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.

Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters

Studies of consumer-resource interactions suggest that individual diet specialisation is empirically widespread and theoretically important to the organisation and dynamics of populations and communities. We used weighted networks to analyze the resource use by sea otters, testing three alternative models for how individual diet specialisation may arise. As expected, individual specialisation was absent when otter density was low, but increased at high-otter density. A high-density emergence of nested resource-use networks was consistent with the model assuming individuals share preference ranks. However, a density-dependent emergence of a non-nested modular network for core resources was more consistent with the competitive refuge model. Individuals from different diet modules showed predictable variation in rank-order prey preferences and handling times of core resources, further supporting the competitive refuge model. Our findings support a hierarchical organisation of diet specialisation and suggest individual use of core and marginal resources may be driven by different selective pressures.

Production of Fructooligosaccharides by Aspergillus phoenicis Biofilm on Polyethylene as Inert Support

Aspergillus phoenicis biofilms on polyethylene as inert support were used to produce fructooligosaccharides (FOS) in media containing 25% (m/V) of sucrose as a carbon source. The maximum production of total FOS (122 mg/mL), with 68% of 1-kestose and 32% of nystose, was obtained in Khanna medium maintained at 30 degrees C for 48 h under orbital agitation (100 rpm). At high concentrations of sucrose (30%, m/V), the recovery of FOS was higher than that observed at a low concentration (5%, m/V). High levels of FOS (242 mg/mL) were also recovered when using the biofilm in sodium acetate buffer with high sucrose concentration (50%, m/V) for 10 h. When the dried biofilm was reused in a fresh culture medium, there was a recovery of approx. 13.7% of total FOS after 72 h of cultivation at 30 C, and 10% corresponded to 1-kestose. The biofilm morphology, analyzed by scanning electron microscope, revealed a noncompact mycelium structure, with unfilled spaces and channels present among the hyphae. The results obtained in this study show that A. phoenicis biofilms may find application for FOS production in a single-step fermentation process, which is cost-effective in terms of reusability, downstream processing and efficiency.

Habitat structure and food resources for wildlife across successional stages in a tropical forest

Tropical forests are experiencing an increase in the proportion of secondary forests as a result of the balance between the widespread harvesting of old-growth forests and the regeneration in abandoned areas. The impacts of such a process on biodiversity are poorly known and intensely debated. Recent reviews and multi-taxa studies indicate that species replacement in wildlife assemblages is a consistent pattern, sometimes stronger than changes in diversity, with a replacement from habitat generalists to old-growth specialists being commonly observed during tropical forest regeneration. However, the ecological drivers of such compositional changes are rarely investigated, despite its importance in assessing the conservation value of secondary forests, and to support and guide management techniques for restoration. By sampling 28 sites in a continuous Atlantic forest area in Southeastern Brazil, we assessed how important aspects of habitat structure and food resources for wildlife change across successional stages, and point out hypotheses on the implications of these changes for wildlife recovery. Old-growth areas presented a more complex structure at ground level (deeper leaf litter, and higher woody debris volume) and higher fruit availability from an understorey palm, whereas vegetation connectivity, ground-dwelling arthropod biomass, and total fruit availability were higher in earlier successional stages. From these results we hypothetize that generalist species adapted to fast population growth in resource-rich environments should proliferate and dominate earlier successional stages, while species with higher competitive ability in resource-limited environments, or those that depend on resources such as palm fruits, on higher complexity at the ground level, or on open space for flying, should dominate older-growth forests. Since the identification of the drivers of wildlife recovery is crucial for restoration strategies, it is important that future work test and further develop the proposed hypotheses. We also found structural and functional differences between old-growth forests and secondary forests with more than 80 years of regeneration, suggesting that restoration strategies may be crucial to recover structural and functional aspects expected to be important for wildlife in much altered ecosystems, such as the Brazilian Atlantic forest. (C) 2012 Elsevier B.V. All rights reserved.

