Purification of the photosynthetic reaction center from <Emphasis Type="Italic">Heliobacterium modesticaldum</Emphasis>

We have developed a purification protocol for photoactive reaction centers (HbRC) from Heliobacterium modesticaldum. HbRCs were purified from solubilized membranes in two sequential chromatographic steps, resulting in the isolation of a fraction containing a single polypeptide, which was identified as PshA by LC–MS/MS of tryptic peptides. All polypeptides reported earlier as unknown proteins (in Heinnickel et al., Biochemistry 45:6756–6764, 2006; Romberger et al., Photosynth Res 104:293–303, 2010) are now identified by mass spectrometry to be the membrane-bound cytochrome c ₅₅₃ and four different ABC-type transporters. The purified PshA homodimer binds the following pigments: 20 bacteriochlorophyll (BChl) g, two BChl g′, two 8¹-OH-Chl a _F, and one 4,4′-diaponeurosporene. It lacks the PshB polypeptide binding the F_A and F_B [4Fe–4S] clusters. It is active in charge separation and exhibits a trapping time of 23 ps, as judged by time-resolved fluorescence studies. The charge recombination rate of the P₈₀₀ ⁺F_X⁻ state is 10–15 ms, as seen before. The purified HbRC core was able to reduce cyanobacterial flavodoxin in the light, exhibiting a K _M of 10 μM and a k _cat of 9.5 s⁻¹ under near-saturating light. There are ~1.6 menaquinones per HbRC in the purified complex. Illumination of frozen HbRC in the presence of dithionite can cause creation of a radical at g = 2.0046, but this is not a semiquinone. Furthermore, we show that high-purity HbRCs are very stable in anoxic conditions and even remain active in the presence of oxygen under low light.     

Molecular modeling study of isoindolines as L-type Ca2+ channel blockers by docking calculations

Two series of isoindolines 1(a–g) and 2(a–g) were found by docking calculations to be possible L-type Ca²⁺ channel (LCC) blockers. The theoretical 3-D model of the outer vestibule and the selective filter of the LCC was provided by Professor Lipkind; this model consists of transmembrane segments S5 and S6 and P-loops contributed by each of four repeats (I, II, III, and IV) of Ca_v 1.2. Therefore, two well-known LCC blockers, nifedipine 3 and (R)-ethosuccinimide 4 were also evaluated, and their binding sites on the LCC were identified and compared with those obtained for 1(a–g) and 2(a–g). Analysis of the results shows that the target compounds tested probably could be LCC blockers, since they interact with or near the glutamic acid residues Glu393, Glu736, Glu1145 and Glu1446 (the EEEE locus), which belong to the LCC selectivity region. The ∆G values for all of the Ca²⁺ channel ligands are between−10.78 and −3.67 (kcal mol⁻¹), showing that LCC-1b, -1e and -1f complexes are more stable than the other compounds tested. Therefore, theoretically calculated dissociation constants K _d (μM) were obtained for all compounds. Comparing these values reveals that compounds 1b (0.0244 μM), 1e (0.0176 μM) and 1f (0.0125 μM) exhibit more affinity for the LCC than the other compounds. This screening shows that the two series of isoindolines probably could act as LCC blockers.     

A role for anions in ATP synthesis and its molecular mechanistic interpretation

ATP, the ‘universal biological energy currency’, is synthesized by utilizing energy either from oxidation of fuels or from light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F₁F₀-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from ADP and inorganic phosphate (P_i). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers 4,4′-diisothiocyanostilbene-2, 2′-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies, attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis. The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293–300, 2010a; J Bioenerg Biomembr 42:301–309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature 172:975–978, 1953; Williams J Theor Biol 1:1–17, 1961; Mitchell Nature 191:144–148, 1961; Mitchell Biol Rev 41:445–502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8–21, 2006a; Process Biochem 41:2218–2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms must be revised.     

