Evaluation of the association of mercury(II) with some dicysteinyl tripeptides

The present study was undertaken to gain insight into the associations of mercury(II) with dicysteinyl tripeptides in buffered media at pH 7.4. We investigated the effects of increasing the distance between cysteinyl residues on mercury(II) associations and complex formations. The peptide–mercury(II) formation constants and their associated thermodynamic parameters in 3-(N-morpholino)propanesulfonic acid (MOPS) buffered solutions were evaluated by isothermal titration calorimetry. Complexes formed in different relative ratios of mercury(II) to cysteinyl peptides in ammonium formate buffered solutions were characterized by LTQ Orbitrap mass spectrometry. The results from these studies show that n-alkyl dicysteinyl peptides (CP 1–4), and an aryl dicysteinyl peptide (CP 5) can serve as effective “double anchors” to accommodate the coordination sites of mercury(II) to form predominantly one-to-one Hg(peptide) complexes. The aryl dicysteinyl peptide (CP 5) also forms the two-to-two Hg₂(peptide)₂ complex. In the presence of excess peptide, Hg(peptide)₂ complexes are also detected. Notably, increasing the distance between the ligating groups or “anchor points” in CP 1–5 does not significantly affect their affinity for mercury(II). However, the enthalpy change (ΔH) values (ΔH₁ ∼ −91 kJ mol⁻¹ and ΔH₂ ∼ −66 kJ mol⁻¹) for complex formation between CP 4 and 5 with mercury(II) are about one and a half times larger than the related values for CP 1, 2 and 3 (ΔH₁ ∼ −66 kJ mol⁻¹ and ΔH₂ ∼ 46 kJ mol⁻¹). The corresponding entropy change (ΔS) values (ΔS₁ ∼ −129 J K⁻¹ mol⁻¹ and ΔS₂ ∼ −116 J K⁻¹ mol⁻¹) of the structurally larger dicysteinyl peptides CP 4 and 5 are less entropically favorable than for CP 1, 2 and 3 (ΔS₁ ∼ −48 J K⁻¹ mol⁻¹ and ΔS₂ ∼ −44 J K⁻¹ mol⁻¹). Generally, these associations result in a decrease in entropy, indicating that these peptide–mercury complexes potentially form highly ordered structures. The results from this study show that dicysteinyl tripeptides are effective in binding mercury(II) and they are promising motifs for the design of multi-cysteinyl peptides for binding more than one mercury(II) ion per peptide.     

A novel immobilization method for nuclease P1 on macroporous absorbent resin with glutaraldehyde cross-linking and determination of its properties

Microbial nuclease P₁ from Penicllium citrinum was immobilized on macroporous absorbent resins: strong polar poly (styrene-co-DVB) resin (SPPSD), polymethacrylic ester resin and poly (styrene-co-DVB)-Br resin. The results showed that SPPSD was the best carrier. Three methods of glutaraldehyde cross-linking were used and simultaneous immobilization and cross-linking (CIS) was demonstrated to be the best method. The functional properties of immobilized nuclease P₁ were studied and compared to those of the free enzyme. The highest enzyme activities of free and immobilized nuclease P₁ were obtained in 0.2 M acetate buffer at pH 4.5 and a temperature of 70 °C. An increase in K_m (from 3.165 to 18.125 mg mL^?1) and a decrease in V_max (from 1667.18 to 443.95 U min^?1 mL^?1) were recorded after immobilization. SPPSD-glutaraldehyde-nuclease P₁ exhibited better thermal stability than the free enzyme. The apparent activation energy (E_a) of the free and immobilized nuclease P₁ was 137.04 kJ mol^?1 and 98.43 kJ mol^?1, respectively, implying that the catalytic efficiency of the immobilized enzyme was restricted by mass-transfer rather than kinetic limit.     

Proposed kinetic mechanism of the production of biodiesel from palm oil using lipase

Experimental determination of the separate effects of palm oil and methanol concentrations on the rate of their enzymatic transesterification was used to propose suitable mechanismic steps and to test the generated kinetic model. The reaction took place in n-hexane organic medium and the lipase used was from Mucor miehei. At a constant methanol concentration of 300 mol m⁻³, it was found that, initially as the palm oil concentration increased, the initial reaction rate increased. However, the initial rate dropped sharply at substrate concentrations larger than 1250 mol m⁻³. Similar behaviour was observed for methanol concentration effect, where at a constant substrate concentration of 1000 mol m⁻³, the initial rate of reaction dropped at methanol concentrations larger than 3000 mol m⁻³. Ping Pong Bi Bi mechanism with inhibition by both reactants was adopted as it best explains the experimental findings. A mathematical model was developed from a proposed kinetic mechanism and was used to identify the regions where the effect of inhibition by both substrates arised. The proposed model equation is essential for predicting the rate of methanolysis of palm oil in a batch or a continuous reactor and for determining the optimal conditions for biodiesel production.     

