Molecular-modeling calculations of enzymatic enantioselectivity taking hydration into account

A new molecular-modeling methodology has been applied to explain enzymatic enantioselectivity in water. This methodology, which combines vacuum molecular mechanics and the continuum solvation method, should provide a more realistic view of the solvent-enzyme and solvent-substrate interactions than the heretofore used approaches involving the vacuum molecular mechanics only. The methodology described herein has been validated using the experimental data on alpha-chymotrypsin's enantioselectivity in the hydrolysis of four chiral substrates. The reasons why the vacuum molecular mechanics, although not taking hydration into account, still in most cases provide a satisfactory approximation of reality are discussed.     

Towards a general framework for including noise impacts in LCA

Purpose  

Several damages have been associated with the exposure of human beings to noise. These include auditory effects, i.e., hearing impairment, but also non-auditory physiological ones such as hypertension and ischemic heart disease, or psychological ones such as annoyance, depression, sleep disturbance, limited performance of cognitive tasks or inadequate cognitive development. Noise can also interfere with intended activities, both in daytime and nighttime. ISO 14'040 also indicated the necessity of introducing noise, together with other less developed impact categories, in a complete LCA study, possibly changing the results of many LCA studies already available. The attempts available in the literature focused on the integration of transportation noise in LCA. Although being considered the most frequent source of intrusive impact, transportation noise is not the only type of noise that can have a malign impact on public health. Several other sources of noise such as industrial or occupational need to be taken into account to have a complete consideration of noise into LCA. Major life cycle inventories (LCI) typically do not contain data on noise emissions yet and characterisation factors are not yet clearly defined. The aim of the present paper is to briefly review what is already available in the field and propose a new framework for the consideration of human health impacts of any type of noise that could be of interest in the LCA practice, providing indications for the introduction of noise in LCI and analysing what data is already available and, in the form of a research agenda, what other resources would be needed to reach a complete coverage of the problem.     

Effectiveness of selection taking into account differences in parental couples for histocompatibility antigens

The connection of the histoincompatibility antigens, determined by the reaction in a mixed culture of lymphocytes of the pair of parents, with the litter of linear mice and live weight of cattle was studied. It was ascertained that the degree of the difference between mates for histocompatibility locus correlated with fruitfulness and productive qualities of the descendants. As a result, a greater quantity of descendants of animals, being more viable, are born. The descendants of the parents, having the high indexes of the reaction in the mixed culture of lymphocytes, are born larger and stronger and retain this advantage during succeeding life periods. The reaction in monozygotic twins has a minimum index. The index of the reaction increases when the relationship between individuals decreases. The method of mixed culture of lymphocytes can be used for prognosis of pairs' combination, for maintenance of the heterogeneity and for determination of the degree of relationship between animals.     

Estimate of the penetrance of genotypes in a monolocus model taking into account environmental factors

Based on ITO matrices, a method for parameter estimation of the monolocus diallele model (MDM) of qualitative trait is described, taking account of non-genetic (environmental) factors. The model parameters, probabilities of relatives' affection, constructing the likelihood function and testing hypotheses of the effect of environmental factors on the penetrations of MDM genotypes are outlined. Examples are given, concerning estimation of epilepsy MDM parameters, taking account of two factors-harmfulness of antenatal ontogenesis period and harmfulness which provokes paroxysms.     

splatche: a program to simulate genetic diversity taking into account environmental heterogeneity

We present a program called splatche (SPatiaL And Temporal Coalescences in Heterogeneous Environments) to simulate the molecular diversity of samples of genes in an environmentally heterogeneous world. Simulations are performed by, first, simulating the colonization of the world using environmental information to constrain migrations and local densities. These simulated densities and migration rates recorded over time and space are then used to simulate genetic diversity under a coalescent framework. The program thus virtually allows the translation of ecological information into molecular diversity, a novel approach that can be used to study the effect of climatic change on genetic diversity.     

