(Table S2) Relative abundance of archaeal 16S rRNA genes in sediment cores

Deep drilling into the marine sea floor has uncovered a vast sedimentary ecosystem of microbial cells (Parkes et al., 1994, doi:10.1038/371410a0; D'Hondt et al., 2004, doi:10.1126/science.1101155). Extrapolation of direct counts of stained microbial cells to the total volume of habitable marine subsurface sediments suggests that between 56 Pg (Parkes et al., 1994, doi:10.1038/371410a0) and 303 Pg (Whitman et al., 1998) of cellular carbon could be stored in this largely unexplored habitat. From recent studies using various culture-independent techniques, no clear picture has yet emerged as to whether Archaea or Bacteria are more abundant in this extensive ecosystem (Schippers et al., doi:10.1038/nature03302; Inagaki et al., doi:10.1073/pnas.0511033103 ; Mauclaire et al., doi:10.1111/j.1472-4677.2004.00035.x; Biddle et al., doi:10.1073/pnas.0600035103). Here we show that in subsurface sediments buried deeper than 1 m in a wide range of oceanographic settings at least 87% of intact polar membrane lipids, biomarkers for the presence of live cells (Biddle et al., doi:10.1073/pnas.0600035103; Sturt et al., 2004, doi:10.1002/rcm.1378), are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols support the lipid-based evidence and indicate that these techniques have previously underestimated archaeal biomass. The lipid concentrations are proportional to those of total organic carbon. On the basis of this relationship, we derived an independent estimate of amounts of cellular carbon in the global marine subsurface biosphere. Our estimate of 90 Pg of cellular carbon is consistent, within an order of magnitude, with previous estimates, and underscores the importance of marine subsurface habitats for global biomass budgets.

Isotopic determination of silicon by mass spectrometry in plants and soils labeled with Si-30

A method for isotopic determination of silicon by mass spectrometry in plants and soils labeled with Si-30 is reported. The development of this method is for use with studies involving the physiological process of absorption, transport, and redistribution of Si in the soil-plant system by use of the stable isotope Si-30 as a tracer. The procedure leads to SiF4 formation, and the isotopic determination of Si was based on the measurements of the (SiF3+)-Si-28, (SiF3+)-Si-29, and (SiF3+)-Si-30 signals. Relative standard deviation of Si-30 abundance measurements (n = 6) were lower than 0.1%, and the detection limit was 0.5 mg Si (dry mass).

Standard Values for Real-Time Transthoracic Three-Dimensional Echocardiographic Dyssynchrony Indexes in a Normal Population

Background: There is a paucity of information describing the real-time 3-dimensional echocardiography (RT3DE) and dyssynchrony indexes (DIs) of a normal population. We evaluate the RT3DE DIs in a population with normal electrocardiograms and 2- and 3-dimensional echocardiographic analyses. This information is relevant for cardiac resynchronization therapy. Methods: We evaluated 131 healthy volunteers (73 were male, aged 46 +/- 14 years) who were referred for routine echocardiography; who presented normal cardiac structure on electrocardiography, 2-dimensional echocardiography, and RT3DE; and who had no history of cardiac diseases. We analyzed 3-dimensional left ventricular ejection fraction, left ventricle end-diastolic volume, left ventricle end-systolic volume, and left ventricular systolic DI% (6-, 12-, and 16-segment models). RT3DE data were analyzed by quantifying the statistical distribution (mean, median, standard deviation [SD], relative SD, coefficient of skewness, coefficient of kurtosis, Kolmogorov-Smirnov test, D`Agostino-Pearson test, percentiles, and 95% confidence interval). Results: Left ventricular ejection fraction ranged from 50% to 80% (66.1% +/- 7.1%); left ventricle end-diastolic volume ranged from 39.8 to 145 mL (79.1 +/- 24.9 mL); left ventricle end-systolic volume ranged from 12.9 to 66 mL (27 +/- 12.1 mL); 6-segment DI% ranged from 0.20% to 3.80% (1.21% +/- 0.66%), median: 1.06, relative SD: 0.5482, coefficient of skewness: 1.2620 (P < .0001), coefficient of Kurtosis: 1.9956 (P = .0039); percentile 2.5%: 0.2900, percentile 97.5%: 2.8300; 12-segment DI% ranged from 0.22% to 4.01% (1.29% +/- 0.71%), median: 1.14, relative SD: 0.95, coefficient of skewness: 1.1089 (P < .0001), coefficient of Kurtosis: 1.6372 (P = .0100), percentile 2.5%: 0.2850, percentile 97.5%: 3.0700; and 16-segment DI% ranged from 0.29% to 4.88% (1.59 +/- 0.99), median: 1.39, relative SD: 0.56, coefficient of skewness: 1.0792 (P < .0001), coefficient of Kurtosis: 0.9248 (P = .07), percentile 2.5%: 0.3750, percentile 97.5%: 3.750. Conclusion: This study allows for the quantification of RT3DE DIs in normal subjects, providing a comparison for patients with heart failure who may be candidates for cardiac resynchronization therapy. (J Am Soc Echocardiogr 2008; 21: 1229-1235)

