Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations

A peptide ${\beta }_2$-${\text{m}}_{21?31}$, which is a fragment from residue 21 to residue 31 of ${\beta }_2$-microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of ${\beta }_2$-${\text{m}}_{21?31}$. From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates.     

Penicillium rubens germination on desiccated and nutrient-depleted conditions depends on the water activity during sporogenesis

Fungal growth often appears in a surrounding where water and nutrients are scarce. The impact of this environment during sporogenesis on subsequent growth is often neglected.This study investigates the effect of water availability during sporogenesis on subsequent early growth. Therefore, a carbon-depleted substrate was constructed. Humidity is then the only parameter of interest. The water conditions during sporogenesis, and during subsequent growth, were varied. This is a stressing environment: no carbon source is present, and water provided solely via the vapour.The lag time, $t_l$, and initial growth rate, ${\mu }_{fp}$, of the germ tubes were monitored.The effect of $a_w$ history on germination and initial growth depends on the $RH$ of the environment. Only at low $RH$ do spores produced at low $a_w$ have a smaller $t_l$ and higher ${\mu }_{fp}$ compared to those grown at high $a_w$. This result was remarkably pronounced when the substrate was also made hydrophobic: growth only occurred when spores were developed at low $a_w$ and placed in high $RH$.Spores grown on lowered $a_w$ attract more water. It is hypothesized that this attraction affects subsequent growth behaviour, and is the reason why growth on hydrophobic glass only prevails in the condition of high $RH$ and lowered $a_w$ history.We demonstrate the influence of cultivation conditions on germination, which becomes more pronounced in a more desiccated environment.     

The mechanisms and process of acephate degradation by hydroxyl radical and hydrated electron

The degradation process of acephate in aqueous solution with OH and ${\text{e}}_{\text{aq}}^{?}$ produced by ⁶⁰Co-γ irradiation and electron pulse radiolysis was studied in the present paper. In the aqueous solution, acephate reacted with ${\text{e}}_{\text{aq}}^{?}$ and transformed to transient species which can absorb weakly in the wavelength range of 300–400?nm and decay very fast. According to the decay of hydrated electron, the reaction rate constant of ${\text{e}}_{\text{aq}}^{?}$ and acephate is (3.51?±?0.076)?×?10⁹?dm³·mol^?1·s^?1. The transient species produced in the reaction of OH and acephate do not distinctly absorb the light in the wavelength range of 300–700?nm, so the decay and kinetics of the transient species cannot determinedirectly. The competing reaction of KSCN oracephate with OH were studied to obtain the reaction rate constant of OH and acephate, which is (9.1?±?0.11)?×?10⁸?dm³·mol^?1·s^?1. Although acetylamide and inorganic ions were determined in the products of the reaction of acephate with OH or ${\text{e}}_{\text{aq}}^{?}$, the concentration of inorganic ions in the products of the reaction of acephate with OH is higher than that in the product of the reaction of acephate with ${\text{e}}_{\text{aq}}^{?}$. Moreover, there were sulfide in the products of the reaction of acephatewith ${\text{e}}_{\text{aq}}^{?}$. The degradation pathways of acephate by OH and ${\text{e}}_{\text{aq}}^{?}$ were also proposed based on the products from GC-MS.     

The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci

For a subdivided population the consequences of dominance and gene flow for the maintenance of multilocus polymorphism, local adaptation, and differentiation are investigated. The dispersing population inhabits two demes in which selection acts in opposite direction. Fitness is determined additively by two linked diallelic loci with arbitrary intermediate dominance (no over- or underdominance). For weak as well as strong migration, the equilibrium structure is derived. As a special case, a continuous-time continent–island model (CI model) is analyzed, with one-way migration from the continent to the island. For this CI model, the equilibrium and stability configuration is obtained explicitly for weak migration, for strong migration, for independent loci, and for complete linkage. For independent loci, the possible bifurcation patterns are derived as functions of the migration rate. These patterns depend strongly on the degree of dominance. The effects of dominance, linkage, and migration on the amount of linkage disequilibrium (LD) and the degree of local adaptation are explored. Explicit formulas are obtained for $D$   $(=x_1{x}_4-x_2{x}_3)$ and $r^2$ (the squared correlation in allelic state). They demonstrate that dominant island alleles increase $D$ and decrease $r^2$. Local adaptation is elevated by dominance of the locally adaptive alleles. The effective migration rate at a linked neutral locus is calculated. If advantageous alleles are dominant, it is decreased only slightly below the actual migration rate. For a quantitative trait that is determined by two additive loci, the influence of dominance on measures of differentiation is studied. Explicit expressions for $Q_{ST}$ and two types of $F_{ST}$ at equilibrium are deduced and their relation is discussed.     

