A new protein domain for binding to DNA through the minor groove

PMID:7925279Protein p6 of the Bacillus subtilis phage phi 29 binds with low sequence specificity to DNA through the minor groove, forming a multimeric nucleoprotein complex that activates the initiation of phi 29 DNA replication. Deletion analysis suggested that the N-terminal part of protein p6, predicted to form an amphipathic alpha-helix, is involved in DNA binding. We have constructed site-directed mutants at the polar side of the putative alpha-helix. DNA binding and activation of initiation of phi 29 DNA replication were impaired in most of the mutant proteins obtained. A 19 amino acid peptide comprising the N-terminus of protein p6 interacted with a DNA fragment containing high-affinity signals for protein p6 binding with approximately 50-fold higher affinity than the peptide corresponding to an inactive mutant. Both wild-type peptide and protein p6 recognized the same sequences in this DNA fragment. This result, together with distamycin competition experiments, suggested that the wild-type peptide also binds to DNA through the minor groove. In addition, CD spectra of the wild-type peptide showed an increase in the alpha-helical content when bound to DNA. All these results indicate that an alpha-helical structure located in the N-terminal region of protein p6 is involved in DNA binding through the minor groove.This work has been supported by grants SROI GM27242-15 from the National Institutes of Health, BIOT-CT91-0268 and CHRX-CT92-0010 from the European Economic Community and PB90/0091 from the Direcci6n General de Investigaci6n Cientffica Tecnica. The institutional help of Fundaci6n Ram6n Areces is also acknowledged. R.Freire was a recipient of a predoctoral fellowship from Comunidad Autonoma de MadridPeer reviewe

Invasive species and habitat degradation in Iberian streams: An analysis of their role in freshwater fish diversity loss

Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives' decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions

Phage Ø29 Protein p6 Is in a Monomer−Dimer Equilibrium That Shifts to Higher Association States at the Millimolar Concentrations Found in Vivo

Protein p6 from Bacillus subtilis phage Ø29 (Mr = 11 800) binds in vitro to DNA forming a large nucleoprotein complex in which the DNA wraps a multimeric protein core. The high intracellular abundance of protein p6 together with its ability to bind the whole Ø29 DNA in vitro strongly suggests that it plays a role in viral genome organization. We have determined by sedimentation equilibrium analysis that protein p6 (1−100 μM range), in the absence of DNA, is in a monomer−dimer equilibrium, with an association constant (K2) of 2 × 105 M-1. The intracellular concentration of protein p6 (1 mM) was estimated measuring the number of copies per cell (7 × 105) and the cell volume (1 × 10-15 L). At concentrations around 1 mM, protein p6 associates into oligomers. This self-association behavior is compatible with a dimer−hexamer model (K2,6 = 3.2 × 108 M-2) or with an isodesmic association of the dimer (K = 950 M-1), because the apparent weight-average molecular mass (Mw,a) does not reach saturation at the highest protein concentrations. The sedimentation coefficients of protein p6 monomer and dimer were 1.4 and 2.0, respectively, compatible with translational frictional ratios (f/fo) of 1.15 and 1.30, which slightly deviate from the hydrodynamics of a rigid globular protein. Taking together these results and considering the structure of the nucleoprotein complex, we speculate that the observed oligomers of protein p6 could mimic a scaffold on which DNA folds to form the nucleoprotein complex in vivo.Peer reviewe

Invasive species and habitat degradation in Iberian streams: an explicit analysis of their role and interactive effects on freshwater fish biodiversity loss