Synthesis of thermo-sensitive polyacrylamide derivatives for affinity precipitation and its application in purification of lysozyme

The thermo-sensitive N-alkyl substituted polyacrylamide polymer was synthesized by radical polymerization and its lower critical solution temperature (LCST) was controlled to be 28 °C. The thermo-sensitive recovery of polymer was over 95% in the presence of 0.05 M NaClO₄. Cibacron Blue F3GA was covalently immobilized onto the polymer via the nucleophilic reaction between the active chlorine atom of its triazine ring and the hydroxyl group of the polymer. The ligands density was 30 μmol g⁻¹ polymer. The adsorption capacity of lysozyme on the polymer was 3.4 mg g⁻¹polymer in affinity precipitation process. And over 90% of adsorbed lysozyme was eluted by 0.5 M KSCN at pH 8.0. When the affinity polymer was applied in the purification of lysozyme from egg white, the purification factor was 28 and lysozyme yield was 80% or so.     

Thresholds for morphological response to light reduction for four tropical seagrass species

Seagrasses worldwide are highly vulnerable to, and at increasing risk from reduced light availability, and robust light thresholds are required for evaluating future impacts of changing light conditions. We tested the morphological response (shoot density and growth) of four Indo-West Pacific seagrass species (Cymodocea serrulata, Halodule uninervis, Halophila ovalis and Zostera muelleri) to six daily light levels ranging from 0 to 23 mol m⁻² d⁻¹ (0–70% surface irradiance) in cool (∼23 °C) and warm temperatures (∼28 °C) over 14 weeks. The impact of light limitation on shoot densities and growth rates was higher at warm than at cool temperatures, and for Z. muelleri and H. ovalis than for C. serrulata and H. uninervis, in terms of both the time taken for the low light treatment to take effect and the predicted time to shoot loss (e.g. 17–143 days at 0 mol m⁻² d⁻¹). Using fitted curves we estimated temperature-dependent thresholds (with estimates of uncertainty) for 50% and 80% protection of growth and shoot density, defined here as “potential light thresholds” in recognition that they were derived under experimental conditions. Potential light thresholds that maintained 50% and 80% of seagrass shoot density fell within the ranges 1.1–5.7 mol m⁻² d⁻¹ and 3.8–10.4 mol m⁻² d⁻¹, respectively, depending on temperature and species. Light thresholds calculated in separate in situ studies for two of the same species produced comparable results. We propose that the upper (rounded) values of 6 mol m⁻² d⁻¹ and 10 mol m⁻² d⁻¹ can be used as potential light thresholds for protecting 50% and 80% of shoot density for these four species over 14 weeks. As management guidelines should always be more conservative than thresholds for biological declines, we used error estimates to provide a quantitative method for converting potential light thresholds into guidelines that satisfy this criterion. The present study demonstrates a new approach to deriving potential light thresholds for acute impacts, describes how they can be applied in management guidelines and quantifies the timescales of seagrass decline in response to light limitation. This method can be used to further quantify cumulative impacts on potential light thresholds.     

Osmoregulation in Dunaliella,Part II: Photosynthesis and starch contribute carbon for glycerol synthesis during a salt stress in Dunaliella tertiolecta

