Adsorption of DNA to mica mediated by divalent counterions: a theoretical and experimental study

The adsorption of DNA molecules onto a flat mica surface is a necessary step to perform atomic force microscopy studies of DNA conformation and observe DNA-protein interactions in physiological environment. However, the phenomenon that pulls DNA molecules onto the surface is still not understood. This is a crucial issue because the DNA/surface interactions could affect the DNA biological functions. In this paper we develop a model that can explain the mechanism of the DNA adsorption onto mica. This model suggests that DNA attraction is due to the sharing of the DNA and mica counterions. The correlations between divalent counterions on both the negatively charged DNA and the mica surface can generate a net attraction force whereas the correlations between monovalent counterions are ineffective in the DNA attraction. DNA binding is then dependent on the fractional surface densities of the divalent and monovalent cations, which can compete for the mica surface and DNA neutralizations. In addition, the attraction can be enhanced when the mica has been pretreated by transition metal cations (Ni(2+), Zn(2+)). Mica pretreatment simultaneously enhances the DNA attraction and reduces the repulsive contribution due to the electrical double-layer force. We also perform end-to-end distance measurement of DNA chains to study the binding strength. The DNA binding strength appears to be constant for a fixed fractional surface density of the divalent cations at low ionic strength (I < 0.1 M) as predicted by the model. However, at higher ionic strength, the binding is weakened by the screening effect of the ions. Then, some equations were derived to describe the binding of a polyelectrolyte onto a charged surface. The electrostatic attraction due to the sharing of counterions is particularly effective if the polyelectrolyte and the surface have nearly the same surface charge density. This characteristic of the attraction force can explain the success of mica for performing single DNA molecule observation by AFM. In addition, we explain how a reversible binding of the DNA molecules can be obtained with a pretreated mica surface.     

Polyamine metabolism during seedling development in rice

The main free amines identified during growth and development of rice seedlings were agmatine, putrescine, spermidine, diaminopropane and tyramine. Amine composition differed according to tissue and stages of development. Conjugated amines were only found in roots. We present evidence that arginine decarboxylase (ADC) regulates putrescine during the development of rice seedlings. When ADC action was blocked by DFMA (-DL-difluoromethylarginine, a specific irreversible inhibitor of ADC), polyamine titers and seedling development were diminished; when agmatine or putrescine was added, normal polyamine titers and growth were restored. The effects of DFMA were concentration dependent. DFMO (-DL-difluoromethylornithine, a specific irreversible inhibitor of ornithine decarboxylase or ODC) promoted growth and development at concentrations below 2 mM. This effect was probably related to its unexplained, but consistently observed slight enhancement of rice ADC. When the increase in the concentration of spermidine was prevented by CHA (cyclohexylammonium sulfate), the number of roots increased and the increase in length of leaves and roots was strongly inhibited. The addition of exogenous spermidine at the time of treatment with CHA reversed the inhibition by CHA.Abbreviations ADC arginine decarboxylase - ODC ornithine decarboxylase - DFMA -DL-difluoromethylarginine - DFMO -DL-difluoromethylornithine - CHA cyclohexylammonium sulfate     

Nitrogen Behaviour and Nitrous Oxide Emission in the Tidal Seine River Estuary (France) as Influenced by Human Activities in the Upstream Watershed

The Seine River estuary (France) is the receptacle of a drainage basin characterised by high population density, heavy industrial activity and intensive agriculture. Whereas nitrate concentrations are high due to diffuse sources in the upstream drainage basin, ammonium mainly originates from the effluents of the Achères wastewater treatment plant (WWTP) downstream from Paris and its suburbs (6.5 million equivalent-inhabitants). Ammonium is mostly nitrified in the tidal freshwater estuary and nitrification causes a strong summer oxygen deficit. Average longitudinal summer profiles of oxygen and nitrogen concentrations for two periods, between 1993–1997 and 1998–2003 in dry hydrological conditions (excluding the wet years 2000 and 2001) clearly reflect the changes due to the improved treatment of wastewater from Paris and its suburbs. On the basis of daily water flux data and twice monthly nitrogen measurements at the boundaries of the upstream freshwater estuarine section (108 km), we calculated nitrification and denitrification fluxes, whose annual averages were 43 and 71 × 10³ kg N d⁻¹ respectively from 1993 to 2003, with summer values (July–September) representing 73 and 57% of the annual fluxes, respectively. The degree of denitrification in the upper estuary appears to be closely related to the nitrification, itself more loosely related to the amount of reduced nitrogen (Kjeldahl) brought by the treated effluents from the Achères WWTP. We estimated the total N₂O emissions to about 40 kg N d⁻¹ (25–60 kg N d⁻¹) in the same sector.     

