A new and general model to describe, characterize, quantify and classify the interactive effects of temperature and pH on the activity of enzymes.

We suggest a new and general model to describe the effects of temperature (T) and pH on the catalytic activity of enzymes. Despite the abundance of models to describe those effects, the current proposals are unsatisfactory, except for specific experimental cases in which the interactive mechanism between the two variables does not exist. For both variables, our solution analyses the activated and deactivated phases of an enzyme as phenomena of different nature. The system is described with independent probability functions. The interactive effects between T and pH are introduced with simple auxiliary functions. These functions describe the variations induced by each variable in the parameters that define the effects of the other. The structure of the resulting equation is, in theory and practice, very regular, which facilitates its use, and it is highly descriptive in different scenarios with or without interactive effects. The model was tested on three different enzymatic systems which are specifically designed to produce data for the evaluation of the effect of T and pH on the enzyme activity (A). Afterwards, our model was validated using results from other authors. Briefly, the authors found that: (1) other available models that were compared with our proposal were inefficient and in all cases our model provided the only statistically consistent solution; (2) in four cases, the enzymatic activity could only be explained if interactive effects are accepted; (3) synergy and antagonism concepts for the interaction between T and pH were described and classified; and (4) our solution is universal and independent of the structure of an enzyme and the reaction concerned.

Crocin bleaching antioxidant assay revisited: application to microplate to analyse antioxidant and pro-oxidant activities.

The crocin bleaching assay (CBA) is a common method for evaluating the antioxidant activity of hydrosoluble samples. It is criticised due to its low reproducibility, problematic quantification of results, differences in reagent preparation, doubtful need for a preheating phase and sensitivity to factors such as temperature, pH, solvents and metals. Here, the critical points of the method were extensively revised, and a highly reproducible procedure for microplate readers redeveloped. The problems of using quantification procedures, disregarding kinetic considerations, are discussed in detail and a model is proposed for quantifying simultaneously anti- and pro-oxidant activities as function of concentration and time. Thus, the combined use of a reproducible procedure and robust mathematical modeling produced consistent and meaningful criteria for comparative characterization of any oxidation modifier, taking into account the dose-time-dependent behaviour. The method was verified by characterising several commercial antioxidants and some metal compounds using the parametric values of the proposed models. The activity of the tested antioxidants decreased in the order ETX>TR>PG>AA>TBHQ>BHA. Others, such as the lipophilic antioxidants of BHT and α-Tocopherol did not show any activity. Interference from metals were for Fe(2+), Fe(3+), Cd(2+), Ni(2+), Mg(2+), Zn(2+) and Sr(2+), slightly antioxidant for Cu(1+) and Cu(2+), and strongly antioxidant for Mn(2+). None of the tested metals showed a pro-oxidant activity.

A critical point: the problems associated with the variety of criteria to quantify the antioxidant capacity.

The oxidant action implies interfering in an autocatalytic process, in which no less than five chemical species are present (oxygen, oxidizable substrate, radicals, antioxidants, and oxidation products); furthermore, reactions of first and second order can take place, and interactions can occur, at several levels of the process. The common and incorrect practice is to use the single-time dose-response of an established antioxidant as a calibration curve to compute the equivalent antioxidant capacity of a sample, which is only tested at one single time-dose, assuming too many false aspects as true. Its use is unreasonable, given the availability of computational applications and instrumental equipment that, combined, provide the adequate tools to work with different variables in nonlinear models. The evaluation of the dose-time dependency of the response of the ß-carotene method as a case study, using the combination of strong quantification procedures and a high amount of results with lower experimental error (applying microplate readers), reveals the lack of meaning of single-time criteria. Also, it demonstrates that, in most of the reactions, the time-dependent response in the oxidation process is inherently nonlinear and should not be standardized at one single time, because it would lead to unreliable results, hiding the real aspects of the response. In food matrices, the application of single-time criteria causes deficiencies in the control of the antioxidant content. Therefore, it is logical that, in the past decade, researchers have claimed consensus to increase the determination and effectiveness of antioxidant responses.

