Санація та реструктуризація : порівняльна характеристика

A novel device for capillary-free mounting of protein crystals is described. A controlled stream of air allows an accurate adjustment of the humidity at the crystal. The crystal is held on the tip of a micropipette. With a video system (CCD camera), the two-dimensional shadow projections of crystals can be recorded for optical analysis. Instead of the micropipette, a standard loop can also be used. Experiments and results for different crystal systems demonstrate the use of this method, also in combination with shock-freezing, to improve crystal order. Working with oxygen-free gases offers the possibility of crystal measurements under anaerobic conditions. Furthermore, the controlled application of arbitrary volatile substances with the gas stream is practicable.</jats:p

Causes and consequences of prolonged dormancy: Why stay belowground?

Prolonged dormancy is a stage in which mature plants fail to resprout during the growing season and instead remain alive belowground. Though it is relatively common, the causes and consequences of this intriguing stage have remained elusive. In this dissertation, I investigate the causes and consequences of prolonged dormancy in a long lived perennial herb, Astragalus scaphoides. First, I use a combination of demography and ecophysiology to study the proximate mechanisms associated with prolonged dormancy. Analysis of a long-term demographic dataset indicates that both endogenous factors (e.g. age, condition, and history) and exogenous factors (e.g. climate and spatial variation) are associated with dormancy. I then investigate the association between stored resources and dormancy. My results indicate that individual plants with low levels of stored available carbon are more likely to enter prolonged dormancy. Surprisingly, individuals increased their mobile carbon concentrations while dormant, presumably by remobilizing structural carbon into mobile forms. Since stored resources integrate past conditions and performance with current state, these results can explain why some individuals remain belowground while others emerge to grow and reproduce. I used matrix models to examine the ultimate causes and consequences of prolonged dormancy. I found evidence that prolonged dormancy acts as a conservative strategy that allows plants to avoid the risk of a variable environment. Further, my results demonstrate that intermediate levels of dormancy result in the highest fitness advantage. Finally, I measured the trade-offs associated with emerging during times of environmental stress. Although plants showed remarkable physiological tolerance to stress, stress led to demographic costs. Therefore, prolonged dormancy is shown to be a beneficial strategy in a variable environment. Together, my research identifies both the proximate causes of prolonged dormancy, as well as the ultimate consequences of remaining belowground during the growing season. Therefore, my research not only identifies why some plants go dormant while others emerge, but also explains the prevalence of this intriguing life stage in the life histories of so many perennial plants

Frequent Fire Alters Nitrogen Transformations in Ponderosa Pine Stands of the Inland Northwest

Recurrent, low-severity fire in ponderosa pine (Pinus ponderosa)linterior Douglas-fir (Pseudotsuga menziesii var. glauca) forests is thought to have directly influenced nitrogen (N) cycling and availability. However, no studies to date have investigated the influence of natural fire intervals on soil processes in undisturbed forests, thereby limiting our ability to understand ecological processes and successional dynamics in this important ecosystem of the Rocky Mountain West. Here, we tested the standing hypothesis that recurrent fire in ponderosa pine/Douglas-fir forests of the Inland Northwest decreases total soil N, but increases N turnover and nutrient availability. We compared soils in stands unburned over the past 69-130 years vs. stands exposed to two or more fires over the last 130 years at seven distinct locations in two wilderness areas. Mineral soil samples were collected from each of the seven sites in June and July of 2003 and analyzed for pH, total C and N, potentially mineralizable N (PMN), and extractable NH4+, NO3, PO4-3, Ca+2, Me, and K+. Nitrogen transformations were assessed at five sites by installing ionic resin capsules in the mineral soil in August of 2003 and by conducting laboratory assays of nitrification potential and net nitrification in aerobic incubations. Total N and PMN decreased in stands subjected to multiple fires. This loss of total N and labile N was not reflected in concentrations of extractable NH4+ and NO3-. Rather, multiple fires caused an increase in NO3- sorbed on ionic resins, nitrification potential, and net nitrification in spite of the burned stands not having been exposed to fire for at least 12-17 years. Charcoal collected from a recent fire site and added to unburned soils increased nitrification potential, suggesting that the decrease of charcoal in the absence of tire may play an important role in N transformations in fire-dependent ecosystems in the long term. Interestingly, we found no consistent effect of fire frequency on extractable P or alkaline metal concentrations. Our results corroborate the largely untested hypothesis that frequent fire in ponderosa pine forests increases inorganic N availability in the long term and emphasize the need to study natural, unmanaged sites in far greater detail