A flexible parametric model for a balanced account of forest carbon fluxes in LCA

Purpose

Despite a mature debate on the importance of a time-dependent account of carbon fluxes in life cycle assessments (LCA) of forestry products, static accounts of fluxes are still common. Time-explicit inventory of carbon fluxes is not available to LCA practitioners, since the most commonly used life cycle inventory (LCI) databases use a static approach. Existing forest models are typically applied to specific study fields for which the detailed input parameters required are available. This paper presents a simplified parametric model to obtain a time-explicit balanced account of the carbon fluxes in a forest for use in LCA. The model was applied to the case of spruce as an example.

Methods

The model calculated endogenous and exogenous carbon fluxes in tons of carbon per hectare. It was designed to allow users to choose (a) the carbon pools to be included in the analysis (aboveground and belowground carbon pools, only aboveground carbon or only carbon in stem); (b) a linear or sigmoidal dynamic function describing biomass growth; (c) a sigmoidal, negative exponential or linear dynamic function describing independently the decomposition of aboveground and belowground biomass; and (d) the forest management features such as stand type, rotation time, thinning frequency and intensity.

Results and discussion

The parametric model provides a time-dependent LCI of forest carbon fluxes per unit of product, taking into account the typically limited data available to LCA practitioners, while providing consistent and robust outcomes. The results obtained for the case study were validated with the more complex CO2FIX. The model ensures carbon balance within spatial and time delimitation defined by the user by accounting for the annual biomass degradation and production in each carbon pool. The inventory can be used in LCA studies and coupled with classic indicators (e.g. global warming potential) to accurately determine the climate impacts over time. The model is applicable globally and to any forest management practice.

Conclusions

This paper proposes a simplified and flexible forest model, which facilitates the implementation in LCA of time-dependent assessments of bio-based products.

     

Modelling of continuous microbial cultivation taking into account the memory effects

The problem of chemostat dynamics modelling for the purpose of control is considered. The "memory" of the culture is explicitly taken into account. Two possibilities for improving the quality of the proposed modelling approaches are discussed. A general model that accounts for the culture `memory' by means of different `memory' functions in the expressions of the specific growth rate and of the specific consumption rate and a polynomial function of the substrate concentration for the yield factor is proposed. The case where the maintenance energy is taken into account is also discussed. Two modifications of the general model (w-type and S-type) are presented. A zero-order `memory' function and a i-function with delay are applied in order to describe the `memory' effects. Continuous growth of the strain Saccharomyces cerevisiae on a glucose limited medium is considered as a case study. Detailed investigations of the variety of models, derived from the general model by applying different `memory' functions and different assumptions are carried out. The results are compared with those previously reported for the same process. It is shown that a significant improvement in predicting the substrate dynamics (not accompanied by any decrease in the quality of the model with respect to the biomass concentration) could be achieved, involving a first- or second-order polynomial function for the yield factor. It is also shown that the quality of the model mainly depends on the way that `memory' function is incorporated. The detailed investigations give priority to the w-type models. In this case past values of both biomass and substrate variables are considered. The time delay models with pure (constant) delay and those which account for the culture `memory' by zero-order `memory' function (adaptability parameter) are compared with respect to their utilization for the purpose of model-based control.     

Kinetic model of alcohol dehydrogenase function taking into account changes in protein conformation

A model of dimeric enzyme functioning is proposed concerning cooperativity of active-sites due to conformation changes. The rates of such changes are estimated from fitting the experimental data on steady-state kinetics of cyclohexanol oxidation.     

A Reed-Frost model taking into account uncertainties in the diagnostic of the infection

In this paper, we model the epidemic course of a pathogen infection within a semi-closed group which generates clinical signals which do not necessarily permit its ready and certain identification. Typical examples of such a pathogen are influenza-type viruses. We allow for time-varying infectivity levels among individuals, and model the probability of infection per contact as a function of the clinical signals. In order to accomplish this, we introduce a modified chain-binomial Reed-Frost model. We obtain an expression for the basic reproduction ratio and determine conditions which guarantee that the epidemic does not survive in the long-term. These conditions being functions of the signal’s distribution, they can be used to design and evaluate interventions, such as treatment protocols.     