Oversimplification and overstandardization in biological methods: sperm bioassays in ecotoxicology as a case of study and a proposal for their reformulation.

An interesting toxicological bioassay (fertilization inhibition in sea urchin) uses as assessment criterion a variable (fertilization ratio) whose variation with time creates two types of difficulties. First, it fails to distinguish between the toxic effect and the spontaneous decline in the sperm activity, causing some inconsistencies. Second, the sensitivity of the fertilization ratio to many other variables of the system requires a complex standardization, constraining the achievement of the method without solving its main problem. Our proposal consists of using a parameter (sperm half-life) as the response of the assay, and describing explicitly the behavior of the system as a simultaneous function of dose and time. This new focus is able to solve the problematic character of the results based on the fertilization ratio and by using the same data set which is required by the conventional approach; it simplifies the protocol, economizes experimental effort, provides unambiguous and robust results, and contributes to the detection of an artefactual temperature effect, which is not very evident under the usual perspective. Potential application of this new approach to the improvement of other formally similar bioassays is finally suggested.

Mathematical modeling of area under the curve assessment criteria to quantify the antioxidant and pro-oxidant capacity: Coffee extracts as a case study.

The development of a convenient mathematical application for testing the antioxidant and pro-oxidant capacity is essential in order to investigate potential sources of new agents and processes. In this regard, authors use the standardized values of the area under the curve of a kinetic profile of a dose-response agent, as a way to bypass the complex process of analyzing the kinetic variations of agents. In general, linear approaches are used, but such patterns frequently lead to unreliable results and misinterpretations, making it extremely difficult to compare the results from different assays. In this work, we have demonstrated the non-linearity of the dose-response area under the curve assessment criteria by means of simulations. A simple non-linear dose-response model was developed to describe the accurate response. As a case study, experimental data of extracts of unroasted coffee beans from five different country-climate locations for the two most common coffee varieties (Robusta and Arabica) were obtained using the ß-carotene and crocin bleaching in vitro assays. Their antioxidant capacity was analyzed in detail and compared with commercial standards. The results show that the antioxidant capacity was greater than some of the commercial standards in terms of its maximum capacity, while when the analyses are based on rate parameters, the coffee extracts show between 6 and 40 times lower values than the standard antioxidants. In addition, to illustrate the advantages of using the standardized area units and the mathematical model developed, other more complex scenarios were recreated. We believe that the model application developed provides a simple alternative to summarize meaningful parameters that characterize the response, facilitates rigorous comparisons among the effects of different compounds and experimental approaches and helps to comprehend multi-variable scenarios.

NOEC and LOEC as merely concessive expedients: two unambiguous alternatives and some criteria to maximize the efficiency of dose-response experimental designs.

NOEC and LOEC (no and lowest observed effect concentrations, respectively) are toxicological concepts derived from analysis of variance (ANOVA), a not very sensitive method that produces ambiguous results and does not provide confidence intervals (CI) of its estimates. For a long time, despite the abundant criticism that such concepts have raised, the field of the ecotoxicology is reticent to abandon them (two possible reasons will be discussed), adducing the difficulty of clear alternatives. However, this work proves that a debugged dose-response (DR) modeling, through explicit algebraic equations, enables two simple options to accurately calculate the CI of substantially lower doses than NOEC. Both ANOVA and DR analyses are affected by the experimental error, response profile, number of observations and experimental design. The study of these effects--analytically complex and experimentally unfeasible--was carried out using systematic simulations with realistic data, including different error levels. Results revealed the weakness of NOEC and LOEC notions, confirmed the feasibility of the proposed alternatives and allowed to discuss the--often violated--conditions that minimize the CI of the parametric estimates from DR assays. In addition, a table was developed providing the experimental design that minimizes the parametric CI for a given set of working conditions. This makes possible to reduce the experimental effort and to avoid the inconclusive results that are frequently obtained from intuitive experimental plans.

