The effects of pH and citrate on the activity of nicotinamide–adenine dinucleotide-specific isocitrate dehydrogenase from pea mitochondria

1. The effect of pH on the co-operative activation of the NAD-specific isocitrate dehydrogenase from pea mitochondria by isocitrate is shown. 2. The interlinked effects of pH on the affinity of the NAD-specific isocitrate dehydrogenase for isocitrate and the dependence of the pH optimum on the substrate concentration are presented. 3. A consideration of the conditions of pH and substrate concentration under which citrate activates the NAD-specific isocitrate dehydrogenase demonstrates similarities between the binding of isocitrate and citrate. 4. A comparison of the effects of citrate and pH on the gross structure of the enzyme is investigated by density-gradient centrifugation. 5. The kinetic interpretations of these results are briefly considered. 6. The metabolic significance of these studies is discussed.     

Dynamic analysis of competition and complementarity for light and N use to understand the yield and the protein content of a durum wheat–winter pea intercrop

In a previous paper [Bedoussac L, Justes E (2009) Plant Soil, doi: 10.1007/s11104-009-0082-2], we showed that intercropping of durum wheat and winter pea increased the yield and protein concentration of durum wheat when early N availability was less than 120 kg N ha^?1. The aim of the present work was to understand these results by analysing intercrop species dynamics for growth, light and N acquisition. A 2-year field experiment was carried out in southwest France with different fertilizer-N levels in order to compare wheat (Triticum turgidum L.) and pea (Pisum sativum L.) grown as sole crops and as an intercrop in a row substitutive design. The advantages of intercropping in low N conditions were due mainly to: (1) better light use (up to 10%), thanks to species dynamic complementarity for leaf area index and height; (2) growth complementarity over time (higher growth rate of wheat until pea flowering and then of pea until wheat flowering); and (3) dynamic complementary N acquisition associated with better wheat N status throughout growth. Disadvantages, underlining poorer complementarity within the intercrop stand, were observed with ample available N in early growth. This induced higher cereal growth during winter, which led to increase interspecies competition by reducing pea light absorption and, consequently, its biomass production.     

Will climate change reduce the effects of a pesticide on amphibians?: partitioning effects on exposure and susceptibility to contaminants

Several studies suggest that global climate change could increase the toxicity of contaminants, but none of these studies explicitly integrate the effects of climate change on both susceptibility and duration of exposure to pollution. For many amphibian and aquatic insect species, exposure to contaminants is probably greatest during their fully aquatic embryonic and larval stages because these stages cannot readily escape water bodies where many contaminants accumulate and concentrate. Hence, by accelerating embryonic and larval development, global warming might reduce the duration of contaminant exposure for these taxa. To test this hypothesis, we isolated the effects of a temperature gradient (13–25 °C) on susceptibility (toxicity at a controlled exposure duration) and exposure of the streamside salamander, Ambystoma barbouri, to the herbicide atrazine (0, 4, 40, and 400 μg L^?1) by quantifying growth, survival, hatching, and metamorphosis under an atrazine exposure duration that was either constant or that depended on time to metamorphosis (and thus temperature). Increasing atrazine concentrations reduced growth, delayed hatching and metamorphosis, and decreased embryonic and larval survival. Increasing temperatures enhanced growth, accelerated development, and reduced survival for embryos but not larvae. With the exception of growth, increasing temperatures generally did not enhance the toxicity of atrazine, but they did generally ameliorate the adverse effects of atrazine by accelerating development and reducing the duration of atrazine exposure. The actual effects of climate change on contaminants remains difficult to predict because temperature changes can affect chemical use, uptake, excretion, biotransformation, fate, transport, and bioavailability. However, this work highlights the importance of explicitly considering how climate change will affect both exposure and toxicity to contaminants to accurately assess risk.     

Assessing effects of radiation on abundance of mammals and predator–prey interactions in Chernobyl using tracks in the snow

To test whether radioactive contamination reduced the abundance of mammals, and whether species differed in susceptibility to radiation, we censused mammals by counting tracks in the snow along 161 100-m line transects around Chernobyl during February 2009. The abundance of mammal tracks was negatively related to level of background radiation, independent of the statistical model, with effects of radiation accounting for a third of the variance. The effect of radiation differed significantly among species. There was a positive relationship between abundance of predators and abundance of prey, modified by the level of background radiation because the number of predators increased disproportionately with the number of prey at high levels of radiation. These findings suggest that predatory mammals aggregate in areas with abundant prey, especially when prey are exposed to high levels of radiation. This study emphasizes the negative effects of level of background radiation on the abundance of mammals and predator–prey interactions.     