In response to an osmotic stress, Dunaliella tertiolecta osmoregulates by metabolizing intracellular glycerol as compatible solute. Upon the application of a salt stress to 0.17 M or 0.7 M NaCl grown D. tertiolecta cells, rates of total glycerol synthesis were substantially higher than that arising from photosynthetic ¹⁴CO₂ fixation into glycerol. The source of this extra carbon is the reserve starch pool. The contribution of carbon from the starch breakdown to glycerol synthesis was estimated from the difference between the total glycerol synthesized and that arising from ¹⁴CO₂ fixation. The maximum observed flux of carbon from ¹⁴CO₂ to glycerol from photosynthesis was of the order of 15–20 μmol ¹⁴C-glycerol mg⁻¹ Chl h⁻¹, whereas the total glycerol synthesis reached about 70 μmol glycerol mg⁻¹ Chl h⁻¹. The contribution of products of starch breakdown to glycerol synthesis increased progressively with increasing salt stress. In light, contrary to prevailing assumptions, both the photosynthesis and the starch breakdown contribute carbon to glycerol biosynthesis. The relative contributions of these two processes in the light, while cells were actively photosynthesizing, depended on the magnitude of the salt stress. On application of dilution stress, the flux of carbon from newly photosynthetically fixed ¹⁴CO₂ into glycerol was reduced progressively with increasing dilution stress that was also accompanied by a decline in total glycerol contents of the cell. The maximum observed rate of glycerol dissimilation was about 135 μmol glycerol mg⁻¹ Chl h⁻¹.     

Environmental indicators for estimating the potential soil respiration rate in alpine zone

Soil respiration is the main form of carbon flux from soil to atmosphere in the global carbon cycle. The effect of temperature on soil respiration rate is important in evaluating the potential feedback of soil organic carbon to global warming. We incubated soils from the alpine meadow zone and upper rocky zone along an altitudinal gradient (4400–5500 m a.s.l.) on the Tibetan Plateau under various temperature and soil moisture conditions. We evaluated the potential effects of temperature and soil moisture on soil respiration and its variation across altitudes. Soil respiration rates increased as the temperature increased. At 60% of soil water content, they averaged 0.21–5.33 μmol g soil⁻¹ day⁻¹ in the alpine meadow zone and 0.11–0.50 μmol g soil⁻¹ day⁻¹ in the rocky zone over the experimental temperature range. Soil respiration rates in the rocky zone did not increase between 25 and 35 °C, probably because of heat stress. Rates of decomposition of organic matter were high in the rocky zone, where the CN ratio was smaller than in the middle altitudes. Soil respiration rates also increased with increasing soil water content from 10% to 80% at 15 °C, averaging 0.04–2.00 μmol g soil⁻¹ day⁻¹ in the alpine meadow zone and 0.03–0.35 μmol g soil⁻¹ day⁻¹ in the rocky zone. Maximum respiration rates were obtained in the middle part of the alpine slope in any case of experimental temperature and soil moisture. The change patterns in soil respiration rate along altitude showed similar change pattern in soil carbon content. Although the altitude is a variable including various environmental factors, it might be used as a surrogate parameter of soil carbon content in alpine zone. Results suggest that temperature, soil moisture and altitude are used as appropriate environmental indicators for estimating the spatial distribution of potential soil respiration in alpine zone.     

The biotransformation of astragalosides by a novel acetyl esterase from Absidia corymbifera AS2

Absidia corymbifera AS2 has been previously screened for effective biotransformation of astragalosides since it is able to catalyze the hydrolysis of acetyl ester moieties. In this study, an acetyl esterase from A. corymbifera AS2 was purified and its catalytic pathways were investigated. The purified enzyme was monomeric, with a molecular mass of 36 kDa, and with optimal activity observed at pH 8.0 and 35 °C. It was stable within pH 7.0–9.5 and at temperatures lower than 45 °C. The K_m and V_max values for p-nitrophenyl acetate was estimated to be 3.76 and 17.64 mmol (min mg)⁻¹, respectively. We found that this enzyme can hydrolyze the acetyl groups at positions O-2 or O-3 of xylopyranosyl residue at the C-3 position of AS-I, isoAS-I, AS-II and isoAS-II, and convert these all to ASI. The pathways of deacetylation catalyzed by this enzyme were also clarified for the first time: AS-II→ASI, isoAS-II→AS-II→ASI, AS-I→(AS-II, isoAS-II)→ASI and isoAS-I→AS-II→ASI. In summary, an acetyl esterase from A. corymbifera AS2 was extracted, which showed unique enzymatic characteristics and enabled clarification of the biotransformation pathways of astragalosides. This enzyme has potential industrial applications, especially for utilizing abundant astragaloside precursors for the production of rare ASI.     

