Decision-making during NHEJ: a network of interactions in human Polμ implicated in substrate recognition and end-bridging

Human Polμ is a DNA polymerase belonging to the X family that has been implicated in the non-homologous end-joining (NHEJ) pathway during repair of double-strand breaks in DNA. Loop1 is a flexible piece of Polμ which has a critical role during terminal transferase and end-joining activities: it acts as a pseudo-template when the template strand is discontinuous or unavailable, whilst diffusing away if present to avoid steric clashes. Mutational analysis and inspection of the 3D structures available allowed us to identify a network of residues in charge of sensing the presence or absence of discontinuities in the template strand, which will in turn determine the final position adopted by Loop1. This network is formed by the previously uncharacterized thumb mini-loop (NSH motif) and the positively charged helix N, which contribute to the correct positioning of Loop1 and to juxtapose the discontinuous template strand during NHEJ of incompatible ends. Accordingly, single mutation of specific conserved residues in these motifs, whilst irrelevant in most of the cases for gap filling, largely affected terminal transferase and end-joining activities. Other point mutations in the ‘hinges’ of Loop1, such as residues Phe³⁸⁵ or Phe³⁸⁹, corroborated the flexibility requirements of this motif.     

Increased incidence of disomic sperm nuclei in a 47,XYY male assessed by fluorescent in situ hybridization (FISH)

Using triple-colour fluorescent in situ hybridization in decondensed sperm heads, we assessed the sex-chromosome distribution in spermatozoa from a 47,XYY male compared with controls. The incidence of spermatozoa with 24,XY (0.30%) and 24,YY (1.01%) disomy was significantly higher than in our control series. Diploid meiocytes present in the ejaculate were mainly 47,XYY (60.6–86.7%), and haploid meiocytes were mainly 24,XY (78.1%).These results suggest that, although the extra Y chromosome is thought to be eliminated during spermatogenesis, XYY germ cells can complete meiosis and produce disomic spermatozoa. Received: 5 August 1996 / Revised: 2 October 1996     

Thinning affects Pinus sylvestris needle decomposition rates and chemistry differently depending on site conditions

Changes in mass and chemical composition of Pinus sylvestris senescent needles were studied over a 5 year period in Mediterranean (MF) and Continental forests (CF) in the Pyrenees under varying levels of thinning (P0: reference, no thinning; P20: removal of 20% basal area, P30: removal of 30% basal area). Decomposition rates were higher in MF (k = 0.423 year^?1) than in CF (k = 0.245 year^?1). However, the maximum decomposition limit was higher in MF (87.9%) compared to CF (78.1%). The relative importance and timing of rainfall, and cellulose and lignin abundance on the decomposition process was similar among both sites. However, air temperature and degree-days only affected CF (the colder site) during the initial stages of decomposition, while litter moisture was significant only in MF (the drier site) in the latter stages of decomposition. Nutrient and carbon dynamics showed temporal patterns similar to those reported in higher latitudes (except for Ca), however, indicators of N mineralization such as C/N and lignin/N at the study sites were lower than values reported in the literature. Decreases in decomposition rates after thinning were higher in MF than in CF, indicating that this ecosystem could, in the short term, be more sensitive to human intervention. Thinning had similar temporary qualitative effects at both sites, slowing decomposition, increasing N and P immobilization and decreasing Ca immobilization. However, quantitative effects of thinning were site dependent in that the magnitude of nutrient immobilization was higher in CF. A conceptual model is presented to explain effects of thinning on litter N dynamics. These temporary changes are not trivial as nutrient immobilization and accumulated organic matter losses over a thinning cycle may affect tree growth particularly during short rotations and intensive fast-growing plantations. Under similar nutrient availability conditions, sites where nutrient release occurs faster may show higher post-thinning tree growth rates.     

