Conformational analysis of protein and nucleic acid fragments with the new grid search algorithm FOUND

The new computer algorithm FOUND, which is implemented as an integrated module of the DYANA structure calculation program, is capable of performing systematic local conformation analyses by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based DYANA target function value. Sets of mutually dependent torsion angles, for example in ribose rings, are treated as a single degree of freedom. The results of the local conformation analysis include allowed torsion angle ranges and stereospecific assignments for diastereotopic substituents, which are then included in the input of a subsequent structure calculation. FOUND can be used for grid searches comprising up to 13 torsion angles, such as the backbone of a complete -helical turn or dinucleotide fragments in nucleic acids, and yields a significantly higher number of stereospecific assignments than the precursor grid search algorithm HABAS.     

Novel Large Apolipoprotein E-Containing Lipoproteins of Density 1.006–1.060 g/ml in Human Cerebrospinal Fluid

Abstract: Although the critical role of apolipoprotein E (apoE) allelic variation in Alzheimer's disease and in the outcome of CNS injury is now recognized, the functions of apoE in the CNS remain obscure, particularly with regard to lipid metabolism. We used density gradient ultracentrifugation to identify apoE-containing lipoproteins in human CSF. CSF apoE lipoproteins, previously identified only in the 1.063–1.21 g/ml density range, were also demonstrated in the 1.006–1.060 g/ml density range. Plasma lipoproteins in this density range include low-density lipoprotein and high-density lipoprotein (HDL) subfraction 1 (HDL₁). The novel CSF apoE lipoproteins are designated HDL₁. No immunoreactive apolipoprotein A-I (apo A-I) or B could be identified in the CSF HDL₁ fractions. Large lipoproteins 18.3 ± 6.6 nm in diameter (mean ± SD) in the HDL₁ density range were demonstrated by electron microscopy. Following fast protein liquid chromatography of CSF at physiologic ionic strength, apoE was demonstrated in particles of average size greater than particles containing apoA-I. The largest lipoproteins separated by this technique contained apoE without apoA-I. Thus, the presence of large apoE-containing lipoproteins was confirmed without ultracentrifugation. Interconversion between the more abundant smaller apoE-HDL subfractions 2 and 3 and the novel larger apoE-HDL₁ is postulated to mediate a role in cholesterol redistribution in brain.     

Metabolic and morphologic properties of single muscle fibers in the rat after spaceflight, Cosmos 1887

The adaptation of a slow (soleus, Sol) and a fast (medial gastrocnemius, MG) skeletal muscle to spaceflight was studied in five young male rats. The flight period was 12.5 days and the rats were killed approximately 48 h after returning to 1 g. Five other rats that were housed in cages similar to those used by the flight rats were maintained at 1 g for the same period of time to serve as ground-based controls. Fibers were classified as dark or light staining for myosin adenosine triphosphatase (ATPase). On the average, the fibers in the Sol of the flight rats atrophied twice as much as those in the MG. Further, the fibers located in the deep (close to the bone and having the highest percentage of light ATPase and high oxidative fibers in the muscle cross section) region of the MG atrophied more than the fibers located in the superficial (away from the bone and having the lowest percentage of light ATPase and high oxidative fibers in the muscle cross-section) region of the muscle. Based on quantitative histochemical assays of single muscle fibers, succinate dehydrogenase (SDH) activity per unit volume was unchanged in fibers of the Sol and MG. However, in the Sol, but not the MG, the total amount of SDH activity in a 10-microns-thick section of a fiber decreased significantly in response to spaceflight. Based on population distributions, it appears that the alpha-glycerophosphate dehydrogenase (GPD) activities were elevated in the dark ATPase fibers in the Sol, whereas the light fibers in the Sol and both fiber types in the MG did not appear to change. The ratio of GPD to SDH activities increased in the dark (but not light) fibers of the Sol and was unaffected in the MG. Immunohistochemical analyses indicate that approximately 40% of the fibers in the Sol of flight rats expressed a fast myosin heavy chain compared with 22% in control rats. Further, 31% of the fibers in the Sol of flight rats expressed both fast and slow myosin heavy chains compared with 8% in control rats. Immunohistochemical changes in the MG were minimal. These data suggest that the magnitude and direction of enzymatic activity and cell volume changes are dependent on the muscle, the region of the muscle, and the type of myosin expressed in the fibers. Further, the ability of fibers to maintain normal or even elevated activities per unit volume of some metabolic enzymes is remarkable considering the marked and rapid decrease in fiber volume.     

