Characterization of the Salmonella typhimurium proteome by semi-automated two dimensional HPLC-mass spectrometry: detection of proteins implicated in multiple antibiotic resistance

The proteome of Salmonella enterica serovar Typhimurium was characterized by 2-dimensional HPLC mass spectrometry to provide a platform for subsequent proteomic investigations of low level multiple antibiotic resistance (MAR). Bacteria (2.15 +/- 0.23 x 10(10) cfu; mean +/- s.d.) were harvested from liquid culture and proteins differentially fractionated, on the basis of solubility, into preparations representative of the cytosol, cell envelope and outer membrane proteins (OMPs). These preparations were digested by treatment with trypsin and peptides separated into fractions (n = 20) by strong cation exchange chromatography (SCX). Tryptic peptides in each SCX fraction were further separated by reversed-phase chromatography and detected by mass spectrometry. Peptides were assigned to proteins and consensus rank listings compiled using SEQUEST. A total of 816 +/- 11 individual proteins were identified which included 371 +/- 33, 565 +/- 15 and 262 +/- 5 from the cytosolic, cell envelope and OMP preparations, respectively. A significant correlation was observed (r(2) = 0.62 +/- 0.10; P < 0.0001) between consensus rank position for duplicate cell preparations and an average of 74 +/- 5% of proteins were common to both replicates. A total of 34 outer membrane proteins were detected, 20 of these from the OMP preparation. A range of proteins (n = 20) previously associated with the mar locus in E. coli were also found including the key MAR effectors AcrA, TolC and OmpF.

A review of biochars’ potential role in the remediation, revegetation and restoration of contaminated soils

Biochars are biological residues combusted under low oxygen conditions, resulting in a porous, low density carbon rich material. Their large surface areas and cation exchange capacities, determined to a large extent by source materials and pyrolysis temperatures, enables enhanced sorption of both organic and inorganic contaminants to their surfaces, reducing pollutant mobility when amending contaminated soils. Liming effects or release of carbon into soil solution may increase arsenic mobility, whilst low capital but enhanced retention of plant nutrients can restrict revegetation on degraded soils amended only with biochars; the combination of composts, manures and other amendments with biochars could be their most effective deployment to soils requiring stabilisation by revegetation. Specific mechanisms of contaminant-biochar retention and release over time and the environmental impact of biochar amendments on soil organisms remain somewhat unclear but must be investigated to ensure that the management of environmental pollution coincides with ecological sustainability.

Geochemistry of natural chromium occurrence in a sandstone aquifer in Bauru Basin, Sao Paulo State, Brazil

Anomalous concentrations of Cr(VI) occur in groundwaters of the Adamantina Aquifer, in a large region in the western state of Sao Paulo, sometimes exceeding the potability limit (0.05 mg L(-1)). To identify the possible geochemical reactions responsible for the occurrence of Cr in groundwater in Urania, borehole rock samples were collected in order to carry out mineralogical and chemical analyses. In addition, multilevel monitoring wells were installed and groundwater samples were analyzed. Analyses of the borehole rock samples show the occurrence of a geochemical anomaly of Cr in the quartzose sandstones (average concentrations of 221 ppm). Chrome-diopside is one of the main minerals contributing to this anomaly, having an average Cr content of 1505 ppm. Sequential extraction experiments indicated weakly adsorbed Cr in the order of 0.54 ppm, and this quantity is enough to provide the Cr concentrations observed in groundwater. Groundwaters from the monitoring wells proved to be stratified, with the highest concentrations of Cr(VI) (0.13 mg L(-1)) being associated with high redox and pH values (over 10) and high concentrations of Na. Geochemical reactions that may explain the release of Cr from the solid phase to groundwater involve the release of Cr(III) from minerals (like chrome-diopside and Cr-Fe hydroxide), followed by oxidation of Cr(III) to Cr(VI), probably related to the reduction of Mn oxides present in the aquifer. Then cation exchange occurs and dissolution of carbonates which increases the pH of groundwater, resulting in the desorption and mobilization of Cr(VI) into groundwater. (C) 2011 Elsevier Ltd. All rights reserved.

