Biochemical and genetic analysis of variant C of caprine αs2-casein (Capra hircus)

Two alleles, A and B, were previously described at the goat α_s2-casein locus. Isoelectric focusing allowed us to subdivide the former one in two new alleles, called A and C. Although α_s2-casein C cannot actually be distinguished from its A counterpart by starch or polyacrylamide gel electrophoresis, it differs from the previous allele by a single substitution Lys (A)/Ile (C) at position 167, which was confirmed at the nucleotide level. The frequencies of the three α_s2-casein alleles A, B and C were estimated to be 0.85, 0.04 and 0.11 in the French dairy breeds ‘Alpine’ and ‘Saanen’.     

Hydraulic acclimation in a Mediterranean oak subjected to permanent throughfall exclusion results in increased stem hydraulic capacitance

Stem water storage capacity and hydraulic capacitance (C_S) play a crucial role in tree survival under drought-stress. To investigate whether C_S adjusts to increasing water deficit, variation in stem water content (StWC) was monitored in vivo for 2 years and related to periodical measurements of tree water potential in Mediterranean Quercus ilex trees subjected either to permanent throughfall exclusion (TE) or to control conditions. Seasonal reductions in StWC were larger in TE trees relative to control ones, resulting in greater seasonal C_S (154 and 80 kg m⁻³ MPa⁻¹, respectively), but only during the first phase of the desorption curve, when predawn water potential was above −1.1 MPa. Below this point, C_S decreased substantially and did not differ between treatments (<20 kg m⁻³ MPa⁻¹). The allometric relationship between tree diameter and sapwood area, measured via electrical resistivity tomography, was not affected by TE. Our results suggest that (a) C_S response to water deficit in the drought-tolerant Q. ilex might be more important to optimize carbon gain during well-hydrated periods than to prevent drought-induced embolism formation during severe drought stress, and (b) enhanced C_S during early summer does not result from proportional increases in sapwood volume, but mostly from increased elastic water.     

Gender and Age Differences in the Suppressive Effect of a 50 Hz Electric Field on the Immobilization-Induced Increase of Plasma Glucocorticoid in Mice

We developed an experimental system to characterize the suppressive effect of extremely low-frequency (ELF) electric fields (EFs) on the stress response. We assessed differences in the EF effects by age and gender. Control, EF-alone, immobilization-alone, and co-treated groups were subjected to an EF (50 Hz, 10 kV/m). Co-treated mice were exposed to the EF for 60 min, with immobilization during the latter half. Our results indicate that the suppressive effects of ELF EFs on the stress response in immobilized mice occur regardless of gender or age. As stress plays an important role in the onset and progression of various diseases, these findings may have broad implications for understanding the efficacy of EFs in animal, and perhaps human, health. Bioelectromagnetics. 2020;41:156–163. © 2019 Bioelectromagnetics Society.     

An evaluation of a novel estimator of linkage disequilibrium

The analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker–phenotype associations. This article introduces a new estimator of a LD parameter (ρ²) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ² could be less frequency dependent than that of the estimator of r², a widely used metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein–Friesian cattle using 771 single-nucleotide polymorphism (SNP) markers and of HapMap III data on 21 991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r² using several scenarios of LD and allelic frequencies. From these studies, it is concluded that ρ² provides a useful metric for the study of LD as the distribution of its estimator is less frequency dependent than that of the standard estimator of r².     

Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans

Traditionally, population genetics focuses on the dynamics of frequencies of alleles acquired by mutations on germ-lines, because only such mutations are heritable. Typical genotyping experiments, however, use DNA from some somatic tissues such as blood, which harbors somatic mutations at the current generation in addition to germ-line mutations accumulated since the most recent common ancestor of the sample. This common practice may sometimes cause erroneous interpretations of polymorphism data, unless we properly understand the role of somatic mutations in population genetics. We here introduce a very basic theoretical framework of population genetics with somatic mutations taken into account. It is easy to imagine that somatic mutations at the current generation simply add individual-specific variations, as errors in mutation detection do. Our theory quantifies this increment under various conditions. We find that the major contribution of somatic mutations plus errors is to very rare variants, particularly to singletons. The relative contribution is markedly large when mutations are deleterious. Because negative selection also increases rare variants, it is important to distinguish the roles of these mutually confounding factors when we interpret the data, even after correcting for demography. We apply this theory to human copy number variations (CNVs), for which the composite effect of somatic mutations and errors may not be negligible. Using genome-wide CNV data, we demonstrate how the joint action of the two factors, selection and somatic mutations plus errors, shapes the observed pattern of polymorphism.     

