Computation of Surface Electrical Potentials of Plant Cell Membranes : Correspondence to Published Zeta Potentials from Diverse Plant Sources

A Gouy-Chapman-Stern model has been developed for the computation of surface electrical potential (ψ0) of plant cell membranes in response to ionic solutes. The present model is a modification of an earlier version developed to compute the sorption of ions by wheat (Triticum aestivum L. cv Scout 66) root plasma membranes. A single set of model parameters generates values for ψ0 that correlate highly with published ζ potentials of protoplasts and plasma membrane vesicles from diverse plant sources. The model assumes ion binding to a negatively charged site (R− = 0.3074 μmol m−2) and to a neutral site (P0 = 2.4 μmol m−2) according to the reactions R− + IΖ ⇌ RIΖ−1 and P0 + IΖ ⇌ PIΖ, where IΖ represents an ion of charge Ζ. Binding constants for the negative site are 21,500 m−1 for H+, 20,000 m−1 for Al3+, 2,200 m−1 for La3+, 30 m−1 for Ca2+ and Mg2+, and 1 m−1 for Na+ and K+. Binding constants for the neutral site are 1/180 the value for binding to the negative site. Ion activities at the membrane surface, computed on the basis of ψ0, appear to determine many aspects of plant-mineral interactions, including mineral nutrition and the induction and alleviation of mineral toxicities, according to previous and ongoing studies. A computer program with instructions for the computation of ψ0, ion binding, ion concentrations, and ion activities at membrane surfaces may be requested from the authors.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands.

We have used an in vitro selection procedure called crosslinking SELEX (SELEX = systematic evolution of ligands by exponential enrichment) to identify RNA sequences that bind with high affinity and crosslink to the Rev protein from human immunodeficiency virus type 1 (HIV-1). A randomized RNA library substituted with the photoreactive chromophore 5-iodouracil was irradiated with monochromatic UV light in the presence of Rev. Those sequences with the ability to photocrosslink to Rev were partitioned from the rest of the RNA pool, amplified, and used for the next round of selection. Rounds of photocrosslinking selection were alternated with rounds of selection for RNA sequences with high affinity to Rev. This iterative, dual-selection method yielded RNA molecules with subnanomolar dissociation constants and high efficiency photocrosslinking to Rev. Some of the RNA molecules isolated by this procedure form a stable complex with Rev that is resistant to denaturing gel electrophoresis in the absence of UV irradiation. In vitro selection of nucleic acids by using modified nucleotides allows the isolation of nucleic acid molecules with potentially limitless chemical capacities to covalently attack a target molecule.

Geoquímica multielementar de sedimentos de corrente no Estado de São Paulo: abordagem através da análise estatística multivariada

Este trabalho apresenta resultados geoquímicos multielementares de sedimentos de corrente no estado de São Paulo, obtidos através do projeto institucional do Serviço Geológico do Brasil denominado \"Levantamento Geoquímico de Baixa Densidade no Brasil\". Dados analíticos de 1422 amostras de sedimento de corrente obtidos por ICP-MS (Inductively Coupled Plasma Mass Spectrometry), para 32 elementos químicos (Al, Ba, Be, Ca, Ce, Co, Cr, Cs, Cu, Fe, Ga, Hf, K, La, Mg, Mn, Mo, Nb, Ni, P, Pb, Rb, Sc, Sn, Sr, Th, Ti, U, V, Y, Zn e Zr), foram processadas e abordadas através da análise estatística uni e multivariada. Os resultados do tratamento dos dados através de técnicas estatísticas univariadas forneceram os valores de background geoquímico (teor de fundo) dos 32 elementos para todo estado de São Paulo. A análise georreferenciada das distribuições geoquímicas unielementares evidenciaram a compartimentação geológica da área. As duas principais províncias geológicas do estado de São Paulo, Bacia do Paraná e Complexo Cristalino, se destacam claramente na maioria das distribuições geoquímicas. Unidades geológicas de maior expressão, como a Formação Serra Geral e o Grupo Bauru também foram claramente destacadas. Outras feições geoquímicas indicaram possíveis áreas contaminadas e unidades geológicas não cartografadas. Os resultados da aplicação de métodos estatísticos multivariados aos dados geoquímicos com 24 variáveis (Al, Ba, Ce, Co, Cr, Cs, Cu, Fe, Ga, La, Mn, Nb, Ni, Pb, Rb, Sc, Sr, Th, Ti, U, V, Y, Zn e Zr) permitiram definir as principais assinaturas e associações geoquímicas existentes em todo estado de São Paulo e correlacioná-las aos principais domínios litológicos. A análise de agrupamentos em modo Q forneceu oito grupos de amostras geoquimicamente correlacionáveis, que georreferenciadas reproduziram os principais compartimentos geológicos do estado: Complexo Cristalino, Grupos Itararé e Passa Dois, Formação Serra Geral e Grupos Bauru e Caiuá. A análise discriminante multigrupos comprovou, estatisticamente, a classificação dos grupos formados pela análise de agrupamentos e forneceu as principais variáveis discriminantes: Fe, Co, Sc, V e Cu. A análise de componentes principais, abordada em conjunto com a análise fatorial pelo método de rotação varimax, forneceram os principais fatores multivariados e suas respectivas associações elementares. O georreferenciamento dos valores de escores fatoriais multivariados delimitaram as áreas onde as associações elementares ocorrem e forneceram mapas multivariados para todo o estado. Por fim, conclui-se que os métodos estatísticos aplicados são indispensáveis no tratamento, apresentação e interpretação de dados geoquímicos. Ademais, com base em uma visão integrada dos resultados obtidos, este trabalho recomenda: (1) a execução dos levantamentos geoquímicos de baixa densidade em todo país em caráter de prioridade, pois são altamente eficazes na definição de backgrounds regionais e delimitação de províncias geoquímicas com interesse metalogenético e ambiental; (2) a execução do mapeamento geológico contínuo em escala adequada (maiores que 1:100.000) em áreas que apontam para possíveis existências de unidades não cartografadas nos mapas geológicos atuais.