The effects of structural variations of thiophene-containing Ru(II) complexes on the acid–base and DNA binding properties

A phenylthiophenyl-bearing Ru(II) complex of [Ru(bpy)₂(Hbptip)](PF₆)₂ {bpy?=?2,2′-bipyridine, Hbptip?=?2-(4-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline} was synthesized and characterized by elemental analysis, ¹H NMR spectroscopy, and electrospray ionization mass spectrometry. The ground- and excited-state acid–base properties of the complex were studied by UV–visible absorption and photoluminescence spectrophotometric pH titrations and the negative logarithm values of the ground-state acid ionization constants were derived to be pK _a1?=?1.31?±?0.09 and pK _a2?=?5.71?±?0.11 with the pK _a2 associated deprotonation/protonation process occurring over 3 pK _a units more acidic than thiophenyl-free parent complex of [Ru(bpy)₂(Hpip)]²⁺ {Hpip?=?2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline}. The calf thymus DNA-binding properties of [Ru(bpy)₂(Hbptip)]²⁺ in Tris–HCl buffer (pH 7.1 and 50?mM NaCl) were investigated by DNA viscosities and density functional theoretical calculations as well as UV–visible and emission spectroscopy techniques of UV–visible and luminescence titrations, steady-state emission quenching by [Fe(CN)₆]^4?, DNA competitive binding with ethidium bromide, DNA melting experiments, and reverse salt effects. The complex was evidenced to bind to the DNA intercalatively with binding affinity being greater than those for previously reported analogs of [Ru(bpy)₂(Hip)]²⁺, [Ru(bpy)₂(Htip)]²⁺, and [Ru(bpy)₂(Haptip)]²⁺ {Hip?=?1H-imidazo[4,5-f][1,10]phenanthroline, Htip?=?2-thiophenimidazo[4,5-f][1,10]phenanthroline, Haptip?=?2-(5-phenylthiophen-2-yl)-1H-imidazo[4,5-f][1,10]phenanthroline}.     

Impact of the spatial scale of grass–legume mixtures on sheep grazing behaviour,preference and intake,and subsequent effects on pasture

The benefits of using white clover in pastures have been widely recognised for many years. However, clover is perceived as being unreliable because of its typically low content, which is spatially and temporally variable, in mixed pastures. One proposed solution to increase the proportion of clover in the diet of grazing animals and composition in the pasture is to spatially separate clover from grass within the same field. In a field experiment ryegrass and white clover were grown in fine mixtures, and in pure alternating strips of ryegrass and clover of 1.5 m, 3 m or 18 m width within a field. Pastures were grazed for two grazing periods of 9 and 12 weeks, and measurements of sward surface height (SSH), herbage mass and composition and clover morphology were taken. Grazing behaviour was also observed. Results showed that spatial separation in the long term, when compared with a fine mixture, increased clover availability (18% to 30% v. 9%, based on standing dry matter) and was not grazed to extinction. Ewes maintained their preference for clover throughout the experiment (selection coefficient 2 to 5), which resulted in a reduction in the SSH of clover in monocultures to <3 cm and significant changes to the morphology of clover (smaller leaves, shorter petioles and thicker stolon), at the expense of maximising their intake. Spatial separation in the short term may therefore allow grazing animals to select their preferred diet; however, in the long term in continuously grazed pasture, their preference for clover depletes its availability.     

Compensatory light utilization of Phalaris arundinacea within the Phalaris arundinacea–Phragmites australis compound community

This study investigated the light utilization characteristics of Phalaris arundinacea within the Phalaris arundinacea-Phragmites australis compound community. The investigation was based on the response curve equation of the net photosynthetic rate-photosynthetic photon flux density (Pn-PPFD) of P. arundinacea and on the distribution of PPFD on the surface canopy of P. arundinacea within the compound community. Results showed that P. arundinacea was able to compensate for substantial reduction in available light, and utilize the weak light within the lower part of the compound community. On the one hand, the density of P. australis within the compound community determined the compensatory light utilization rate (CLUR) of P.arundinacea. On the other hand, the CLUR amplitude of P. arundinacea within the compound community with the same P. australis density was relatively small in a day. The results can help people to regulate P. arundinacea-P. australis compound communities to maintain a long-term, stable coexistence in the constructed wetlands.

Abbreviations: CK – control; CLUR, compensatory light utilization rate; LER, light extinction rates; Pn, net photosynthetic rate; PPFD, photosynthetic photon flux density.     

