The Interaction of DNA with Bacteriophage φ29 Connector: A Study by AFM and TEM

The connector of bacteriophage φ29 is involved in DNA packaging during viral morphogenesis and we have studied itsin vitrobinding to DNA using either linear or circular DNA. The protein–DNA complexes have been analyzed by transmission electron microscopy (TEM) and by atomic force microscopy (AFM) of samples directly deposited on mica. TEM showed the presence of a specific binding due to the interaction of the protein with the free ends of the DNA. The study of these samples by AFM showed two major types of morphologies: The interaction of the connector with circular DNA revealed that the strands of DNA that enter and exit the protein complex form an angle with a mean value of 132°. Nevertheless, when the connector was incubated with linear DNA (and later circularized), there was an additional bend angle of about 168°. Further morphological analysis of the latter samples by AFM revealed a structure of the protein–DNA complex consistent with the DNA traversing the connector, probably through the inner channel. On the other hand, images from the samples obtained by incubation of the connector with circular DNA were consistent with an interaction of the DNA with the outer side of the connector.     

Impact of enzyme concentration and residence time on apparent activity recovery in jump dilution analysis

Jump dilution analysis is commonly used to evaluate the reversibility of inhibition and to quantify the residence time of the inhibitor–enzyme complex. During hit and lead characterization, one sometimes observes apparently linear progress curves after jump dilution that display activity recoveries that are intermediate between those expected for fully reversible and irreversible inhibition. Computer simulations of progress curves after jump dilution indicate that seemingly linear progress curves can result when dealing with tight-binding inhibitors if substoichiometric concentrations of inhibitor are preincubated with enzyme. In this situation, the activity recovered is comparable to that expected for instantaneously reversible inhibitors. In addition, simulations demonstrate that intermediate values of activity recovery may be observed for compounds with modestly slow dissociation rates (i.e., residence times >0 min but ?20 min) when the attending curvature of the data is not accounted for. The observation of intermediate values of recovery can, thus, serve as an indication of either modest residence time or a contaminating inactivator within an inhibitor sample, in either case prompting greater scrutiny of the test compound.     

Exposure to road traffic noise and cognitive development in schoolchildren in Barcelona,Spain: A population-based cohort study

BackgroundRoad traffic noise is a prevalent and known health hazard. However, little is known yet about its effect on children’s cognition. We aimed to study the association between exposure to road traffic noise and the development of working memory and attention in primary school children, considering school-outdoor and school-indoor annual average noise levels and noise fluctuation characteristics, as well as home-outdoor noise exposure.Methods and findingsWe followed up a population-based sample of 2,680 children aged 7 to 10 years from 38 schools in Barcelona (Catalonia, Spain) between January 2012 to March 2013. Children underwent computerised cognitive tests 4 times (n = 10,112), for working memory (2-back task, detectability), complex working memory (3-back task, detectability), and inattentiveness (Attention Network Task, hit reaction time standard error, in milliseconds). Road traffic noise was measured indoors and outdoors at schools, at the start of the school year, using standard protocols to obtain A-weighted equivalent sound pressure levels, i.e., annual average levels scaled to human hearing, for the daytime (daytime LAeq, in dB). We also derived fluctuation indicators out of the measurements (noise intermittency ratio, %; and number of noise events) and obtained individual estimated indoor noise levels (LAeq) correcting for classroom orientation and classroom change between years. Home-outdoor noise exposure at home (Lden, i.e., EU indicator for the 24-hour annual average levels) was estimated using Barcelona’s noise map for year 2012, according to the European Noise Directive (2002). We used linear mixed models to evaluate the association between exposure to noise and cognitive development adjusting for age, sex, maternal education, socioeconomical vulnerability index at home, indoor or outdoor traffic-related air pollution (TRAP) for corresponding school models or outdoor nitrogen dioxide (NO₂) for home models. Child and school were included as nested random effects.The median age (percentile 25, percentile 75) of children in visit 1 was 8.5 (7.8; 9.3) years, 49.9% were girls, and 50% of the schools were public. School-outdoor exposure to road traffic noise was associated with a slower development in working memory (2-back and 3-back) and greater inattentiveness over 1 year in children, both for the average noise level (e.g., ‒4.83 points [95% CI: ‒7.21, ‒2.45], p-value < 0.001, in 2-back detectability per 5 dB in street levels) and noise fluctuation (e.g., ‒4.38 [‒7.08, ‒1.67], p-value = 0.002, per 50 noise events at street level). Individual exposure to the road traffic average noise level in classrooms was only associated with inattentiveness (2.49 ms [0, 4.81], p-value = 0.050, per 5 dB), whereas indoor noise fluctuation was consistently associated with all outcomes. Home-outdoor noise exposure was not associated with the outcomes. Study limitations include a potential lack of generalizability (58% of mothers with university degree in our study versus 50% in the region) and the lack of past noise exposure assessment.ConclusionsWe observed that exposure to road traffic noise at school, but not at home, was associated with slower development of working memory, complex working memory, and attention in schoolchildren over 1 year. Associations with noise fluctuation indicators were more evident than with average noise levels in classrooms.