Eficiência de uso de nitrogênio pela cana-de-açúcar: diferenças genotípicas, preferência por amônio e emissão de N2O

O uso ineficiente do nitrogênio (N) é um problema global, que pode diminuir a sustentabilidade da produção agrícola da cana-de-açúcar para fins energéticos devido às emissões de N2O oriundas da fertilização nitrogenada. A eficiência de utilização de nitrogênio (EUN) tem sido pouco estudada em genótipos de cana-de-açúcar, o que pode ser preocupante devido a importância da cultura para o país. O objetivo desse estudo foi avaliar a EUN de genótipos de cana-de-açúcar, verificando se genótipos contrastantes tem preferência de absorção por amônio ao invés de nitrato, e checar se extratos radiculares de Brachiaria humidicola e Saccharum spontaneum aumentam a eficiência de utilização de N pela cultura. Para isso três experimentos foram desenvolvidos em condições controladas em casa-de-vegetação e câmara de crescimento. No primeiro deles, 18 genótipos foram submetidos a dois níveis de N: limitante (baixo N) e suficiente (alto N). Posteriormente, quatro genótipos selecionados quanto a EUN do primeiro experimento, foram cultivados em câmara de crescimento por 69 dias, onde receberam quantidades conhecidas de N-fertilizante marcado ou no 15NH4+ ou no 15NO3-, sendo avaliados 24 e 72 horas após a aplicação do fertilizante marcado. Um terceiro ensaio foi realizado, em que extratos radiculares de Brachiaria humidicola (BCH) e Saccharum spontaneum (SCS) foram aplicados ao solo com o intuito de verificar seu potencial como inibidor da nitrificação, comparando-os com a dicianodiamida (DCD), e seu efeito para o aumento do aproveitamento do N pela cana-de-açúcar. No experimento de EUN verificou-se grande variação entre os genótipos. Dos 18 genótipos avaliados, seis foram classificados como responsivos a N e eficientes na utilização de N, três foram não eficientes e responsivos; dois foram eficientes e não responsivos, e sete não eficientes e não responsivos. Esse resultado comprova que a recomendação da adubação nitrogenada pode realmente estar pouco precisa, pois não leva em consideração a EUN de cada genótipo, sendo realizada uma aplicação genérica. As medições de fotossíntese mostraram que os genótipos mais eficientes na utilização do N, não necessariamente possuem as taxas fotossintéticas mais elevadas, estando a EUN diretamente relacionada à quantidade de raízes das plantas. No segundo trabalho, verificou-se que o N na planta proveniente do fertilizante (NPPF), 72 horas após a aplicação do N, foi 36% menor quando a fonte marcada foi NO3-, atestando que a cana-de-açúcar tem preferência de absorção por amônio em relação ao nitrato nos primeiros dias após a adubação nitrogenada. Por fim, os resultados do terceiro ensaio mostraram que a aplicação de sulfato de amônio (SA), associado ao inibidor sintético DCD, manteve os valores de N-NO3- baixos ao longo de todo período de avaliação (durante 60 dias), enquanto que com SA, SA+BCH e SA+SCS houve um aumento na concentração de nitrato no solo já a partir de 15 dia após a fertilização. O uso de DCD reduziu o fluxo médio de N2O durante o período de avaliação em relação ao uso isolado do fertilizante, o que não foi observado com o uso de extratos de raízes de Brachiaria humidicola e Saccharum spontaneum