Disappearing Plants: Why They Hide and How They Return

Prolonged dormancy is a life-history stage in which mature plants fail to resprout for one or more growing seasons and instead remain alive belowground. Prolonged dormancy is relatively common, but the proximate causes and consequences of this intriguing strategy have remained elusive. In this study we tested whether stored resources are associated with remaining belowground, and investigated the resource costs of remaining belowground during the growing season. We measured stored resources at the beginning and end of the growing season in Astragalus scaphoides, an herbaceous perennial in southwest Montana, USA. At the beginning of the growing season, dormant plants had lower concentrations of stored mobile carbon (nonstructural carbohydrates, NSC) than did emergent plants. Surprisingly, during the growing season, dormant plants gained as much NSC as photosynthetically active plants, an increase most likely due to remobilization of structural carbon. Thus, low levels of stored NSC were associated with remaining belowground, and remobilization of structural carbon may allow for dormant plants to emerge in later seasons. The dynamics of NSC in relation to dormancy highlights the ability of plants to change their own resource status somewhat independently of resource assimilation, as well as the importance of considering stored resources in understanding plant responses to the environment

Vulnerability of grassland seed banks to resource-enhancing global changes

AbstractSoil seed banks represent reservoirs of diversity in the soil that may increase resilience of communities to global changes. Two global change factors that can dramatically alter the composition and diversity of aboveground communities are nutrient enrichment and increased rainfall. In a full-factorial nutrient and rainfall addition experiment in an annual Californian grassland, we asked whether shifts in aboveground composition and diversity were reflected in belowground seed banks. Nutrient and rainfall additions increased exotic and decreased native abundances, while rainfall addition increased exotic richness, both in aboveground communities and seed banks. Under nutrient addition, forbs and short-statured plants were replaced by grasses and tall-statured species, both above and below ground, and whole-community responses to the treatments were similar. Structural equation models indicated that especially nutrient addition effects on seed banks were largely indirect via aboveground communities. However, rainfall addition also had a direct negative effect on native species richness and abundance of species with high specific leaf area (SLA) in seed banks, showing that seed banks are sensitive to the direct effects of temporary increases in rainfall. Our findings highlight the vulnerability of seed banks in annual, resource-poor grasslands to shifts in compositional and trait changes in aboveground communities and show how invasion of exotics and depletion of natives are critical for these above-belowground compositional shifts. Our findings suggest that seed banks have limited potential to buffer resource-poor annual grasslands from the community changes caused by resource enrichment.Abstract Soil seed banks represent reservoirs of diversity in the soil that may increase resilience of communities to global changes. Two global change factors that can dramatically alter the composition and diversity of aboveground communities are nutrient enrichment and increased rainfall. In a full-factorial nutrient and rainfall addition experiment in an annual Californian grassland, we asked whether shifts in aboveground composition and diversity were reflected in belowground seed banks. Nutrient and rainfall additions increased exotic and decreased native abundances, while rainfall addition increased exotic richness, both in aboveground communities and seed banks. Under nutrient addition, forbs and short-statured plants were replaced by grasses and tall-statured species, both above and below ground, and whole-community responses to the treatments were similar. Structural equation models indicated that especially nutrient addition effects on seed banks were largely indirect via aboveground communities. However, rainfall addition also had a direct negative effect on native species richness and abundance of species with high specific leaf area (SLA) in seed banks, showing that seed banks are sensitive to the direct effects of temporary increases in rainfall. Our findings highlight the vulnerability of seed banks in annual, resource-poor grasslands to shifts in compositional and trait changes in aboveground communities and show how invasion of exotics and depletion of natives are critical for these above-belowground compositional shifts. Our findings suggest that seed banks have limited potential to buffer resource-poor annual grasslands from the community changes caused by resource enrichment

