Role of unfolded state heterogeneity and en-route ruggedness in protein folding kinetics

In order to improve our understanding of the physical bases of protein folding, there is a compelling need for better connections between experimental and computational approaches. This work addresses the role of unfolded state conformational heterogeneity and en-route intermediates, as an aid for planning and interpreting protein folding experiments. The expected kinetics were modeled for different types of energy landscapes, including multiple parallel folding routes, preferential paths dominated by one primary folding route, and distributed paths with a wide spectrum of microscopic folding rate constants. In the presence of one or more preferential routes, conformational exchange among unfolded state populations slows down the observed rates for native protein formation. We find this to be a general phenomenon, taking place even when unfolded conformations interconvert much faster than the "escape" rate constants to folding. Dramatic kinetic deceleration is expected in the presence of an increasing number of folding-incompetent unfolded conformations. This argues for the existence of parallel folding paths involving several folding-competent unfolded conformations, during the early stages of protein folding. Deviations from single-exponential behavior are observed for unfolded conformations exchanging at comparable rates or more slowly than folding events. Analysis of the effect of en-route (on-path) intermediate formation and landscape ruggedness on folding kinetics leads to the following unexpected conclusions: (1) intermediates, which often retard native state formation, may in some cases accelerate folding, and (2) rugged landscapes, usually associated with stretched exponentials, display single-exponential behavior in the presence of late high-friction paths.     

Testosterone and paternal care in East African foragers and pastoralists

The 'challenge hypothesis' posits that testosterone facilitates reproductive effort (investment in male-male competition and mate-seeking) at the expense of parenting effort (investment in offspring and mates). Multiple studies, primarily in North America, have shown that men in committed relationships, fathers, or both maintain lower levels of testosterone than unpaired men. Data from non-western populations, however, show inconsistent results. We hypothesized that much of this cross-cultural variation can be attributed to differential investment in mating versus parenting effort, even among married fathers. Here, we directly test this idea by comparing two neighbouring Tanzanian groups that exhibit divergent styles of paternal involvement: Hadza foragers and Datoga pastoralists. We predicted that high levels of paternal care by Hadza fathers would be associated with decreased testosterone in comparison with non-fathers, and that no such difference between fathers and non-fathers would be evident in Datoga men, who provide minimal direct paternal care. Twenty-seven Hadza men and 80 Datoga men between the ages of 17 and 60 provided morning and afternoon saliva samples from which testosterone was assayed. Measurements in both populations confirmed these predictions, adding further support to the hypothesis that paternal care is associated with decreased testosterone production in men.     

Construction costs, payback times, and the leaf economics of carnivorous plants

Understanding how different plant species and functional types "invest" carbon and nutrients is a major goal of plant ecologists. Two measures of such investments are "construction costs" (carbon needed to produce each gram of tissue) and associated "payback times" for photosynthesis to recover construction costs. These measurements integrate among traits used to assess leaf-trait scaling relationships. Carnivorous plants are model systems for examining mechanisms of leaf-trait coordination, but no studies have measured simultaneously construction costs of carnivorous traps and their photosynthetic rates to determine payback times of traps. We measured mass-based construction costs (CC(mass)) and photosynthesis (A(mass)) for traps, leaves, roots, and rhizomes of 15 carnivorous plant species grown under greenhouse conditions. There were highly significant differences among species in CC(mass) for each structure. Mean CC(mass) of carnivorous traps (1.14 ± 0.24 g glucose/g dry mass) was significantly lower than CC(mass) of leaves of 267 noncarnivorous plant species (1.47 ± 0.17), but all carnivorous plants examined had very low A(mass) and thus, long payback times (495-1551 h). Our results provide the first clear estimates of the marginal benefits of botanical carnivory and place carnivorous plants at the "slow and tough" end of the universal spectrum of leaf traits.     

Energetics and the evolution of carnivorous plants--Darwin's 'most wonderful plants in the world'

Carnivory has evolved independently at least six times in fiveangiosperm orders. In spite of these independent origins, thereis a remarkable morphological convergence of carnivorous planttraps and physiological convergence of mechanisms for digestingand assimilating prey. These convergent traits have made carnivorousplants model systems for addressing questions in plant moleculargenetics, physiology, and evolutionary ecology. New data showthat carnivorous plant genera with morphologically complex trapshave higher relative rates of gene substitutions than do thosewith simple sticky traps. This observation suggests two alternativemechanisms for the evolution and diversification of carnivorousplant lineages. The ‘energetics hypothesis’ positsrapid morphological evolution resulting from a few changes inregulatory genes responsible for meeting the high energeticdemands of active traps. The ‘predictable prey capturehypothesis’ further posits that complex traps yield morepredictable and frequent prey captures. To evaluate these hypotheses,available data on the tempo and mode of carnivorous plant evolutionwere reviewed; patterns of prey capture by carnivorous plantswere analysed; and the energetic costs and benefits of botanicalcarnivory were re-evaluated. Collectively, the data are moresupportive of the energetics hypothesis than the predictableprey capture hypothesis. The energetics hypothesis is consistentwith a phenomenological cost–benefit model for the evolutionof botanical carnivory, and also accounts for data suggestingthat carnivorous plants have leaf construction costs and scalingrelationships among leaf traits that are substantially differentfrom those of non-carnivorous plants. Key words: Carnivorous plants, competition, construction costs, cost–benefit model, Darwin, energetics, niche overlap, phylogeny, prey capture, universal spectrum of leaf traits Received 6 May 2008; Revised 5 June 2008 Accepted 16 June 2008     

Nectar,not colour,may lure insects to their death

We experimentally demonstrate in the field that prey of the carnivorous plant Sarracenia purpurea are attracted to sugar, not to colour. Prey capture (either all taxa summed or individual common taxa considered separately) was not associated with total red area or patterning on pitchers of living pitcher plants. We separated effects of nectar availability and coloration using painted ‘pseudopitchers’, half of which were coated with sugar solution. Unsugared pseudopitchers captured virtually no prey, whereas pseudopitchers with sugar solution captured the same amount of prey as living pitchers. In contrast to a recent study that associated red coloration with prey capture but that lacked controls for nectar availability, we infer that nectar, not colour, is the primary means by which pitcher plants attract prey.     

Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models

Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.     

Small artery elasticity is decreased in patients with systemic lupus erythematosus without increased intima media thickness

Introduction  

The objectives of this study were to determine small arterial elasticity (SAE) in systemic lupus erythematosus (SLE) and to investigate its relationship with intima media thickness (IMT), accumulation of advanced glycation end products (AGEs), endothelial activation and inflammation.     

Regulation of the adaptation to zinc deficiency in plants

The molecular mechanisms by which plants sense their micronutrient status, and adapt to their environment in order to ensure a sufficient micronutrient supply, are poorly understood. Zinc is an essential micronutrient for all living organisms. when facing a shortage in zinc supply, plants adapt by enhancing the zinc uptake capacity. The molecular regulators controlling this adaptation were recently identified. in this mini-review, we highlight recent progress in understanding the adaptation to zinc deficiency in plants and discuss the future challenges to fully unravel its molecular basis.Key words: adaptation, zinc deficiency, biofortification, molecular regulators, plant nutritionIn an increasingly populated world, agricultural production is an essential element of social development. Agriculture is the primary source of all nutrients required for human life, and nutrient sufficiency is the basis for good health and welfare of the human population.¹ Soils with zinc deficiency are widespread in the world, affecting large areas of cultivated soils in India, Turkey, China, Brazil and Australia,^2,3 making zinc the most common crop micronutrient deficiency.⁴ In addition, risk of inadequate zinc diet and zinc malnutrition are estimated to affect one-third of the global human population, i.e., around two billion people.⁵ Most affected are people living in developing countries, where diets are rich in cereal-based foods. Cereal grains are rich in phytate, which is a potent anti-nutrient, limiting micronutrient bioavailability.⁶ Zinc deficiency in crop production can be easily ameliorated through zinc fertilization, making agronomic biofortification an important strategy,³ however in the poorer regions, the required infrastructure to provide a reliable supply of zinc fertilizers of sufficient quality, is often not available. In those situations, biofortified crops, in which the zinc status of crops is genetically improved by selective breeding or via biotechnology, offer a rural-based intervention that will more likely reach the population.⁷ Different traits can be targeted to developing such improved crops, such as plant zinc deficiency tolerance, zinc use efficiency and the accumulation of zinc in edible parts. However, insufficient knowledge on the molecular mechanisms and the regulation of the zinc homeostasis network in plants is a serious bottleneck when pursuing zinc biofortification.     

Canopy and litter ant assemblages share similar climate–species density relationships

Tropical forest canopies house most of the globe''s diversity, yet little is known about global patterns and drivers of canopy diversity. Here, we present models of ant species density, using climate, abundance and habitat (i.e. canopy versus litter) as predictors. Ant species density is positively associated with temperature and precipitation, and negatively (or non-significantly) associated with two metrics of seasonality, precipitation seasonality and temperature range. Ant species density was significantly higher in canopy samples, but this difference disappeared once abundance was considered. Thus, apparent differences in species density between canopy and litter samples are probably owing to differences in abundance–diversity relationships, and not differences in climate–diversity relationships. Thus, it appears that canopy and litter ant assemblages share a common abundance–diversity relationship influenced by similar but not identical climatic drivers.     

c-kitpos GATA-4 high rat cardiac stem cells foster adult cardiomyocyte survival through IGF-1 paracrine signalling

Background

Resident c-kit positive (c-kit^pos) cardiac stem cells (CSCs) could be considered the most appropriate cell type for myocardial regeneration therapies. However, much is still unknown regarding their biological properties and potential.

Methodology/Principal Findings

We produced clones of high and low expressing GATA-4 CSCs from long-term bulk-cultured c-kit^pos CSCs isolated from adult rat hearts. When c-kit^pos GATA-4 high expressing clonal CSCs (cCSCs) were co-cultured with adult rat ventricular cardiomyocytes, we observed increased survival and contractility of the cardiomyocytes, compared to cardiomyocytes cultured alone, co-cultured with fibroblasts or c-kit^pos GATA-4 low expressing cCSCs. When analysed by ELISA, the concentration of IGF-1 was significantly increased in the c-kit^pos GATA-4 high cCSC/cardiomyocyte co-cultures and there was a significant correlation between IGF-1 concentration and cardiomyocyte survival. We showed the activation of the IGF-1 receptor and its downstream molecular targets in cardiomyocytes co-cultured with c-kit^pos GATA-4 high cCSCs but not in cardiomyocytes that were cultured alone, co-cultured with fibroblasts or c-kit^pos GATA-4 low cCSCs. Addition of a blocking antibody specific to the IGF-1 receptor inhibited the survival of cardiomyocytes and prevented the activation of its signalling in cardiomyocytes in the c-kit^pos GATA-4 high cCSC/cardiomyocyte co-culture system. IGF-1 supplementation or IGF-1 high conditioned medium taken from the co-culture of c-kit^pos GATA-4 high cCSCs plus cardiomyocytes did extend the survival and contractility of cardiomyocytes cultured alone and cardiomyocytes co-cultured with c-kit^pos GATA-4 low cCSCs.

Conclusion/Significance

c-kit^pos GATA-4 high cCSCs exert a paracrine survival effect on cardiomyocytes through induction of the IGF-1R and signalling pathway.