The binding of 1,N6-ethenoNAD to bovine liver glutamate dehydrogenase: studies using the time-correlated single photon counting fluorescence technique

The time-correlated single photon counting (TCPC) fluorescence technique has been used as a novel approach to investigate ligand-protein interaction, for the case of the binding of the fluorescent coenzyme analogue 1,N6-ethenoNAD (epsilon NAD) to bovine liver glutamate dehydrogenase in the presence of glutarate, a substrate analogue which stabilizes the complex. System calibration was performed using solutions of epsilon ADP and carefully purified epsilon NAD mixed at variable molar ratios (pH 7.0, 0.05 M sodium phosphate buffer, 20 degrees C). The fluorescence lifetimes obtained after deconvolution were 2.4 ns (for epsilon NAD) and 23 ns (for epsilon ADP), in good agreement with literature values obtained under similar conditions. epsilon NAD binds to glutamate dehydrogenase in the presence of 50 mM glutarate, with a fluorescence quantum yield enhancement factor, Q, of about 17-fold, as previously reported (Favilla, R. and Mazzini, A. (1984) Biochim. Biophys. Acta 48-57). For this system, fluorescence lifetime values were obtained after deconvolution as 2.4 ns for free epsilon NAD and 21 ns for bound epsilon NAD. These values did not vary appreciably with enzyme concentration nor with degree of saturation, thus reflecting the existence of only one spectroscopically relevant type of complex. Addition of either GTP or ADP did not affect the lifetime of epsilon NAD bound to the enzyme, but only its affinity, thus allowing calculations of binding strengths. In the case of a simple binding (i.e., in the absence of GTP) the dissociation constant of the complex could be derived from a simple relationship, in which only the ratio between the pre-exponential factors and the parameter gamma, which represents the molar fraction of epsilon NAD molecules free in solution in the open conformation, are to be taken into account. The results are in good agreement with those reported by some of us (reference above) using a steady-state fluorescence technique, which by itself is, however, unable to resolve the number of relevant species present in the system.     

Spectral composition of shade light in coastal-zone oak forests in SE Bulgaria,and relationships with leaf area index: a first overview

Major knowledge gaps exist with respect to light-quality regimes in the coastal-zone Strandzha Quercus frainetto (Q.f.) forest region adjoining the southern Bulgarian Black Sea. This paper presents preliminary results that help narrow these gaps. In conjunction with leaf area index (LAI) field campaigns we undertook measurements with an array of 7 broad-band (ca 40 nm) sensors covering the range 0.40–0.94 μm, plus 1 sensor for UVB (0.297 μm peak) and 1 for photosynthetically active radiation (PAR). Measurements focused on inside-forest shade conditions at sites 0 to ca 15 km from the Black Sea and at altitudes up to ca 120 m above sea level. Some of the sites were also studied using a high-resolution spectroradiometer. A sequential measuring strategy was necessary. This involves potentially large uncertainties, here addressed through estimations of the variability around the sinusoidal course of daylight. Light-quality regimes were found to be in general support of earlier studies of deciduous forests. Our data from the broad-band sensors and from the spectroradiometer are mutually supportive. They indicate a stronger red-shift below Q.f. canopies than below canopies in enclaves dominated by Fagus orientalis and Pinus sylvestris. Transmission in the range 0.50–0.55 μm increases beneath the three types of canopies, most pronounced in the Q.f. case. Analysis of relationships between the inside-forest to open-field irradiance ratio and LAI supports the use of Beer’s Law. We found a fairly strong relationship between the red (0.66 μm) to far-red (0.73 μm) irradiance ratios (R/FR) and LAI for the Q.f. forest. In quantitative terms, the result is new for this Q.f. region, and suggests further research to explore whether a two-sensor approach (0.66 and 0.73 μm) might offer possibilities for further low-cost mapping of the spatio-temporal patterns of R/FR and LAI in Strandzha. Such mapping would assist in further studies of the region’s forest biogeochemistry and vitality.     

The effects of manipulation of sedimentary iron and organic matter on sediment biogeochemistry and seagrasses in a subtropical carbonate environment

The microbial metabolism of organic matter (OM) in seagrass beds can create sulfidic conditions detrimental to seagrass growth; iron (Fe) potentially has ameliorating effects through titration of the sulfides and the precipitation of iron-sulfide minerals into the sediment. In this study, the biogeochemical effects of Fe availability and its interplay with sulfur and OM on sulfide toxicity, phosphorous (P) availability, seagrass growth and community structure were tested. The availability of Fe and OM was manipulated in a 2 × 2 factorial experiment arranged in a Latin square, with four replicates per treatment. The treatments included the addition of Fe, the addition of OM, the addition of both Fe and OM as well as no addition. The experiment was conducted in an oligotrophic, iron-deficient seagrass bed. Fe had an 84.5% retention efficiency in the sediments with the concentration of Fe increasing in the seagrass leaves over the course of the experiment. Porewater chemistry was significantly altered with a dramatic decrease in sulfide levels in Fe addition plots while sulfide levels increased in the OM addition treatments. Phosphorus increased in seagrass leaves collected in the Fe addition plots. Decreased sulfide stress was evidenced by heavier δ³⁴S in leaves and rhizomes from plots to which Fe was added. The OM addition negatively affected seagrass growth but increased P availability; the reduced sulfide stress in Fe added plots resulted in elevated productivity. Fe availability may be an important determinant of the impact that OM has on seagrass vitality in carbonate sediments vegetated with seagrasses.     