Relation between sedimentary framework and hydrogeology in the Guarani Aquifer System in Sao Paulo state, Brazil

This paper presents the results of a new investigation of the Guarani Aquifer System (SAG) in Sao Paulo state. New data were acquired about sedimentary framework, flow pattern, and hydrogeochemistry. The flow direction in the north of the state is towards the southwest and not towards the west as expected previously. This is linked to the absence of SAG outcrop in the northeast of Sao Paulo state. Both the underlying Piramboia Formation and the overlying Botucatu Formation possess high porosity (18.9% and 19.5%, respectively), which was not modified significantly by diagenetic changes. Investigation of sediments confirmed a zone of chalcedony cement close to the SAG outcrop and a zone of calcite cement in the deep confined zone. The main events in the SAG post-sedimentary history were: (1) adhesion of ferrugineous coatings on grains, (2) infiltration of clays in eodiagenetic stage, (3) regeneration of coatings with formation of smectites, (4) authigenic overgrowth of quartz and K-feldspar in advanced eodiagenetic stage, (5) bitumen cementation of Piramboia Formation in mesodiagenetic stage, (6) cementation by calcite in mesodiagenetic and telodiagenetic stages in Piramboia Formation, (7) formation of secondary porosity by dissolution of unstable minerals after appearance of hydraulic gradient and penetration of the meteoric water caused by the uplift of the Serra do Mar coastal range in the Late Cretaceous, (8) authigenesis of kaolinite and amorphous silica in unconfined zone of the SAG and cation exchange coupled with the dissolution of calcite at the transition between unconfined and confined zone, and (9) authigenesis of analcime in the confined SAG zone. The last two processes are still under operation. The deep zone of the SAG comprises an alkaline pH, Na-HCO(3) groundwater type with old water and enriched delta(13)C values (<-3.9), which evolved from a neutral pH, Ca-HCO(3) groundwater type with young water and depleted delta(13)C values (>-18.8) close to the SAG outcrop. This is consistent with a conceptual geochemical model of the SAG, suggesting dissolution of calcite driven by cation exchange, which occurs at a relatively narrow front recently moving downgradient at much slower rate compared to groundwater flow. More depleted values of delta(18)O in the deep confined zone close to the Parana River compared to values of relative recent recharged water indicate recharge occur during a period of cold climate. The SAG is a ""storage-dominated"" type of aquifer which has to be managed properly to avoid its overexploitation. (C) 2011 Elsevier Ltd. All rights reserved.

Bacterial Community Composition in Brazilian Anthrosols and Adjacent Soils Characterized Using Culturing and Molecular Identification

Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

Detection of adulterations in processed coffee with cereals and coffee husks using capillary zone electrophoresis

The proposed method for the identification of adulteration was based on the controlled acid hydrolysis of xylan and starch present in some vegetable adulterants, followed by the analysis of the resulting xylose and glucose, which are the monosaccharides that compose, respectively, the two polysaccharides. The acid hydrolysis with HCl increases the ionic strength of the sample, which impairs the electrophoretic separation. Thus, a neutralization step based on anion exchange resin was necessary. The best separations were obtained in NaOH 80 mmol/L, CTAB 0.5 mmol/L, and methanol 30% v/v. Because of the high value of pH, monosaccharides are separated as anionic species in such running electrolyte. The LOQ for both monosaccharides was 0.2 g for 100 g of dry matter, which conforms to the tolerable limits.

Determination of amino acids by capillary electrophoresis-electrospray ionization-mass spectrometry: An evaluation of different protein hydrolysis procedures

In this work, a CE equipment, online hyphenated to an IT MS analyzer by a linear sheath liquid interface promoting ESI, was used to develop a method for quantitative determination of amino acids. Under appropriate conditions (BGE composition, 0.8% HCOOH, 20% CH(3)OH; sheath liquid composition, 0.8% HCOOH, 60% methanol; V(ESI), +4.50 W), analytical curves of all amino acids from 3 to 80 mg/L were recorded presenting acceptable linearity (r > 0.99). LODs in the range of 16-172 mu mol/L were obtained. BSA, a model protein, was submitted to different hydrolysis procedures (classical acid and basic, and catalyzed by the H(+) form of a cation exchanger resin) and its amino acid profiles determined. In general, the resin-mediated hydrolysis yields were overall similar or better than those obtained by classical acid or basic hydrolysis. The resulting experimental-to-theoretical BSA concentration ratios served as correction factors for the quantitation of amino acids in Brazil nut resin generated hydrolysates.