ß-Carotene assay revisited. application to characterize and quantify antioxidant and prooxidant activities in a microplate.

The ß-carotene bleaching assay, a common method for evaluating antioxidant activity, has been widely criticized due to its low reproducibility, problematic quantification, complex reagent preparation, and interference of different factors (temperature, pH, solvents, and metals). In this work we have examined the effects of these factors and developed a highly reproducible procedure for microplate assay, evaluated the critical points of the method, and proposed a kinetic model for quantifying both antioxidant and prooxidant activities. The application of these tools produced very consistent results, which provide robust and meaningful criteria to compare in detail the characteristics of several well-known commercial antioxidants, as well as several predictable prooxidants, and can be easily applied to natural extracts, food samples, and many other type of compounds. As an example, we have tested a set of commercial antioxidants and some typical lipophilic prooxidants. The activity of the tested antioxidants decreased in the following order: ethoxyquin ≫ α-tocopherol > butylhydroxyanisole > butylhydroxytoluene ≫ propyl gallate. On the other hand, hemoglobin and Fe(2+), Fe(3+), Co(2+), and Cu(2+) showed a strong prooxidant effect, and the activity was null in Cd(2+), Ni(2+), and Sr(2+), slightly antioxidant in Mg(2+), and strongly antioxidant in Zn(2+) and Mn(2+).

Mouse bioassay for palytoxin. Specific symptoms and dose-response against dose-death time relationships.

Nowadays, a variety of protocols are applied to quantitate palytoxin. However, there is not desirable agreement among them, the confidence intervals of the basic toxicological parameters are too wide and the formal descriptions lack the necessary generality to establish comparisons. Currently, the mouse bioassay is the most accepted one to categorize marine toxins and it must constitute the reference for other methods. In the present work, the mouse bioassay for palytoxin is deeply analyzed and carefully described showing the initial symptoms of injected mice which are presented here in the first time. These symptoms clearly differ from the more common marine toxins described up to now. Regarding to the toxicological aspects two considerations are taking into account: (i) the empiric models based in the dose-death time relationships cause serious ambiguities and (ii) the traditional moving average method contains in its regular use any inaccuracy elements. Herein is demonstrated that the logistic equation and the accumulative function of Weibull's distribution (with the modifications proposed) generate satisfactory toxicological descriptions in all the respects.

Growth and metabolic features of lactic acid bacteria in media with hydrolysed fish viscera. An approach to bio-silage of fishing by-products.

The reparameterization of two classic growth models (the logistic and Gompertz equations), and the dynamic modification of the integrated form of the first of these, was applied to the description of the kinetics and metabolic behaviour of six strains of lactic acid bacteria in four media: three of these from visceral waste from fishing products, and one commercial medium. The descriptions obtained -always consistent models and statistically significant parameters- provided a wide range of reliable numerical values on notable characteristics of microbial growth and bioproductions, which allowed the assessment of the individual systems by direct comparison, and also the suggesting of the potentially most suitable groups (of species of fish and of bacteria) for bio-silage processes.

The notion of hormesis and the dose-response theory: a unified approach.

According to an opinion which is vigorous and insistently defended for approximately one decade, hormesis (the response of a biological entity to an effector, with stimulatory results at low doses and inhibitory results at high doses) radically puts into question the classic theory of dose-response (DR) relationships and demands a profound revision of environmental protection policies. Herein we show that DR theory, with the modifications which we propose, allows the modelling of various kinds of biphasic responses which are phenomenologically similar to hormetic ones and of well-defined origin, as well as responses which have been treated as genuinely hormetic. Our descriptive approach may also represent a useful resource for experimental design, directed towards identifying some of the potentially heterogeneous mechanisms which underlie the hormetic phenomenon. Finally, it also allows to discuss some factors which prevent the use of the notion of hormesis-perhaps useful in a clinical context, under strictly controlled conditions-to make decisions on environmental protection measures.

