Identification of archaeal proteins that affect the exosome function in vitro

Abstract Background The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors. Results Here, we show that the proteins PaSBDS and PaNip7, which bind preferentially to poly-A and AU-rich RNAs, respectively, affect the Pyrococcus abyssi exosome activity in vitro. PaSBDS inhibits slightly degradation of a poly-rA substrate, while PaNip7 strongly inhibits the degradation of poly-A and poly-AU by the exosome. The exosome inhibition by PaNip7 appears to depend at least partially on its interaction with RNA, since mutants of PaNip7 that no longer bind RNA, inhibit the exosome less strongly. We also show that FITC-labeled PaNip7 associates with the exosome in the absence of substrate RNA. Conclusions Given the high structural homology between the archaeal and eukaryotic proteins, the effect of archaeal Nip7 and SBDS on the exosome provides a model for an evolutionarily conserved exosome control mechanism.

Storage of bovine reproductive tissues and RNA extracts on ice for 24h or repeated freeze–thaw cycles do not affect RNA integrity

The aims of this study were to test (i) the effect of time of tissue and RNA extracts storage on ice and (ii) the effect of repeated freeze–thaw cycles on RNA integrity and gene expression of bovine reproductive tissues. Fragments of endometrium (ENDO), corpus luteum (CL) and ampulla (AMP) were subdivided and incubated for 0, 1, 3, 6, 12 or 24 h on ice. RNA extracts were incubated on ice for 0, 3, 12 or 24 h, or exposed to 1, 2, 4 or 6 freeze–thaw cycles. RNA integrity number (RIN) was estimated. Expression of progesterone receptor (PGR) and cyclophilin genes from RNA extracts stored on ice for 0 or 24 h, and 1 or 6 freeze–thaw cycles was measured by qPCR. Tissue and RNA extract incubation on ice, and repeated freeze–thaw cycles did not affect RIN values of RNA from ENDO, CL or AMP. Storage on ice or exposure to freeze–thaw cycles did not affect Cq values for PGR or cyclophilin genes. In conclusion, neither generalized RNA degradation nor specific RNA degradation was affected by storage of tissue or RNA extracts on ice for up to 24 h, or by up to 6 freeze–thaw cycles of RNA extracts obtained from bovine ENDO, CL and AMP.

Sucrose Substitutes Affect the Cariogenic Potential of Streptococcus mutans Biofilms

Streptococcus mutans is considered the primary etiologic agent of dental caries and contributes significantly to the virulence of dental plaque, especially in the presence of sucrose. To avoid the role of sucrose on the virulence factors of S. mutans, sugar substitutes are commonly consumed because they lead to lower or no production of acids and interfere with biofilm formation. This study aimed to investigate the contribution of sugar substitutes in the cariogenic potential of S. mutans biofilms. Thus, in the presence of sucrose, glucose, sucralose and sorbitol, the biofilm mass was quantified up to 96 h, the pH of the spent culture media was measured, the expression of biofilm-related genes was determined, and demineralization challenge experiments were conduct in enamel fragments. The presence of sugars or sugar substitutes profoundly affected the expression of spaP, gtfB, gtfC, gbpB, ftf, vicR and vicX in either biofilm or planktonic cells. The substitution of sucrose induced a down-regulation of most genes involved in sucrose-dependent colonization in biofilm cells. When the ratio between the expression of biofilm and planktonic cells was considered, most of those genes were down-regulated in biofilm cells in the presence of sugars and up-regulated in the presence of sugar substitutes. However, sucralose but not sorbitol fulfilled the purpose of reducing the cariogenic potential of the diet since it induced the biofilm formation with the lowest biomass, did not change the pH of the medium and led to the lowest lesion depth in the cariogenic challenge

Disparity in regional and systemic circulatory capacities: do they affect the regulation of the circulation?

[EN] In this review we integrate ideas about regional and systemic circulatory capacities and the balance between skeletal muscle blood flow and cardiac output during heavy exercise in humans. In the first part of the review we discuss issues related to the pumping capacity of the heart and the vasodilator capacity of skeletal muscle. The issue is that skeletal muscle has a vast capacity to vasodilate during exercise [approximately 300 mL (100 g)(-1) min(-1)], but the pumping capacity of the human heart is limited to 20-25 L min(-1) in untrained subjects and approximately 35 L min(-1) in elite endurance athletes. This means that when more than 7-10 kg of muscle is active during heavy exercise, perfusion of the contracting muscles must be limited or mean arterial pressure will fall. In the second part of the review we emphasize that there is an interplay between sympathetic vasoconstriction and metabolic vasodilation that limits blood flow to contracting muscles to maintain mean arterial pressure. Vasoconstriction in larger vessels continues while constriction in smaller vessels is blunted permitting total muscle blood flow to be limited but distributed more optimally. This interplay between sympathetic constriction and metabolic dilation during heavy whole-body exercise is likely responsible for the very high levels of oxygen extraction seen in contracting skeletal muscle. It also explains why infusing vasodilators in the contracting muscles does not increase oxygen uptake in the muscle. Finally, when approximately 80% of cardiac output is directed towards contracting skeletal muscle modest vasoconstriction in the active muscles can evoke marked changes in arterial pressure.

Does depth and sedimentation interact with sea urchings to affect algal assemblage patterns on eastern atlantic reefs?