The diversity of life on Earth is under the so called biodiversity crisis, which is specially pressing in freshwater ecosystems. Habitat loss and degradation and invasive species are commonly cited as the main causes. Distinguishing the role of each extinction driver and their potential interactions through a mechanistic understanding of impact is crucial for achieving conservation goals. 2. We analyze whether freshwater fish invasive species are mere passengers co-occurring in the biodiversity loss process driven by habitat degradation or as main drivers of the decline of native fish communities in an Iberian basin. Moreover, since few invaded ecosystems are free from habitat loss and degradation, we also tested whether native species simply responded to the abundance of invasive species or if habitat degradation modified the functional relationships between natives and invasive species. 3. We found invasive species to be leading the decline of freshwater fish native communities, while habitat degradation neither played an active role nor influenced invasive species per capita effect on natives. Lower reaches and areas close to reservoirs held the most seriously injured fish communities independently of their habitat degradation status. Then Mediterranean freshwater fish show some resilience to habitat perturbations while invasive species should be raised to the center of attention of conservation actions. Moreover, the essential ecological role that hydrologically stable reaches might play for native communities’ persistence in highly fluctuating environments, such as the Mediterranean, is endangered by the proliferation of invasive species in those environments. 4. Synthesis and applications: Conservation efforts to reduce biodiversity loss among Mediterranean areas freshwater fish communities should focus on mitigating the effect of invasive species especially in better conserved areas. However, the high cost and low efficiency of management actions against invasive species may difficult the effective fight against invasive threats, while new tools such as harder legislation could help reduce the current introduction rates. The roles of different drivers leading the decay of native communities should not be directly extrapolated across taxonomic groups and/or environments, but be analyzed in different particular situations in order to tackle objective management plans facing the current biodiversity problem

Comparison of Game-Related Statistics in Men¿s International Championships between Winning and Losing Teams according to Margin of Victory

The aims of this study were (i) to compare water polo game-related statistics by game outcome (winning and losing teams) and margins of victory (close games, unbalanced games, and very unbalanced games), and (ii) to identify characteristics that mark the differences in performances for each group of margin of victory. The game-related statistics of the 308 men¿s matches played in seven International Championships (Olympic Games, World and European Championships) were analysed. A cluster analysis established three groups (close games, unbalanced games, and very unbalanced games) according to the margin of victory. Differences between game outcomes (winning or losing teams) and margins of victory (close, unbalanced, and very unbalanced games) were determined using the chi-squared statistic, also calculating the effect sizes of the differences. A discriminant analysis was then performed applying the sample-splitting method according to game outcome (winning and losing teams) by margin of victory. It was found that the game-related statistics differentiate the winning from the losing teams in each final score group, with 7 (offensive and defensive) variables differentiating winners from losers in close games, 16 in unbalanced games, and 11 in very unbalanced games. In all three types of game, the game-related statistics were shown to discriminate performance (85% or more), with two variables being discriminatory by game outcome (winning or losing teams) in all three cases: shots and goalkeeper-blocked shots

Physical exercise, detraining and lipid profile in obese children: a systematic review

Introducción. El desentrenamiento es la pérdida de las mejoras obtenidas por el ejercicio físico/entrenamiento tras su cese, aspecto poco estudiado en población infantil obesa. Así, el propósito del presente estudio fue evaluar los efectos del desentrenamiento sobre el perfil lipídico (HDL, LDL, colesterol total y triglicéridos) en niños obesos. Población y métodos. Los estudios fueron recuperados mediante la búsqueda en siete bases de datos. Dicha búsqueda se limitó a programas de ejercicio físico de, al menos, ocho semanas de duración y su desentrenamiento, y se evaluó el perfil lipídico de niños obesos. Se calculó el tamaño del efecto (TE), sus intervalos de confianza del 95% y la heterogeneidad de los estudios a través de la Q de Cochrane (modelo de efectos aleatorios). Resultados. Cinco estudios cumplieron los criterios de inclusión y fueron seleccionados para su revisión (n= 330). En general, los resultados intragrupo (postest vs. desentrenamiento) mostraron que, tras el desentrenamiento, el nivel en sangre del colesterol HDL (TE= 0,12) y el colesterol total aumentaron (TE= 1,41). Del mismo modo, los resultados intergrupo (grupo experimental vs. grupo control) confirmaron el aumento del colesterol HDL tras el desentrenamiento (TE= 0,49). Conclusiones. Los resultados de esta revisión sistemática sugieren que el desentrenamiento tras un programa de ejercicio físico no genera una pérdida significativa de los beneficios obtenidos sobre el perfil lipídico de los niños obesos. No obstante, debido al número de estudios analizados y a la heterogeneidad observada en los análisis y en el tiempo considerado como desentrenamiento (de 12 a 48 semanas), se requiere un mayor número de estudios de calidad para obtener resultados más concluyentes.Introduction. Detraining is the loss of improvements obtained through the participation in physical exercise/training after training cessation, an aspect that has been poorly studied in obese child population. Therefore, the purpose of this study was to assess the effects of detraining on the lipid profile (HDL, LDL, total cholesterol and triglycerides) of obese children. Population and Methods. Studies were collected through a search across seven databases. The search was limited to physical exercise programs that lasted, at least, eight weeks and the corresponding detraining, with an assessment of obese children lipid profile. Effect size (ES), 95% confidence intervals and study heterogeneity were estimated using Cochran’s Q test (random effects model). Results. Five studies complied with the inclusion criteria and were selected for review (n= 330). In general, intra-group results (posttest versus detraining) indicated that, following detraining, blood levels of HDL cholesterol (ES= 0.12) and total cholesterol (ES= 1.41) were increased. Likewise, inter-group results (experimental group versus control group) confirmed the increase of HDL cholesterol following detraining (ES= 0.49). Conclusions. The results of this systematic review suggest that detraining after a physical exercise program does not lead to a significant loss of the benefits gained in relation to the lipid profile of obese children. However, given the number of analyzed studies and the heterogeneity observed in the analyses and the period defined as detraining (12 to 48 weeks), a higher number of well designed studies is required to obtain more conclusive results