Lipase-catalyzed interfacial polymerization of ω-pentadecalactone in aqueous biphasic medium: A mechanistic study

The synthetic activity of lipases in biphasic o/w systems was investigated with respect to their use in the synthesis of polyester chains via transesterification reactions. Lipase-catalyzed ring-opening polymerization (ROP) of pentadecalactone (ω-PDL) dispersed in water was used as a model reaction to understand the synthetic activity of lipases in biphasic o/w system. We conducted a systematic investigation of the influence of reaction conditions on the macromolecular characteristics of oligo(ω-PDL) encompassing chemical, thermophysical and colloidal properties of the reaction medium. A model was proposed assuming Michaelis–Menten interfacial kinetics followed by chain extension via lipase-catalyzed linear polycondensation. The solidification of oligo(ω-PDL) chains with a degree of polymerization of approximately three was identified as a major factor limiting the molecular weight of obtained oligomers to ∼870 g mol⁻¹, despite the fast reaction rate and complete conversion of ω-PDL. The addition of toluene into the dispersed phase at a volumetric ratio of 0.3–0.5 of toluene to ω-PDL allowed us to circumvent this problem and increase the molecular weight of obtained oligomers up to 1460 g mol⁻¹. The molecular weight of polymer product according to this model was thus inversely related to the weight ratio percentage of interfacial lipase PS to ω-PDL per droplet and correspondingly correlated with the activity of lipase. Taking into account all these parameters allowed increasing the molar mass of oligo(ω-PDL) from 870 g mol⁻¹ to 3507 g mol⁻¹.     

Mechanical response and deformation mechanics of Type IV pili investigated using steered coarse-grained molecular dynamics simulation

Type IV pili are long filamentous structures on the surface of bacteria, which can be rapidly assembled or disassembled with pilin subunits by molecular motors. They can generate force during retraction and are involved in many bacterial functions. Steered molecular dynamics simulations with coarse-grained MARTINI models are carried out to investigate the mechanical behaviors of pili under tension. Our study is the first to report a Young's modulus of 0.80 ± 0.07 GPa and a spring constant of 1294.6 ± 116.5 kJ mol⁻¹ nm⁻² for pilus. Our results show the mechanical responses of pili are different from those described by the worm-like chain model and the van der Waal's interactions play a critical role in the mechanical responses. Moreover, the effects of pulling rates and virtual spring constants of pilus on Young's modulus are studied and two distinct morphological stages with the conformational changes appear during the extension of pilus are observed. This work provide insight into the mechanics and the deformation mechanism of pilus assembly.     

Improvement of succinate production by overexpression of a cyanobacterial carbonic anhydrase in Escherichia coli

Succinate fermentation was investigated in Escherichia coli strains overexpressing cyanobacterium Anabaena sp. 7120 ecaA gene encoding carbonic anhydrase (CA). In strain BL21 (DE3) bearing ecaA, the activity of CA was 21.8 U mg⁻¹ protein, whereas non-detectable CA activity was observed in the control strain. Meanwhile, the activity of phosphoenolpyruvate carboxylase (PEPC) increased from 0.2 U mg⁻¹ protein to 1.13 U mg⁻¹ protein. The recombinant bearing ecaA reached a succinate yield of 0.39 mol mol⁻¹ glucose at the end of the fermentation. It was 2.1-fold higher than that of control strain which was just 0.19 mol mol⁻¹ glucose. EcaA gene was also introduced into E. coli DC1515, which was deficient in glucose phosphotransferase, lactate dehydrogenase and pyruvate:formate lyase. Succinate yield can be further increased to 1.26 mol mol⁻¹ glucose. It could be concluded that the enhancement of the supply of HCO₃⁻ in vivo by ecaA overexpression is an effective strategy for the improvement of succinate production in E. coli.     

Urease immobilization on biotinylated polypyrrole coated ChemFEC devices for urea biosensor development

In this report, we describe a novel strategy for the design of a clinical urea biosensor using a process based on assembled multilayer systems. Biotinylated enzyme (urease–subiotin) was immobilized on the biotinylated polypyrrole coated Chemical field effect capacitance (ChemFEC) devices using the high avidin–biotin affinity. The immobilized enzyme activity was checked by its catalytic conversion of urea into carbon dioxide and ammonia. Electrochemical response of the bridge system constructed on Si/SiO₂/Si₃N₄ electrodes to urea addition was evaluated using the capacity–potential measurements. In addition, contact-angle measurements were carried out to control the change of surface energy and their components before and after each layer formation. The developed urea biosensor demonstrates high performances: a good sensitivity of 50 mV/pUrea in the linear urea concentration range from 10⁻⁴ to 10⁻¹ M and an excellent operational stability after three weeks of continuous use. The immobilized urease was characterised through its apparent Michaelis–Menten constant (5 mM) and the activation energy of the enzymatic reaction (20 kJ mol⁻¹). It was also shown that capacitive measurements can be used to quantify the interaction between molecular systems, based on avidin and biotin molecules.     