Species distribution modeling and molecular markers suggest longitudinal range shifts and cryptic northern refugia of the typical calcareous grassland species Hippocrepis comosa (horseshoe vetch)

Calcareous grasslands belong to the most diverse, endangered habitats in Europe, but there is still insufficient information about the origin of the plant species related to these grasslands. In order to illuminate this question, we chose for our study the representative grassland species Hippocrepis comosa (Horseshoe vetch). Based on species distribution modeling and molecular markers, we identified the glacial refugia and the postglacial migration routes of the species to Central Europe. We clearly demonstrate that H. comosa followed a latitudinal and due to its oceanity also a longitudinal gradient during the last glacial maximum (LGM), restricting the species to southern refugia situated on the Peninsulas of Iberia, the Balkans, and Italy during the last glaciation. However, we also found evidence for cryptic northern refugia in the UK, the Alps, and Central Germany. Both species distribution modeling and molecular markers underline that refugia of temperate, oceanic species such as H. comosa must not be exclusively located in southern but also in western of parts of Europe. The analysis showed a distinct separation of the southern refugia into a western cluster embracing Iberia and an eastern group including the Balkans and Italy, which determined the postglacial recolonization of Central Europe. At the end of the LGM, H. comosa seems to have expanded from the Iberian refugium, to Central and Northern Europe, including the UK, Belgium, and Germany.     

Temperature increase and fluctuation induce phytoplankton biodiversity loss – Evidence from a multi‐seasonal mesocosm experiment

Global climate change scenarios predict lake water temperatures to increase up to 4°C and extreme weather events, including heat waves and large temperature fluctuations, to occur more frequently. Such changes may result in a reorganization of the plankton community structure, causing shifts in diversity and structure toward a community dominated by fewer species that are more adapted to endure warmer and irregular temperature conditions. We designed a long‐term (8 months) mesocosm experiment to explore how ambient water temperature (C: control), induced increased temperature (T: +4°C), and temperature fluctuations (F: ±4°C relative to T) change phytoplankton phenology, taxonomical diversity, and community structure, and how such changes affected zooplankton abundance and composition. Synthesis. Our results show that T and F relative to C significantly decreased phytoplankton diversity. Moreover, there was a clear effect of the temperature treatments (T and F) on phytoplankton size structure that resulted in a significantly lower growth of large species (i.e., large Chlorophyta) compared to C. Decreased diversity and evenness in the T and F treatments pushed the community toward the dominance of only a few phytoplankton taxa (mainly Cyanobacteria and Chlorophyta) that are better adapted to endure warmer and more irregular temperature conditions. The observed shift toward Cyanobacteria dominance may affect trophic energy transfer along the aquatic food web.     

Differences in photoperiod‐induced diapause plasticity among different populations of the bark beetle Ips typographus and its predator Thanasimus formicarius

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Functional flower traits and their diversity drive pollinator visitation

Recent studies have shown that the diversity of flowering plants can enhance pollinator richness and visitation frequency and thereby increase the resilience of pollination. It is assumed that flower traits explain these effects, but it is still unclear which flower traits are responsible, and knowing that, if pollinator richness and visitation frequency are more driven by mass‐ratio effects (mean trait values) or by trait diversity. Here, we analyse a three‐year data set of pollinator observations collected in a European grassland plant diversity experiment (The Jena experiment). The data entail comprehensive flower trait measurements, including reward traits (nectar and pollen amount), morphological traits (height, symmetry, area, colour spectra) and chemical traits (nectar‐amino acid and nectar‐sugar concentration). We test if pollinator species richness and visitation frequency of flower communities depend on overall functional diversity combining all flower traits within a community, single trait diversities (within trait variation) and community‐weighted means of the single traits, using Bayesian inference. Overall functional diversity did not affect pollinator species richness, but reduced visitation frequency. When looking at individual flower traits separately, we found that single trait diversity of flower reflectance and flower morphology were important predictors of pollinator visitation frequency. Moreover, independent of total flower abundance, community‐weighted means of flower height, area, reflectance, nectar‐sugar concentration and nectar‐amino acid concentration strongly affected both pollinator species richness and visitation frequency. Our results, challenge the idea that functional diversity always positively affects ecosystem functions. Nonetheless, we demonstrate that both single trait diversity and mass‐ratio effects of flower traits play an important role for diverse and frequent flower visits, which underlines the functionality of flower traits for pollination services.     

Action without awareness: reaching to an object you do not remember seeing

Background

Previous work by our group has shown that the scaling of reach trajectories to target size is independent of obligatory awareness of that target property and that “action without awareness” can persist for up to 2000 ms of visual delay. In the present investigation we sought to determine if the ability to scale reaching trajectories to target size following a delay is related to the pre-computing of movement parameters during initial stimulus presentation or the maintenance of a sensory (i.e., visual) representation for on-demand response parameterization.