What is the role of adherence to 24-hour movement guidelines in relation to physical fitness components among adolescents?

Background: Physical inactivity, excessive sedentary time, and lack of sleep time have been independently associated with lower health-related physical fitness. However, little is known about the combined association between 24-h movement guidelines (i.e., physical activity, recreational screen time, and sleep duration) and components of physical fitness. Objective: The main aim was to examine the likelihood of having high/very high levels on different components of physical fitness based on meeting with 24-h movement guidelines. Methods: In this cross-sectional study, 1276 Spanish youths (13.07±0.86; 55.88% boys), aged 11–16 years, completed self-reported questionnaires on physical activity, recreational screen time, and sleep duration. Physical fitness components were assessed by 20-m shuttle-run test, standing long jump test, handgrip strength test, and 4×10-m shuttle-run test. Meeting 24-h movement guidelines was defined as: 9–11h/day (children aged 5–13) or 8–10h/day (adolescents aged 14–17) of sleep, ≤2h/day of recreational screen time and at least 60min/day of moderateto-vigorous physical activity. The probability of having a high/very high score for each physical fitness components (i.e., ≥60th centile according to the normative cut-off points for European adolescents) in relation to adherence to 24-h movement guidelines was analyzed using a series of binary logistic regressions. Results: Participants who met the three 24-h movement guidelines were more likely to have high/very high for cardiorespiratory fitness (OR=3.31; 95% CI: 1.79, 6.14; p<0.001), standing long jump (OR=1.91; 95% CI: 1.06, 3.45; p=0.031), muscular fitness (OR=2.05; 95% CI: 1.09, 3.86; p=0.048) and physical fitness (OR=1.99; 95% CI: 1.08, 3.66; p=0.012), but not for handgrip strength (OR=1.15; 95% CI: 0.64, 2.01; p=0.636) and speed/agility (OR=1.65; 95% CI: 0.92, 2.96; p=0.093), compared to those who did not meet all three recommendations. Conclusion: Since meeting the three 24-h movement guidelines increased the likelihood of having higher levels in most physical fitness components, it seems necessary to promote these movement behaviors early in life, as they could serve as a gateway for improving health-related fitness in future generations.This study has been funded by the European Community and the Ministry of Economy of Extremadura (IB16193). We gratefully acknowledge the financial support of the Ministry of Economy and Infrastructures and European Community. Dr. Tapia-Serrano is supported by the Junta of Extremadura (PD18015) and European Social Fund (FSE). In addition, this research has been funded by the European Regional Development Fund, The FSE, and the Junta of Extremadura, with grant numbers GR21124. Dr. López-Gil is a Margarita Salas Fellow (Universidad Pública de Navarra – 1225/2022). Dr. García-Hermoso is a Miguel Servet Fellow (Instituto de Salud Carlos III-FSE – CP18/0150)