Vegetation Changes to the Okavango Delta, Botswana; A Comparison Between Managed and Non-Managed Areas

This capstone explores vegetation changes in the Okavango Delta area of Botswana. Spatial analyses were conducted using Moderate Resolution Imaging Spectroradiometer Normalized Difference Vegetation Index satellite imagery and Geographic Information System land management data to compare vegetation changes within managed areas to determine whether management practices have had beneficial or adverse impacts. Rainfall, logging, and livestock data were utilized to attempt to find a link to precipitation, logging, or overgrazing. After analysis the livestock data were the only one that showed a correlation to the vegetation changes observed. Of the vegetation cover types analyzed, forest showed the most change, a significant decrease. Little difference in vegetation changes was found in the managed areas, indicating that land management techniques are ineffective.

Towards the Design of a Textile Chemical Ontology

The main goal of this paper is to present the initial version of a Textile Chemical Ontology, to be used by textile professionals with the purpose of conceptualising and representing the banned and harmful chemical substances that are forbidden in this domain. After analysing different methodologies and determining that “Methontology” is the most appropriate for the purposes, this methodology is explored and applied to the domain. In this manner, an initial set of concepts are defined, together with their hierarchy and the relationships between them. This paper shows the benefits of using the ontology through a real use case in the context of Information Retrieval. The potentiality of the proposed ontology in this preliminary evaluation encourages extending the ontology with a higher number of concepts and relationships, and validating it within other Natural Language Processing applications.

Pursuing Chemical Efficiency by Using Supported Organocatalysts for Asymmetric Reactions under Aqueous Conditions

Over the past decade, a great effort has been made by the chemical community to improve the efficiency of organic transformations and allow sustainable processes. Merging the use of supported and recyclable organocatalysts and aqueous conditions for the asymmetric synthesis of valuable molecules, has led to outstanding contributions in the area of green chemistry. Recent progresses in the field include the implementation of these methodologies in the large scale production of chiral molecules using automated flow chemistry.