Local dispersion of the Eucalyptus leaf beetle Chrysophtharta bimaculata (Coleoptera: Chrysomelidae), and implications for forest protection

1. Chrysophtharta bimaculata is a native chrysomelid species that can cause chronic defoliation of plantation and regrowth Eucalyptus forests in Tasmania, Australia. Knowledge of the dispersion pattern of C. bimaculata was needed in order to assess the efficiency of an integrated pest management (IPM) programme currently used for its control. 2. Using data from yellow flight traps, local populations of C. bimaculata adults were monitored over a season at spatial scales relevant to commercial forestry: within a 50-ha operational management unit (a forestry 'coupe') and between coupes. In addition, oviposition was monitored over a season at a subset of the between-coupe sites. 3. Dispersion indices (Taylor's Power Law and Iwao's Mean Crowding regression method) demonstrated that C. bimaculata adults were spatially aggregated within and between coupes, although the number of egg-batches laid at the between-coupe scale was uniform. Spatial autocorrelation analysis showed that trap-catches at the within-coupe level were similar (positively autocorrelated) to a radius distance of approximately 110 m, and then dissimilar (negatively autocorrelated) at approximately 250 m. At the between-coupe scale, no repeatable spatial autocorrelation patterns were observed. 4. For any individual site, rapid changes in beetle density were observed to be associated with loosely aggregated flights of beetles into and out of that site. Peak adult catches (> the weekly mean plus standard deviation trap-catch) for a site occurred for a period of 2.0 +/- 0.22 weeks at a time (n = 37), with normally only one or two peaks per site per season. Peak oviposition events for a site occurred on average 1.4 +/- 0.11 times per season and lasted 1.5 +/- 0.12 weeks. 5. Analysis of an extensive data set (n = 417) demonstrated that adult abundance at a site was positively correlated with egg density, but negatively correlated with tree damage (caused by conspecifics) and the presence of conspecific larvae. There was no relationship between adult abundance and a visual estimate of the amount of young foliage on trees. 6. Adults of C. bimaculata are show n to occur in relatively small, mobile aggregations. This means that pest surveys must be both regular (less than 2 weeks apart) and intensive (with sampling points no more than 150 m apart) if beetle populations are to be monitored with confidence. Further refinement of the current IPM strategy must recognize the problems posed by this temporal and spatial patchiness, particularly with regard to the use of biological insecticides, such as Bacillus thuringiensis, for which only a very short operational window exists.