Climatic oscillations shape the phylogeographical structure of Atlantic Forest fire-eye antbirds (Aves: Thamnophilidae)

In the present study, mitochondrial (mt)DNA sequence data were used to examine the genetic structure of fire-eye antbirds (genus Pyriglena) along the Atlantic Forest and the predictions derived from the river hypothesis and from a Last Glacial Maximum Pleistocene refuge paleomodel were compared to explain the patterns of genetic variation observed in these populations. A total of 266 individuals from 45 populations were sampled over a latitudinal transect and a number of phylogeographical and population genetics analytical approaches were employed to address these questions. The pattern of mtDNA variation observed in fire-eye antbirds provides little support for the view that populations were isolated by the modern course of major Atlantic Forest rivers. Instead, the data provide stronger support for the predictions of the refuge model. These results add to the mounting evidence that climatic oscillations appear to have played a substantial role in shaping the phylogeographical structure and possibly the diversification of many taxa in this region. However, the results also illustrate the potential for more complex climatic history and historical changes in the geographical distribution of Atlantic Forest than envisioned by the refuge model. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 900824.

Glandular trichomes on aerial and underground organs in Chrysolaena species (Vernonieae - Asteraceae): Structure, ultrastructure and chemical composition

Although the occurrence of glandular trichomes is frequently reported for aerial vegetative organs, many questions still remain opened about the presence of such trichomes in underground systems. Here, we present, for the first time, a comparative study concerning the structure, ultrastructure and chemical aspects of both, the aerial and underground glandular trichomes of two different Chrysolaena species, C obovata and C platensis. Glandular trichomes (GTs) were examined using LM, SEM, and TEM and also analyzed by GC-MS and HPLC coupled to UV/DAD and HR-ESI-MS (HPLC-UV-MS). In both aerial (leaf and bud) and underground (rhizophore) organs, the GTs are multicellular, biseriate and formed by five pairs of cells: a pair of support cells, a pair of basal cells, and three pairs of secreting cells. These secreting cells have, at the beginning of secretory process, abundance of smooth ER. The same classes of secondary metabolites are biosynthesized and stored in both aerial and underground GTs of C platensis and C obovata. These GTs from aerial and underground organs have similar cellular and sub-cellular anatomy, however the belowground trichomes show a higher diversity of compounds when compared to those from the leaves. We also demonstrate by means of HPLC-UV-DAD that the sesquiterpene lactones are located inside the trichomes and that hirsutinolides are not artifacts. (C) 2012 Elsevier GmbH. All rights reserved.

Structure of the N=50 As, Ge, Ga nuclei

The level structures of the N = 50 As-83, Ge-82, and Ga-81 isotones have been investigated by means of multi-nucleon transfer reactions. A first experiment was performed with the CLARA PRISMA setup to identify these nuclei. A second experiment was carried out with the GASP array in order to deduce the gamma-ray coincidence information. The results obtained on the high-spin states of such nuclei are used to test the stability of the N = 50 shell closure in the region of Ni-78 (Z = 28). The comparison of the experimental level schemes with the shell-model calculations yields an N = 50 energy gap value of 4.7(3) MeV at Z = 28. This value, in a good agreement with the prediction of the finite-range liquid-drop model as well as with the recent large-scale shell model calculations, does not support a weakening of the N = 50 shell gap down to Z = 28. (c) 2012 Elsevier B.V. All rights reserved.

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

Brazilian urban population genetic structure reveals a high degree of admixture

Advances in genotyping technologies have contributed to a better understanding of human population genetic structure and improved the analysis of association studies. To analyze patterns of human genetic variation in Brazil, we used SNP data from 1129 individuals - 138 from the urban population of Sao Paulo, Brazil, and 991 from 11 populations of the HapMap Project. Principal components analysis was performed on the SNPs common to these populations, to identify the composition and the number of SNPs needed to capture the genetic variation of them. Both admixture and local ancestry inference were performed in individuals of the Brazilian sample. Individuals from the Brazilian sample fell between Europeans, Mexicans, and Africans. Brazilians are suggested to have the highest internal genetic variation of sampled populations. Our results indicate, as expected, that the Brazilian sample analyzed descend from Amerindians, African, and/or European ancestors, but intermarriage between individuals of different ethnic origin had an important role in generating the broad genetic variation observed in the present-day population. The data support the notion that the Brazilian population, due to its high degree of admixture, can provide a valuable resource for strategies aiming at using admixture as a tool for mapping complex traits in humans. European Journal of Human Genetics (2012) 20, 111-116; doi:10.1038/ejhg.2011.144; published online 24 August 2011