A Computational Analysis of Localized Ca<Superscript>2+</Superscript>-Dynamics Generated by Heterogeneous Release Sites

We investigate the role of heterogeneous expression of IP₃R and RyR in generating diverse elementary Ca²⁺ signals. It has been shown empirically (Wojcikiewicz and Luo in Mol. Pharmacol. 53(4):656–662, 1998; Newton et al. in J. Biol. Chem. 269(46):28613–28619, 1994; Smedt et al. in Biochem. J. 322(Pt. 2):575–583, 1997) that tissues express various proportions of IP₃ and RyR isoforms and this expression is dynamically regulated (Parrington et al. in Dev. Biol. 203(2):451–461, 1998; Fissore et al. in Biol. Reprod. 60(1):49–57, 1999; Tovey et al. in J. Cell Sci. 114(Pt. 22):3979–3989, 2001). Although many previous theoretical studies have investigated the dynamics of localized calcium release sites (Swillens et al. in Proc. Natl. Acad. Sci. U.S.A. 96(24):13750–13755, 1999; Shuai and Jung in Proc. Natl. Acad. Sci. U.S.A. 100(2):506–510, 2003a; Shuai and Jung in Phys. Rev. E, Stat. Nonlinear Soft Matter Phys. 67(3 Pt. 1):031905, 2003b; Thul and Falcke in Biophys. J. 86(5):2660–2673, 2004; DeRemigio and Smith in Cell Calcium 38(2):73–86, 2005; Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005), so far all such studies focused on release sites consisting of identical channel types. We have extended an existing mathematical model (Nguyen et al. in Bull. Math. Biol. 67(3):393–432, 2005) to release sites with two (or more) receptor types, each with its distinct channel kinetics. Mathematically, the release site is represented by a transition probability matrix for a collection of nonidentical stochastically gating channels coupled through a shared Ca²⁺ domain. We demonstrate that under certain conditions a previously defined mean-field approximation of the coupling strength does not accurately reproduce the release site dynamics. We develop a novel approximation and establish that its performance in these instances is superior. We use this mathematical framework to study the effect of heterogeneity in the Ca²⁺-regulation of two colocalized channel types on the release site dynamics. We consider release sites consisting of channels with both Ca²⁺-activation and inactivation (“four-state channels”) and channels with Ca²⁺-activation only (“two-state channels”) and show that for the appropriate parameter values, synchronous channel openings within a release site with any proportion of two-state to four-state channels are possible, however, the larger the proportion of two-state channels, the more sensitive the dynamics are to the exact spatial positioning of the channels and the distance between channels. Specifically, the clustering of even a small number of two-state channels interferes with puff/spark termination and increases puff durations or leads to a tonic response.     

Singlet oxygen formation and chlorophyll a triplet excited state deactivation in the cytochrome b6f complex from Bryopsis?corticulans

We have attempted to investigate the correlation between the detergent-perturbed structural integrity of the Cyt b ₆ f complex from the marine green alga Bryopsis corticulans and its photo-protective properties, for which the nonionic detergents n-octyl-β-d-glucopyranoside (β-OG) and n-dodecyl-β-d-maltoside (β-DM), respectively, were used for the preparation of Cyt b ₆ f, and the singlet oxygen (¹O₂*) production as well as the triplet excited-state chlorophyll a (³Chl a*) formation and deactivation were examined by spectroscopic means. Near-infrared luminescence of ¹O₂ * (~1,270 nm) on photo-irradiation was detected for the β-OG preparation where the complex is mainly in oligomeric state, but not for the β-DM one in which the complex exists in dimeric form. Under anaerobic condition, photo-excitation of Chl a in the β-DM preparation generated ³Chl a* with a lower quantum yield of Φ_T ~ 0.02 and a longer lifetime of ~600 μs with respect to those as in the case of β-OG preparation, Φ_T ~ 0.12 and 200–300 μs. These results prove that the enzymatically active and intact Cyt b ₆ f complex on photo-excitation tends to produce little ³Chl a* or ¹O₂ *, which implies that the pigment–protein assembly of Cyt b ₆ f complex per se is crucial for photo-protection. F. Ma and X.-B. Chen contributed equally to this work.     

Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples

Background  

HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations [1–3]. It would be useful to develop automated analyses of HIV sequence polymorphism that are able to predict drug resistance mutations, and to distinguish different types of functional roles among such mutations, for example, those that directly cause drug resistance, versus those that play an accessory role. Detecting functional interactions between mutations is essential for this classification. We have adapted a well-known measure of evolutionary selection pressure (K _a /K _s ) and developed a conditional K _a /K _s approach to detect important interactions.     

Relationships between photosystem II efficiency and photochemical reflectance index under different levels of illumination: comparison among species grown at high- and low elevations through different seasons

Previously, we found a significant association between photosystem II efficiency (ΦPSII) and photochemical reflectance index (PRI) measured at predawn among different species at different elevations and throughout several seasons. However, this relationship has not been evaluated under varied levels of illumination. Here, we used the Taiwan species Pinus taiwanensis (a conifer distributed at 750–3,000 m a.s.l.), Stranvaesia niitakayamensis (an evergreen tree, 1,700–3,100 m) and two Miscanthus spp. (perennial C₄ Gramineae, coastline–3,200 m) to elucidate the ΦPSII–PRI relationship. We studied six levels of photosynthetic photon flux density (PPFD) (0, 200, 400, 800, 1,200 and 2,000 μmol m⁻² s⁻¹) over several growth seasons at high (2,600 m a.s.l.) and low (800 m a.s.l.) elevation sites. In comparing the same species or genus, ΦPSII and PRI were closely correlated in darkness or under the same level of PPFD, with data obtained from different seasons and elevations pooled for regression analysis. Because both the intercept and slope of the ΦPSII–PRI equation showed a negative curvilinear correlation with PPFD, we could fit an empirical regression model, ΦPSII = c + d·ln(PPFD) + e·[ln(PPFD)]² + f·PRI + g·PRI·ln(PPFD) + h·PRI·[ln(PPFD)]², for multiple regression analysis. Using this model, we found a close correlation between the estimated and measured ΦPSII (r ² = 0.842−0.937, P < 0.001) for all four species examined and for mango (Mangifera indica) measured under both artificial illumination and sunlight (data from Weng et al. 2010). This empirical regression model could simulate both seasonal and diurnal variations of leaf-scale photosynthetic efficiency at high and low elevations.     

Induction of a non-specific permeability transition in mitochondria from Yarrowia lipolytica and Dipodascus (Endomyces) magnusii yeasts

In this study we used tightly-coupled mitochondria from Yarrowia lipolytica and Dipodascus (Endomyces) magnusii yeasts, possessing a respiratory chain with the usual three points of energy conservation. High-amplitude swelling and collapse of the membrane potential were used as parameters for demonstrating induction of the mitochondrial permeability transition due to opening of a pore (mPTP). Mitochondria from Y. lipolytica, lacking a natural mitochondrial Ca²⁺ uptake pathway, and from D. magnusii, harboring a high-capacitive, regulated mitochondrial Ca²⁺ transport system (Bazhenova et al. J Biol Chem 273:4372–4377, 1998a; Bazhenova et al. Biochim Biophys Acta 1371:96–100, 1998b; Deryabina and Zvyagilskaya Biochemistry (Moscow) 65:1352–1356, 2000; Deryabina et al. J Biol Chem 276:47801–47806, 2001) were very resistant to Ca²⁺ overload. However, exposure of yeast mitochondria to 50–100 μM Ca²⁺ in the presence of the Ca²⁺ ionophore ETH129 induced collapse of the membrane potential, possibly due to activation of the fatty acid-dependent Ca²⁺/nH⁺-antiporter, with no classical mPTP induction. The absence of response in yeast mitochondria was not simply due to structural limitations, since large-amplitude swelling occurred in the presence of alamethicin, a hydrophobic, helical peptide, forming voltage-sensitive ion channels in lipid membranes. Ca²⁺- ETH129-induced activation of the Ca²⁺/H⁺-antiport system was inhibited and prevented by bovine serum albumin, and partially by inorganic phosphate and ATP. We subjected yeast mitochondria to other conditions known to induce the permeability transition in animal mitochondria, i.e., Ca²⁺ overload (in the presence of ETH129) combined with palmitic acid (Mironova et al. J Bioenerg Biomembr 33:319–331, 2001; Sultan and Sokolove Arch Biochem Biophys 386:37–51, 2001), SH-reagents, carboxyatractyloside (an inhibitor of the ADP/ATP translocator), depletion of intramitochondrial adenine nucleotide pools, deenergization of mitochondria, and shifting to acidic pH values in the presence of high phosphate concentrations. None of the above-mentioned substances or conditions induced a mPTP-like pore. It is thus evident that the permeability transition in yeast mitochondria is not coupled with Ca²⁺ uptake and is differently regulated compared to the mPTP of animal mitochondria.     