A distributed and energy‑efficient KNN for EEG classification with dynamic money‑saving policy in heterogeneous clusters

Universidad de Granada/CBUASpanish Ministry of Science, Innovation, and Universities under Grants PGC2018-098813-B-C31,PID2022-137461NB-C32ERDF fund. Funding for open access charge: University of Granada/ CBU

The effects of habitat and prey availability on otter (Lutra lutra) diet and distribution in the Sierra Norte de Sevilla Natural Park

La nutria está ampliamente distribuida en el Parque Natural Sierra Norte de Sevilla y en su entorno inmediato. En el área de estudio la nutria tendió a intensificar el uso del hábitat desde los tramos de cabecera hacia los tramos más bajos. Como era de esperar la disponibilidad de alimento fue también un factor decisivo para explicar el uso del hábitat por la nutria. El análisis de la dieta reveló que la presa más importante fue el barbo (Barbus sclateri). Existió una elevada correlación entre el tamaño medio y máximo de los barbos y el uso del hábitat por la nutria, de manera que ésta utilizó más los tramos con barbos de mayor talla. Esta misma correlación se observó también para las bogas (Chondrostoma willkommii). La nutria consumió hasta 20 tipos de presas distintas en el área de estudio: 11 especies de peces (barbo, calandino, pez sol, colmilleja, cachuelo, boga, pardilla y trucha), siete vertebrados no peces (rana, sapo, urodelos, culebra de agua, aves y micromamíferos) y dos invertebrados (cangrejo rojo americano e insectos). De todas ellas las más importantes, en orden decreciente, fueron el barbo, seguido a gran distancia por el cangrejo rojo (Procambarus clarkii) y la rana común (Rana perezi). En conjunto, en este resultado destaca sobremanera la importancia que adquirieron los peces en la dieta de la nutria. El 61% de los individuos consumidos y el 84% de la biomasa correspondió a peces. La dieta de la nutria varió según las condiciones ambientales y, en general, se ajustó a las presas disponibles en cada lugar. Sin embargo, cuando se comparó la abundancia de presas en el medio y en la dieta se observó que la nutria mostró preferencia o rechazo por algunas especies y/o tallas de las que seleccionó las mayores, salvo en el caso del pez sol (Lepomis gibbosus), en el que este patrón se invertía. En la situación actual y a la luz de los resultados obtenidos se puede concluir que el estado de conservación de la nutria en el Parque Natural Sierra Norte de Sevilla parece bueno o muy bueno.__________________________The otter is widespread through all the Parque Natural Sierra Norte de Sevilla and surrounding areas. We found that the otter varied its intensity of use of habitat in the course of the portion of the longitudinal gradient defined as headwaters-middle reaches. The otter tended to use more intensively middle reaches instead of headwaters, related to food sources availability. The otter fed on 20 different preys: 11 different freshwater fish species (The Iberian barbell, calandino, the sun fish, the Iberian sandsmelt, the Iberian chub, the Iberian nase, pardilla and common trout), seven vertebrates no fishes (common frogs, common toads, urodels, water snakes, birds y micromamifers) and two invertebrates (the red swamp crayfish and insects). Within all these preys the Iberian barbell (Barbus sclateri), the red swamp crayfish (Procambarus clarkii) and common frog (Rana perezi) stood out in this order of preference. 61% of preys and 84% of total biomass corresponded to freshwater fish individuals. This fact underlines the high importance that freshwater fishes had for the otters´ diet within the study area. However, otter’s diet showed a faithfully pattern in relation to preys availability, since they mainly fed on the most available preys. This general pattern must be specified, as the otter tended to select or reject some fish species and/or fish sizes. Long sized fishes were specially consumed except for the sun fish (Lepomis gibbosus) with which this general pattern appeared inverted. In summary we can say that the Sierra Norte´s otter population is in good or very good health