Structure–Function Relationships in the Human P-Glycoprotein (ABCB1): Insights from Molecular Dynamics Simulations

P-Glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette superfamily of transporters, and it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping compounds out of cells. P-gp contributes to a reduction in toxicity, and has broad substrate specificity. It is involved in the failure of many cancer and antiviral chemotherapies due to the phenomenon of multidrug resistance (MDR), in which the membrane transporter removes chemotherapeutic drugs from target cells. Understanding the details of the ligand–P-gp interaction is therefore critical for the development of drugs that can overcome the MDR phenomenon, for the early identification of P-gp substrates that will help us to obtain a more effective prediction of toxicity, and for the subsequent outdesign of substrate properties if needed. In this work, a series of molecular dynamics (MD) simulations of human P-gp (hP-gp) in an explicit membrane-and-water environment were performed to investigate the effects of binding different compounds on the conformational dynamics of P-gp. The results revealed significant differences in the behaviour of P-gp in the presence of active and non-active compounds within the binding pocket, as different patterns of movement were identified that could be correlated with conformational changes leading to the activation of the translocation mechanism. The predicted ligand–P-gp interactions are in good agreement with the available experimental data, as well as the estimation of the binding-free energies of the studied complexes, demonstrating the validity of the results derived from the MD simulations.     

An attempt to predict pork drip loss from pH and colour measurements or near infrared spectra using artificial neural networks

The ability to predict meat drip loss by using either near infrared spectra (SPECTRA) or different meat quality (MQ) measurements, such as pH₂₄, Minolta L^∗, a^∗, b^∗, along with different chemometric approach, was investigated. Back propagation (BP) and counter propagation (CP) artificial neural networks (ANN) were used and compared to PLS (partial least squares) regression. Prediction models were created either by using MQ measurements or by using NIR spectral data as independent predictive variables. The analysis consisted of 312 samples of longissimus dorsi muscle. Data were split into training and test set using 2D Kohonen map. The error of drip loss prediction was similar for ANN (2.2–2.6%) and PLS models (2.2–2.5%) and it was higher for SPECTRA (2.5–2.6%) than for MQ (2.2–2.3%) based models. Nevertheless, the SPECTRA based models gave reasonable prediction errors and due to their simplicity of data acquisition represent an acceptable alternative to classical meat quality based models.     

Verification of the geological origin of bottled mineral water using artificial neural networks

As a first step towards objective and cost-efficient verification of the geographical origin of commercially sold mineral water, we determined up to what extent the chemical composition of mineral water can be linked to the geology of the local water source. For this purpose, a dataset consisting of 145 European mineral water samples from a known geology was analysed using counter-propagation artificial neural networks (CP-ANNs) with supervised learning algorithm. The models were tested for recall ability (RA) and validated with a leave-one-out cross validation (LOO-CV).     

Relevance for food sciences of quantitative spatially resolved element profile investigations in wheat (Triticum aestivum) grain

Bulk element concentrations of whole grain and element spatial distributions at the tissue level were investigated in wheat (Triticum aestivum) grain grown in Zn-enriched soil. Inductively coupled plasma mass spectrometry and inductively coupled plasma optical emission spectrometry were used for bulk analysis, whereas micro-proton-induced X-ray emission was used to resolve the two-dimensional localization of the elements. Soil Zn application did not significantly affect the grain yield, but did significantly increase the grain Ca, Fe and Zn concentrations, and decrease the grain Na, P and Mo concentrations; bulk Mg, S, K, Mn, Cu, Cd and Pb concentrations remained unchanged. These changes observed in bulk element concentrations are the reflection of tissue-specific variations within the grain, revealing that Zn application to soil can lead to considerable alterations in the element distributions within the grain, which might ultimately influence the quality of the milling fractions. Spatially resolved investigations into the partitioning of the element concentrations identified the tissues with the highest element concentrations, which is of utmost importance for accurate prediction of element losses during the grain milling and polishing processes.     

Micro-PIXE study of Ag in digestive glands of a nano-Ag fed arthropod (Porcellio scaber, Isopoda, Crustacea)

Micro-proton induced X-ray emission (micro-PIXE) method was applied to study the micro-localization of silver (Ag) in digestive glands of a terrestrial arthropod (Porcellio scaber) after feeding on silver nanoparticles (nano-Ag) dosed food. The aim of our work was to assess whether feeding on nano-Ag results in the assimilation of silver (Ag) in digestive gland cells. To study micro-localization and elemental distribution of Ag, the animals were fed on food dosed with nanoparticles for 14 days under controlled laboratory conditions. At the end of the feeding exposure, the animals were dissected and digestive glands prepared for micro-PIXE analyses and TEM investigation. The results obtained by micro-PIXE documented high amounts of Ag inside S-cells of the digestive gland epithelium; however, TEM investigation did not show particle aggregates inside digestive gland cells. Also no adverse effect on feeding behavior was recorded what is a measure of toxic effects. We explain the presence of Ag inside the cells as a result of the assimilation of dissoluted Ag ions from ingested nano-Ag particles. Assimilation of excessive amounts of ingested metal ions in S-cells is a well known metal detoxification mechanism in isopods. We discuss the advantages of using micro-PIXE for the micro-localization of elements in biological tissue in studies of interactions between nanoparticles and biological systems.     