Kinetic models of photosystem II should accommodate the effect of donor side quenching on variable chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence in the microseconds time range

Quantitative data on laser flash-induced variable fluorescence in the 100 ns to 1 ms time range (Belyaeva et al. in Photosynth Res 98:105–119, 2008) confirming those of others (Steffen et al. in Biochemistry 40:173–180, 2001, Biochemistry 44:3123–3132, 2005; Belyaeva et al. in Biophysics 51(6):976–990, 2006), need a substantial correction with respect to magnitude of the normalized variable fluorescence associated with single turnover-induced charge separation in RCs of PS II. Their data are conclusive with the involvement of donor side quenching, the release of which occurs with a rate constant in the range of tens of ms⁻¹, and presumed to be associated with reduction of Y_\textz ⁺ Y_{\text{z}}^{ + } by the OEC.     

Thalamocortical transformations of periodic stimuli: the effect of stimulus velocity and synaptic short-term depression in the vibrissa–barrel system

Recent works on the response of barrel neurons to periodic deflections of the rat vibrissae have shown that the stimulus velocity is encoded in the corti cal spike rate (Pinto et al., Journal of Neurophysiology, 83(3), 1158–1166, 2000; Arabzadeh et al., Journal of Neuroscience, 23(27), 9146–9154, 2003). Other studies have reported that repetitive pulse stimulation produces band-pass filtering of the barrel response rate centered around 7–10 Hz (Garabedian et al., Journal of Neurophysiology, 90, 1379–1391, 2003) whereas sinusoidal stimulation gives an increasing rate up to 350 Hz (Arabzadeh et al., Journal of Neuroscience, 23(27), 9146–9154, 2003). To explore the mechanisms underlying these results we propose a simple computational model consisting in an ensemble of cells in the ventro-posterior medial thalamic nucleus (VPm) encoding the stimulus velocity in the temporal profile of their response, connected to a single barrel cell through synapses showing short-term depression. With sinusoidal stimulation, encoding the velocity in VPm facilitates the response as the stimulus frequency increases and it causes the velocity to be encoded in the cortical rate in the frequency range 20–100 Hz. Synaptic depression does not suppress the response with sinusoidal stimulation but it produces a band-pass behavior using repetitive pulses. We also found that the passive properties of the cell membrane eventually suppress the response to sinusoidal stimulation at high frequencies, something not observed experimentally. We argue that network effects not included here must be important in sustaining the response at those frequencies.

Chemical and physical-chemical characteristics of dietary fibres from Ulva lactuca (L.) Thuret and Enteromorpha compressa (L.) Grev.

Dietary fibres from Ulva lactuca (L.) Thuret (sea lettuce) and Enteromorpha compressa (L.) Grev. (A.O. nori) were measured according to a ‘standard’ method and a ‘physiological’ protocol simulating the gastric and intestinal environments. U. lactuca contained 15.8–8.0% soluble and 24.2–32.6% insoluble fibres according to the ‘standard’ and ‘physiological’ methods, respectively. For E. compressa, these values were 14.9–15.9 and 21.6–28.7%, respectively. For both algae, the composition suggests that the soluble fibres were xylorhamnoglycuronans sulphates and insoluble fibres were essentially composed of glucans. No marked chemical compositional variation was observed between soluble fractions extracted under the simulated gastric and intestinal conditions. Fibres in both algae are hydrophilic but the water holding capacities were higher after extraction of soluble fibres (5.5–9.5 g g⁻¹ for the dry algae; 14.0–16.0 g g⁻¹ for the standard insoluble fibres). Water soluble fibres demonstrated low intrinsic viscosities at 37 °C in buffers, particularly those from E. compressa (36.0–36.5 ml g⁻¹), and was affected by pH for those of U. lactuca (147.5 ml g⁻¹ at pH 3.0 and 175.0 ml g⁻¹ at pH 7.3).     