The antigenic interrelationship between the endoflagella of Treponema phagedenis biotype Reiter and Treponema pallidum Nichols strain. I. Treponemicidal activity of cross-reactive endoflagellar antibodies against T. pallidum

Treponemicidal activity against Treponema pallidum, Nichols strain, by anti-endoflagellar antibodies and the presence of antigenic interrelationships between the endoflagella of Treponema phagedenis biotype Reiter (TPR) and T. pallidum have been demonstrated. SDS-PAGE profiles of purified endoflagella from both organisms were similar, identifying five polypeptide bands for TPR (37,000, 33,000 doublet, 30,000, and 27,000 daltons) and five polypeptide bands for T. pallidum (35,000, 33,000 doublet, 30,000, and 27,000 daltons). Antiserum against TPR endoflagella identified identical bands on Western blots of TPR, T. pallidum, and the respective endoflagellar preparations. Western blots confirmed the presence of antibodies in normal human serum (NHS) against the 33,000 dalton treponemal endoflagellar proteins. The complement-dependent treponemicidal activity of NHS against T. pallidum was completely removed by absorption with purified TPR endoflagella. Furthermore, rabbit antisera against TPR endoflagella were reactive in the Treponema pallidum immobilization (TPI) test. These findings demonstrate that anti-endoflagellar antibodies are treponemicidal against T. pallidum. A possible mechanism for this activity is discussed in relation to the subsurface location of endoflagella.     

In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species

The coronavirus disease COVID-19 constitutes the most severe pandemic of the last decades having caused more than 1 million deaths worldwide. The SARS-CoV-2 virus recognizes the angiotensin converting enzyme 2 (ACE2) on the surface of human cells through its spike protein. It has been reported that the coronavirus can mildly infect cats, and ferrets, and perhaps dogs while not pigs, mice, chicken and ducks. Differences in viral infectivity among different species or individuals could be due to amino acid differences at key positions of the host proteins that interact with the virus, the immune response, expression levels of host proteins and translation efficiency of the viral proteins among other factors. Here, first we have addressed the importance that sequence variants of different animal species, human individuals and virus isolates have on the interaction between the RBD domain of the SARS-CoV-2 spike S protein and human angiotensin converting enzyme 2 (ACE2). Second, we have looked at viral translation efficiency by using the tRNA adaptation index. We find that integration of both interaction energy with ACE2 and translational efficiency explains animal infectivity. Humans are the top species in which SARS-CoV-2 is both efficiently translated as well as optimally interacting with ACE2. We have found some viral mutations that increase affinity for hACE and some hACE2 variants affecting ACE2 stability and virus binding. These variants suggest that different sensitivities to coronavirus infection in humans could arise in some cases from allelic variability affecting ACE2 stability and virus binding.     

On the anatomical definition of arterial networks in blood flow simulations: comparison of detailed and simplified models

Biomechanics and Modeling in Mechanobiology - The goal of this work is to assess the impact of vascular anatomy definition degree in the predictions of blood flow models of the arterial network. To...     

Absence of regional differences in the size and oxidative capacity of diaphragm muscle fibers

The oxidative capacity and cross-sectional area of muscle fibers were compared between the costal and crural regions of the cat diaphragm and across the abdominal-thoracic extent of the muscle. Succinate dehydrogenase (SDH) activity of individual fibers was quantified using a microphotometric procedure implemented on an image-processing system. In both costal and crural regions, population distributions of SDH activities were unimodal for both type I and II fibers. The continuous distribution of SDH activities for type II fibers indicated that no clear threshold exists for the subclassification of fibers based on differences in oxidative capacity (e.g., the classification of fast-twitch glycolytic and fast-twitch oxidative glycolytic fiber types). No differences in either SDH activity or cross-sectional area were noted between fiber populations of the costal and crural regions. Differences in SDH activity and cross-sectional area were noted, however, between fiber populations located on the abdominal and thoracic sides of the costal region. Both type I and II fibers on the abdominal side of the costal diaphragm were larger and more oxidative than comparable fibers on the thoracic side.     

Fractionation and amino acid composition of an aspartic acid-containing thermal proteinoid population

The heterogeneity of an aspartic acid-containing thermal polymer population has been studied by anion exchange chromatography, amino acid analysis of the resulting fractions and data processing by the principal components method. By using stepwise or continuous gradients of ionic strength both saw-toothed or bell-shaped elution profiles were obtained. This behaviour and the amino acid composition of analyzed fractions suggest a relatively high degree of heterogeneity in the polymer population although less than theoretically expected. This conclusion is compared with the findings reported in proteinoids made by similar procedures.