Two new spirostanol saponins from the the roots and rhizomes of Tupistra chinensis

Two new spirostanol saponins (1) and (2), together with three known saponins (3–5), were isolated from the roots and rhizomes of Tupistra chinensis, and their structures were determined as (20S, 22R)-spirost-25(27)-en-1β, 3β, 4β, 5β-tetraol-5-O-β-d-glucopyranoside (1) and (20S, 22R)-spirost-25(27)-en-1β, 3β, 5β-triol-5-O-β-d-glucopyranoside (2), (20S, 22R)-spirost-25(27)-en-1β, 2β, 3β, 4β, 5β-pentaol-5-O-β-d-glucopyranoside (3), Δ²⁵⁽²⁷⁾-pentrogenin (4) and ranmogenin A (5) on the basis of physicochemical properties and spectral analysis. The isolated compounds were evaluated for their cytotoxic activities against A549 and H1299 tumor cell lines in vitro. Among them, compound 2 showed cytotoxicities against A549 cells (IC₅₀ 52.66 ± 3.12 μmol L⁻¹) and H1299 cells (IC₅₀ 57.29 ± 2.51 μmol L⁻¹), respectively.     

Forming nanoparticles of α-amylase and embedding them into solid surfaces

In the current work nanoparticles (NPs) of α-amylase were generated in an aqueous solution using high-intensity ultrasound, and were subsequently immobilized on polyethylene (PE) films, or polycarbonate (PC) plates, or on microscope glass slides. The α-amylase NPs coated on the solid surfaces have been characterized by ESEM, TEM, FTIR, XPS and AFM. The substrates immobilized with α-amylase were used for hydrolyzing soluble potato starch to maltose. The amount of enzyme introduced in the substrates, leaching properties, and the catalytic activity of the immobilized enzyme were compared. The catalytic activity of the amylase deposited on the three solid surfaces was compared to that of the same amount of free enzyme at different pHs and temperatures. α-Amylase coated on PE showed the best catalytic activity in all the examined parameters when compared to native amylase, especially at high temperatures. When immobilized on glass, α-amylase showed better activity than the native enzyme over all pH and temperature values studied. However, the immobilization on PC did not improve the enzyme activity at any pH and any temperature compared to the free amylase. The kinetic parameters, K_m and V_max were also calculated. The amylase coated PE showed the most favorable kinetic parameters (K_m = 5 g L⁻¹ and V_max = 5E−07 mol mL⁻¹ min⁻¹). In contrast, the anchored enzyme-PC exhibited unfavorable kinetic parameters (K_m = 16 g L⁻¹, V_max = 4.2E−07 mol mL⁻¹ min⁻¹). The corresponding values for amylase-glass were K_m = 7 g L⁻¹, V_max = 1.8E−07 mol mL⁻¹ min⁻¹, relative to those obtained for the free enzyme (K_m = 6.6 g L⁻¹, V_max = 3.3E−07 mol mL⁻¹ min⁻¹).     

Pyruvate producing biocatalyst with constitutive NAD-independent lactate dehydrogenases

Production of pyruvate from lactate through biocatalysis is a valuable process for its simple composition of reaction system and convenience of recovery. Biocatalyst with lactate-induced NAD-independent lactate dehydrogenases (iLDHs) can effectively catalyze lactate into pyruvate. To reduce the cost of biocatalyst preparation caused by indispensable lactate addition, the mutants with constitutive iLDH of Pseudomonas sp. XP-M2 were screened. Mutant XP-LM exhibited high iLDHs activities in minimal salt medium with cheap substrate glucose as the carbon source. The biocatalyst (8.2 g dry cell weight l⁻¹) containing 169.8 U l⁻¹ l-iLDH was prepared with 20 g 1⁻¹ glucose. The cost-effective biocatalyst prepared from the mutant XP-LM could efficiently catalyze lactate into pyruvate with high yield (0.961 mol mol⁻¹). Based on the different thermostability of d-iLDH and l-iLDH in the biocatalyst, whole cells of the strain might also have the potential in production of pyruvate and d-lactate from racemic lactate.     