Combined 1H-Detected solid-state NMR spectroscopy and electron cryotomography to study membrane proteins across resolutions in native environments

Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted system

Predicting evolutionarily stable strategies from functional responses of Sonoran Desert annuals to precipitation

For many decades, researchers have studied how plants use bet-hedging strategies to insure against unpredictable, unfavourable conditions. We improve upon earlier analyses by explicitly accounting for how variable precipitation affects annual plant species' bet-hedging strategies. We consider how the survival rates of dormant seeds (in a 'seed bank') interact with precipitation responses to influence optimal germination strategies. Specifically, we incorporate how response to resource availability (i.e. the amount of offspring (seeds) generated per plant in response to variation in desert rainfall) influences the evolution of germination fractions. Using data from 10 Sonoran Desert annual plants, we develop models that explicitly include these responses to model fitness as a function of precipitation. For each of the species, we identify the predicted evolutionarily stable strategies (ESSs) for the fraction of seeds germinating each year and then compare our estimated ESS values to the observed germination fractions. We also explore the relative importance of seed survival and precipitation responses in shaping germination strategies by regressing ESS values and observed germination fractions against these traits. We find that germination fractions are lower for species with higher seed survival, with lower reproductive success in dry years, and with better yield responses in wet years. These results illuminate the evolution of bet-hedging strategies in an iconic system, and provide a framework for predicting how current and future environmental conditions may reshape those strategies

Prolonged dormancy interacts with senescence for two perennial herbs

1. Senescence is characterized by a decline in survival, fecundity and reproductive value with age among adult individuals. Simple age-dependent life cycles progress forward through developmental stages, with each successive stage being characterized by age-specific vital rates. In contrast, size- or stage-based life cycles for perennial plants are more complex and often include stasis and retrogression to previous vegetative or reproductive life stages, indicating possible slowing or even reversing the developmental progress. 2. Many plants remain in nonemergent, below-ground stages during the growing season (prolonged dormancy), which may affect the process of senescence. Stasis in the dormant stage implies that senescence is interrupted while plants are below-ground. 3. We explored the underlying assumptions of size- or stage-based life cycle graphs and developed four different demographic models for how prolonged dormancy may mediate the relationship between age and vital rates. We then tested these models using more than 20 years of demographic data on 2 perennial herbs, Astragalus scaphoides and Silene spaldingii. 4. Results from model fitting suggest that prolonged dormancy interacts with the age dependence of vital rates. The model using true biological age (time since germination) of emergent and dormant plants to estimate vital rates was never the best model for our data. For both species, the model assuming that dormancy resets plants to the same postdormant state experienced earlier in life independent of their predormant age resulted in the best fit, though not for every vital rate. 5. Older Astragalus plants had declining annual survival probabilities and reproductive value, suggesting senescence. Silene showed the opposite pattern for reproductive value that increased with age, indicating negative senescence. 6. Synthesis. Using long-term demographic data from two perennial herbs, this study shows mixed evidence for senescence in perennial plants. Our results indicate that prolonged dormancy interacts with the age dependence of vital rates and may sometimes retard the process of senescence

Arl3 regulates a transport system for farnesylated cargo

Arl3 is a small G-protein that is found exclusively in ciliated organisms. In addition, knocking out of Arl3 results in a plethora of ciliopathies. Arl3 is known to bind the photoreceptor (specialized cilia) specific PDE delta subunit (PDE6D), which in turn bind to prenylated proteins. The significance of this interaction and the function of Arl3 in cilia are poorly understood. Here in this study, by solving the crystal structure of a fully modified prenylated (farnesylated) Rheb in complex with PDE6D and comparing it to a structure of PDE6D in complex with the Arl3 homologue Arl2, we show that Arl3 is an allosteric regulator of PDE6D. Arl3, in a nucleotide dependent manner, releases the farnesylated cargo bound to PDE6D. We explain the molecular mechanism of this release and we further verify the mechanism in vitro and by live cell imaging. Based on this study we hypothesize that Arl3 regulate the targeting of prenylated cargo in and out the cilia