Effect of manganese spatial distribution in the soil profile on wheat growth in rice–wheat rotation

Manganese (Mn) deficiency in wheat under rice (Oryza sativa L.) and wheat (Triticum aestivum L.) rotation is an important problem in most rice-growing areas in China. A field survey, field trials and a soil column experiment were conducted to determine the relationship between Mn leaching and distribution in soil profiles and paddy rice cultivation and the effects of Mn distribution in soil profiles on wheat growth and its response to Mn fertilization. At five field sites surveyed, total Mn and active Mn concentrations in the topsoil layers under rice–wheat rotations were only 42% and 11%, respectively, of those under systems without paddy rice. Both total and available Mn increased with soil depth in soils with rice–wheat rotations, showing significant spatial variability of Mn in the soil profile. Manganese leaching was the main pathway for Mn loss in coarse-textured soil with high pH, while excessive Mn uptake was the main pathway for Mn loss in clay-textured and acid soil. When Mn was deficient in the topsoil, sufficient Mn in the subsoil contributed to better growth and Mn nutrition of wheat but insufficient Mn in the subsoil resulted in Mn deficiency in wheat.     

Assessing the effects of management on forest growth across France: insights from a new functional–structural model

Background and Aims

The structure of a forest stand, i.e. the distribution of tree size features, has strong effects on its functioning. The management of the structure is therefore an important tool in mitigating the impact of predicted changes in climate on forests, especially with respect to drought. Here, a new functional–structural model is presented and is used to assess the effects of management on forest functioning at a national scale.

Methods

The stand process-based model (PBM) Castanea was coupled to a stand structure module (SSM) based on empirical tree-to-tree competition rules. The calibration of the SSM was based on a thorough analysis of intersite and interannual variability of competition asymmetry. The coupled Castanea–SSM model was evaluated across France using forest inventory data, and used to compare the effect of contrasted silvicultural practices on simulated stand carbon fluxes and growth.

Key Results

The asymmetry of competition varied consistently with stand productivity at both spatial and temporal scales. The modelling of the competition rules enabled efficient prediction of changes in stand structure within the Castanea PBM. The coupled model predicted an increase in net primary productivity (NPP) with management intensity, resulting in higher growth. This positive effect of management was found to vary at a national scale across France: the highest increases in NPP were attained in forests facing moderate to high water stress; however, the absolute effect of management on simulated stand growth remained moderate to low because stand thinning involved changes in carbon allocation at the tree scale.

Conclusions

This modelling approach helps to identify the areas where management efforts should be concentrated in order to mitigate near-future drought impact on national forest productivity. Around a quarter of the French temperate oak and beech forests are currently in zones of high vulnerability, where management could thus mitigate the influence of climate change on forest yield     

Activation of extrasynaptic δ-GABAA receptors globally or within the posterior-VTA has estrous-dependent effects on consumption of alcohol and estrous-independent effects on locomotion

Recent reports support higher than expected rates of binge alcohol consumption among women and girls. Unfortunately, few studies have assessed the mechanisms underlying this pattern of intake in females. Studies in males suggest that alcohol concentrations relevant to the beginning stages of binge intoxication may selectively target tonic GABAergic inhibition mediated by GABA_A receptor subtypes expressing the δ-subunit protein (δ-GABA_ARs). Indeed, administration of agonists that interact with these δ-GABA_ARs prior to alcohol access can abolish binge drinking behavior in male mice. These δ-GABA_ARs have also been shown to exhibit estrous-dependent plasticity in regions relevant to drug taking behavior, like the hippocampus and periaqueductal gray. The present experiments were designed to determine whether the estrous cycle would alter binge drinking, or our ability to modulate this pattern of alcohol use with THIP, an agonist with high selectivity and efficacy at δ-GABA_ARs. Using the Drinking-in-the-Dark (DID) binge-drinking model, regularly cycling female mice were given 2 h of daily access to alcohol (20%v/v). Vaginal cytology or vaginal impedance was assessed after drinking sessions to track estrous status. There was no fluctuation in binge drinking associated with the estrous cycle. Both Intra-posterior-VTA administration of THIP and systemic administration of the drug was also associated with an estrous cycle dependent reduction in drinking behavior. Pre-treatment with finasteride to inhibit synthesis of 5α-reduced neurosteroids did not disrupt THIP's effects. Analysis of δ-subunit mRNA from posterior-VTA enriched tissue samples revealed that expression of this GABA_A receptor subunit is elevated during diestrus in this region. Taken together, these studies demonstrate that δGABA_ARs in the VTA are an important target for binge drinking in females and confirm that the estrous cycle is an important moderator of the pharmacology of this GABA_A receptor subtype.     