Desenvolvimento de um método potenciométrico para deteção de salmonella typhimurium

A Salmonella é um microrganismo responsável por grande parte das doenças alimentares, podendo por em causa a saúde pública da área contaminada. Uma deteção rápida, eficiente e altamente sensível e extremamente importante, sendo um campo em franco desenvolvimento e alvo de variados e múltiplos estudos na comunidade cientifica atual. Foi desenvolvido um método potenciométrico para a deteção de Salmonellas, com elétrodos seletivos de iões, construídos em laboratório com pontas de micropipetas, fios de prata e sensores com composição otimizada. O elétrodo indicador escolhido foi um ESI seletivo a cadmio, para redução da probabilidade de interferências no método, devido a pouca abundancia do cadmio em amostras alimentares. Elétrodos seletivos a sódio, elétrodos de Ag/AgCl de simples e de dupla juncão foram também construídos e caracterizados para serem aplicados como elétrodos de referência. Adicionalmente otimizaram-se as condições operacionais para a analise potenciométrica, nomeadamente o elétrodo de referencia utilizado, condicionamento dos elétrodos, efeito do pH e volume da solução amostra. A capacidade de realizar leituras em volumes muito pequenos com limites de deteção na ordem dos micromolares por parte dos ESI de membrana polimérica, foi integrada num ensaio com um formato nao competitivo ELISA tipo sanduiche, utilizando um anticorpo primário ligado a nanopartículas de Fe@Au, permitindo a separação dos complexos anticorpo-antigénio formados dos restantes componentes em cada etapa do ensaio, pela simples aplicação de um campo magnético. O anticorpo secundário foi marcado com nanocristais de CdS, que são bastante estáveis e é fácil a transformação em Cd2+ livre, permitindo a leitura potenciométrica. Foram testadas várias concentrações de peroxido de hidrogénio e o efeito da luz para otimizar a dissolução de CdS. O método desenvolvido permitiu traçar curvas de calibração com soluções de Salmonellas incubadas em PBS (pH 4,4) em que o limite de deteção foi de 1100 CFU/mL e de 20 CFU/mL, utilizando volumes de amostra de 10 ƒÊL e 100 ƒÊL, respetivamente para o intervalo de linearidade de 10 a 108 CFU/mL. O método foi aplicado a uma amostra de leite bovino. A taxa de recuperação media obtida foi de 93,7% } 2,8 (media } desvio padrão), tendo em conta dois ensaios de recuperação efetuados (com duas replicas cada), utilizando um volume de amostra de 100 ƒÊL e concentrações de 100 e 1000 CFU/mL de Salmonella incubada.

Biotic factors and occurrence of Lutzomyia longipalpis in endemic area of visceral leishmaniasis, Mato Grosso do Sul, Brazil

The relationships between environmental exposure to risk agents and health conditions have been studied with the aid of remote sensing imagery, a tool particularly useful in the study of vegetation cover. This study aims to evaluate the influence of environmental variables on the spatial distribution of the abundance of Lutzomyia longipalpis and the reported canine and human visceral leishmaniasis (VL) cases at an urban area of Campo Grande, state of Mato Grosso do Sul. The sandfly captures were performed in 13 residences that were selected by raffle considering four residences or collection station for buffer. These buffers were generated from the central house with about 50, 100 and 200 m from it in an endemic area of VL. The abundance of sandflies and human and canine cases were georreferenced using the GIS software PCI Geomatica. The normalized difference vegetation index (NDVI) and percentage of land covered by vegetation were the environmental variables extracted from a remote sensing IKONOS-2 image. The average NDVI was considered as the complexity of habitat and the standard deviation as the heterogeneity of habitat. One thousand three hundred sixty-seven specimens were collected during the catch. We found a significant positive linear correlation between the abundance of sandflies and the percentage of vegetation cover and average NDVI. However, there was no significant association between habitat heterogeneity and the abundance of these flies.

Electrothermal AAS determination of Ni in soft drinks using Co as the internal standard

A method for the direct determination of Ni in soft drinks by graphite furnace atomic absorption spectrometry using a transversely heated graphite atomizer (THGA), Zeeman-effect background corrector, and Co as the internal standard (IS) is proposed. Magnesium nitrate was used to stabilize both Ni and Co. All diluted samples (1+1) in 0.2% (v/v) HNO3 and reference solutions [5.0-50 mu g L-1 Ni in 0.2% (v/v) HNO3] were spiked with 50 mu g L-1 Co. For a 20-mu L sample dispensed into the atomizer, correlations between the ratio of absorbance of Ni to absorbance of Co and the analyte concentration were close to 0.9996. The relative standard deviation of the measurements varied from 0.5 to 3.4% and 1.0 to 7.0% (n=12) with and without IS, respectively. Recoveries within 98-104% for Ni spikes were obtained using IS. The characteristic mass was calculated as 43 pg Ni and the limit of detection was 1.4 mu g L-1. The accuracy of the method was checked for the direct determination of Ni in soft drinks and the results obtained with IS were better than those without IS.