In a cohort study, Maria Foraster and colleagues study associations between exposure to road traffic noise at schools, and trajectories of working memory and inattentiveness among schoolchildren aged 7 to 10 years in Barcelona, Spain.     

Sodium bicarbonate and sodium citrate: ergogenic aids?

Numerous studies have used exogenous administration of sodium bicarbonate (NaHCO(3)) and sodium citrate (Na-citrate) in an attempt to enhance human performance. After ingestion of NaHCO(3) and Na-citrate, two observations have been made: (a) There was great individual variability in the ergogenic benefit reached, which can be attributed to the level of physical conditioning of the subjects and to their tolerance of the buffer substance; and (b) the subjects who had ingested NaHCO(3) and Na-citrate show higher levels of pH, bicarbonate, and lactate ions concentrations in their exercising blood than do the subjects who had ingested the placebo. A majority of the studies have suggested that the ingestion of both substances provides an ergogenic effect due to the establishment and maintenance of an elevated pH level during exercise. However, the exact mechanism by which the ergogenic effects occur has not been demonstrated conclusively. Sodium bicarbonate and Na-citrate seem to be effective in activities with a sufficient duration to generate a difference in the hydrogen ion gradient, characterized by a very high intensity and involving large muscular groups. However, in activities of equally high intensity, but with longer duration, the results obtained have been conflicting and inconclusive.     

Large T antigen on the simian virus 40 origin of replication: a 3D snapshot prior to DNA replication

Large T antigen is the replicative helicase of simian virus 40. Its specific binding to the origin of replication and oligomerization into a double hexamer distorts and unwinds dsDNA. In viral replication, T antigen acts as a functional homolog of the eukaryotic minichromosome maintenance factor MCM. T antigen is also an oncoprotein involved in transformation through interaction with p53 and pRb. We obtained the three-dimensional structure of the full-length T antigen double hexamer assembled at its origin of replication by cryoelectron microscopy and single-particle reconstruction techniques. The double hexamer shows different degrees of bending along the DNA axis. The two hexamers are differentiated entities rotated relative to each other. Isolated strands of density, putatively assigned to ssDNA, protrude from the hexamer-hexamer junction mainly at two opposite sites. The structure of the T antigen at the origin of replication can be understood as a snapshot of the dynamic events leading to DNA unwinding. Based on these results a model for the initiation of simian virus 40 DNA replication is proposed.     

Effects of short vs. long rest period between sets on elbow-flexor muscular endurance during resistance training to failure

This study aimed to examine short-term resistance training effects of resting period length between sets on maximal number of repetitions and mean velocity over a moderate-intensity (60% of the maximum voluntary isometric contraction [MVIC]) set to failure on elbow-flexor muscles. The MVIC and surface electromyographic activity (sEMG) were also measured. Twenty-one untrained subjects were divided into 3 groups: short rest between sets (1 minute; SR), long rest between sets (4 minutes; LR), and nontraining control group (CG). The SR and LR performed 3 sets to failure in an arm-curl machine, 2 days per week for 5 weeks, with moderate loads (60-75% of the MVIC). The LR completed a significantly higher (31.6%, p < 0.05) total training volume than the SR. Both training groups enhanced the maximal number of repetitions to failure, with no significant differences in the magnitude of gains. The posttraining average velocity achieved by the SR at 40, 50, 60, 70, 80, and 90% of the total number of repetitions completed was significantly higher (p < 0.05) than the corresponding average velocity achieved on pretraining conditions, whereas no significant differences were observed in the LR. No significant changes in the MVIC or sEMG were observed in any group. We conclude that short-term elbow-flexor resistance training to failure, allowing 1 or 4 minutes of rest between sets, induces similar gains concerning local muscular endurance. Nevertheless, only the SR training approach reduced the rate of decline in the average repetition velocity during a set to failure. This can be of some importance in sport modalities in which not only the maximal number of repetitions (e.g., muscle endurance), but also a greater maintenance of high repetition velocities, may be critical for performance.