Brownian dynamics simulations of ion atmospheres around polyalanine and B-DNA: effects of biomolecular dielectric

We have extended an earlier Brownian dynamics simulation algorithm for simulating the structural dynamics of ions around biomolecules to accommodate dielectric inhomogeneity. The electrostatic environment of a biomolecule immersed in water was obtained by numerically solving the Poisson equation with the biomolecule treated as a low dielectric region and the solvent treated as a high dielectric region. Instead of using the mean-field type approximations of ion interactions as in the Poisson-Boltzmann model, the ions were treated explicitly by allowing them to evolve dynamically under the electrostatic field of the biomolecule. This model thus accounts for ion-ion correlations and the finite-size effects of the ions. For a 13-residue alpha-helical polyalanine and a 12-base-pair bp B-form DNA, we found that the choice of the dielectric constant of the biomolecule has much larger effects on the mean ionic structure around the biomolecule than on the fluctuational and dynamical properties of the ions surrounding the biomolecule.     

Enzymatic synthesis of two novel non-reducing oligosaccharides using transfructosylation activity with β-fructofuranosidase from Arthrobacter globiformis

Two novel non-reducing oligosaccharides together with tri- and tetra-saccharides were synthesized by transfructosylation activity from sucrose as a donor and cellobiose or cellotriose as an acceptor with a purified beta-fructofuranosidase from Arthrobacter globiformis IFO 3062, and these oligosaccharides were identified as O-beta-D-glucopyranosyl-(1-->4)-alpha-D-glucopyranosyl-(1-->2)-alpha,beta-D-fructofuranoside and O-beta-D-glucopyranosyl-(1-->4)-beta-D-glucopyranosyl-(1-->4)-alpha-D-glucopyranosyl-(1-->2)-alpha,beta-D-fructofuranoside by spectrometric analyses. Both oligosaccharides were stable under condition at 100 degrees C for 30 min, and showed no degradation at pH 2.     

Free amino acids and biogenic amines in red and white muscle of tuna stored in controlled atmospheres

Summary. This paper analyses the presence of and changes in free amino acids and biogenic amines in red and white muscle of bigeye tuna during storage in controlled atmospheres with 2 gas mixes containing different concentrations of CO₂ and O₂. Levels of amines were generally higher in white than in red muscle, with the exception of putrescine and spermidine. Levels of biogenic amines increased (p<0.05) throughout storage, commencing later in red than in white muscle. A correlation between the amino acid histidine and the biogenic amine histamine was observed, but only in white muscle. Only in the case of tryptophan did white and red muscle differ (p<0.05) in terms of essential free amino acid content. They also differed in anserine content. Concentrations of the non-essential FAAs glutamic acid, glycine and alanine were higher in red than in white muscle. The effectiveness of the atmospheres was reflected in the evolution of both biogenic amines and FAAs. Gas mix 1, containing a higher concentration of CO₂, was the more effective.     

Vacuum packing: a model system for laboratory-scale silage fermentations

AIMS: To determine the utility of vacuum-packed polythene bags as a convenient, flexible and cost-effective alternative to fixed volume glass vessels for lab-scale silage studies. METHODS AND RESULTS: Using perennial ryegrass or red clover forage, similar fermentations (as assessed by pH measurement) occurred in glass tube and vacuum-packed silos over a 35-day period. As vacuum-packing devices allow modification of initial packing density, the effect of four different settings (initial packing densities of 0.397, 0.435, 0.492 and 0.534 g cm(-3)) on the silage fermentation over 16 days was examined. Significant differences in pH decline and lactate accumulation were observed at different vacuum settings. Gas accumulation was apparent within all bags and changes in bag volume with time was observed to vary according to initial packing density. CONCLUSIONS: Vacuum-packed silos do provide a realistic model system for lab-scale silage fermentations. SIGNIFICANCE AND IMPACT OF THE STUDY: Use of vacuum-packed silos holds potential for lab-scale evaluations of silage fermentations, allowing higher throughput of samples, more consistent packing as well as the possibility of investigating the effects of different initial packing densities and use of different wrapping materials.     

Microbiological, biochemical and sensory assessment of mussels (Mytilus galloprovincialis) stored under modified atmosphere packaging