“Perchance to dream?”: Assessing the effects of dispersal strategies on the fitness of expanding populations

Unraveling the patterns of animals’ movements is crucial to understanding the basics of biogeography, tracking range shifts resulting from climate change, and predicting and preventing biological invasions. Many researchers have modeled animals’ dispersal under the assumptions of various movement strategies, either predetermined or directed by external factors, but none have compared the effects of different movement strategies on population survival and fitness. In this paper, using an agent-based model with a landscape divided into cells of varying quality, we compare the ecological success of three movement and habitat selection strategies (MHSSs): (i) Smart, in which animals choose the locally optimal cell; (ii) Random, in which animals move randomly between cells without taking into account their quality; (iii) Dreamer, in which animals attempt to find a habitat of dream whose quality is much higher than that of the habitat available on the map. We compare the short-term success of these MHSSs in good, medium and bad environments. We also assess the effect of temporal variation of habitat quality (specifically, winter harshness) on the success of each MHSS. Success is measured in terms of survival rate, dispersal distance, accumulated energy and quality of settled habitat. The most general conclusion is that while survival rate, accumulated energy and quality of settled habitat are affected primarily by overall habitat composition (proportions of different habitat types in the landscape), dispersal distance depends mainly on the MHSS. In medium and good environments, the Dreamer strategy is highly successful: it simultaneously outperforms the Smart strategy in dispersal distance and the Random strategy in terms of the other metrics.     

Effect of glycerol–water binary mixtures on the structure and dynamics of protein solutions

We have performed 20?ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30, and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The solvent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the incoherent intermediate scattering function, shows a nonmonotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water-containing solvents, but different from the pure glycerol case. The increase in the number of protein–glycerol hydrogen bonds in glycerol–water binary mixtures explains the slowing down of protein dynamics as the glycerol content increases. We also explored the dynamic behavior of the hydration layer. We show that the short length scale dynamics of this layer are insensitive to glycerol concentration. However, the long length scale behavior shows a significant dependence on glycerol content. We also provide insights into the behavior of bound and mobile water molecules.     

Effects of the light–dark cycle on diurnal rhythms of diet-induced thermogenesis in humans

This study aimed to clarify the effect of light exposure during the daytime and nighttime on diet-induced thermogenesis (DIT), which is one kind of energy expenditure, and the contribution of autonomic nervous activities (ANA) to the mechanism behind such effects. We found that the light–dark cycle significantly induced a diurnal rhythm of DIT, with afternoon levels tending to be higher than nighttime levels. By contrast, no such rhythms were observed under constant light or dark conditions. There were also no significant differences in ANA between the light conditions. These findings demonstrate that a diminished light–dark cycle leads to disruption of the diurnal rhythm of metabolism and so the retention of ordinary light–dark cycles may be recommended for health maintenance.     

Investigating the effects of subthalamic Nucleus–Deep brain stimulation on the voice quality

Abstract

Introduction: Deep brain stimulation (DBS) is a standard surgical treatment method which is generally applied to subthalamic nucleus in Parkinson’s patients in cases where medical treatment is insufficient in treating the motor symptoms. It is known that Subthalamic Nucleus Deep Brain Stimulation (STN-DBS) treats many motor symptoms. However, the results of studies on speech and voice vary. The aim of the study is analysing the effect of STN-DBS on the characteristics of voice.

Materials/methods: A total of 12 patients, (8 male–4 female) with an age average of 58.8?±?9.6, who have been applied DBS surgery on STN included in the study. The voice recordings of the patients have been done prior to surgery and 6?months after the surgery. The evaluation of voice has been carried out through the instrumental method. The patients’ voice recordings of the /a,e,i/ vowels have been done. The obtained recordings were evaluated by the Praat programme and the effects on jhitter, shimmer, fundamental frequency (F0) and noise harmonic rate (NHR) were analysed.

Results: Numerical values of F0 of all female participants have been decreased for all of the vowels postoperatively. In the females; jhitter and fraction parameters were found to be significantly different (0.056 and 0.017, perspectively) for the vowel /e/. In addition, p values in the shimmer for vowels /e,i/ were thought to be clinically significant (.087, .079 and .076) respectively. All these changes in second measurements were found to indicate worsening vocal quality after the DBS in females. In males, there is not any significant difference observed between two measures in any of the parameters of any vowels.

Conclusions: Acoustic voice quality deteriorated after STN-DBS predominantly for females however this deterioration was not prominent audio-perceptually. This finding commented as a result of the fact that that voice quality deviance of the participants was not severe.     