Ni catalyst on mixed support of CeO2-ZrO2 and Al2O3: Effect of composition of CeO2-ZrO2 solid solution on the methane steam reforming reaction

In this study, catalysts containing 5 wt.% Ni deposited on a support composed of a CeO2-ZrO2 solid solution deposited on alumina were tested in the steam reforming of methane. The supports, with various ratios of Ce to Zr, were prepared by co-precipitation of the oxide precursors, followed by calcination in synthetic air. The catalysts were then prepared by Ni impregnation of the supports. The prepared solids were characterized by temperature-programmed reduction with H-2 (TPR-H-2), in situ X-ray diffraction (XRD) and X-ray absorption near-edge structure (XANES) spectroscopy. The XRD analysis confirmed the formation of a solid solution between ZrO2 and CeO2. In the catalytic tests, it was found that catalysts with higher Ce content did not exhibit deactivation during 6 h of reaction. The catalyst with highest Ce content, Ni(0.8Ce0.2Zr)AI, provided the best result, with the highest rate of conversion of methane and the lowest carbon deposition, which may be partly due to the smaller Ni-0 crystallites in this sample and also the segregated CeO2 particles may have favored H2O adsorption which could lead to higher C gasification. (C) 2012 Elsevier B.V. All rights reserved.

Unraveling the structure of sugarcane bagasse after soaking in concentrated aqueous ammonia (SCAA) and ethanol production by Scheffersomyces (Pichia) stipitis

Abstract Background Fuel ethanol production from sustainable and largely abundant agro-residues such as sugarcane bagasse (SB) provides long term, geopolitical and strategic benefits. Pretreatment of SB is an inevitable process for improved saccharification of cell wall carbohydrates. Recently, ammonium hydroxide-based pretreatment technologies have gained significance as an effective and economical pretreatment strategy. We hypothesized that soaking in concentrated aqueous ammonia-mediated thermochemical pretreatment (SCAA) would overcome the native recalcitrance of SB by enhancing cellulase accessibility of the embedded holocellulosic microfibrils. Results In this study, we designed an experiment considering response surface methodology (Taguchi method, L8 orthogonal array) to optimize sugar recovery from ammonia pretreated sugarcane bagasse (SB) by using the method of soaking in concentrated aqueous ammonia (SCAA-SB). Three independent variables: ammonia concentration, temperature and time, were selected at two levels with center point. The ammonia pretreated bagasse (SCAA-SB) was enzymatically hydrolysed by commercial enzymes (Celluclast 1.5 L and Novozym 188) using 15 FPU/g dry biomass and 17.5 Units of β-glucosidase/g dry biomass at 50°C, 150 rpm for 96 h. A maximum of 28.43 g/l reducing sugars corresponding to 0.57 g sugars/g pretreated bagasse was obtained from the SCAA-SB derived using a 20% v/v ammonia solution, at 70°C for 24 h after enzymatic hydrolysis. Among the tested parameters, pretreatment time showed the maximum influence (p value, 0.053282) while ammonia concentration showed the least influence (p value, 0.612552) on sugar recovery. The changes in the ultra-structure and crystallinity of native SCAA-SB and enzymatically hydrolysed SB were observed by scanning electron microscopy (SEM), x-ray diffraction (XRD) and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The enzymatic hydrolysates and solid SCAA-SB were subjected to ethanol fermentation under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) by Scheffersomyces (Pichia) stipitis NRRL Y-7124 respectively. Higher ethanol production (10.31 g/l and yield, 0.387 g/g) was obtained through SSF than SHF (3.83 g/l and yield, 0.289 g/g). Conclusions SCAA treatment showed marked lignin removal from SB thus improving the accessibility of cellulases towards holocellulose substrate as evidenced by efficient sugar release. The ultrastructure of SB after SCAA and enzymatic hydrolysis of holocellulose provided insights of the degradation process at the molecular level.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

Abstract Background The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated. Methods The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches. Results Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis. Conclusion Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.