Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Descriptors of Posidonia oceanica meadows: Use and application

The conservation of the coastal marine environment requires the possession of information that enables the global quality of the environment to be evaluated reliably and relatively quickly. The use of biological indicators is often an appropriate method. Seagrasses in general, and Posidonia oceanica meadows in particular, are considered to be appropriate for biomonitoring because of their wide distribution, reasonable size, sedentary habit, easy collection and abundance and sensitivity to modifications of littoral zone. Reasoned management, on the scale of the whole Mediterranean basin, requires standardized methods of study, to be applied by both researchers and administrators, enabling comparable results to be obtained. This paper synthesises the existing methods applied to monitor P. oceanica meadows, identifies the most suitable techniques and suggests future research directions. From the results of a questionnaire, distributed to all the identified laboratories working on this topic, a list of the most commonly used descriptors was drawn up, together with the related research techniques (e.g. standardization, interest and limits, valuation of the results). It seems that the techniques used to study meadows are rather similar, but rarely identical, even though the various teams often refer to previously published works. This paper shows the interest of a practical guide that describes, in a standardized way, the most useful techniques enabling P. oceanica meadows to be used as an environmental descriptor. Indeed, it constitutes the first stage in the process. (c) 2005 Elsevier Ltd. All rights reserved.Peer reviewe

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

Sugarcane root length density and distribution from root intersection counting on a trench-profile

Root length density (RLD) is a critical feature in determining crops potential to uptake water and nutrients, but it is difficult to be measured. No standard method is currently available for assessing RLD in the soil. In this study, an in situ method used for other crops for studying root length density and distribution was tested for sugarcane (Saccharum spp.). This method involved root intersection counting (RIC) on a Rhodic Eutrudox profile using grids with 0.05 x 0.05 m and modeling RLD from RIC. The results were compared to a conventional soil core-sampled method (COR) (volume 0.00043 m³). At four dates of the cropping season in three tillage treatments (plowing soil, minimum tillage and direct planting), with eight soil depths divided in 0.1 m soil layer (between 0-0.6 and 1.6-1.8 m) and three horizontal distances from the row (0-0.23, 0.23-0.46 and 0.46-0.69 m), COR and RIC methods presented similar RLD results. A positive relationship between COR and RIC was found (R² = 0.76). The RLD profiles considering the average of the three row distances per depth obtained using COR and RIC (mean of four dates and 12 replications) were close and did not differ at each depth of 0.1 m within a total depth of 0.6 m. Total RLD between 0 and 0.6 m was 7.300 and 7.100 m m-2 for COR and RIC respectively. For time consumption, the RIC method was tenfold less time-consuming than COR and RIC can be carried out in the field with no need to remove soil samples. The RLD distribution in depth and row distance (2-D variability) by RIC can be assessed in relation to the soil properties in the same soil profiles. The RIC method was suitable for studying these 2-D (depth and row distance in the soil profile) relationships between soil, tillage and root distribution in the field.A densidade de comprimento de raízes (DCR) é uma característica importante para determinar o potencial de absorção de água e nutrientes das plantas, mas é difícil de ser medida. Nenhum método padrão está atualmente disponível para avaliar a DCR no solo. Neste estudo, um método in situ usado em outras culturas para estudo da densidade de comprimento e distribuições das raízes foi testado para a cana-de-açúcar (Saccharum spp.). O método envolveu contagem de intersecções de raízes (CIR) no perfil de um Latossolo Vermelho eutroférrico, usando grade com quadrículas de 0.05 x 0.05 m, modelizando a DCR a partir da CIR. Os resultados foram comparados com o método do trado cilíndrico (TRA) (volume de 0.00043 m-3). Em quatro épocas durante o ciclo em três manejos do solo (plantio convencional, cultivo mínimo e plantio direto), em oito profundidades divididas a cada 0.1 m (entre 0 - 0.6 e 1.6 - 1.8 m) e três distâncias horizontais em relação à linha de plantio (0 - 0.23, 0.23 - 0.46 e 0.46 - 0.69 m), os métodos TRA e CIR apresentaram resultados de DCR similares. Encontrou-se positiva entre TRA e CIR (R² = 0,76). As DCRs nos perfis, considerando as médias das três distâncias da linha por profundidade, obtida utilizando-se de TRA e CIR (média de quatro datas e 12 repetições), foram próximas e não diferiram a cada 0.1 m de profundidade até 0.6 m de profundidade. A DCR total entre 0 e 0.6 m foi de 7.300 e 7.100 m m-2 para TRA e CIR, respectivamente. Para o tempo de realização, o método CIR foi 10 vezes mais rápido do que TRA e o método CIR pode ser realizado no campo, sem necessidade de remover amostras de solo. A distribuição da DCR em profundidade e distância da linha (variabilidade 2D) pelo método CIR pode ser avaliada em relação às propriedades do solo nos mesmos perfis do solo. O método CIR foi apropriado para estudos dessas relações 2D (profundidade e distância da linha no perfil do solo) entre solo, manejo e distribuição de raízes no campo