Taking into account water use impacts in the LCA of biofuels: an Argentinean case study

Purpose  

The assessment of biofuels has until now mainly focused on energy demand and greenhouse gas emissions. Only little attention has been given to other impacts, although the general importance of water use for the life cycle assessment (LCA) of agricultural products has been recognized in recent publications. The aim of this work is to assess in detail the water consumption along a biofuel production chain taking into account irrigation efficiencies, levels of water scarcity, and type of feedstock, and to integrate those results in a full LCA. Furthermore, we compare the results for biofuels from various feedstocks and regions with conventional petrol.     

Management of athletic training taking into account individual heart rate variability characteristics

This article presents a new approach to planning and timely adjusting athletic trainings according to the data of the quick analysis of heart rate variability. It has been shown that individual types of regulation are different not only in the autonomic balance, but also in the degree of endurance of training and competition loads.     

Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence

Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.     

Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility

A detailed theoretical study has been made for five antibiotics which all bind selectively to AT sequences in the minor groove of B-DNA: SN-18071, NSC-101327, distamycin-2, distamycin-3 and netropsin. The optimal complexes were found for systems in which the flexibility of DNA, as well as that of the antibiotics, was taken into account. Explicit, mobile counterions and a dielectric function modelling aqueous solution were also included. The binding geometries of the most strongly interacting antibiotics, distamycin-3 and netropsin, are compared in considerable detail and it is shown that notable differences exist between them. The results for netropsin are also discussed in the light of recent disagreements concerning its exact binding location within DNA.     

On the importance of taking into account agricultural practices when defining conservation priorities for regional planning

Conserving biodiversity in managed landscapes requires the definition of spatial conservation priorities. The systematic conservation planning tools which are used to define these conservation priorities, assess the vulnerability of different locations by combining two different elements: some measurement of the biological assets in question, and some measurement of the key processes which threaten these biological assets. For instance, in cumulative impact mapping, maps of individual human activities that impact ecosystems (hereafter referred to as ‘stressor’ for individual maps and ‘cumulative stressor’ for combined maps) are overlaid with maps of ecosystem vulnerability, in order to estimate the overall ecological impact of human activities on natural ecosystems. These tools are appealing because they are easy to use and inform regional land planning. However, given that once these spatial conservation priorities are defined they potentially have far-reaching consequences, there is a need to test their robustness and reliability. Here we propose to investigate how the uncertainties related to the estimation of a cumulative stressor layer affect the definition of spatial conservation priorities. We conduct a sensitivity analysis of the different ways of estimating major stressors related to human activities (transport, urbanization and population) with a specific focus on agriculture. We show that spatial conservation priorities are little sensitive to most of the parameters and input data used to estimate the cumulative stressor map. In particular, they are not very sensitive to changes in spatially overlapping stressors, i.e. those which overlap spatially with other stressors. However, our analyses also reveal that spatial conservation priorities are highly sensitive to how the agriculture stressor is defined. These results highlight the importance of better understanding how agricultural activities impact biodiversity and establishing how more accurate information on agricultural practices can be used to define spatial conservation priorities.     

A precise method for the quantitation of proteins taking into account their amino acid composition.

A method for the quantitation of protein in biological material is described which gives the same response for all proteins irrespective of their amino acid composition. The method is based on the ninhydrin reaction of amino acids released after total acid hydrolysis of 5- to 20-μl solutions containing 1 to 100 μg of protein. The ammonia is released from the hydrolysate by diffusion and the amino acids are quantitated without fractionation using the continuous-flow system of an amino acid analyzer. Calibration is obtained with solutions of known amino acid content. The protein of a sample is calculated by multiplying the nanomoles of total amino acids found by a conversion factor F. F is the weight in micrograms of 1 nmol of the specific mixture of amino acid residues that the protein of the sample is composed of F has to be determined once for all further quantitations of the same material by quantitative amino acid analysis following standard procedures. By this method as little as 30 ng of protein per aliquot of hydrolysate analyzed can be determined.