Low expression of Neu2 sialidase in the thymus of SM/J mice—existence of neuraminidase positive cells “Neu-medullocyte” in the murine thymus

We have already reported that the homogenate of the A/J mouse thymus shows a high sialidase activity at the neutral pH region and that in both soluble and membrane fractions optimal pH was 6.5–7 (Kijimoto-Ochiai et al., Glycoconj. J., 20:375–384, 2004). In the present study, we investigated the level of sialidase activities in the thymus of the SM/J mouse, a mouse strain that we know to have a Neu1^a allele that reveals a low level of sialidase activity in the liver. We found that while in the A/J thymus the soluble sialidase activity at pH 6.5 was high, the SM/J thymus lacked all such activity. A QTL analysis of SMXA recombinant inbred strains showed that soluble sialidase activity correlated well with the D1Mit8/9 marker on chromosome 1. The murine whole DNA-sequence data and the results of our FISH analysis (Kotani et al., Biochem. Biophys. Res. Comm., 286:250–258, 2001) showed that this location is consistent with the position of Neu2 gene. We confirmed that it is hard to detect the Neu2 enzyme of the SM/J mouse thymus by an anti-Neu2 antibody using a Western blot analysis. We also found that while the mRNA expression of Neu2 was quite normal in the SM/J mouse liver, it was very low in the SM/J mouse thymus. We therefore conclude that the lack of soluble sialidase activity in the SM/J mouse thymus is due to the thymus-specific low expression level of the Neu2 gene. We have previously shown that the sialidase positive cell which contains the Mac-1 and immunoglobulin, and which is located sparsely in the corticomedullar region or medullary region of the A/J mouse thymus (Kijimoto-Ochiai et al., Glycoconj. J., 20:375–384, 2004). We showed now in this paper that the detection of this cell in the SM/J mouse thymus at pH 7.0 was difficult. We propose, therefore, to name the cell “Neu-medullocyte”.     

Thermal clamping of temperature-regulating flowers reveals the precision and limits of the biochemical regulatory mechanism

The flowers of several families of seed plants warm themselves when they bloom. In some species, thermogenesis is regulated, increasing the rate of respiration at lower ambient temperature (T _a) to maintain a somewhat stable floral temperature (T _f). The precision of this regulation is usually measured by plotting T _f over T _a. However, such measurements are influenced by environmental conditions, including wind speed, humidity, radiation, etc. This study eliminates environmental effects by experimentally ‘clamping’ T _f at constant, selected levels and then measuring stabilized respiration rate. Regulating flowers show decreasing respiration with rising T _f (Q ₁₀ < 1). Q ₁₀ therefore becomes a measure of the biochemical ‘precision’ of temperature regulation: lower Q ₁₀ values indicate greater sensitivity of respiration to T _f and a narrower range of regulated temperatures. At the lower end of the regulated range, respiration is maximal, and further decreases in floral temperature cause heat production to diminish. Below a certain tissue temperature (‘switching temperature’), heat loss always exceeds heat production, so thermoregulation becomes impossible. This study compared three species of thermoregulatory flowers with distinct values of precision and switching temperature. Precision was highest in Nelumbo nucifera (Q ₁₀ = 0.16) moderate in Symplocarpus renifolius (Q ₁₀ = 0.48) and low in Dracunculus vulgaris (Q ₁₀ = 0.74). Switching temperatures were approximately 30, 15 and 20°C, respectively. There were no relationships between precision, switching temperature or maximum respiration rate. High precision reveals a powerful inhibitory mechanism that overwhelms the tendency of temperature to increase respiration. Variability in the shape and position of the respiration–temperature curves must be accounted for in any explanation of the control of respiration in thermoregulatory flowers.     