Methodology/Principal Findings

Participants completed immediate or delayed (i.e., 2000 ms) perceptual reports and reaching responses to different sized targets under non-masked and masked target conditions. For the reaching task, the limb associated with a trial (i.e., left or right) was not specified until the time of response cuing: a manipulation that prevented participants from pre-computing the effector-related parameters of their response. In terms of the immediate and delayed perceptual tasks, target size was accurately reported during non-masked trials; however, for masked trials only a chance level of accuracy was observed. For the immediate and delayed reaching tasks, movement time as well as other temporal kinematic measures (e.g., times to peak acceleration, velocity and deceleration) increased in relation to decreasing target size across non-masked and masked trials.

Conclusions/Significance

Our results demonstrate that speed-accuracy relations were observed regardless of whether participants were aware (i.e., non-masked trials) or unaware (i.e., masked trials) of target size. Moreover, the equivalent scaling of immediate and delayed reaches during masked trials indicates that a persistent sensory-based representation supports the unconscious and metrical scaling of memory-guided reaching.     

Alterations in carbohydrate metabolism and its regulation in PPARalpha null mouse hearts

Although a shift from fatty acids (FAs) to carbohydrates (CHOs) is considered beneficial for the diseased heart, it is unclear why subjects with FA beta-oxidation defects are prone to cardiac decompensation under stress conditions. The present study investigated potential alterations in the myocardial utilization of CHOs for energy production and anaplerosis in 12-wk-old peroxisome proliferator-activating receptor-alpha (PPARalpha) null mice (a model of FA beta-oxidation defects). Carbon-13 methodology was used to assess substrate flux through energy-yielding pathways in hearts perfused ex vivo at two workloads with a physiological substrate mixture mimicking the fed state, and real-time RT-quantitative polymerase chain reaction was used to document the expression of selected metabolic genes. When compared with that from control C57BL/6 mice, isolated working hearts from PPARalpha null mice displayed an impaired capacity to withstand a rise in preload (mimicking an increased venous return as it occurs during exercise) as reflected by a 20% decline in the aortic flow rate. At the metabolic level, beyond the expected shift from FA (5-fold down) to CHO (1.5-fold up; P < 0.001) at both preloads, PPARalpha null hearts also displayed 1) a significantly greater contribution of exogenous lactate and glucose and/or glycogen (2-fold up) to endogenous pyruvate formation, whereas that of exogenous pyruvate remained unchanged and 2) marginal alterations in citric acid cycle-related parameters. The lactate production rate was the only measured parameter that was affected differently by preloads in control and PPARalpha null mouse hearts, suggesting a restricted reserve for the latter hearts to enhance glycolysis when the energy demand is increased. Alterations in the expression of some glycolysis-related genes suggest potential mechanisms involved in this defective CHO metabolism. Collectively, our data highlight the importance of metabolic alterations in CHO metabolism associated with FA oxidation defects as a factor that may predispose the heart to decompensation under stress conditions even in the fed state.     

Resveratrol induces catalytic bioscavenger paraoxonase 1 expression and protects against chemical warfare nerve agent toxicity in human cell lines

Current advances in enzyme bioscavenger prophylactic therapy against chemical warfare nerve agent (CWNA) exposure are moving towards the identification of catalytic bioscavengers that can degrade large doses of organophosphate (OP) nerve agents without self destruction. This is a preferred method compared to therapy with the purified stoichiometric bioscavenger, butyrylcholinesterase, which binds OPs 1:1 and would thus require larger doses for treatment. Paraoxonase-1 (PON-1) is one such catalytic bioscavenger that has been shown to hydrolyze OP insecticides and contribute to detoxification in animals and humans. Here we investigated the effects of a common red wine ingredient, Resveratrol (RSV), to induce the expression of PON-1 in the human hepatic cell line HC04 and evaluated the protection against CWNA simulants. Dose-response curves showed that a concentration of 20 microM RSV was optimal in inducing PON-1 expression in HC04 cells. RSV at 20 microM increased the extracellular PON-1 activity approximately 150% without significantly affecting the cells. Higher doses of RSV were cytotoxic to the cells. Resveratrol also induced PON-1 in the human lung cell line A549. RSV pre-treatment significantly (P = 0.05) protected the hepatic cells against exposure to 2x LD(50) of soman and sarin simulants. However, lung cells were protected against soman simulant exposure but not against sarin simulant exposure following RSV treatment. In conclusion, these studies indicate that dietary inducers, such as RSV, can up-regulate PON-1, a catalytic bioscavenger, which can then hydrolyze and protect against CWNA-induced toxicity, providing a prospective new method to protect against CWNA exposure.