Radio frequency radiation causes no nonthermal damage in enzymes and living cells

The ability of radio frequency radiation (RFR) to exert irreversible nonthermal (i.e., not caused by accompanying heat) effects on biologics has been widely debated due to a relative paucity of comprehensive critical details in published reports dealing with this issue. In this study, we used rigorous control over experimental conditions to determine whether continuous RFR nonthermally affects commercially important enzymes and live bacterial and human cells using three most commonly used frequencies in current RF identification technology, namely 2.45 GHz, 915 MHz, and 13.56 MHz. Diverse biological samples were exposed to RFR under deliberately harsh conditions to increase the likelihood of observing such effects should they exist. Enzymatic activities of horseradish peroxidase and β‐galactosidase in aqueous solution exhibited no statistically discernable consequences of even very intense RFR. Likewise, with putative thermal effects excluded, the viabilities of bacteria (both gram‐positive and gram‐negative) and of human cells were not detectably compromised by such an RFR exposure. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Local and Regional vs. Global Contingency Testing

Contingency analysis of r × c-tables is systematized as follows: Global contingency testing based on the total chisquare under H₀ of independent row and column variables is least favorable to exhaustive interpretation. Local contingency testing based on chi-square components of the individual cells of an r × c-table and realized in Configural frequency analysis (KRAUTH and LIENERT, 1973) is more favourable to substantive interpretation. Compromising between global and local contingency testing leads to so-called generalized local and regional contingency testing. Every contingency testing (local, regional and naturally global) is including all N individuals of a sample supposed to have been drawn randomly from a defined population. Extension to 3-and t-dimensional contingency analysis is outlined, and biomedical applications are discussed.     

A More Powerful Simultaneous Test Procedure in Configural Frequency Analysis

In the Configural Frequency Analysis (CFA) of KRAUTH and LIENERT (1973 a, b), overfrequented (or underfrequented) cells in multivariate contingency tables are identified by simultaneous binomial tests. As an alternative, finite and asymptotic tests are proposed, which are derived from the (exact conditional) generalized hypergeometrical distribution of the cell frequencies. These tests allow for considerably more powerful decisions than do the conservative binomial tests.     

Intrageneric amplification of horse microsatellite markers with emphasis on the Przewalski's horse (E. pmewalskii)

Primer sequences flanking 13 microsatellite loci isolated from the domestic horse (E. caballus) were successfully used to amplify homologous loci in the Przewalski's horse (E. przewalskii). The results demonstrate that the level of polymorphism at all 13 loci in the Przewalski's horse was comparable to that in the domestic horse and the overall exclusion probability in the Przewalski's horse was calculated to be 0.9994. The results suggest that it should be possible to use E. caballus-derived microsatellite markers to provide parentage verification and additional valuable information to the captive management of E. przewalskii. The ability to amplify corresponding loci in the remaining five species of the genus was also confirmed, illustrating the general application of markers isolated from the domestic horse to the evaluation of polymorphism in the other six species of the genus.     

Evaluation of the Influence of Magnetic Field on Female Users of an Induction Hob in Ergonomically Sound Exposure Situations

The hypothesis being tested was that the exposure of female workers to the electromagnetic field (EMF) emitted by an induction hob (IHb) meeting public exposure limitations (evaluated according to EN/IEC 62233) is also compliant with European Directive 2013/35/EU on workers’ protection. The electric field induced in three female models in a realistic ergonomically comfortable posture near IHb was evaluated using numerical models of 25 kHz EMF sources (IHb covered by cooking vessels). It was found that, in analyzed ergonomically comfortable exposure situations, the electric field induced in the user's body may exceed public and workers’ limits when the vessels do not match the dimensions of IHb's heating zone. This can even be the case when IHb complies with Conformité Européenne labeling requirements (i.e. EMF exposure falls below public limits 30 cm away from IHb edge). In the 36 exposure scenarios analyzed, statistically significant differences were found when the distances from IHb and vessel dimension, and the height and body mass index of models in exposure scenarios varied, but not between the use of models of pregnant and nonpregnant women. The use of IHb complying with European requirements on general public protection does not ensure that EMF exposure to workers complies with the relevant limits. Adequate protection measures need to address these occupational environmental hazards. © 2020 Bioelectromagnetics Society.