Complete Genome Sequence of Mycoplasma suis and Insights into Its Biology and Adaption to an Erythrocyte Niche

Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+) kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems.

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun to elucidate the demographic history of the species, as well as patterns of population structure and patterns of linkage disequilibrium within its genome. Such studies will be greatly enhanced by new genomic tools and recent large-scale efforts to map genomic variation. To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum. Results: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, interpopulation differentiation, and the degree to which allele frequencies are correlated between populations. Conclusions: The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.

Bulk structures of PtO and PtO(2) from density functional calculations

Platinum plays an important role in catalysis and electrochemistry, and it is known that the direct interaction of oxygen with Pt surfaces can lead to the formation of platinum oxides (PtO(x)), which can affect the reactivity. To contribute to the atomistic understanding of the atomic structure of PtO(x), we report a density functional theory study of the atomic structure of bulk PtO(x) (1 <= x <= 2). From our calculations, we identified a lowest-energy structure (GeS type, space group Pnma) for PtO, which is 0.181 eV lower in energy than the structure suggested by W. J. Moore and L. Pauling [J. Am. Chem. Soc. 63, 1392 (1941)] (PtS type). Furthermore, two atomic structures were identified for PtO(2), which are almost degenerate in energy with the lowest-energy structure reported so far for PtO(2) (CaCl(2) type). Based on our results and analysis, we suggest that Pt and O atoms tend to form octahedron motifs in PtO(x) even at lower O composition by the formation of Pt-Pt bonds.

Coexistence of forest and savanna in an Amazonian area from a geological perspective

Question: How can the coexistence of savanna and forest in Amazonian areas with relatively uniform climates be explained? Location: Eastern Marajo Island, northeast Amazonia, Brazil. Methods: The study integrated floristic analysis, terrain morphology, sedimentology and delta(13)C of soil organic matter. Floristic analysis involved rapid ecological assessment of 33 sites, determination of occurrence, specific richness, hierarchical distribution and matrix of floristic similarity between paired vegetation types. Terrain characterization was based on analysis of Landsat images using 4(R), 5(G) and 7(B) composition and digital elevation model (DEM). Sedimentology involved field descriptions of surface and core sediments. Finally, radiocarbon dating and analysis of delta(13)C of soil profile organic matter and natural ecotone forest-savanna was undertaken. Results: Slight tectonic subsidence in eastern Marajo Island favours seasonal flooding, making it unsuitable for forest growth. However, this area displays slightly convex-up, sinuous morphologies related to paleochannels, covered by forest. Terra-firme lowland forests are expanding from west to east, preferentially occupying paleochannels and replacing savanna. Slack, running water during channel abandonment leads to disappearance of varzea/gallery forest at channel margins. Long-abandoned channels sustain continuous terra-firme forests, because of longer times for more species to establish. Recently abandoned channels have had less time to become sites for widespread tree development, and are either not vegetated or covered by savanna. Conclusion: Landforms in eastern Marajo Island reflect changes in the physical environment due to reactivation of tectonic faults during the latest Quaternary. This promoted a dynamic history of channel abandonment, which controlled a set of interrelated parameters (soil type, topography, hydrology) that determined species location. Inclusion of a geological perspective for paleoenvironmental reconstruction can increase understanding of plant distribution in Amazonia.

Improved xylitol production in media containing phenolic aldehydes: application of response surface methodology for optimization and modeling of bioprocess

BACKGROUND: The combined effects of vanillin and syringaldehyde on xylitol production by Candida guilliermondii using response surface methodology (RSM) have been studied. A 2(2) full-factorial central composite design was employed for experimental design and analysis of the results. RESULTS: Maximum xylitol productivities (Q(p) = 0.74 g L(-1) h(-1)) and yields (Y(P/S) = 0.81 g g(-1)) can be attained by adding only vanillin at 2.0 g L(-1) to the fermentation medium. These data were closely correlated with the experimental results obtained (0.69 +/- 0.04 g L(-1) h(-1) and 0.77 +/- 0.01 g g(-1)) indicating a good agreement with the predicted value. C. guilliermondii was able to convert vanillin completely after 24 h of fermentation with 94% yield of vanillyl alcohol. CONCLUSIONS: The bioconversion of xylose into xylitol by C. guilliermondii is strongly dependent on the combination of aldehydes and phenolics in the fermentation medium. Vanillin is a source of phenolic compound able to improve xylitol production by yeast. The conversion of vanillin to alcohol vanilyl reveals the potential of this yeast for medium detoxification. (C) 2009 Society of Chemical Industry