Proteases production by two Vibrio species on residuals marine media.

A comparative study was carried out on the growth and production of alkaline proteases by two Vibrio species using different marine peptones from fish viscera residues. The bacteria tested, Vibrio anguillarum and Vibrio splendidus, are producers of high levels of proteolytic enzymes which act as factors of virulence in fish cultures, causing high mortality rates. The kinetic assays and subsequent comparison with the parameters obtained from the adjustment to various mathematical models, highlighted the potential interest of the media formulated, for their possible production on an industrial scale, particularly the production of proteases by V. anguillarum growing in rainbow trout and squid peptones.

Preliminary tests on nisin and pediocin production using waste protein sources. Factorial and kinetic studies.

Lactic acid bacteria, the object of current interest as bacteriocin producers, are microorganisms with complex requirements for peptidic sources, making them appropriate indicators for testing the suitability of formulations based on proteinaceous wastes for use as microbiological media. Different peptones obtained from visceral and fish muscle residues promoted growth of lactic acid bacteria when applied individually or in combination. Kinetic parameters and bacteriocin production were similar and, in some cases (pediocin), far superior (>500%) to those obtained with bactopeptones and commercial media specifically recommended for lactic acid bacteria growth. Visceral residues, especially when subjected to a brief process of autohydrolysis at 20 degrees C, were more efficient for bacterial growth than muscle, even when muscle was treated with pepsin.

Effects of aeration on growth and on production of bacteriocins and other metabolites in cultures of eight strains of lactic acid bacteria.

In general, it is accepted that the production of bacteriocins in lactic acid bacteria cultures implies moderately to highly restrictive conditions regarding the availability of oxygen. However, the situation appears to be more complex, probably owing to the facultative anaerobic character of these microorganisms. By studying the culture of eight strains of lactic acid bacteria carried out in vessels with different loads of medium within an interval that determines linearly the minimum availability of oxygen, the existence of three types of behavior was highlighted: production increases (1) with the availability of oxygen, (2) with the restriction of this availability, and (3) toward both extremes of these conditions, diminishing in intermediate situations. These behaviors affected not only the production of bacteriocins, but also their metabolic character (in the Luedeking and Piret sense), as well as the production of other characteristic metabolites, such as lactic acid, acetic acid, and ethanol.

Stimulation of bacteriocin production by dialyzed culture media from different lactic acid bacteria.

The cross-effects of dialyzed postincubates (with a cut-off at 1000 Da) on the biomass and bacteriocin production of six strains of lactic acid bacteria were studied, and a predominance of stimulating responses was found, the characteristics of which suggested merely nutritional effects or the presence of precursor fragments of the bacteriocins. Additionally, cluster analysis of the detected responses provides an approach to define groups of highly compatible (potential consortia) or doubtfully compatible strains of lactic acid bacteria. Such a definition, which does not claim taxonomic value, has practical interest, however, in cases (e.g., silage production) in which it is convenient to use mixed inocula including strains able to establish positive interactions.

Peptones from autohydrolysed fish viscera for nisin and pediocin production.

Various peptones obtained from hydrolysed visceral homogenates of four fishery residues showed their suitability for promoting the growth of lactic acid bacteria, micro-organisms with particularly complex requirements regarding peptidic nutrients. The assay of several treatments with two bacterial species, producers of the two main bacteriocins (nisin and pediocin) demostrated that optimum conditions only imply a brief autohydrolysis at natural pH and room temperature, with subsequent steam-flow stabilisation. Later kinetic analysis of the cultures of both bacteria in the best media provided parameters which, for production of both biomass and bacteriocins (the latter behaved in the majority of cases as a mixed metabolite), indicate comparable or superior results to those found in costly commercial media, specifically recommended for culture of lactic acid bacteria.

Pediocin production by Pediococcus acidilactici in solid state culture on a waste medium: process simulation and experimental results.