Analysis of minerals from Arctic Ocean sediments

The Arctic Ocean System is a key player regarding the climatic changes of Earth. Its highly sensitive ice Cover, the exchange of surface and deep water masses with the global ocean and the coupling with the atmosphere interact directly with global climatic changes. The output of cold, polar water and sea ice influences the production of deep water in the North Atlantic and controls the global ocean circulation ("the conveyor belt"). The Arctic Ocean is surrounded by the large Northern Hemisphere ice sheets which not only affect the sedimentation in the Arctic Ocean but also are supposed to induce the Course of glacials and interglacials. Terrigenous sediment delivered from the ice sheets by icebergs and meltwater as well as through sea ice are major components of Arctic Ocean sediments. Hence, the terrigenous content of Arctic Ocean sediments is an outstanding archive to investigate changes in the paleoenvironment. Glazigenic sediments of the Canadian Arctic Archipelago and surface samples of the Arctic Ocean and the Siberian shelf regions were investigated by means of x-ray diffraction of the bulk fraction. The source regions of distinct mineral compositions were to be deciphered. Regarding the complex circumpolar geology stable christalline shield rocks, active and ancient fold belts including magmatic and metamorphic rocks, sedimentary rocks and wide periglacial lowlands with permafrost provide a complete range of possible mineral combinations. Non- glaciated shelf regions mix the local input from a possible point source of a particular mineral combination with the whole shelf material and function as a sampler of the entire region draining to the shelf. To take this into account, a literature research was performed. Descriptions of outcropping lithologies and Arctic Ocean sediments were scanned for their mineral association. The analyses of glazigenic and shelf sediments yielded a close relationship between their mineral composition and the adjacent source region. The most striking difference between the circumpolar source regions is the extensive outcrop of carbonate rocks in the vicinity of the Canadian Arctic Archipelago and in N Greenland while siliciclastic sediments dominate the Siberian shelves. In the Siberian shelf region the eastern Kara Sea and the western Laptev Sea form a destinct region defined by high smectite, (clino-) pyroxene and plagioclase input. The source of this signal are the extensive outcrops of the Siberian trap basalt in the Putorana Plateau which is drained by the tributaries of the Yenissei and Khatanga. The eastern Laptev Sea and the East Siberian Sea can also be treated as one source region containing a feldspar, quartz, illite, mica, and chlorite asscciation combined with the trace minerals hornblende and epidote. Franz Josef Land provides a mineral composition rich in quartz and kaolinite. The diverse rock suite of the Svalbard archipelago distributes specific mineral compositions of highly metamorphic christalline rocks, dolomite-rich carbonate rocks and sedimentary rocks with a higher diagenetic potential manifested in stable newly built diagenetic minerals and high organic maturity. To reconstruct the last 30,000 years as an example of the transition between glacial and interglacial conditions a profile of sediment cores, recovered during the RV Polarstern" expedition ARK-VIIIl3 (ARCTIC '91), and additional sediment cores around Svalbard were investigated. Besides the mineralogy of different grain size fractions several additional sedimentological and organo-geochemical Parameterswere used. A detailed stratigraphic framework was achieved. By exploiting this data set changes in the mineral composition of the Eurasian Basin sediments can be related to climatic changes. Certain mineral compositions can even be associated with particular transport processes, e.g. the smectitel pyroxene association with sea ice transport from the eastern Kara Sea and the western Laptev Sea. Hence, it is possible to decipher the complex interplay between the influx of warm Atlantic waters into the Southwest of the Eurasian Basin, the waxing and waning of the Svalbard1Barents- Sea- and Kara-Sea-Ice-Sheets, the flooding of the Siberian shelf regions and the surface and deep water circulation. Until now the Arctic Ocean was assumed to be a rather stable System during the last 30,000 years which only switched from a completely ice covered situation during the glacial to seasonally Open waters during the interglacial. But this work using mineral assemblages of sediment cores in the vicinity of Svalbard revealed fast changes in the inflow of warm Atlantic water with the Westspitsbergen Current (< 1000 years), short periods of advances and retreats of the marine based Eurasian ice sheets (1000-3000 years), and short melting phases (400 years?). Deglaciation of the marine-based Eurasian and the land-based north American and Greenland ice sheets are not simultaneous. This thesis postulates that the Kara Sea Ice Sheet released an early meltwater signal prior to 15,000 14C years leading the Barents Sea Ice Sheet while the western land-based ice sheets are following later than 13,500 14C years. The northern Eurasian Basin records the shift between iceberg and sea-ice material derived from the Canadian Arctic Archipelago and N-Greenland and material transported by sea-ice and surface currents from the Siberian shelf region. The phasing of the deglaciation becomes very obvious using the dolomite and quartd phyllosilicate record. It is also supposed that the flooding of the Laptev Sea during the Holocene is manifested in a stepwise increase of sediment input at the Lomonosov Ridge between the Eurasian and Amerasian Basin. Depending on the strength of meltwater pulses from the adjacent ice sheets the Transpolar Drift can probably be relocated. These movements are traceable by the distribution of indicator minerals. Based on the outcome of this work the feasibility of bulk mineral determination can be qualified as excellent tool for paleoenvironmental reconstructions in the Arctic Ocean. The easy preparation and objective determination of bulk mineralogy provided by the QUAX software bears the potential to use this analyses as basic measuring method preceding more time consuming and highly specialised mineralogical investigations (e.g. clay mineralogy, heavy mineral determination).

Risk Criticism : Precautionary Reading in an Age of Environmental Uncertainty /

'Risk Criticism: Reading in an Age of Manufactured Uncertainties' is a study of literary and cultural responses to global environmental risk that offers an environmental humanities approach to understanding risk in an age of unfolding ecological catastrophe. In 2015, the Bulletin of the Atomic Scientists re-set its iconic Doomsday Clock to three minutes to midnight, as close to the apocalypse as it has been since 1953. What pushed its hands was, however, not just the threat of nuclear weapons, but also other global environmental risks that the Bulletin judged to have risen to the scale of the nuclear, including climate change and innovations in the life sciences. If we may once have believed that the end of days would come in a blaze of nuclear firestorm (or the chill of the subsequent nuclear winter), we now suspect that the apocalypse may be much slower, creeping in as chemical toxin, climate change, or bio- or nano- technologies run amok. Taking inspiration from the questions raised by the Bulletin’s synecdochical “nuclear,” 'Risk Criticism' aims to generate a hybrid form of critical practice that brings “nuclear criticism”—a subfield of literary studies that has been, since the Cold War, largely neglected—into conversation with ecocriticism, the more recent approach to environmental texts in literary studies. Through readings of novels, films, theater, poetry, visual art, websites, news reports, and essays, 'Risk Criticism' tracks the diverse ways in which environmental risks are understood and represented today.