Regulation of neuropeptide expression in the brain by neurotrophins

Neurotrophins, which are structurally related to nerve growth factor, have been shown to promote survival of various neurons. Recently, we found a novel activity of a neurotrophin in the brain: Brain-derived neurotrophic factor (BDNF) enhances expression of various neuropeptides. The neuropeptide differentiation activity was then compared among neurotrophins both in vivo and in vitro. In cultured neocortical neurons, BDNF and neurotrophin-5 (NT-5) remarkably increased levels of neuropeptide Y and somatostatin, and neurotrophin-3 (NT-3) also increased these peptides but required higher concentrations. At elevating substance P, however, NT-3 was as potent as BDNF. In contrast, NGF had negligible or no effect. Neurotrophins administered into neonatal brain exhibited slightly different potencies for increasing these neuropeptides: The most marked increase in neuropeptide Y levels was obtained in the neocortex by NT-5, whereas in the striatum and hippocampus by BDNF, although all three neurotrophins increased somatostatin similarly in all the brain regions examined. Overall spatial patterns of the neuropeptide induction were similar among the neurotrophins. Neurons in adult rat brain can also react with the neurotrophins and alter neuropeptide expression in a slightly different fashion. Excitatory neuronal activity and hormones are known to change expression of neurotrophins. Therefore, neurotrophins, neuronal activity, and hormones influence each other and all regulate neurotransmitter/peptide expression in developing and mature brain. Physiological implication of the neurotransmitter/peptide differentiation activities is also discussed.     

Inverse Relationship between Polyamine Levels and the Degree of Phenotypic Alteration Induced by the Root-Inducing, Left-Hand Transferred DNA from Agrobacterium rhizogenes

Floral induction in plants is a paradigm for signal perception, transduction, and physiological response. The introduction of root-inducing, left-hand transferred DNA (Ri T-DNA) into the genomes of several plants results in modifications of flowering (D Tepfer [1984] Cell 47: 959-967), including a delay in flowering in tobacco (Nicotiana tabacum). Conjugated polyamines are markers for flowering in numerous species of plants. In tobacco their accumulation is correlated with the onset of flowering (F Cabanne et al. [1981] Physiol Plant 53: 399-404). Using tobacco, we have explored the possibility of a correlation between the expression of Ri TL-DNA and changes in polyamine metabolism. We made use of two levels of phenotypic change, designated T and T′, that retard flowering by 5 to 10 and 15 to 20 days, respectively. We show that delay in flowering is correlated with a reduction in polyamine accumulation and with a delay in appearance of conjugated polyamines, and we propose that genes carried by the Ri TL-DNA intervene either directly in polyamine metabolism or that polyamine metabolism is closely linked to direct effects of Ri T-DNA expression.     

Effect of Hormone Treatment on Growth Bud Formation and Free Amine and Hydroxycinnamoyl Putrescine Levels in Leaf Explant of Nicotiana tabacum Cultivated in Vitro