The production of pediocin by Pediococcus acidilactici was comparatively studied in submerged and solid-state culture, using polyurethane foam particles soaked in commercial (MRS) and waste media with various supplements, where product concentrations were 15 times higher in MRS medium. For the solid state analysis, cultures were treated by successive compression and refilling of tubular minireactors equipped with a piston, without the need for reinoculation. This method was found to be simple, reproducible, and easily controllable, allowing culture productivity to be maintained for long periods of time without alterations in the basic properties of the system. In addition, yields were found to be superior compared to those from submerged culture. The system kinetics were modeled on the basis of widely accepted assumptions with a good fit to the experimental results and observed biomass fluctuations less evident than those predicted by the kinetic model.

Substrate inhibition of Pediococcus acidilactici by glucose on a waste medium. Simulations and experimental results.

AIMS: The possibility of substrate inhibition by glucose on biomass and pediocin production was studied in cultures of Pediococcus acidilactici on a residual medium. METHODS AND RESULTS: Calculation of the substrate inhibition coefficient in the context of microbial growth is generally laborious, and very prone to experimental error. However, a simulation combining logistic and Monod kinetics equations demonstrates that quantitative evidence for this type of inhibition, without the possibility of misinterpretation, can be obtained through the comparison of punctual preasymptotic productions as a function of substrate concentration. SIGNIFICANCE AND IMPACT OF THE STUDY: It was concluded that glucose had an inhibitory effect on growth, but not on bacteriocin production.

Survival of lactic acid bacteria in seawater: a factorial study.

A feasibility study of lactic bacteria as potential probiotics in larval cultures of marine fish was performed by investigating the survival of five strains of lactic bacteria in seawater by readily standardized procedures at different temperatures and salinities. These conditions were chosen in such a way that their combinations define a complete first-order factorial design. Depending on the strain and the ambient conditions, the survival adhered to first-order kinetics in some cases, and to the Gompertz equation in others. The half lives (t0.5) calculated from these models were subsequently introduced as responses to the factorial designs, estimating the coefficients of empirical equations that describe the group effect of temperature and salinity on t0.5. Simply additive effects were found in two cases, a negative first-order interaction in another case, while another two required second-order models.

An empirical model for describing the effects of nitrogen sources on nisin production.

AIMS: A study on the effects of tryptone and yeast extract on nisin production by Lactococcus lactis was carried out using a second order rotatable factorial design. METHODS AND RESULTS: The results show that both ingredients increased nisin production, although a small decrease in nisin levels was noted at high tryptone concentrations. In view of the low vitamin content of tryptone, the amino acids present in both tryptone and yeast extract may be responsible for these observations. CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY: The observed response suggests that maintaining tryptone concentrations in the centre of the domain and increasing the concentration of yeast extract would be ideal conditions for nisin production. However, when the economic aspects are considered, it appears that low concentrations of yeast extract and reasonably high concentrations of tryptone are optimal.

Joint effect of nisin, CO2, and EDTA on the survival of Pseudomonas aeruginosa and Enterococcus faecium in a food model system.

A study on the joint effect of either nisin or Nisaplin, headspace CO2 levels, and EDTA on the survival of Pseudomonas aeruginosa and Enterococcus faecium was carried out in a water-soluble fish muscle extract at 3 degrees C using a second-order rotatable factorial design. E. faecium was completely deactivated by all processing after 2 days of storage. In contrast, P. aeruginosa was much less susceptible to treatments, and cell death was satisfactorily described by two models. Nisin increased cell death, whereas Nisaplin (commercial form of nisin) was not suitable, as it caused undesirable interference, presumably due to its co-compounds. Interactions between Nisaplin or nisin and either EDTA or CO2 were found to be nonstatistically significant. Factors that could account for this unexpected lack of synergism are discussed. However, a statistically significant positive interaction was found between CO2 and EDTA. This finding could allow CO2 levels to be decreased and hence to reduce the main disadvantages of CO2 application, namely, exudation and acidification.