A show cave management: Anthropogenic CO2 in atmosphere of Výpustek Cave (Moravian Karst,Czech Republic)

Anthropogenic impact on CO₂ levels was studied in the Bear Chamber of the Výpustek Cave, a show cave in the Moravian Karst (Czech Republic), during a period of active ventilation and enhanced attendance. The study showed that the natural CO₂ levels were controlled by (i) the natural CO₂ influxes from soils/epikarst (up to ∼5.64 × 10⁻² mol s⁻¹); and, (ii) the advective CO₂ fluxes out of cave atmosphere (up to 4.66 × 10⁻² mol s⁻¹). During visitor presence, the anthropogenic CO₂ flux into the chamber reached up to ∼0.13 mol s⁻¹ and exceeded all other CO₂ fluxes. The reachable anthropogenic steady states at sufficient duration of stay (up to 2.65 × 10⁻¹ mol m⁻³) could exceed the natural CO₂ levels by factor of more than nine based on the number of visitors. Recession analysis of anthropogenic pulses showed that intervals between individual visitor groups would have to be up to ∼6 h long if the cave environment has to return to natural conditions. As such pauses between individual tours are hardly realizable, a risk analysis was conducted to find the consequences of breaking natural conditions. It showed that the condition under which dripwater becomes aggressive to calcite (i.e., the point when P_CO2 in cave atmosphere exceeds the hypothetical CO₂ concentrations in epikarst that has participated on the water formation, P_CO2(H) = 10^−1.56) is potentially reachable under extreme conditions only (enormous visitor stay period and visitor number). In case of condensed water, however, any increase in CO₂ concentration will cause an increase of water aggressiveness to calcite. Therefore, in the periods and sites of enhanced condensation, it is important to strive for preservation of natural conditions.     

Immobilization of lipase on epoxy-activated Purolite® A109 and its post-immobilization stabilization

In this study, Purolite^® A109, polystyrenic macroporous resin, was used as immobilization support due to its good mechanical properties and high particle diameter (400 μm), which enables efficient application in enzyme reactors due to lower pressure drops. The surface of support had been modified with epichlorhydrine and was tested in lipase immobilization. Optimized procedure for support modification proved to be more efficient than conventional procedure for hydroxy groups (at 22 °C for 18 h), since duration of procedure was shortened to 40 min by performing modification at 52 °C resulting with almost doubled concentration of epoxy groups (563 μmol g⁻¹). Lipase immobilized on epoxy-modified support showed significantly improved thermal stability comparing to both, free form and commercial immobilized preparation (Novozym^® 435). The highest activity (47.5 IU g⁻¹) and thermal stability (2.5 times higher half-life than at low ionic strength) were obtained with lipase immobilized in high ionic strength. Thermal stability of immobilized lipase was further improved by blocking unreacted epoxy groups on supports surface with amino acids. The most efficient was treatment with phenylalanine, since in such a way blocked immobilized enzyme retained 65% of initial activity after 8 h incubation at 65 °C, while non-blocked derivative retained 12%.     

Seasonal variations in photosynthetic irradiance response curves of macrophytes from a Mediterranean coastal lagoon

The main photosynthesis and respiration parameters (dark respiration rate, light saturated production rate, saturation irradiance, photosynthetic efficiency) were measured on a total of 23 macrophytes of the Thau lagoon (2 Phanerogams, 5 Chlorophyceae, 10 Rhodophyceae and 6 Phaeophyceae). Those measurements were performed in vitro under controlled conditions, close to the natural ones, and at several seasons. Concomitantly, measurements of pigment concentrations, carbon, phosphorous and nitrogen contents in tissues were performed. Seasonal intra-specific variability of photosynthetic parameters was found very high, enlightening an important acclimatation capacity. The highest photosynthetic capacities were found for Chlorophyceae (e.g. Monostroma obscurum thalli at 17 °C, 982 μmol O₂ g⁻¹ dw h⁻¹ and 9.1 μmol O₂ g⁻¹ dw h⁻¹/μmol photons m⁻² s⁻¹, respectively for light saturated net production rate and photosynthetic efficiency) and Phanerogams (e.g. Nanozostera noltii leaves at 25 °C, 583 μmol O₂ g⁻¹ dw h⁻¹ and 2.6 μmol O₂ g⁻¹ dw h⁻¹/μmol photons m⁻² s⁻¹ respectively for light saturated net production rate and photosynthetic efficiency). As expected, species with a high surface/volume ratio were found to be more productive than coarsely branched thalli and thick blades shaped species. Contrary to R_d (ranging 6.7–794 μmol O₂ g⁻¹ dw h⁻¹, respectively for Rytiphlaea tinctoria at 7 °C and for Dasya sessilis at 25 °C) for which a positive relationship with water temperature was found whatever the species studied, the evolution of P/I curves with temperature exhibited different responses amongst the species. The results allowed to show summer nitrogen limitation for some species (Gracilaria bursa-pastoris and Ulva spp.) and to propose temperature preferences based on the photosynthetic parameters for some others (N. noltii, Zostera marina, Chaetomorpha linum).     

