Parameterization and optimization of the menthol force field for molecular dynamics simulations

Menthol’s various biological properties render it a useful component for medical and cosmetological applications, while its three centers of asymmetry mean that it can be used in a range of organic reactions. Menthol-substituted ionic liquids (ILs) have been found to exhibit promising antimicrobial and antielectrostatic properties, as well as being useful in organic catalysis and biochemical studies. However, so far, a force field designed and validated specifically for the menthol molecule has not been constructed. In the present work, the validation and optimization of force field parameters with regard to the ability to reproduce the macroscopic properties of menthol is presented. The set of optimized potentials for liquid simulations all atom (OPLS-AA) compatible parameters was tested and carefully tuned. The refinement of parameters included fitting of partial atomic charges, optimization of Lennard-Jones parameters, and recalculation of the dihedral angle parameters needed to reproduce quantum energy profiles. To validate the force field, a variety of physicochemical properties were calculated for liquid menthol. Both thermodynamic and kinetic properties were taken into account, including density, surface tension, enthalpy of vaporization, and shear viscosity. The obtained force field was proven to accurately reproduce the properties of the investigated compound while being fully compatible with the OPLS-AA force field.

     

Ecological validity of social interaction tests in rats and mice

Different rat and mouse models are used in studies of social interactions. Simple behavioral measures, which are commonly used in the laboratory, allow to perform relatively short experiments and to use multiple brain manipulation techniques. However, too much focus on the simplest behavioral models generates a serious risk of reducing ecological validity or even studying phenomena which would never happen outside of the laboratory. In this review, we discuss the suitability of mice and rats as model organisms for studying social behaviors, with focus on social transmission of fear paradigms. First, we briefly introduce the concept of domestication and what impact it had on laboratory rodents. Then, we present two aspects of social behaviors, sociability and dominance, which are crucial for social organization in these species. Finally, we present experimental models used for studying how animals transmit information about danger between each other, and how these models may reflect what happens in the natural environment. We discuss the difficulties that arise from our limited knowledge of rat and mouse ecology, especially their social life. We also explore the subject of balancing ecological validity and controllability in rodent models of social behaviors, the latter being particularly important for studying brain activity. Although it is very challenging, an efficient program for social neuroscience research should, in our opinion, aim at bridging the gap between laboratory and field studies.     

Species composition of semi-natural mesic grasslands as a factor influencing the methane yield of plant biomass (Central Europe)

Semi-natural lowland and mountain mesic meadows are grasslands rich in species, and their conservation status depends on treatments such as mowing or grazing livestock. In many countries, the condition of grasslands is deteriorating because of their inappropriate use or abandonment. This study aimed to determine the effects of the species composition of plant communities and functional plant groups on the methane yield from biomass harvested from mesic grasslands in the Sudetes Mountains. Biogas potential analysis was performed based on biomass samples collected from Poland and the Czech Republic. The biogas potential was determined in 40 day-long batch anaerobic digestion tests. The average methane yield obtained from the biomass was 246 ± 16 NL CH₄ kg^?1 VS, whereas the methane yield per hectare was 870 ± 203 m³ CH₄ ha^?1. Plant communities comprising different dominant species had no effect on the methane yield but affected the methane yield per hectare. Additionally, the species composition of grasslands with a higher percentage of forbs had lower biomass yield, resulting in lower methane yields per hectare. The continuity of the low-intensity management of mountain grassland, which can be provided by the utilization of their biomass for bioenergy production, sustains high biodiversity and ensures appropriate meadow conservation.     

Cold‐ and menthol‐evoked membrane potential changes in the moss Physcomitrella patens: influence of ion channel inhibitors and phytohormones