Degradation of aromatic amino acids by Rhodococcus erythropolis

A Gram-positive Rhodococcus erythropolis strain S1 was shown to assimilate aromatic amino acids such as L-phenylalanine, L-tyrosine, L-tryptophan, D-phenylalanine, D-tyrosine and D-tryptophan, which were utilized not only as the sole carbon source but also as a suitable nitrogen source. The highest growth on these aromatic amino acids occurred at a temperature of 30°C. L-Phenylalanine, L-tyrosine and L-tryptophan degradative pathways would appear to be independent, and to be induced alternatively. The strain S1 also showed the ability to assimilate peptides which consisted of only L-phenylalanine and L-tyrosine.     

Macrophage catabolism of lipid A is regulated by endotoxin stimulation

Lipopolysaccharide (LPS) is a Gram-negative bacterial glycolipid that is believed to cause, by virtue of its stimulatory actions on macrophages and other eukaryotic cells, the life-threatening symptoms associated with Gram-negative infections. Macrophages both respond to and catabolically deactivate LPS. The lipid A moiety of LPS is responsible for the stimulatory actions of LPS on macrophages. We have previously developed methods employing a radiolabeled bioactive lipid A precursor, 4'-32P-lipid IVA, to study the interaction of this class of lipids with animal cells (Hampton, R. Y., Golenbock, D. T., and Raetz, C. R. H. (1988). J. Biol. Chem. 263, 14802-14807). In the current work, we have examined the uptake and catabolism of 4'-32P-lipid IVA by the RAW 264.7 cell line in serum-containing medium at physiological temperatures and have studied the effect of LPS stimulation on the ability of these cells to catabolize lipid IVA. RAW 264.7 macrophage-like cells avidly take up 4'-32P-lipid IVA under cell culture conditions at nanomolar concentrations. Uptake of lipid IVA was accompanied by lysosomal dephosphorylation of a fraction of the lipid to yield 4'-monophosphoryl lipid IVA. Chemically generated 4'-monophosphoryl lipid IVA was found to be substantially less bioactive than lipid IVA in the RAW cell, indicating that this catabolic dephosphorylation results in detoxification. In uptake experiments of 3-4 h duration, all metabolism of lipid IVA is blocked by ligands of the macrophage scavenger receptor. In longer experiments (24 h), both scavenger receptor-dependent and -independent uptake are responsible for the lysosomal catabolism of lipid IVA. Preincubation of RAW 264.7 cells with LPS caused dose-dependent inhibition of lipid IVA dephosphorylation. Sufficient LPS stimulation resulted in essentially complete inhibition of lipid IVA catabolism in both short- and long-term uptake experiments. This effect occurred at physiologically relevant concentrations of LPS (IC50 less than 1 ng/ml), and our data indicate that LPS-induced blockade of lipid IVA catabolism was due to the resultant physiological stimulation of the cells, and not inhibition of dephosphorylation by competition for uptake or enzymatic sites or by simple sequestration of labeled lipid IVA by LPS aggregates. We suggest that in the macrophage, LPS can modulate its own catabolism by virtue of its pharmacological properties. This effect of LPS could play a role in LPS pathophysiology as well as in macrophage biology.     

Spatio-temporal patterns generated by Salmonella typhimurium.

We present experimental results on the bacterium Salmonella typhimurium which show that cells of chemotactic strains aggregate in response to gradients of amino acids, attractants that they themselves excrete. Depending on the conditions under which cells are cultured, they form periodic arrays of continuous or perforated rings, which arise sequentially within a spreading bacterial lawn. Based on these experiments, we develop a biologically realistic cell-chemotaxis model to describe the self-organization of bacteria. Numerical and analytical investigations of the model mechanism show how the two types of observed geometric patterns can be generated by the interaction of the cells with chemoattractant they produce.     

Possible role of metal ionophore against zinc induced cognitive dysfunction in <Emphasis Type="SmallCaps">d-</Emphasis>galactose senescent mice

Metal ionophores are considered as potential anti-dementia agents, and some are currently undergoing clinical trials. Many metals are known to accumulate and distribute abnormally in the aging brain. Alterations in zinc metal homeostasis in the glutaminergic synapse could contribute to ageing and the pathophysiology of Alzheimer’s disease (AD). The present study was designed to investigate the effect of metal ionophores on long term administration of zinc in D-galactose induced senescent mice. The ageing model was established by combined administration of zinc and D-galactose to mice for 6 weeks. A novel metal ionophore, PBT-2 was given daily to zinc-induced d-galactose senescent mice. The cognitive behaviour of mice was monitored using the Morris Water Maze. The anti-oxidant status and amyloidogenic activity in the ageing mouse was measured by determining mito-oxidative parameters and deposition of amyloid β (Aβ) in the brain. Systemic administration of both zinc and D-galactose significantly produced memory deficits, mito-oxidative damage, heightened acetylcholinesterase enzymatic activity and deposition of amyloid-β. Treatment with PBT-2 significantly improved behavioural deficits, biochemical profiles, cellular damage, and curbed the deposition of APP in zinc-induced senescent mice. These findings suggest that PBT-2, acting as a metal protein attenuating compound, may be helpful in the prevention of AD or alleviation of ageing.