Accumulation of phycocyanin in heterotrophic and mixotrophic cultures of the acidophilic red alga Galdieria sulphuraria

The relationship between light intensity, nitrogen availability and pigmentation was investigated in mixotrophic and heterotrophic cultures of the unicellular red alga Galdieria sulphuraria 074G, a potential host for production of the blue pigment, phycocyanin (PC). During the exponential growth phase of batch cultures, G. sulphuraria 074G contained 2–4 mg phycocyanin per g dry weight. In carbon-limited and nitrogen-sufficient batch cultures grown in darkness, this value increased to 8–12 mg g⁻¹ dry weight during the stationary phase, whereas the phycocyanin content in nitrogen-deficient cells decreased to values below 1 mg g⁻¹ dry weight during stationary phase. Light intensities between 0 and 100 μmol photons m⁻² s⁻¹ had no influence on phycocyanin accumulation in mixotrophic cultures grown on glucose or fructose, while light stimulated phycocyanin synthesis in cultures grown on glycerol, in which the phycocyanin content in stationary phase was increased from 10 mg g⁻¹ dry weight in darkness to 20 mg g⁻¹ dry weight at a light intensity of 80 μmol photons m⁻² s⁻¹. At higher light intensities, less phycocyanin accumulated than at lower intensities, irrespective of the carbon substrate used. In carbon-limited continuous flow cultures grown on glucose or glycerol at a dilution rate of 0.63 day⁻¹, corresponding to 50% of the maximum specific growth rate, the highest steady-state phycocyanin content of 15–28 mg g⁻¹ dry weight was found at 65 μmol photons m⁻² s⁻¹. In contrast to the apparent glucose repression of light-induced PC synthesis observed in batch cultures, no glucose repression of the light stimulation was observed in continuous flow cultures because the glucose concentration in the culture supernatant always remained at limiting levels. Despite the fact that G. sulphuraria 074G contains less phycocyanin than some other microalgae and cyanobacteria, the ability of G. sulphuraria 074G to grow and synthesize phycocyanin in heterotrophic or mixotrophic cultures makes it an interesting alternative to the cyanobacterium, Spirulina platensis presently used for synthesis of phycocyanin.     

Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations

Ram2 from Pediococcus acidilactici is a rhamnosidase from the glycoside hydrolase family 78. It shows remarkable selectivity for rutinose rather than para-nitrophenyl-alpha-l-rhamnopyranoside (p-NPR). Molecular dynamics simulations were performed using a homology model of this enzyme, in complex with both substrates. Free energy calculations lead to predicted binding affinities of −34.4 and −30.6 kJ mol⁻¹ respectively, agreeing well with an experimentally estimated relative free energy of 5.4 kJ mol⁻¹. Further, the most relevant binding poses could be determined. While p-NPR preferably orients its rhamnose moiety toward the active site, rutinose interacts most strongly with its glucose moiety. A detailed hydrogen bond analysis confirms previously implicated residues in the active site (Asp217, Asp222, Trp226, Asp229 and Glu488) and quantifies the importance of individual residues for the binding. The most important amino acids are Asp229 and Phe339 which are involved in many interactions during the simulations. While Phe339 was observed in more simulations, Asp229 was involved in more persistent interactions (forming an average of at least 2 hydrogen bonds during the simulation). These analyses directly suggest mutations that could be used in a further experimental characterization of the enzyme. This study shows once more the strength of computer simulations to rationalize and guide experiments at an atomic level.