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.     

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.     

Fungi associated with black pepper plants in Quang Tri province (Vietnam), and interaction between Meloidogyne incognita and Fusarium solani

During a survey of nurseries and plantations of black pepper plants in Quang Tri province in Vietnam during the rainy season of 2007, nine fungal taxa were isolated from the roots of the black pepper plants. Fusarium solani was found in about one out of four black pepper root samples examined but not in the nurseries and also not from black pepper plants younger than five years growing in plantations. Since in these nurseries about one out of two black pepper plants examined had yellow leaves, this observation suggests that another pathogen must be the initial cause of the yellowing of the leaves. A likely pathogenic candidate is M. incognita which was extracted from every single black pepper plant examined in the nurseries. During the same survey, we also observed that F. solani was not isolated from the roots of black pepper plants that did not had yellow leaves and that the percentage of black pepper plants with yellow leaves increased with increased frequency of occurrence of F. solani. This observation indicates that F. solani plays a role in the yellowing of the leaves of black pepper plants in a later stage of the development of the plants. The results of a greenhouse experiment showed the negative effects inoculation with M. incognita alone or in combination with F. solani may have on the percentage of black pepper plants with yellow leaves and on plant growth. No effect of inoculation with F. solani before, at the same time, or two weeks after inoculation with M. incognita on root galling and nematode reproduction was observed.     

High frequency residues: A new set of signals for detectability studies of an X-ray imaging system

A new set of signals for studying detectability of an X-ray imaging system is presented. The results obtained with these signals are intended to complement the NEQ results.The signals are generated from line spread profiles by progressively removing their lower frequency components and the resulting high frequency residues (HFRs) form the set of signals to be used in detectability studies. Detectability indexes for these HFRs are obtained using a non-prewhitening (NPW) observer and a series of edge images are used to obtain the HFRs, the covariance matrices required by the NPW model and the MTF and NPS used in NEQ calculations. The template used in the model is obtained by simulating the processes of blurring and sampling of the edge images. Comparison between detectability indexes for the HFRs and NEQ are carried out for different acquisition techniques using different beam qualities and doses.The relative sensitivity shown by detectability indexes using HFRs is higher than that of NEQ, especially at lower doses. Also, the different observers produce different results at high doses: while the ideal Bayesian observer used by NEQ distinguishes between beam qualities, the NPW used with the HFRs produces no differences between them.Delta functions used in HFR are the opposite of complex exponential functions in terms of their support in the spatial and frequency domains. Since NEQ can be interpreted as detectability of these complex exponential functions, detectability of HFRs is presented as a natural complement to NEQ in the performance assessment of an imaging system.     

Nonthermal electromagnetic fields: From first messenger to therapeutic applications

Nonthermal pulsed electromagnetic fields, from low frequency to pulse-modulated radio frequency, have been successfully employed as adjunctive therapy for the treatment of delayed and non-union fractures, fresh fractures and chronic wounds. Recent increased understanding of the mechanism of action of electromagnetic fields (EMF) has permitted technologic advances allowing the development of EMF devices which are portable and disposable, can be incorporated into dressings, supports and casts, and can be used over clothing. This broadens the use of non-pharmacological, non-invasive EMF therapy to the treatment of postoperative pain and edema to enhance surgical recovery. EMF therapy is rapidly becoming a standard part of surgical care, and new, more significant, clinical applications for osteoarthritis, brain and cardiac ischemia and traumatic brain injury are in the pipeline. This study reviews recent evidence which suggests that calmodulin (CaM)-dependent nitric oxide signaling is involved in cell and tissue response to weak nonthermal EMF signals. There is abundant evidence that EMF signals can be configured a priori to increase the rate of CaM activation, which, in turn, can modulate the biochemical cascades living cells and tissues employ in response to external insult. Successful applications in pilot clinical trials, coupled with evidence at the cellular and animal levels, provide support that EMF is a first messenger that can modulate the response of challenged biological systems.     

A HEMATOLOGICAL STUDY IN MICE FOR EVALUATION OF LEUKEMOGENESIS BY EXTREMELY LOW FREQUENCY MAGNETIC FIELDS

OF1 mice were chronically exposed to a 50-Hz sinusoidal East–West magnetic field of 15 μT (rms), in order to make a peripheral blood study for a leukemogenic evaluation of this non-ionizing radiation. Mating and pregnancy of ancestors (first generation), and birth, lactation, and development of second-generation female mice until adulthood occurred in the experimental field. A hematological study of both control and exposed 14- to 15-week-old and 50- to 52-week-old, second-generation females was realized. Individual diagnosis of specimens and statistical analysis of results revealed a high incidence of blood leukoproliferative disorders in 14- to 15-week-old exposed females (relative risk [RR] = 3.00, p = 0.0033), despite the resistance of this strain of mice to developing malignancies under normal environmental conditions before they are 26 weeks old. Especially elevated incidences of lymphocytic (RR = 6.50, p = 0.0021) and chronic (RR = 4.00, p = 0.0153) leukemias were associated with medium-term (14–15 weeks) exposure. After 50–52 weeks of exposure, the mortality of exposed mice was 30% versus 0% of control mice. From dead exposed females, 67% revealed some type of malignancy. Corresponding RR for blood leukoproliferative disorders of those exposed which survived was 2.57 (p = 0.0351). Especially important was the proportion of chronic leukemias after long-term (50–52 weeks) exposure (RR = 8.57, p = 0.0118). Moreover, a statistically nonsignificant increase of lymphoblastic–myeloblastic leukemias pointed to a relation between age of specimen and type of alteration. We suggest that the increase in blood leukemias in OF1 mice agrees with the results of numerous epidemiological studies.     

Temperature-Sensitive Behavior of Paramecium caudatum

SYNOPSIS. The effect of temperature on the behavior of swimming cells of Paramecium caudatum has been investigated by photographic analyses of their tracks in uniform temperature, in temperature gradient, or in temperature changing with time. When the cells were placed in the temperature gradient, the frequency of discontinuous directional changes of cells swimming toward the optimal temperature, the temperature of the culture, was much lower than that of the cells swimming in the opposite direction. This difference in the frequency of directional changes explained the observed accumulation of the cells at - the optimal temperature. When the temperature was suddenly changed toward the optimum, a transient decrease of the frequency of directional changes was observed and when the temperature was changed in the reverse direction, a transient increase of the frequency was noted. This transient response to the temperature change was the origin of the dependence of the frequency of directional changes on the swimming direction in the temperature gradient. Finally, the relation between the magnitude of the transient response and the rate of the temperature change was derived.