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Understanding the transfer of polychlorinated dibenzo- p -dioxins (PCDDs) and dibenzofurans (PCDFs) as well as polychlorinated biphenyls (PCBs) from oral exposure into cow's milk is not purely an experimental endeavour, as it has produced a large corpus of theoretical work. This work consists of a variety of predictive toxicokinetic models in the realms of health and environmental risk assessment and risk management. Their purpose is to provide mathematical predictive tools to organise and integrate knowledge on the absorption, distribution, metabolism and excretion processes. Toxicokinetic models are based on more than 50 years of transfer studies summarised in part I of this review series. Here in part II, several of these models are described and systematically classified with a focus on their applicability to risk analysis as well as their limitations. This part of the review highlights the opportunities and challenges along the way towards accurate, congener-specific predictive models applicable to changing animal breeds and husbandry conditions. [ABSTRACT FROM AUTHOR]

Polychlorinated dibenzo- para -dioxins (PCDDs) and dibenzofurans (PCDFs) (collectively and colloquially referred to as 'dioxins') as well as polychlorinated biphenyls (PCBs) are persistent and ubiquitous environmental contaminants that may unintentionally enter and accumulate along the food chain. Owing to their chronic toxic effects in humans and bioaccumulative properties, their presence in feed and food requires particular attention. One important exposure pathway for consumers is consumption of milk and dairy products. Their transfer from feed to milk has been studied for the past 50 years to quantify the uptake and elimination kinetics. We extracted transfer parameters (transfer rate, transfer factor, biotransfer factor and elimination half-lives) in a machine-readable format from seventy-six primary and twenty-nine secondary literature items. Kinetic data for some toxicologically relevant dioxin congeners and the elimination half-lives of dioxin-like PCBs are still not available. A well-defined selection of transfer parameters from literature was statistically analysed and shown to display high variability. To understand this variability, we discuss the data with an emphasis on influencing factors, such as experimental conditions, cow performance parameters and metabolic state. While no universal interpretation could be derived, a tendency for increased transfer into milk is apparently connected to an increase in milk yield and milk fat yield as well as during times of body fat mobilisation, for example during the negative energy balance after calving. Over the past decades, milk yield has increased to over 40 kg/d during high lactation, so more research is needed on how this impacts feed to food transfer for PCDD/Fs and PCBs. [ABSTRACT FROM AUTHOR]

Background: During food or feed contamination events, it is of utmost importance to ensure their rapid resolution to minimize impact on human health, animal health and finances. The existing Rapid Alert System for Food and Feed (RASFF) is used by the European Commission, national competent authorities of member countries and the European Food Safety Authority to report information on any direct or indirect human health risk arising from food or feed, or serious risks to animal health or the environment in relation to feed. Nevertheless, no methods exist to to collectively evaluate this vast source of supply chain information. Methods: To aid in the extraction, evaluation and visualization of the data in RASFF notifications, we present the Rapid Alert Supply Network Extractor (RASNEX) open-source tool available from https://doi.org/10.5281/zenodo.4322555 freely. Among RASNEX's functions is the graphical mapping of food and feed supply chain operators implicated in contamination events. RASNEX can be used during ongoing events as a support tool for risk analysis using RASFF notifications as input. Results: In a first use case, we showcase the functionality of RASNEX with the RASFF notification on a 2017/2018 contamination event in eggs caused by the illegal use of fipronil. The information in this RASFF notification is used to visualize nine different flows of main and related food products. In a second use case, we combine RASFF notifications from different types of food safety hazards (Salmonella spp., fipronil and others) to obtain wider coverage of the visualized egg supply network compared to the first use case. Actors in the egg supply chain were identified mainly for Italy, Poland and Benelux. Other countries (although involved in the egg supply chain) were underrepresented. Conclusions: We hypothesize that biases may be caused by inconsistent RASFF reporting behaviors by its members. These inconsistencies may be counteracted by implementing standardized decision-making tools to harmonize decisions whether to launch a RASFF notification, in turn resulting in a more uniform future coverage across European food and feed supply chains with RASNEX. [ABSTRACT FROM AUTHOR]