Assessment of groundwater recharge and water fluxes of the Guarani Aquifer System, Brazil

The groundwater recharge and water fluxes of the Guarani Aquifer System in the state of Sao Paulo in Brazil were assessed through a numeric model. The study area (6,748 km(2)) comprises Jacar,-Gua double dagger A(0) and Jacar,-Pepira River watersheds, tributaries of the Tiet River in the central region of the state. GIS based tools were used in the storage, processing and analysis of data. Main hydrologic phenomena were selected, leading to a groundwater conceptual model, taking into account the significant outcrops occurring in the study area. Six recharge zones were related to the geologic formation and structures of the semi-confined and phreatic aquifer. The model was calibrated against the baseflows and static water levels of the wells. The results emphasize the strong interaction of groundwater flows between watersheds and the groundwater inflow into the rivers. It has been concluded that lateral groundwater exchanges between basins, the deep discharges to the regional system, and well exploitation were not significant aquifer outflows when compared to the aquifer recharge. The results have shown that the inflows from the river into the aquifer are significant and have the utmost importance since the aquifer is potentially more vulnerable in these places.

Multicriteria analysis in decision making under information uncertainty

This paper presents results of research related to multicriteria decision making under information uncertainty. The Bell-man-Zadeh approach to decision making in a fuzzy environment is utilized for analyzing multicriteria optimization models (< X, M > models) under deterministic information. Its application conforms to the principle of guaranteed result and provides constructive lines in obtaining harmonious solutions on the basis of analyzing associated maxmin problems. This circumstance permits one to generalize the classic approach to considering the uncertainty of quantitative information (based on constructing and analyzing payoff matrices reflecting effects which can be obtained for different combinations of solution alternatives and the so-called states of nature) in monocriteria decision making to multicriteria problems. Considering that the uncertainty of information can produce considerable decision uncertainty regions, the resolving capacity of this generalization does not always permit one to obtain unique solutions. Taking this into account, a proposed general scheme of multicriteria decision making under information uncertainty also includes the construction and analysis of the so-called < X, R > models (which contain fuzzy preference relations as criteria of optimality) as a means for the subsequent contraction of the decision uncertainty regions. The paper results are of a universal character and are illustrated by a simple example. (c) 2007 Elsevier Inc. All rights reserved.

A Geometric Approach for Turbo Decoding of Reed-Solomon Codes in QAM Modulation Schemes

This work studies the turbo decoding of Reed-Solomon codes in QAM modulation schemes for additive white Gaussian noise channels (AWGN) by using a geometric approach. Considering the relations between the Galois field elements of the Reed-Solomon code and the symbols combined with their geometric dispositions in the QAM constellation, a turbo decoding algorithm, based on the work of Chase and Pyndiah, is developed. Simulation results show that the performance achieved is similar to the one obtained with the pragmatic approach with binary decomposition and analysis.

Local search multiuser detection

In this work, a wide analysis of local search multiuser detection (LS-MUD) for direct sequence/code division multiple access (DS/CDMA) systems under multipath channels is carried out considering the performance-complexity trade-off. It is verified the robustness of the LS-MUD to variations in loading, E(b)/N(0), near-far effect, number of fingers of the Rake receiver and errors in the channel coefficients estimates. A compared analysis of the bit error rate (BER) and complexity trade-off is accomplished among LS, genetic algorithm (GA) and particle swarm optimization (PSO). Based on the deterministic behavior of the LS algorithm, it is also proposed simplifications over the cost function calculation, obtaining more efficient algorithms (simplified and combined LS-MUD versions) and creating new perspectives for the MUD implementation. The computational complexity is expressed in terms of the number of operations in order to converge. Our conclusion pointed out that the simplified LS (s-LS) method is always more efficient, independent of the system conditions, achieving a better performance with a lower complexity than the others heuristics detectors. Associated to this, the deterministic strategy and absence of input parameters made the s-LS algorithm the most appropriate for the MUD problem. (C) 2008 Elsevier GmbH. All rights reserved.