Evaluation of Bi as internal standard to minimize matrix effects on the direct determination of Pb in vinegar by graphite furnace atomic absorption spectrometry using Ru permanent modifier with co-injection of Pd/Mg(NO3)(2)

Bismuth was evaluated as an internal standard for the direct determination of Pb in vinegar by graphite furnace atomic absorption spectrometry using Ru as a permanent modifier with co-injection of Pd/Mg(NO3)(2). The correlation coefficient of the graph plotted from the non-nalized absorbance signals of Bi versus Pb was r=0.989. Matrix effects were evaluated by analyzing the slope ratios between the analytical curve, and analytical curves obtained from Pb additions in red and white wine vinegar obtained from reference solutions prepared in 0.2% (v/v) HNO3, samples. The calculated ratios were around 1.04 and 1.02 for analytical curves established applying an internal standard and 1.3 and 1.5 for analvtical curves without. Analytical curves in the 2.5-15 pg L-1 Pb concentration interval were established using the ratio Pb absorbance to Bi absorbance versus analvte concentration, and typical linear correlations of r=0.999 were obtained. The proposed method was applied for direct determination of Pb in 18 commercial vinegar samples and the Pb concentration varied from 2.6 to 31 pg L-1. Results were in agreement at a 95% confidence level (paired t-test) with those obtained for digested samples. Recoveries of Pb added to vinegars varied from 96 to 108% with and from 72 to 86% without an internal standard. Two water standard reference materials diluted in vinegar sample were also analyzed and results were in agreement with certified values at a 95% confidence level. The characteristic mass was 40 pg Pb and the useful lifetime of the tube was around 1600 firings. The limit of detection was 0.3 mu g L-1 and the relative standard deviation was <= 3.8% and <= 8.3% (n = 12) for a sample containing, 10 mu L-1 Pb with and without internal standard, respectively. (C) 2007 Elsevier B.V. All rights reserved.

Arsenic as internal standard to correct for interferences in the determination of antimony by hydride generation in situ trapping graphite furnace atomic absorption spectrometry

The feasibility of using internal standardization (IS) to correct for interferences in hydride generation with in situ trapping in graphite furnace was evaluated. Arsenic was chosen as internal standard for Sb determination and Ir was used as permanent modifier. Fluctuations in the main parameters that affect the analytical results were minimized by IS and an effective contribution was verified in the studies of liquid phase interferences. Cobalt and Ni2+ were selected to illustrate the potential use of IS on the correction of interference by transition metals. The application of IS allows the Sb determination in samples containing up to 20-fold higher concentration of the Co2+ and Ni2+ when compared to the procedure without IS. The relative standard deviation of measurements varied from 0.3% to 0.7% and from 1.1% to 3.2% with and without IS, respectively. Recoveries within 92% and 107% of spiked aqueous solution containing Sb(III) and Sb(V) were found. (c) 2005 Elsevier B.V. All rights reserved.

Combined search for the standard model Higgs boson decaying to bb̄ using the D0 run II data set

We present the results of the combination of searches for the standard model Higgs boson produced in association with a W or Z boson and decaying into bb̄ using the data sample collected with the D0 detector in pp̄ collisions at √s=1.96TeV at the Fermilab Tevatron Collider. We derive 95% C.L. upper limits on the Higgs boson cross section relative to the standard model prediction in the mass range 100GeV≤M H≤150GeV, and we exclude Higgs bosons with masses smaller than 102 GeV at the 95% C.L. In the mass range 120GeV≤M H≤145GeV, the data exhibit an excess above the background prediction with a global significance of 1.5 standard deviations, consistent with the expectation in the presence of a standard model Higgs boson. © 2012 American Physical Society.