Glucosinolate Profiles Change During the Life Cycle and Mycorrhizal Colonization in a Cd/Zn Hyperaccumulator <Emphasis Type="Italic">Thlaspi praecox</Emphasis> (Brassicaceae)

Thlaspi praecox Wulfen (Brassicaceae) is a perennial Cd/Zn hyperaccumulating plant species that forms functional arbuscular mycorrhizal (AM) symbiosis. Glucosinolates (GS) were studied in different organs of field-collected T. praecox at differing plant developmental stages. Additionally, AM colonization was recorded. Total GS concentrations and profiles of nine individual GS varied during the plant life cycle. Novel individual GS that were related to specific developmental phases, mainly to flowering and seed production, were identified. The highest total GS and sinalbin concentrations in rosette leaves were found in the vegetative phase, possibly contributing to protection of young, palatable leaves. The lowest were found in roots during the flowering and the seeding phases. Increased total GS concentrations in roots and enhanced aliphatic GS, especially glucobrassicanapin, in the senescence phase may protect roots from herbivory during winter and early spring. The presence of glucotropaeolin and the absence of glucobrassicanapin in the flowering phase coincided with peak AM colonization. This is the first report on GS profiles in an AM and metal-hyperaccumulating plant.     

Shear tests on full scale storey‐height specimens constructed with thermally insulating clay unit masonry with thin‐layer mortar

The paper presents results of a series of 6 in‐plane shear tests on storey‐height clay unit masonry panels [1] with thin‐layer mortar, carried out in addition to previous test campaigns [2], [3], and [4]. The walls were constructed with unfilled thermally insulating clay units with a thermal conductivity of λ = 0.09 W/(m · K). The current design rules for clay unit masonry according to DIN EN 1996‐1‐1/NA [5] are conservative compared to the presented test results for thermally insulating clay unit masonry.     

Elemental analysis of edible grains by micro-PIXE: Common buckwheat case study

The aim of this study was the adaptation of the micro-PIXE method for analysis of nutritionally relevant heavy elements in different tissues of the grain of common buckwheat (Fagopyrum esculentum), as a representative nutritionally interesting grain food source. At 57% of the buckwheat grain biomass, the endosperm was a modest nutrient source when compared to the cotyledons, at 17% of the biomass. These latter contained high concentrations of trace elements, representing 91% of the total grain Zn, 87% for P, 70% for S, 62% for Mg, 60% for K, 54% for Cu, 53% for Mn and 35% for Fe. The husk provided storage for 85% of the total Ca, 84% for Al, 83% for Si, 76% for Cl, 69% for Ti and 46% for Fe. Knowledge on these preferential elemental constitutions of the different grain tissues makes the possibility of designing target products with nutritionally optimal constitution more feasible. These data represent a basis for a more targeted approach to nutritional improvement of grains intended for human consumption.     

Application of temporal temperature gradient gel electrophoresis for characterisation of fungal endophyte communities of Salix caprea L. in a heavy metal polluted soil

Fungal endophytes can affect the heavy metal uptake of their host plants and increase the tolerance of their host plants to heavy metal stress. Therefore, in the present study, a wide-range screening of the fungal endophyte communities was conducted to determine the fungal distribution and diversity on S. caprea roots on a metal polluted site. Fungal communities were screened using amplification with the 5.8S-ITS2-28S part of the rDNA operon, with the resulting amplicons analysed by temporal temperature gradient gel electrophoresis (TTGE) and sequencing. This technique is reproducible and shows good coverage of ascomycete and basidiomycete taxa, as 68% and 32% of all of the sequences, respectively. No clear shift in fungal ITS-TTGE profiles from S. caprea roots was seen along the secondary succession stages. Ascomycetes dominated the more polluted plots, while there was a greater diversity of basidiomycetes in the less polluted and control plots, suggesting greater tolerance of ascomycetes in comparison with basidiomycete fungi. The high diversity of DSEs was confirmed at the highly metal-enriched locations, with species belonging to the genera Phialophora, Phialocephala and Leptodontidium. Furthermore, the DSE colonisation of S. caprea roots and the frequency of the sequences showing affinity towards DSE genus Phialophora, showed good correspondence with soil Pb, Cd and plant-available P concentrations, possibly indicating that DSEs improve metal tolerance of willows to high heavy metal contamination.