Undesirable substances in feed can transfer into foods of animal origin after ingestion by livestock animals. These contaminants in food may threaten consumer health. Commonly, feeding trials are conducted with animals to assess the transfer of undesirable substances into animal tissues or milk. Such feeding trials explore the effects of the various physiological systems (e.g., ruminant and non-ruminant gastro-intestinal tracts) as well as different livestock production intensities on transfer. Using alternative methods to mimic the complex physiological processes of several organs is highly challenging. This review proposes a potential cascade of in vitro and ex vivo models to investigate the transfer of contaminants from feed into foods of animal origin. One distinct challenge regarding the models for ruminants is the simulation of the forestomach system, with the rumen as the anaerobic fermentation chamber and its epithelial surfaces for absorption. Therefore, emphasis is placed on in vitro systems simulating the rumen with its microbial ecosystem as well as on ex vivo systems to replicate epithelial absorption. Further, the transfer from blood into milk must be evaluated by employing a suitable model. Finally, in silico approaches are introduced that can fill knowledge gaps or substitute in vitro and ex vivo models. Physiologically-based toxicokinetics combines the information gained from all alternative methods to simulate the transfer of ingested undesirable substances into foods of animal origin. [ABSTRACT FROM AUTHOR]

Experiments show that a ligand–receptor complexformed bybinding a bivalent ligand (D) in which the two ligating units arejoined covalently by a flexible polymeric spacer (S) can be ordersof magnitude more stable than the corresponding complex formed withmonomeric ligands. Although molecular models rationalizing this “enhancementeffect” have been proffered, they ignore spacer–receptor(S–R) interactions, which can substantially influence the relativestability of complexes. Here, the results of a computational studydesigned to assess the impact of S–R interactions in the prototypicbivalent complex are presented and compared to results of experiments.The S–R interactions mimicking general features of biologicalsystems are modeled by contoured R surfaces with hills (or depressions)at the binding sites. In the fictitious limit of vanishing S–Rinteractions, the enhancement is pronounced, as observed in experiments.For strictly repulsive S–R interactions (hard R surface), theenhancement vanishes, or even reverses. This is particularly the caseif the R surface is convex (i.e., rising between the binding sites),while the enhancement is only moderately reduced if the R surfaceis concave. Alternatively, a weak S–R attraction close to theR surface can increase the enhancement. It is concluded that largeenhancement should be observed only if both features are present:a concave R surface plus a weak S–R attraction. The latteroccurs for spacer material such as polyethylene glycol (PEG), whichis weakly hydrophobic and thus attracted by protein surfaces. It isshown that the enhancement of bivalent binding can be characterizedby a single key parameter, which may also provide guidelines for thedesign of multivalent complexes with large enhancement effect. [ABSTRACT FROM AUTHOR]

Highlights: [•] A pharmacokinetic model was combined with a probabilistic model to gain a decision tool for risk management. [•] The German dioxin incident of winter 2010/2011 can be described by the tool. [•] Clearing rates for the congener 1,2,3,4,7,8-HxCDD were determined from experimental data (Hoogenboom et al., 2004). [•] The approach demonstrated here is a showcase how a risk assessment in the case of contaminated feeding can be performed. [Copyright &y& Elsevier]

Understanding the transfer of polychlorinated dibenzo- p -dioxins and dibenzofurans (PCDD/Fs) in farm animals is essential for ensuring food safety, but such information for suckler ewes ( Ovis aries ) has been lacking. This work quantifies the accumulation, tissue distribution, and depuration kinetics of PCDD/Fs in these animals. Six suckler ewes (EXP group) were exposed to PCDD/Fs through contaminated hay (2.3-12.7 ng toxic-equivalent kg -1 dry matter) and then allowed to depurate by switching to noncontaminated hay from 29 days of lactation. Four control ewes were fed continuously with noncontaminated hay. At different time points covering depuration, weaning and slaughter, PCDD/F analysis of milk (three time points), blood and sternal adipose tissue (five time points), Longissimus thoracis muscle, liver, and empty body homogenate at slaughter (188 days of depuration) was performed. A relevant PCDD/F bioaccumulation was observed from oral intake in milk and adipose tissue (biotransfer factors of 1.24 and 1.06 day kg -1 lipids for the sum toxic-equivalent, respectively) in the EXP ewes, especially for penta- and hexa-chlorinated congeners. The EXP ewes' adipose tissue started at 10-fold the EU maximum level (ML) and showed depuration below the ML after 130 days. Specific PCDD/F accumulation in the ewe liver was observed, especially for dibenzofurans. These toxicokinetic data can inform recommendations to ensure the chemical safety of sheep food products.