Microelectrode measurements carried out on leaf cells from Physcomitrella patens revealed that a sudden temperature drop and application of menthol evoked two types of different‐shaped membrane potential changes. Cold stimulation evoked spike‐type responses. Menthol depolarized the cell membrane with different rates. When it reached above 1 mV s^?1, the full response was recorded. Characteristic for the full responses was also a few‐minute plateau of the membrane potential recorded after depolarization. The influence of inhibitors of calcium channels (5 mM Gd³⁺), potassium channels (5 mM Ba²⁺), chloride channels (200 μM Zn²⁺, 50 μM niflumic acid) and proton pumps (10 μM DES), an activator of calcium release from intracellular stores (Sr²⁺), calcium chelation (by 400 μM EGTA) and phytohormones (50 μM auxin, 50 μM abscisic acid (ABA), 500 μM salicylic acid) on cold‐ and menthol‐evoked responses was tested. Both responses are different in respect to the ion mechanism: cold‐evoked depolarizations were influenced by Ba²⁺ and DES; in turn, menthol‐evoked potential changes were most effectively blocked by Zn²⁺. Moreover, the effectiveness of menthol in generation of full responses was reduced after administration of auxin or ABA, i.e. phytohormones known for their participation in responses to cold and regulation of proton pumps. The effects of DES indicated that one of the main conditions for generation of menthol‐evoked responses is inhibition of the proton pump activity. Our results indicate that perception of cold and menthol by plants proceeds in different ways due to the differences in ionic mechanism and hormone dependence of cold‐ and menthol‐evoked responses.     

Predicting ratings of perceived exertion in youth soccer using decision tree models

The purpose of this study was to determine the effectiveness of white-box decision tree models (DTM) for predicting the rating of perceived exertion (RPE). The second aim was to examine the relationship between RPE and external measures of intensity in youth soccer training at the group and individual level. Training load data from 18 youth soccer players were collected during an in-season competition period. A total of 804 training observations were undertaken, with a total of 43 ± 17 sessions per player (range 12–76). External measures of intensity were determined using a 10 Hz GPS and included total distance (TD, m/min), high-speed running distance (HSR, m/min), PlayerLoad (PL, n/min), impacts (n/min), distance in acceleration/deceleration (TD ACC/TD DEC, m/min) and the number of accelerations/decelerations (ACC/DEC, n/min). Data were analysed with decision tree models. Global and individualized models were constructed. Aggregated importance revealed HSR as the strongest predictor of RPE with relative importance of 0.61. HSR was the most important factor in predicting RPE for half of the players. The prediction error (root mean square error [RMSE] 0.755 ± 0.014) for the individualized models was lower compared to the population model (RMSE 1.621 ± 0.001). The findings demonstrate that individual models should be used for the assessment of players’ response to external load. Furthermore, the study demonstrates that DTM provide straightforward interpretation, with the possibility of visualization. This method can be used to prescribe daily training loads on the basis of predicted, desired player responses (exertion).     

The low-resolution structural models of hepatitis C virus RNA subdomain 5BSL3.2 and its distal complex with domain 3′X point to conserved regulatory mechanisms within the Flaviviridae family

Subdomain 5BSL3.2 of hepatitis C virus RNA lies at the core of a network of distal RNA–RNA contacts that connect the 5′ and 3′ regions of the viral genome and regulate the translation and replication stages of the viral cycle. Using small-angle X-ray scattering and NMR spectroscopy experiments, we have determined at low resolution the structural models of this subdomain and its distal complex with domain 3′X, located at the 3′-terminus of the viral RNA chain. 5BSL3.2 adopts a characteristic ‘L’ shape in solution, whereas the 5BSL3.2–3′X distal complex forms a highly unusual ‘Y’-shaped kissing junction that blocks the dimer linkage sequence of domain 3′X and promotes translation. The structure of this complex may impede an effective association of the viral polymerase with 5BSL3.2 and 3′X to start negative-strand RNA synthesis, contributing to explain the likely mechanism used by these sequences to regulate viral replication and translation. In addition, sequence and shape features of 5BSL3.2 are present in functional RNA motifs of flaviviruses, suggesting conserved regulatory processes within the Flaviviridae family.     

The assessment of LIF in uterine flushing--a possible new diagnostic tool in states of impaired fertility

The objective of this study was to assess the LIF (leukemia inhibitory factor) concentration in uterine flushing and serum (ELISA) of women with proven fertility, infertile women and women with recurrent miscarriage. In addition, progesterone level was determined in serum. A decreased production of LIF in the uterine microenvironment was found in states of impaired fertility. With a cut-off point of 8.23 pg/ml for LIF level in uterine flushings we have achieved 86.7% sensitivity and 100% specificity in detection of women with idiopathic infertility compared to fertile controls. No correlation between LIF in serum and uterine flushing was demonstrated, rendering LIF measurements in serum useless for diagnosis of impaired infertility. We conclude that LIF measurement in uterine flushing could be a useful diagnostic tool to predict unsuccessful implantation.