Structural elements of the C-terminal domain of subunit E (E<Subscript>133-222</Subscript>) from the <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> V<Subscript>1</Subscript>V<Subscript>O</Subscript> ATPase determined by solution NMR spectroscopy

Subunit E of the vacuolar ATPase (V-ATPase) contains an N-terminal extended α helix (Rishikesan et al. J Bioenerg Biomembr 43:187–193, 2011) and a globular C-terminal part that is predicted to consist of a mixture of α-helices and β-sheets (Grüber et al. Biochem Biophys Res Comm 298:383–391, 2002). Here we describe the production, purification and 2D structure of the C-terminal segment E_133-222 of subunit E from Saccharamyces cerevisiae V-ATPase in solution based on the secondary structure calculation from NMR spectroscopy studies. E_133-222 consists of four β-strands, formed by the amino acids from K136-V139, E170-V173, G186-V189, D195-E198 and two α-helices, composed of the residues from R144-A164 and T202-I218. The sheets and helices are arranged as β1:α1:β2:β3:β4:α2, which are connected by flexible loop regions. These new structural details of subunit E are discussed in the light of the structural arrangements of this subunit inside the V₁- and V₁V_O ATPase.     

On the Calibration of a Size-Structured Population Model from Experimental Data

The aim of this work is twofold. First, we survey the techniques developed in Perthame and Zubelli (Inverse Probl 23(3):1037–1052, 2007), Doumic et al. (Inverse Probl 25, 2009) to reconstruct the division (birth) rate from the cell volume distribution data in certain structured population structured population models. Secondly, we implement such techniques on experimental cell volume distributions available in the literature so as to validate the theoretical and numerical results. As a proof of concept, we use the experimental data experimental data reported in the classical work of Kubitschek (Biophys J 9(6):792–809, 1969) concerning Escherichia coli in vitro experiments measured by means of a Coulter transducer-multichannel analyzer system (Coulter Electronics, Inc., Hialeah, FL, USA). Despite the rather old measurement technology, the reconstructed division rates still display potentially useful biological features.     

Cl Anion-Dependent Mg-ATPase

We studied, in the rat brain, the synaptosomal and microsomal membrane fractions of Cl⁻ ion-activated, Mg²⁺-dependent ATPase, satisfying the necessary kinetic peculiarities of transport ATPases, by a novel method of kinetic analysis of the multisite enzyme systems: (1) the [Mg-ATP] complex constitutes the substrate of the enzymic reaction; (2) the V = f(Cl⁻) dependence-reflecting curve is bell-shaped; (3) substrate dependence, V = f(S), curves at a constant concentration of free ligands (Mg_f, ATP_f, Cl⁻); (4) as known from the literature, in the process of reaction a phosphorylated intermediate is formed (Gerencser, Crit Rev Biochem Mol Biol 31:303–337, 1996). We report on the Cl-ATPase molecular mechanism and its place in the “P-type ATPase” classification.     

Effect of nitrate and glucose addition on denitrification and nitric oxide reductase (<Emphasis Type="Italic">cnorB</Emphasis>) gene abundance and mRNA levels in <Emphasis Type="Italic">Pseudomonas mandelii</Emphasis> inoculated into anoxic soil

The effect of glucose addition (0 and 500 μg C g⁻¹ soil) and nitrate (NO₃) addition (0, 10, 50 and 500 μg NO₃–N g⁻¹ soil) on nitric oxide reductase (cnorB) gene abundance and mRNA levels, and cumulative denitrification were quantified over 48 h in anoxic soils inoculated with Pseudomonas mandelii. Addition of glucose-C significantly increased cnorB _p (P. mandelii and related species) mRNA levels and abundance compared with soil with no glucose added, averaged over time and NO₃ addition treatments. Without glucose addition, cnorB _p mRNA levels were higher when 500 μg NO₃–N g⁻¹ soil was added compared with other NO₃ additions. In treatments with glucose added, addition of 50 μg NO₃–N g⁻¹ soil resulted in higher cnorB _p mRNA levels than soil without NO₃ but was not different from the 10 and 500 μg NO₃–N g⁻¹ treatments. cnorB _p abundance in soils without glucose addition was significantly higher in soils with 500 μg NO₃–N g⁻¹ soil compared to lower N-treated soils. Conversely, addition of 500 μg NO₃–N g⁻¹ soil resulted in lower cnorB _p abundance compared with soil without N-addition. Over 48 h, cumulative denitrification in soils with 500 μg glucose-C g⁻¹ soil, and 50 or 500 μg NO₃–N g⁻¹ was higher than all other treatments. There was a positive correlation between cnorB _p abundance and cumulative denitrification, but only in soils without glucose addition. Glucose-treated soils generally had higher cnorB _p abundance and mRNA levels than soils without glucose added, however response of cnorB _p abundance and mRNA levels to NO₃ supply depended on carbon availability.     