Seed development, yield and quality of two palm species growing in different tropical forest types in SE Brazil: implications for ecological restoration

Natural forest remnants have been set as seed production fields to supply seeds of native tree species for tropical forest restoration, but the effect of different forest types on seed production has not been accessed to date for palm species. In this work, we studied seed development, yield, and quality of two palm species in different tropical forest types in SE Brazil. Seed production of palmiteiro (Euterpe edulis) and queen-palm (Syagrus romanzoffiana), which are largely used in restoration efforts due to their importance for vertebrate frugivores, were studied in natural remnants of Atlantic Rainforest, Restinga Forest, Seasonally Dry Forest, and Cerrado Forest. We studied seed development, yield, size, and germination of seed lots produced in some of these forest types, including seeds harvested in 2008, 2009, and both years. Seed yield and quality, as well as seed dry mass in 2009, were higher for palmiteiro seeds produced in the Atlantic Rainforest, while queen-palm seeds produced at the Restinga Forest showed the higher mass and yield, but the lowest physiological potential. Consequently, these natural differences of seed yield and quality have to be taken into account for establishing standards for seed commercialization and analysis, seed pricing, and seedling production in forest nurseries.

Antioxidant capacity of Brazilian fruit, vegetables and commercially-frozen fruit pulps

Several epidemiological and research studies suggest that a high intake of foods rich in natural antioxidants increases the antioxidant capacity of the plasma and reduces the risk of some kinds of cancers, heart diseases, and stroke. These health benefits are attributed to a variety of constituents, including vitamins, minerals, fiber, and numerous phytochemicals, such as flavonoids. Thus, in addition to measuring the composition of the usual macronutrients and micronutrients, it seems important to also measure the antioxidant capacity of foods. For this purpose, 28 foods including fruits, vegetables and commercially-frozen fruit pulps were analyzed for antioxidant capacity. The antioxidant capacity of the foods varied from 0.73 to 19.8 mu mol BHT equiv/g. The highest values were observed for wild mulberries (19.8 mu mol BHT equiv/g), acai fruit pulp (18.2 mu mol BHT equiv/g) and watercress (9.6 mu mol BHT equiv/g). The antioxidant capacities are only indicative of the potential of the bioactive compounds; however, these data are important to explore and understand the role of fruit, vegetables and other foods in health promotion. (C) 2009 Elsevier Inc. All rights reserved.

Isoflavones and antioxidant capacity of Peruvian and Brazilian lupin cultivars

Seed coats, cotyledons and hypocotyls from six Peruvian (Lupinus mutabilis Sweet) and two Brazilian (Lupinus albus and Lupinus angustifolius) lupin cultivars were assessed regarding their content of isoflavones and antioxidant capacity. Genistein and a genistein derivative were detected in seed coats and cotyledons from Peruvian cultivars. Total isoflavones ranged from 9.8 to 87, 16.1 to 30.8 and 1.3 to 6.1 mg/100 g of sample in fresh weight (expressed as genistein) in seed coat, cotyledon and hypocotyl fractions, respectively, from mutabilis species, whereas no isoflavones were detected in L. angustifolius and L. albus. A significant correlation (r = 0.99) was found between the total isoflavone levels and the antioxidant capacity measured by the 2,2-diphenyl-1-picrylhydrazyl radical-scavenging method in all fractions of Peruvian samples. No condensed tannins were detected in any of the lupin cultivars. The H-6 Andean cultivar is promising for its high isoflavone content and antioxidant capacity. Insights from this study indicate that lupin cultivars of the mutabilis species have similar isoflavone profiles and that isoflavones are more concentrated in the cotyledon seed fraction than in the seed coat or hypocotyl fractions. (C) 2008 Elsevier Inc. All rights reserved.