Biosynthetic pathways to dichloroimines; precursor incorporation studies on terpene metabolites in the tropical marine sponge Stylotella aurantium

The biosynthetic origin of the dichloroimine functional group in the marine sponge terpene metabolites stylotellanes A ( 3) and B ( 4) was probed by the use of [C-14]-labelled precursor experiments. Incubation of the sponge Stylotella aurantium with [C-14]-labelled cyanide or thiocyanate resulted in radioactive terpenes in which the radiolabel was shown by hydrolytic chemical degradation to be associated specifically with the dichloroimine carbons. Additionally, label from both precursors was incorporated into farnesyl isothiocyanate ( 2). A time course experiment with [ 14C]cyanide revealed that the specific activity for farnesyl isothiocyanate decreases over time, but increases for stylotellane B ( 4), consistent with the rapid formation of farnesyl isothiocyanate ( 2) from inorganic precursors followed by a slower conversion to stylotellane B ( 4). The advanced precursors farnesyl isothiocyanate ( 2) and farnesyl isocyanide ( 5) were supplied to S. aurantium, and shown to be incorporated efficiently into stylotellane A ( 3) and B ( 4). Feeding of [C-14]-farnesyl isothiocyanate ( 2) resulted in a higher incorporation of label than with [C-14]-farnesyl isocyanide ( 5). Farnesyl isocyanide was incorporated into farnesyl isothiocyanate in agreement with labelling studies in other marine sponges. Both farnesyl isocyanide and isothiocyanate were further incorporated into axinyssamide A ( 11) as well as the cyclized dichloroimines (12)-(14), ( 16) that represent more advanced biosynthetic products of this pathway. These results identify the likely biosynthetic pathway leading to the major metabolites of S. aurantium.

Blanchaquinone: A new anthraquinone from an Australian Streptomyces sp.

Chemical analysis of an Australian Streptomyces species yielded a range of known anthracyclines and biosynthetically related metabolites, including daunomycin (1), E-rhodomycinone (2), 11-hydroxyauramycinone (3), 11-hydroxysulfurmycinone (4), aklavinone (5), bisanhydro-gamma-rhodomycinone (6), and the anthraquinone 7, as well as the hitherto unreported blanchaquinone (8). The structure assigned to 8 was secured by detailed spectroscopic analysis and correlation to known analogues, such as the anthraquinone 7. This account also represents the first natural occurrence of 3, 4, and 7 and the first spectroscopic characterization of 11-hydroxysulfurmycinone (4).

AMS dating of rock art in the Laura Region, Cape York Peninsula, Australia - protocols and results of recent research

The authors describe rock art dating research in Australia using the oxalate method While the array of dates obtained (which range from c. 1200 to c. 25000 BP) show a satisfactory correlation with other archaeological data, there are mismatches which suggest that some motifs were often imitated by later artists, and/or that the mineral accretions continued to form periodically, perhaps continuously, as a regional phenomenon over a long period of time.

Mechanics of cellular adhesion to artificial artery templates

We are using polymer templates to grow artificial artery grafts in vivo for the replacement of diseased blood vessels. We have previously shown that adhesion of macrophages to the template starts the graft formation. We present a study of the mechanics of macrophage adhesion to these templates on a single cell and single bond level with optical tweezers. For whole cells, in vitro cell adhesion densities decreased significantly from polymer templates polyethylene to silicone to Tygon (167, 135, and 65 cells/mm(2)). These cell densities were correlated with the graft formation success rate (50%, 25%, and 0%). Single-bond rupture forces at a loading rate of 450 pN/s were quantified by adhesion of trapped 2-mm spheres to macrophages. Rupture force distributions were dominated by nonspecific adhesion (forces, < 40 pN). On polystyrene, preadsorption of fibronectin or presence of serum proteins in the cell medium significantly enhanced adhesion strength from a mean rupture force of 20 pN to 28 pN or 33 pN, respectively. The enhancement of adhesion by fibronectin and serum is additive (mean rupture force of 43 pN). The fraction of specific binding forces in the presence of serum was similar for polystyrene and polymethyl-methacrylate, but specific binding forces were not observed for silica. Again, we found correlation to in vivo experiments, where the density of adherent cells is higher on polystyrene than on silica templates, and can be further enhanced by fibronectin adsorption. These findings show that in vitro adhesion testing can be used for template optimization and to substitute for in-vivo experiments.