Partitioning particulate scattering and absorption into contributions of phytoplankton and non-algal particles in winter in Lake Taihu (China)

Light scattering, backscattering, and absorption coefficients of particles were observed at 62 locations in Lake Taihu (China) in November 2008. A method using a priori knowledge and the measured data was proposed to partition particulate scattering and absorption into contributions of phytoplankton and non-algal particles. The results showed that phytoplankton weakly contributed to the particulate scattering and backscattering with the mean b _ph/b _p values usually below 10% and b _bph/b _bt values of 0.3–3.9% in the whole visible light spectrum, and an approximate relationship of b _bt ≈ b _bp ≈ b _bnap was regarded as reasonable in Lake Taihu. In contrast with scattering and backscattering, phytoplankton made more contributions to the particulate absorption with the mean a _ph/a _p values varying in a wide range of about 20–70%. Both the scattering and absorption spectra of non-algal particles can be modeled well by corresponding methods. A power function model was used to simulate the scattering spectra, which presented high predictive accuracies with MAPE values usually below 5% and RMSE values below 1.5 m⁻¹, while the spectral absorption model also performed well with mean S _nap being 0.0052 nm⁻¹ (standard deviation, SD = 0.0010 nm⁻¹). As to the phytoplankton absorption, a quadratic function model used was considered to have a good performance with corresponding parameters being supported at each wavelength in the spectral range of 400–700 nm. Additionally, two basic bio-optical parameters were determined, that is, b _nap^*(550) = 0.604 m² g⁻¹ and a _ph^*(675) = 0.0288 m² mg⁻¹. Overall, these results obtained in the present study supply us with new knowledge about optical properties of suspended particulates in an inland and highly turbid lake (Lake Taihu), which are beneficial to the development of analytical models of water color remote sensing.     

Kinetic and thermodynamic behaviour of wall-bound peroxidase from wheat leaves infected with stripe rust

We have identified two types of peroxidases (POX), one ionically and one covalently bound to the particulate fraction, in stripe rust-infected and -uninfected wheat (Triticum aestivum L.) leaves. The cell walls contained a high level of POX, of which 73–76% was extractable by 1% NaCl and 24–26% by 5 mM EDTA in infected and non-infected leaves of HD 2329. The NaCl-released POX constituted the predominant fraction. Both NaCl- and EDTA-extracted POX exhibited maximum activity at pH 5.0 and had a K _m (enzyme–substrate affinity measure) value of 1.61–1.70 and 1.64–1.67 mM, respectively, with o-dianisidine as the substrate. The V _max (maximum catalytic rate) in the two extractions ranged between 7.06–7.45 and 6.65–7.82 μmol min⁻¹ g⁻¹ fresh weight. A temperature optimum of 50°C was observed for both the NaCl- and EDTA-released fractions. The two POX fractions showed a differential response to metal ions, suggesting their distinctive nature. Sodium azide inhibited POX activity markedly, which suggested the presence of heme as a prosthetic group. Inhibition of wall-bound POX by iodine and the regeneration of activity by mercaptoethanol suggested the involvement of cysteine in the active site of the enzyme. These two forms showed greater differences in terms of thermodynamic properties, such as the energy of activation (E _a) and enthalpy change (ΔH), while entropy (ΔS) and free energy changes were similar. The results further show that pathogen infection of the leaves of this susceptible wheat cultivar induces an increase in the activity and kinetics of POX, which may be critical in the response of the plant cell to infection.