AIMS: To determine the microbiological, biochemical and sensory changes of mussels during storage under aerobic, vacuum packaging (VP) and modified atmosphere packaging (MAP) conditions at 4 degrees C, and to determine shelf-life of mussels under the same packaging conditions using the above assessment parameters. METHODS AND RESULTS: Aqua-cultured mussels (Mytilus galloprovincialis) were obtained from a local culture farm, packaged aerobically under VP and MAP (50%/50% CO2/N2: M1, 80%/20% CO2/N2: M2, 40%/30%/30% CO2/N2/O2: M3), and stored at 4 degrees C. Quality evaluation was carried out using microbiological, chemical and sensory analyses. Microbiological results revealed that the M2 and VP delayed microbial growth compared with that of air-packaged samples. The effect was more pronounced for total viable count (TVC), Pseudomonas spp., lactic acid bacteria (LAB) and H2S-producing bacteria. TVC was reduced by 0.9-1.0, Pseudomonas spp. by 0.7-0.8, LAB by 1.0-2.2, H2S-producing bacteria by 0.7-1.2. Enterobacteriaceae were not significantly affected by MAP conditions. Of the chemical indices determined, the total volatile basic nitrogen and trimethylamine nitrogen values remained lower than the proposed acceptability limits of 35 mg N 100 g(-1) and 12 mg N 100 g(-1), respectively, after 15 days of storage. Both the VP and air-packaged mussel samples exceeded these limits. The thiobarbituric acid value of all MAP and VP mussels remained lower than the proposed acceptability limit of 1 mg malondialdehyde kg(-1). The air-packaged samples exceeded this limit. All samples retained desirable sensory characteristics during the first 8 days of storage. CONCLUSIONS: Based on odour and taste evaluation, the M1 and M3 samples remained acceptable until ca day 11-12, the M2 samples remained acceptable until ca day 14-15 days while the VP and air-packaged mussel samples remained acceptable until ca days 10-11 and 8-9 of storage respectively. Based primarily on sensory, but also on biochemical and microbiological parameters determined, M2 gas mixture was the most effective for mussel preservation achieving a shelf-life of ca 14-15 days. SIGNIFICANCE AND IMPACT OF THE STUDY: MAP (M2) can be used to increase the shelf-life of refrigerated mussels. A shelf-life extension of refrigerated mussels by ca 5-6 days under MAP may be obtained.     

The greenhouse gas value of ecosystems

As society faces the urgent need to mitigate climate change, it is critical to understand how various ecosystems contribute to the climate, and to express these contributions in terms that are meaningful to policymakers, economists, land managers, and other nonscience interest holders. Efforts to mitigate climate change call for quantification of the full greenhouse gas (GHG) effects of land use decisions, yet we lack an appropriate metric of the full GHG implications of maintaining a given ecosystem over a multiple year time frame. Here, we propose the concept of greenhouse gas value (GHGV) of ecosystems, which accounts for potential GHG release upon clearing of stored organic matter, annual GHG flux, and probable GHG exchanges resulting from disturbance. It treats these ecosystem–atmosphere exchanges in a time‐sensitive manner, thereby providing an appropriate framework for computing of the GHG consequences of any land use decision. To illustrate this concept, we provide estimates of the GHGV of various biome types (based on data compiled from the literature), disturbance regimes, and decisions on the treatment of time. We show that natural ecosystems generally have high GHGV's, whereas managed ecosystems generally have lower or negative GHGV's; that GHGV decreases with increasing probability of disturbance, and that decisions on the treatment of time can be important, affecting some ecosystem types more strongly than others. In addition, we show how GHGV may be used to quantify the full GHG effects of land‐use or land‐cover change in a thorough and rigorous manner. Finally, we provide comparisons of GHGV to other major paradigms for valuing the GHG contributions of ecosystems, showing that – for many purposes –GHGV is the most appropriate method of quantifying the GHG services of ecosystems.     

The effect of addition of olive oil and "Aceto balsamico di Modena" wine vinegar in conjunction with active atmosphere packaging on the microbial and sensory quality of "Lollo Verde" lettuce and rocket salad

Fresh rocket “Eruca Sativa” and lettuce “Lollo Verde” leaves were stored with the addition of olive oil and wine vinegar “Aceto balsamico di Modena” under modified atmosphere packaging (MAP) (5% O₂/10% CO₂/85% N₂ for MAP A and 2% O₂/5% CO₂/93% N₂ for MAP B). The microbial (mesophilic, psychrotrophic bacteria and Enterobacteriacae), physical (color and firmness) and sensory parameters of samples were studied in relation to storage time (up to 10 days at 5 ± 1 °C). The effect of wine vinegar and the application of both MAP treatments reduced the growth of all bacteria populations (p < 0.05). Samples with olive oil stored under MAP A gave the best score for overall impression (3 and 2.1 for MAP A and B respectively at the 9th day of storage) while the addition of vinegar limited sensory shelf-life to 3 days (p < 0.05). Firmness was negatively affected by wine vinegar while samples with olive oil stored under MAP A maintained firmness close to normal. Color attributes were maintained better under both MAP treatments (p < 0.05).     

Modelling O2 and O2 unidirectional fluxes in plants. IV: Role of conductance and laws of its regulation in C3 plants

Numerous studies focus on the measurement of conductances for CO₂ transfer in plants and especially on their regulatory effects on photosynthesis. Measurement accuracy is strongly dependent on the model used and on the knowledge of the flow of photochemical energy generated by light in chloroplasts. The only accurate and precise method to quantify the linear electron flux (responsible for the production of reductive energy) is the direct measurement of O₂ evolution, by ¹⁸O₂ labelling and mass spectrometry. The sharing of this energy between the carboxylation (P) and the oxygenation of photorespiration (PR) depends on the plant specificity factor (Sp) and on the corresponding atmospheric concentrations of CO₂ and O₂ ( André, 2013). The concept of plant specificity factor simplifies the equations of the model. It gives a new expression of the effect of the conductance (g) between atmosphere and chloroplasts. Its quantitative effect on photosynthesis is easy to understand because it intervenes in the ratio of the plant specificity factor (Sp) to the specificity of Rubisco (Sr). Using this ‘simple’ model with the data of ¹⁸O₂ experiments, the calculation of conductance variations in response to CO₂ and light was carried out.