The mutual information (MI) expansion is applied to two molecular systems to probe algorithms that serve to estimate conformational entropy differences more precisely. The individual terms of the MI expansion are evaluated with a histogram method. Internal coordinates are used to avoid spurious correlations, which would require higher order terms in the MI expansion. Two approaches are applied that compensate for systematic errors that occur with a histogram method: (1) Simulation data are balanced by using the same number of coordinate sets (frames) for both conformer domains considered for the entropy difference computation. Balancing puts fluctuations of the histogram bin contents on the same level for both conformer domains, allowing efficient error cancellation. (2) Bias correction compensates for systematic deviations due to a finite number of frames per bin. Applying both corrections improves the precision of entropy differences drastically. Estimates of entropy differences are compared to thermodynamic benchmarks of a simple polymer model and trialanine, where excellent agreement was found. For trialanine, the average error for the estimated conformational entropy difference is only 0.3 J/(mol K), which is 100 times smaller than without applying the two corrections. Guidelines are provided for efficiently estimating conformational entropies. The program ENTROPICAL, used for the computations, is made available, which can be used for molecular dynamics or Monte Carlo simulation data on macromolecules like oligopeptides, polymers, proteins, and ligands.

We constructed an accurate polyether force field for implicit solvent (IS) molecular dynamics (MD) simulations that matches local and global conformations of 1,2-dimethoxy-ethane (DME) and polyethylene glycol (PEG), respectively. To make appropriate force field adjustments for IS models of PEG, we used long-term MD simulation data of 1 μs in explicit solvent (ES) based on the most recent CHARMM35 ether force field that includes adjustments for PEG in explicit water. In IS models, competition of attractive van der Waals (vdW) interactions between solute-solute and solute-solvent atom pairs is often not considered explicitly. As a consequence, the attractive vdW interactions between solute atom pairs that remain in IS models explicitly can yield equilibrium structures that are too compact. This behavior was observed in the present study comparing MD simulation data of the DME and PEG ES model with corresponding IS models that use generalized Born (GB) electrostatics combined with positive surface energy terms favoring compact structures. To regain balance of attractive vdW interactions for IS models, we considered the IS generalized Born with simple switching (GBSW) model in detail, where we turned off surface energy terms and reduced attractive vdW interactions to 90%, or we used alternatively even slightly negative surface energies. However, to obtain quantitatively the same local and global distributions of PEG conformers as in ES, we needed additional force field adjustments involving torsion potentials and 1-4 and 1-5 atom pair Coulomb interactions. This CHARMM ether force field, specifically optimized for IS simulation conditions, is equally valid for dimeric and polymeric ethylene glycol. To explore the conformational space of PEG with MD simulations, an IS GBSW model requires 2 orders of magnitude less CPU time than the corresponding ES model. About a factor of 5 of this gain in efficiency is due to the lack of solvent viscosity in IS models.

Systematic model investigations of the molecular interactions of fluorinated amino acids within native protein environments substantially improve our understanding of the unique properties of these building blocks. A rationally designed heterodimeric coiled coil peptide (VPE/VPK) and nine variants containing amino acids with variable fluorine content in either position a16 or d19 within the hydrophobic core were synthesized and used to evaluate the impact of fluorinated amino acid substitutions within different hydrophobic protein microenvironments. The structural and thermodynamic stability of the dimers were examined by applying both experimental (CD spectroscopy, FRET, and analytical ultracentrifugation) and theoretical (MD simulations and MM-PBSA free energy calculations) methods. The coiled coil environment imposes position-dependent conformations onto the fluorinated side chains and thus affects their packing and relative orientation towards their native interaction partners. We find evidence that such packing effects exert a significant influence on the contribution of fluorine-induced polarity to coiled coil folding.

Non-linear correlations based on mutual information are evaluated to measure statistical dependencies among data points measured from metabolism in two dimensional space. While the Pearson correlation coefficient is only rigorously applicable to characterize strictly linear correlations with Gaussian noise, the mutual information coefficient is more generally valid. Here, we use recent distribution-free (non-parametric) mutual information estimators based on k-nearest neighbor distances. The mutual information algorithm of Kraskov et al. is found to yield estimates with low systematic and statistical error. The significance of the different methods is probed for artificial sets of tens to hundreds of data points, a size currently typical for metabolomic data. We analyze experimental data on metabolite concentrations from Arabidopsis thaliana by using these procedures. The mutual information was able to detect additional non-linear correlations undetectable for the Pearson coefficient.

A method is presented to calculate thermodynamic conformational entropy of a biomolecule from molecular dynamics simulation. Principal component analysis (the quasi-harmonic approximation) provides the first decomposition of the correlations in particle motion. Entropy is calculated analytically as a sum of independent quantum harmonic oscillators. The largest classical eigenvalues tend to be more anharmonic and show statistical dependence beyond correlation. Their entropy is corrected using a numerical method from information theory: the k-nearest neighbor algorithm. The method calculates a tighter upper limit to entropy than the quasi-harmonic approximation and is likewise applicable to large solutes, such as peptides and proteins. Together with an estimate of solute enthalpy and solvent free energy from methods such as MMPB/SA, it can be used to calculate the free energy of protein folding as well as receptor-ligand binding constants.