Strategies in the use of light energy by Genipa spruceana Steyerm seedlings subjected to flooding

In an attempt to elucidate strategies in the use of light energy by G. spruceana seedlings subjected to flooding, we investigated the capacity of light capture and use of light energy by G. spruceana in three growing conditions: 1- absence of flooding (SA), 2- partially flooded (PA) and 3- totally flooded (TA). Destructive and non-destructive measurements, such as specific leaf area, chloroplast pigment (chlorophyll and carotenoids) content and fluorescence analyses, were made at regular intervals over a period of 90 days. All parameters decreased in seedlings subjected to flooding. Plants of treatment TA dropped all of their leaves after 30 days of complete submergence. Chloroplast pigment content differed between treatments SA and TA after 30 days from the start of the experiment; whereas SA and PA plants only differed for this variable after 90 days. Plants subjected to flooding (PA and TA) exhibited high dissipation of photochemical de-excitation (DIo/ABS), indicating a limited efficiency of light energy use. This fact was proven by the performance index (PI ABS) only in analyses after 90 days, and no significant difference was verified for PI ABS among treatments up to 30 days. Therefore, considering that G. spruceana seedlings subjected to flooding reduced the chloroplast pigment content more quickly than PI ABS, we suggest that the light energetic flux in G. spruceana seedlings subjected to flooding, in the beginning, is more restricted to a decrease in the structures that captures light (reduction chlorophyll pigment content) than how the photosynthetic apparatus functions (alterations in photochemical efficiency of photosystem II).Na tentativa de elucidar estratégias de utilização da energia luminosa em plantas jovens de Genipa spruceana Steyerm submetidas ao alagamento, nós investigamos a capacidade de captura e uso de energia luminosa em G. spruceana sob três condições de crescimento1- ausência de alagamento (SA), 2- plantas parcialmente alagadas (PA) e 3- plantas totalmente alagadas (TA). Medidas de área foliar específica, teores de pigmentos cloroplastídicos e fluorescência da clorofila a foram feitas em intervalos regulares no período de 90 dias. Todos os parâmetros analisados diminuíram em condições de alagamento (PA e TA). Aos 30 dias, as plantas no tratamento TA sofreram abscisão foliar. Os teores dos pigmentos cloroplastídicos (clorofilas e carotenóides) entre os tratamentos SA e TA diferiram aos 30 dias. Ao passo que, somente foi possível verificar diferenças entre os tratamentos SA e PA aos 90 dias. As plantas submetidas ao alagamento (PA e TA) exibiram alta dissipação de energia de excitação (DIo/ABS) indicando limitada eficiência na utilização da energia luminosa. Este fato foi comprovado pelos resultados do índice de desempenho (PI ABS) somente ao fim do período experimental (90 dias). Mas, não foi verificado diferença para PI ABS entre os tratamentos aos 30 dias. Portanto, considerando que G. spruceana submetidas ao tratamento TA reduziram seus teores de clorofilas mais rapidamente do que decrescem seus PI ABS, sugere-se que o fluxo de energia luminosa em plântulas de G. spruceana sob alagamento total, no início, é mais restringido pelo decréscimo na estrutura de captura de luz (diminuição dos pigmentos cloroplastídicos) do que no funcionamento do aparato fotossintético (alterações na eficiência fotoquímica do fotossistema II)