Use of intertidal areas by shrimps (Decapoda) in a brazilian Amazon estuary

O presente trabalho investigou a ocupação e a correlação da abundância de camarões em relação às variáveis ambientais nos diferentes habitats (manguezal, marisma e afloramento rochoso) em um estuário amazônico. As coletas foram realizadas em agosto e novembro de 2009, na maré baixa de sizígia na praia do Areuá, situada na RESEX Mãe Grande de Curuçá, Pará, totalizando 20 poças. Em cada ambiente foram registrados os fatores físicoquímicos (pH, salinidade e temperatura) e mensuradas a área (m²) e o volume (m³) de cada poça através da técnica de batimetria. A média do pH, salinidade, temperatura, área e volume das poças-de-maré foram 8,75 (± 0,8 desvio padrão) 35,45 (± 3), 29,49 °C (± 2,32), 27,41 m² (± 41,18) e 5,19 m³ (± 8,01), respectivamente. Foi capturado um total de 4.871 indivíduos, distribuídos em três famílias e quatro espécies: Farfantepenaeus subtilis (marinha) a mais frequente (98,36%), seguida de Alpheus pontederiae (0,76%) (estuarina), Macrobrachium surinamicum (0,45%) e Macrobrachium amazonicum (0,43%) predominantemente dulcícolas. As espécies F. subtilis e A. pontederiae ocorreram nos três habitats, enquanto que M. surinamicum ocorreu no afloramento rochoso e marisma e M. amazonicum somente no marisma. O pH e a temperatura foram os descritores ambientais mais importantes que afetaram significativamente a densidade e a biomassa dos camarões.

Ferramenta computacional para identificação de micro-organismos com base em assinaturas genômicas

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Profiling of alterations in platelet proteins during storage of platelet concentrates

BACKGROUND: The quality of platelet concentrates (PCs) is primarily determined in vitro by selective methods (e.g., pH, aggregometry), which provide only limited information on certain platelet (PLT) characteristics. In contrast, proteomic technologies provide a comprehensive overview of the PLT proteome. High interassay variability, however, limits meaningful assessment of samples taken from the same product over time or before and after processing. STUDY DESIGN AND METHODS: Differential in-gel electrophoresis (DIGE) and mass spectrometry were applied to analyze changes in the PLT proteome during storage of PCs. RESULTS: DIGE provides a comprehensive and reproducible overview of the cytoplasmic PLT proteome (median standard deviation of protein spot intensities, 5%-9%). Although 97 percent of cytosolic PLT proteins remained unchanged over a 9-day storage period, septin 2 showed characteristic alterations that preceded by several days more widespread alterations affecting numerous other proteins. Also beta-actin and gelsolin are potential marker proteins for changes in the PLT proteome. Interestingly septin 2 and gelsolin are affected during apoptosis, indicating that apoptosis in PCs may have an impact on PLT storage. CONCLUSION: DIGE is a tool for comprehensively assessing the impact of storage on the global proteome profile of therapeutic PCs. Most of the changes detected are in high-abundance PLT proteins.

n-Alkane analyses from an transect of marine surface sediments off southwest Africa

An isobathic transect of marine surface sediments from 1°N to 28°S off southwest Africa was used to further evaluate the potential of the chain length distribution and carbon stable isotope composition of higher plant n-alkanes as proxies for continental vegetation and climate conditions. We found a strong increase in the n-C29-33 weighted mean average d13C values from -33 per mil near the equator to around -26 per mil further south. Additionally, C25-35n-alkanes reveal a southward trend of increasing average chain length from 30.0 to 30.5. The data reflect the changing contribution of plants employing different photosynthetic pathways (C3 and C4) and/or being differently influenced by the environmental conditions of their habitat. The C4 plant proportions calculated from the data (ca. 20% for rivers draining the rainforest, to ca. 70% at higher latitude) correspond to the C4 plant abundance in continental catchment areas postulated by considering prevailing wind systems and river outflows. Furthermore, the C4 plant contribution to the sediments correlates with the mean annual precipitation and aridity at selected continental locations in the postulated catchment areas, suggesting that the C4 plant fraction in marine sediments can be used to assess these environmental parameters.