Molecular modeling and QSAR studies of a set of indole and benzimidazole derivatives as H(4) receptor antagonists

Histamine is an important biogenic amine, which acts with a group of four G-protein coupled receptors (GPCRs), namely H(1) to H(4) (H(1)R - H(4)R) receptors. The actions of histamine at H(4)R are related to immunological and inflammatory processes, particularly in pathophysiology of asthma, and H(4)R ligands having antagonistic properties could be helpful as antiinflammatory agents. In this work, molecular modeling and QSAR studies of a set of 30 compounds, indole and benzimidazole derivatives, as H(4)R antagonists were performed. The QSAR models were built and optimized using a genetic algorithm function and partial least squares regression (WOLF 5.5 program). The best QSAR model constructed with training set (N = 25) presented the following statistical measures: r (2) = 0.76, q (2) = 0.62, LOF = 0.15, and LSE = 0.07, and was validated using the LNO and y-randomization techniques. Four of five compounds of test set were well predicted by the selected QSAR model, which presented an external prediction power of 80%. These findings can be quite useful to aid the designing of new anti-H(4) compounds with improved biological response.

Brazilian Network of Food Data Systems and LATINFOODS Regional Technical Compilation Committee: Food composition activities (2006-2009)

The Brazilian Network of Food Data Systems (BRASILFOODS) has been keeping the Brazilian Food Composition Database-USP (TBCA-USP) (http://www.fcf.usp.br/tabela) since 1998. Besides the constant compilation, analysis and update work in the database, the network tries to innovate through the introduction of food information that may contribute to decrease the risk for non-transmissible chronic diseases, such as the profile of carbohydrates and flavonoids in foods. In 2008, data on carbohydrates, individually analyzed, of 112 foods, and 41 data related to the glycemic response produced by foods widely consumed in the country were included in the TBCA-USP. Data (773) about the different flavonoid subclasses of 197 Brazilian foods were compiled and the quality of each data was evaluated according to the USDAs data quality evaluation system. In 2007, BRASILFOODS/USP and INFOODS/FAO organized the 7th International Food Data Conference ""Food Composition and Biodiversity"". This conference was a unique opportunity for interaction between renowned researchers and participants from several countries and it allowed the discussion of aspects that may improve the food composition area. During the period, the LATINFOODS Regional Technical Compilation Committee and BRASILFOODS disseminated to Latin America the Form and Manual for Data Compilation, version 2009, ministered a Food Composition Data Compilation course and developed many activities related to data production and compilation. (C) 2010 Elsevier Inc. All rights reserved.

Undergraduate teaching of ideal and real fluid flows: The value of real-world experimental projects

This study describes the pedagogical impact of real-world experimental projects undertaken as part of an advanced undergraduate Fluid Mechanics subject at an Australian university. The projects have been organised to complement traditional lectures and introduce students to the challenges of professional design, physical modelling, data collection and analysis. The physical model studies combine experimental, analytical and numerical work in order to develop students’ abilities to tackle real-world problems. A first study illustrates the differences between ideal and real fluid flow force predictions based upon model tests of buildings in a large size wind tunnel used for research and professional testing. A second study introduces the complexity arising from unsteady non-uniform wave loading on a sheltered pile. The teaching initiative is supported by feedback from undergraduate students. The pedagogy of the course and projects is discussed with reference to experiential, project-based and collaborative learning. The practical work complements traditional lectures and tutorials, and provides opportunities which cannot be learnt in the classroom, real or virtual. Student feedback demonstrates a strong interest for the project phases of the course. This was associated with greater motivation for the course, leading in turn to lower failure rates. In terms of learning outcomes, the primary aim is to enable students to deliver a professional report as the final product, where physical model data are compared to ideal-fluid flow calculations and real-fluid flow analyses. Thus the students are exposed to a professional design approach involving a high level of expertise in fluid mechanics, with sufficient academic guidance to achieve carefully defined learning goals, while retaining sufficient flexibility for students to construct there own learning goals. The overall pedagogy is a blend of problem-based and project-based learning, which reflects academic research and professional practice. The assessment is a mix of peer-assessed oral presentations and written reports that aims to maximise student reflection and development. Student feedback indicated a strong motivation for courses that include a well-designed project component.