Foliar explants of Nicotiana tabacum cv Xanthi n.c. were cultured on four different media: a basal medium, basal medium plus benzyladenine, basal medium plus 2,4-dichlorophenoxyacetic acid (2,4-D), and the basal medium containing both hormones. No differentiation or cell division occurred in leaf explants cultured on the basal medium. Addition of benzyladenine caused the formation of buds on the explants, while 2,4-D caused callus formation and proliferation. Likewise, only callus was formed when explants were cultured on medium containing both hormones, but growth was significantly greater than that of callus grown on a medium containing 2,4-D alone. The levels of amines and hydroxycinnamoyl putrescines were determined in the four types of explants. In nongrowing explants, amines (except an aromatic amine, tyramine) and hydroxycinnamoyl putrescines were always at a low level and only small changes in their concentrations were observed. In callus cultures, amine (except an aromatic amine, phenethylamine) and hydroxycinnamoyl putrescine levels were higher than those found in bud cultures. In all the media, transitory accumulation of aromatic amines occurred after a few days of culture. Higher levels of hydroxycinnamoyl putrescines were attained in callus cultures with a slow growth rate (2,4-D alone) than in callus cultures with a fast growth rate (benzyladenine + 2,4-D). The formation of buds was accompanied by significant changes in putrescine and hydroxycinnamoyl putrescine levels. Increasing levels were found during the first 14 days in culture when cell multiplication was rapid, followed by a sharp decline after 20 days in culture as the rate of cell division decreased and differentiation took place. The relationship among amines, hydroxycinnamoyl putrescines, and cell division and bud formation is discussed.     

Effect of cinnamoyl putrescines on in vitro cell multiplication and differentiation of tobacco explants

Hydroxycinnamoyl putrescines promote the cell multiplication of leaf discs of a tobacco mutant, RMB₇, cultivatedin vitro on the Murashige and Skoog medium. This mutant never accumulates these molecules during its development and does not enter in floweirng. Maximal effect is obtained at 2.5·10^–4M. The same molecules inhibit bud formation ofNicotiana tabacum var. Xanthi nc, at 5·10^–5 M but promote callus formation. From 10^–4 M to 5·10^–3 M they strongly inhibit cell multiplication and bud formation without toxic effect. Their possible role in plant metabolism is discussed.Abbreviations IAA indole 3-acetic-acid - BA benzyladenine     

Changing root and shoot architecture with the rolA gene from Agrobacterium rhizogenes: Interactions with gibberellic acid and polyamine metabolism

The effects of rolA on root and shoot architecture have been ascribed to a deficiency in gibberellic acid (GA₃) and to changes in polyamine metabolism. Using tobacco, we examined interactions among GA₃, a polyamine accumulation inhibitor (α-DL-difluoromethylornithine or DFMO) and the rolA gene controlled by the 35S CaMV promoter. We measured the effects of these three agents on architecture and polyamine accumulation in excised roots and whole plants grown in vitro. Previous work showed that DFMO or genetic transformation with the rolA gene from Agrobacterium rhizogenes, controlled by the 35S promoter (P_35S-rolA), caused excised tobacco roots to grow faster with altered root system architecture. We show that gibberellic acid (GA₃) reversed the effects of DFMO on the architecture of excised root systems, but neither reversed the effects of DFMO on growth, nor the changes in growth and architecture associated with P_35S-rolA. GA₃ treatment alone resulted in increased agmatine levels, suggesting that the inhibition of the effects of DFMO on architecture was through a stimulation of the arginine decarboxylase (ADC) pathway, GA₃ alone also inhibited the accumulation of putrescine and tyramine conjugates in excised roots. In tobacco plants growing in vitro DFMO and P_35S-rolA were associated with reduced shoot height, which was partially restored by GA₃ treatment; however, GA₃ also stimulated shoot height in the controls. GA₃ did not lessen the leaf wrinkling associated with P_35S-rolA. P_35S-rolA increased root number in young seedlings in vitro, and increased root system length in seedlings grown in soil. As in excised roots, the developmental changes linked to DFMO and P_35S-rolA were accompanied by reductions in putrescine titers. GA₃ treatment stimulated putrescine accumulation in stems and leaves, and partially reversed the negative effects of DFMO and P_35S-rolA on putrescine accumulation in roots, stems and leaves. Again, the restoration of putrescine pools appeared to be through a stimulation of the ADC pathway, since agmatine accumulated in plants exposed to GA₃. In general, the effects of DFMO and P_35S-rolA on phenotype and polyamine metabolism were coordinated, and in many cases these effects were similarly modulated by GA₃, reinforcing the previous conclusion that the phenotypic effects of rolA in roots and shoots occur through interference with polyamine metabolism and that the putrescine conjugates are particularly important in regulating root system growth and architecture. We were unable, however, to discem consistent evidence for a direct role for GA₃ in establishing the RolA phenotype.