Analysis of the cytotoxic effects of ruthenium–ketoconazole and ruthenium–clotrimazole complexes on cancer cells

Ruthenium-based compounds have intriguing anti-cancer properties, and some of these novel compounds are currently in clinical trials. To continue the development of new metal-based drug combinations, we coupled ruthenium (Ru) with the azole compounds ketoconazole (KTZ) and clotrimazole (CTZ), which are well-known antifungal agents that also display anticancer properties. We report the activity of a series of 12 Ru–KTZ and Ru–CTZ compounds against three prostate tumor cell lines with different androgen sensitivity, as well as cervical cancer and lymphoblastic lymphoma cell lines. In addition, human cell lines were used to evaluate the toxicity against non-transformed cells and to establish selectivity indexes. Our results indicate that the combination of ruthenium and KTZ/CTZ in a single molecule results in complexes that are more cytotoxic than the individual components alone, displaying in some cases low micromolar CC₅₀ values and high selectivity indexes. Additionally, all compounds are more cytotoxic against prostate cell lines with lower cytotoxicity against non-transformed epidermal cell lines. Some of the compounds were found to primarily induce cell death via apoptosis yet weakly interact with DNA. Our studies also demonstrate that the cytotoxicity induced by our Ru-based compounds is not directly related to their ability to interact with DNA.     

Effects of far-red light on fluorescence induction in infiltrated pea leaves under diminished ΔpH and Δφ components of the proton motive force

Chlorophyll fluorescence induction curves induced by an actinic pulse of red light follow different kinetics in dark-adapted plant leaves and leaves preilluminated with far-red light. This influence of far-red light was abolished in leaves infiltrated with valinomycin known to eliminate the electrical (Δφ) component of the proton-motive force and was strongly enhanced in leaves infiltrated with nigericin that abolishes the ΔpH component. The supposed influence of ionophores on different components of the proton motive force was supported by differential effects of these ionophores on the induction curves of the millisecond component of chlorophyll delayed fluorescence. Comparison of fluorescence induction curves with the kinetics of P700 oxidation in the absence and presence of ionophores suggests that valinomycin facilitates a build-up of a rate-limiting step for electron transport at the site of plastoquinone oxidation, whereas nigericin effectively removes limitations at this site. Far-red light was found to be a particularly effective modulator of electron flows in chloroplasts in the absence of ΔpH backpressure on operation of the electron-transport chain.     

The effect of pH on the characteristics of the binding of nicotinamide–adenine dinucleotide by nicotinamide–adenine dinucleotide specific isocitrate dehydrogenase from pea mitochondria

1. The effect of pH on the V(max.) and concentration of NAD(+) at half-maximum velocity at a constant isocitrate concentration was examined, and the results were related to the requirements for binding of H(+) ions to the enzyme. 2. The effect of varying the NAD(+) concentration on the pH optimum with constant isocitrate concentration was studied. 3. A comparison has been made between the effect of isocitrate concentration on the characteristics of binding of NAD(+) and the effect of NAD(+) concentration on the characteristics of isocitrate binding at three different pH values. 4. The mechanistic and metabolic significance of these studies is considered.     

Theoretical studies on the reaction mechanism of PP1 and the effects of different oxidation states of the Mn–Mn center on the mechanism

Protein phosphatase 1 (PP1) is a dinuclear metalloenzyme that catalyzes the dephosphorylation of serine and threonine residues. In this work, the catalytic reaction mechanism of PP1 was theoretically investigated by hybrid density functional theory. Firstly, an initial model of the Mn(II)–Mn(II) active site of PP1 was constructed on the basis of the high-resolution crystal structure, and stationary points along the reaction pathway were optimized and analyzed. The calculations provide strong support for the mechanism of the dephosphorylation by PP1 and suggest that His125 plays the role of donating a proton to the leaving group. Furthermore, reaction models with the Mn–Mn centers at different oxidation states [Mn(III)–Mn(II) and Mn(III)–Mn(III) centers] were designed. Our calculations show that increasing the oxidation state of one or both Mn(II) can shorten the bond lengths between the metal ions and the ligands, and increase the energy barrier of the related reactions. We found it interesting that artificially adding a negatively charged hydroxy ligand into the Mn(III)–Mn(II) center can recover the shortened coordination bonds and lower the increased energy barrier. Our investigation suggests that the definite oxidation states of the metal centers should be significantly correlated to the negative charges of the ligands not only in phosphoprotein phosphatases, but also in purple acid phosphatases and Escherichia coli 5′-nucleotidase. This means that all the members of phosphoprotein phosphatases adopt homodivalent centers, and suggests the heterovalent active sites of purple acid phosphatases have evolved from homodivalent ones.