[EN]A range of factors may affect the composition and abundance of macroalgae on subtidal rocky reefs. We experimentally determined the interactive effect of the occurrence of the long-spine sea urchin, Diadema antillarum, depth and sedimentation levels on macroalgal assemblage structure on eastern Atlantic rocky reefs. Specifically, we manipulated sea urchin densities (removal of all individuals vs. untouched controls at natural densities) on rocky reefs devoid of erect vegetation, and predicted (1) that removal of sea urchins would differently affect macroalgal assemblage structure between deep (16-18 m) and shallow (8-9 m) reef strata, and that (2) the effect of sea urchin removal on macroalgae would be altered under different scenarios of sedimentation (ambient vs. enhanced). Experimental circular plots (2 m in diameter) were set up at 3 locations at Gran Canaria (Canarian Archipelago), and were maintained and monitored every 4 wk for 1 y. At the end of the experimental period, the structure of the algal assemblages differed between urchin treatments and depth strata, with a larger cover of turf and bushlike algae where urchins were removed and at the shallow reef stratum. More important, differences in algal assemblage structure between urchin treatments were irrespective of sedimentation levels, but shifted from the shallow to the deep stratum. This interactive effect was, in turn, observed for bushlike algae, as a result of a larger magnitude of response (i.e., larger cover) in the shallow stratum relative to the deep stratum, but was not detected for either turf or crustose coralline algae. These results highlight the importance of sorne physical conditions (here, differences in depth) to interact with biotic processes (here, urchin abundance) to create patterns in the organization of subtidal and benthic assemblages

Reliability and consistency affect the integration of visual depth cues

Abstract Originalsprache (englisch) Visual perception relies on a two-dimensional projection of the viewed scene on the retinas of both eyes. Thus, visual depth has to be reconstructed from a number of different cues that are subsequently integrated to obtain robust depth percepts. Existing models of sensory integration are mainly based on the reliabilities of individual cues and disregard potential cue interactions. In the current study, an extended Bayesian model is proposed that takes into account both cue reliability and consistency. Four experiments were carried out to test this model's predictions. Observers had to judge visual displays of hemi-cylinders with an elliptical cross section, which were constructed to allow for an orthogonal variation of several competing depth cues. In Experiment 1 and 2, observers estimated the cylinder's depth as defined by shading, texture, and motion gradients. The degree of consistency among these cues was systematically varied. It turned out that the extended Bayesian model provided a better fit to the empirical data compared to the traditional model which disregards covariations among cues. To circumvent the potentially problematic assessment of single-cue reliabilities, Experiment 3 used a multiple-observation task, which allowed for estimating perceptual weights from multiple-cue stimuli. Using the same multiple-observation task, the integration of stereoscopic disparity, shading, and texture gradients was examined in Experiment 4. It turned out that less reliable cues were downweighted in the combined percept. Moreover, a specific influence of cue consistency was revealed. Shading and disparity seemed to be processed interactively while other cue combinations could be well described by additive integration rules. These results suggest that cue combination in visual depth perception is highly flexible and depends on single-cue properties as well as on interrelations among cues. The extension of the traditional cue combination model is defended in terms of the necessity for robust perception in ecologically valid environments and the current findings are discussed in the light of emerging computational theories and neuroscientific approaches.

Micropollutants affect the ability of phytoplankton communities to track environmental changes

Human activities strongly influence environmental processes, and while human domination increases, biodiversity progressively declines in ecosystems worldwide. High genetic and phenotypic variability ensures functionality and stability of ecosystem processes through time and increases the resilience and the adaptive capacity of populations and communities, while a reduction in functional diversity leads to a decrease in the ability to respond in a changing environment. Pollution is becoming one of the major threats in aquatic ecosystem, and pharmaceutical and personal care products (PPCPs) in particular are a relatively new group of environmental contaminants suspected to have adverse effects on aquatic organisms. There is still a lake of knowledge on the responses of communities to complex chemical mixtures in the environment. We used an individual-trait-based approach to assess the response of a phytoplankton community in a scenario of combined pollution and environmental change (steady increasing in temperature). We manipulated individual-level trait diversity directly (by filtering out size classes) and indirectly (through exposure to PPCPs mixture), and studied how reduction in trait-diversity affected community structure, production of biomass and the ability of the community to track a changing environment. We found that exposure to PPCPs slows down the ability of the community to respond to an increasing temperature. Our study also highlights how physiological responses (induced by PPCPs exposure) are important for ecosystem processes: although from an ecological point of view experimental communities converged to a similar structure, they were functionally different.

Obesity, age, sex, diagnosis, and fixation mode differently affect early cup failure in total hip arthroplasty: a matched case-control study of 4420 patients

Studies about the influence of patient characteristics on mechanical failure of cups in total hip replacement have applied different methodologies and revealed inconclusive results. The fixation mode has rarely been investigated. Therefore, we conducted a detailed analysis of the influence of patient characteristics and fixation mode on cup failure risks.

Transmission dynamics of Chlamydia trachomatis affect the impact of screening programmes

To assess the impact of screening programmes in reducing the prevalence of Chlamydia trachomatis, mathematical and computational models are used as a guideline for decision support. Unfortunately, large uncertainties exist about the parameters that determine the transmission dynamics of C. trachomatis. Here, we use a SEIRS (susceptible-exposed-infected-recovered-susceptible) model to critically analyze the turnover of C. trachomatis in a population and the impact of a screening programme. We perform a sensitivity analysis on the most important steps during an infection with C. trachomatis. Varying the fraction of the infections becoming symptomatic as well as the duration of the symptomatic period within the range of previously used parameter estimates has little effect on the transmission dynamics. However, uncertainties in the duration of temporary immunity and the asymptomatic period can result in large differences in the predicted impact of a screening programme. We therefore analyze previously published data on the persistence of asymptomatic C. trachomatis infection in women and estimate the mean duration of the asymptomatic period to be longer than anticipated so far, namely 433 days (95% CI: 420-447 days). Our study shows that a longer duration of the asymptomatic period results in a more pronounced impact of a screening programme. However, due to the slower turnover of the infection, a substantial reduction in prevalence can only be achieved after screening for several years or decades.