Protein crystal’s shape and polymorphism prediction within the limits resulting from the exploration of the Miyazawa–Jernigan matrix

A computer study of the prediction of the protein crystal’s shape and polymorphism of crystal’s structures within the limits resulting from the exploration of the Miyazawa–Jernigan matrix is presented. In this study, a coarse-graining procedure was applied to prepare a two-dimensional growth unit, where instead of full atom representation of the protein a two-type (hydrophobic–hydrophilic, HP) aminoacidal representation was used. The interaction energies between hydrophobic ($E_{\text{HH}}$) aminoacids were chosen from the well-known HP-type models ($E_{\text{HH}}\in [-4\text{,}-3\text{,}-2.3\text{,}-1]$), whereas interaction energies between hydrophobic and hydrophilic aminoacids ($E_{\text{HP}}$) as well as interaction energies between hydrophilic aminoacids ($E_{\text{PP}}$) were chosen from the range: $<-1\text{,}1>$, but not all values from this range fulfiled limitations resulting from the exploration of the Miyazawa–Jernigan matrix. Exploring every positively vetted combinations of energy interactions a polymorphism of the unit cell was observed what led to the fact that different final crystal’s shapes were obtained.     

Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics,possible effects on chromatin structure

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as $K\to Q$. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins.Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state ($q=+8$) is essentially a random coil, hyper-acetylated H4 ($q=+3$) is virtually as compact and stable as a globular protein of the same number of amino-acids.Conformational ensembles of acetylated H4 match the corresponding $K\to X$ substitutions only approximately: based on the ensemble similarity, we propose $K\to M$ as a possible alternative to the commonly used $K\to Q$.Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.     

Sleep Apnea Detection from Single-Lead ECG Using Features Based on ECG-Derived Respiration (EDR) Signals

Background and objective

One of the important applications of non-invasive respiration monitoring using ECG signal is the detection of obstructive sleep apnea (OSA). ECG-derived respiratory (EDR) signals, contribute to useful information about apnea occurrence. In this paper, two EDR extraction methods are proposed, and their application in automatic OSA detection using single-lead ECG is investigated.

Biological maturity at birth,the course of the subsequent ontogenetic stages and age at menarche

The main aim of the study was to assess the influence of biological maturity at birth on growth processes in the subsequent years and during puberty in girls. The material of this study comes from the outpatient clinic cards and cross-sectional research on girls from the province of Wielkopolska in Poland. It includes data of 527 girls. The influence of perinatal maturity on body weight in the later stages of ontogeny was determined with the use of the Kruskal–Wallis test and the Mann–Whitney U test. In order to determine the relationship between perinatal maturity and age at menarche, the survival analysis module was used.The results show a diverse influence of perinatal maturity on the values of body weight achieved in later years of life. The indicated predictive factors included both birth weight and gestational age. In the examined girls menarche occurred between the 10th year and the 17th year of life $(\overline{X}=12.87$, s = 1.26; Me = 13 years). The comparison showed a significant variation in age at menarche depending on the length of pregnancy (log-rank ${\chi }_2^2=27.068$, p < 0.0001) and birth weight (log-rank ${\chi }_2^2=23.241$, p < 0.0001). There was no variation in maturation of the examined girls conditioned by the occurrence of intra-uterine growth retardation (log-rank ${\chi }_2^2=2.046$, p > 0.05). Remote prognoses as to the postnatal development of preterm-born children and/or children with low birth weight indicate adverse influence of these variables on age at menarche. Perinatal biological maturity of a newborn conditions the course of postnatal development.