Characterization of organic matter from composting of different residues by physicochemical and spectroscopic methods

Chemical and spectroscopic methods were used to characterize organic matter transformations during the composting process. Four different residue mixtures were studied: P1 - garden trimmings (GT) only, P2 - GT plus fresh cattle manure, P3 - GT plus orange pomace and P4 - GT plus filter cake. The thermophilic phase was not reached in PI compost, but the P2, P3 and P4 composts showed all three typical process phases. The thermophilic phase and CEC/C ratio stabilized after 90 days, while C/N ratio and the ash content stabilized after 60 days. The increasing E(4)/E(6) ratio indicated oxidation reactions occurring during the process in the material from P2, P3 and P4. The (13)C NMR and FTIR results suggested extraction of both pectin and lignin in the HA-like fraction. The CEC/C ratio, temperature and E(4)/E(6) ratio showed that within 90 days P2, P3 and P4 composts were humified. However, material from P1 did not show characteristics of humified compost. From these data, it is apparent that C/N ratio and ash content are not reliable methods for monitoring the composting process. (C) 2009 Elsevier Ltd. All rights reserved.

Modificação estrutural de bentonitas nacionais : caracterização e estudos de adsorção

São apresentados os aspectos teóricos, práticos e bibliográficos envolvidos no desenvolvimento da tese de doutorado intitulada Modificação estrutural de bentonitas nacionais: caracterização e estudos de adsorção. O trabalho consistiu no desenvolvimento de um material adsorvente a partir de bentonitas, do tipo montmorilonitas, modificadas estruturalmente com o objetivo de aumentar sua capacidade de adsorção de poluentes, orgânicos e inorgânicos. O estudo visa incrementar o valor agregado deste recurso mineral e insere-se na área de tratamento de efluentes líquidos usando adsorventes não tradicionais, eficientes e de baixo custo em substituição ao carvão ativado ou às resinas de troca iônica. Foram estudadas as propriedades físicas e químicas; distribuição de tamanho de partículas, área superficial, potenciais eletrocinéticos, capacidade de troca catiônica, composição mineralógica, morfologia superficial e espaçamento basal, bem como as propriedades adsorptivas dos argilominerais não tratados e modificados, não modificadas e pilarizadas respectivamente. Também são discutidos os mecanismos de adsorção envolvidos e o desenvolvimento de um reator contínuo (adsorção em flocos) e de separação sólido/líquido. As modificações estruturais dos argilominerais foram realizadas via homoionização com cloreto de cálcio e posterior intercalação com compostos orgânicos com ação quelante de metais. A FENAN, bentonita obtida pela intercalação com Orto Fenantrolina (OF), foi a que apresentou melhor viabilidade técnica em termos de adsorção, adsorção/dessorção, floculação e de acumulação de poluentes na forma floculada e não floculada. Adicionalmente os estudos de reversibilidade da intercalação revelaram a alta estabilidade da OF na FENAN, em soluções fortemente ácidas, onde aproximadamente 90% da OF permanece ligada à superfície da argila. A quantidade de OF adsorvida na forma de unidades micelares foi de 112 mg por grama de bentonita a pH 8,5 ± 0,5. A caracterização das bentonitas, via difração de Raios X, análise térmica, microscopia eletrônica de varredura e por microscopia de força atômica, revelou que as FENAN possuem um comportamento estrutural muito estável ao longo da seqüência de adsorção/dessorção e que após a adsorção de poluentes inorgânicos, o quelato metálico formado apresenta alta estabilidade dentro da estrutura da organobentonita. A capacidade de acumulação alcançada nas FENAN foi de 110 mg de Cu/g de bentonita, valor superior à de diversos materiais adsorventes alternativos propostos em outros trabalhos similares. Os estudos de acumulação das FENAN floculadas – FENANFLOC, indicaram que a presença de floculante, na quantidade utilizada, não afeta significativamente a capacidade de remoção das bentonitas modificadas. Este comportamento apresentado, permitiu o desenvolvimento do Reator Expandido de Flocos Adsorventes (REFA), cujas características e parâmetros operacionais são discutidos em detalhe. Finalmente, os resultados são discutidos em termos dos fenômenos interfaciais envolvidos e dos potenciais práticos deste novo adsorvente e da nova técnica de adsorção em flocos no REFA.

Avaliação do potencial antiinflamatório, anticoagulante e hemorrágico de heparinóides presentes em "Artemia franciscana"

Heparan sulfate (HS) and Heparin (Hep) glycosaminoglycans (GAGs) are heterogeneous and highly charged polysaccharides. HS is structurally related to Hep but is much less substituted with sulfo groups than heparin and has a more varied structure (or sequence). Because of structural similiarities between these two polymers, they have been described together as heparinoids . Both chains bind a variety of proteins and mediate various physiologically important processes including, blood coagulation, cell adhesion and growth factor regulation. Heparinoids with structural characteristics similar to these described from HS and/or Hep from mammalian tissues have been isolated from different species of invertebrates, although only a few heparinoids from unusual sources have been characterized. The present study describes the presence of unusual heparinoids population from Artemia franciscana, isolated after proteolysis and fractionation by ion exchange resin and named, F-3.0M. The study model in vivo were hemostasis (rat tail scarification) and inflamatoty activity. The tests in vitro were used for coagulations assays (PT and APTT). The analyse of the heparinoids eluted with 3,0M NaCl showed electrophoretic migration in different buffer systems a single band with a behaviour intermediate between those of mammalian HEP and HS. The main products obtained from Artemia heparinoids after enzymatic degradation with heparitinases I and II from F. heparinum were N-sulphated disaccharides (∆U-GlcNS,6S/ ∆U,2S-GlcNS and ∆U-GlcNS) and N-acetylated disaccharides (∆U, GlcNAc). This heparinoid had a lower hemorrhagic effect (400μg/ml) when compared to unfractiionated heparins(25μg/ml).The results also suggest a negligible APTT activity of this heparinoid (62.2s). No action was observed on PT indicating that F-3.0M haven t action on the extrinsic pathway. The results showed that the fraction F- 3.0M have inhibitory effect on migration of leukocytes, 64.5% in the concentration of 10 μg/ml (P<0.001). The search for new heparin and/or heparan sulphates analogs devoid of anticoagulant activity is an atractive alternative and may open up a wide variety of new therapeutic applications

Soil CO2 emission and its relation to soil properties in sugarcane areas under Slash-and-burn and Green harvest

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Culturas de cobertura e sua influência na fertilidade do solo sob sistema de plantio direto (SPD)

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

Small relief shape variations influence spatial variability of soil chemical attributes

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

Atributos do solo sob pastagens em sistema de sequeiro e irrigado

A pecuária é uma das atividades econômicas mais importantes da região do cerrado, sendo que o sucesso dessa atividade é dependente do sistema de manejo e de gramíneas forrageiras adaptadas às condições edafoclimáticas da região. Objetivou-se, neste tabalho, avaliar os atributos do solo em áreas sob pastagens com capim-Tanzânia (Panicum maximum Jacq. cv. Tanzânia) e braquiarão [Brachiaria brizantha (Hochst ex A. Rich.) Stapf. cv. Marandu], em sistema de sequeiro e irrigado no município de Rio Verde, GO. O experimento foi instalado no Centro Tecnológico Comigo, em um Latossolo Vermelho-Amarelo Distrófico típico, em 16 parcelas com 450m² cada. Adotou-se o delineamento em blocos completamente casualisados, referindo-se aos quatro tratamentos: capim-Tanzânia e braquiarão com e sem irrigação, com quatro repetições. Foram realizadas análises de atributos físicos (estabilidade de agregados) e químicas (pH, cálcio, magnésio, potássio, fósforo, acidez potencial, capacidade de troca catiônica, saturação por bases e conteúdo de matéria orgânica). Os atributos químicos variaram em ambas as profundidades, decorrentes principalmente da ação da calagem e adubação do solo independente da ausência ou presença de irrigação. Os tratamentos com capim-Tanzânia e braquiarão sem irrigação apresentaram os maiores teores de matéria orgânica e tiveram os maiores valores do diâmetro médio geométrico (DMG). A maior porcentagem dos agregados ficou retida na peneira de > 2,0mm de malha. A irrigação não afetou a produção de massa seca do capim-Tanzânia e braquiarão.

Extraction methods and availability of phosphorus for soybean in soils from Parana State, Brazil

In studies on the evaluation of methodologies for the analysis of soil, phosphorus (P) has been the single most studied aspect, due to the complexity of this dynamic element in soil. However, these studies have been limited regarding soil conditions in Paranaa. The present study aimed to evaluate the efficiency of the Mehlich-1, Mehlich-3 and ion exchange resin methods in the evaluation of available P for soybean (Glycine max) in the soils of Paranaa State. Twelve soil samples collected from the upper 0-20 cm were planted with soybean for a period of 42 days in the greenhouse. The ability to extract soil P followed the order of decreasing average amount of extracted P: Mehlich-3 > resin > Mehlich-1. The correlation coefficients between the content of P extracted by Mehlich-1, Mehlich-3 and resin and the amount of P accumulated in the plants were 0.86, 0.90 and 0.93, respectively. Mehlich-1, Mehlich-3 and resin showed similar efficiency in the evaluation of P availability to plants and, under conditions of natural fertility and in soils that had received no application of poorly natural reactive phosphates, can be used to quantify the concentrations of P in the soils of Parana State.