Seawater carbonate chemistry, sample density and Strongylocentrotus purpuratus size, filtering and respiration rate during experiments, 2011

Anthropogenic CO2 emissions are acidifying the world's oceans. A growing body of evidence is showing that ocean acidification impacts growth and developmental rates of marine invertebrates. Here we test the impact of elevated seawater pCO2 (129 Pa, 1271 µatm) on early development, larval metabolic and feeding rates in a marine model organism, the sea urchin Strongylocentrotus purpuratus. Growth and development was assessed by measuring total body length, body rod length, postoral rod length and posterolateral rod length. Comparing these parameters between treatments suggests that larvae suffer from a developmental delay (by ca. 8%) rather than from the previously postulated reductions in size at comparable developmental stages. Further, we found maximum increases in respiration rates of + 100 % under elevated pCO2, while body length corrected feeding rates did not differ between larvae from both treatments. Calculating scope for growth illustrates that larvae raised under high pCO2 spent an average of 39 to 45% of the available energy for somatic growth, while control larvae could allocate between 78 and 80% of the available energy into growth processes. Our results highlight the importance of defining a standard frame of reference when comparing a given parameter between treatments, as observed differences can be easily due to comparison of different larval ages with their specific set of biological characters.

Collection of aboveground community and species-specific plant biomass from the Jena Experiment (time series since 2002).

This data set comprises time series of aboveground community plant biomass (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of several experiments at the field site of a large grassland biodiversity experiment (the Jena Experiment; see further details below). Aboveground community biomass was normally harvested twice a year just prior to mowing (during peak standing biomass twice a year, generally in May and August; in 2002 only once in September) on all experimental plots in the Jena Experiment. This was done by clipping the vegetation at 3 cm above ground in up to four rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned by random selection of new coordinates every year within the core area of the plots. The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for the biomass measures on the community level are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship. The following series of datasets are contained in this collection: 1. Plant biomass form the Main Experiment: In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). 2. Plant biomass from the Dominance Experiment: In the Dominance Experiment, 206 grassland plots of 3.5 x 3.5 m were established from a pool of 9 species that can be dominant in semi-natural grassland communities of the study region. In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 3, 4, 6, and 9 species). 3. Plant biomass from the monoculture plots: In the monoculture plots the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species like the other experiments in May 2002. All plots were maintained by bi-annual weeding and mowing.

Predictable hydrodynamic conditions explain temporal variations in the density of benthic foraging seabirds in a tidal stream environment

Tidal stream turbines could have several direct impacts upon pursuit-diving seabirds foraging within tidal stream environments (mean horizontal current speeds > 2 ms−1), including collisions and displacement. Understanding how foraging seabirds respond to temporally variable but predictable hydrodynamic conditions immediately around devices could identify when interactions between seabirds and devices are most likely to occur; information which would quantify the magnitude of potential impacts, and also facilitate the development of suitable mitigation measures. This study uses shore-based observational surveys and Finite Volume Community Ocean Model outputs to test whether temporally predictable hydrodynamic conditions (horizontal current speeds, water elevation, turbulence) influenced the density of foraging black guillemots Cepphus grylle and European shags Phalacrocorax aristotelis in a tidal stream environment in Orkney, United Kingdom, during the breeding season. These species are particularly vulnerable to interactions with devices due to their tendency to exploit benthic and epi-benthic prey on or near the seabed. The density of both species decreased as a function of horizontal current speeds, whereas the density of black guillemots also decreased as a function of water elevation. These relationships could be linked to higher energetic costs of dives in particularly fast horizontal current speeds (>3 ms−1) and deeper water. Therefore, interactions between these species and moving components seem unlikely at particularly high horizontal current speeds. Combining this information, with that on the rotation rates of moving components at lower horizontal current speeds, could be used to assess collision risk in this site during breeding seasons. It is also likely that moderating any device operation during both lowest water elevation and lowest horizontal current speeds could reduce the risk of collisions for these species in this site during this season. The approaches used in this study could have useful applications within Environmental Impact Assessments, and should be considered when assessing and mitigating negative impacts from specific devices within development sites.

Toward controlled growth of helicity-specific carbon nanotubes

The underlying mechanisms for the nucleation of carbon nanotubes as well as their helicity, remain elusive. Here, using van der Waals dispersion force calculations implemented within density functional theory, we study the cap formation, believed to be responsible for the chirality of surface-catalyzed carbon nanotubes. We find the energetics associated with growth along different facets to be independent of the surface orientation and that the growth across an edge along the axis of the metal particle leads to a perfect honeycomb lattice in a curved geometry. The formation of defects in the graphene matrix, which bend the carbon plane, requires that two or more graphene embryos with significantly different growth axis merge. Such scenario is only possible at the front- or back-end of the metal particle where growth symmetry is broken. The graphene embryos reconstruct their hexagonal structure into pentagons, heptagons, and octagons counterpart to accommodate the tube curvature.

Air Pollution and High Density Lipoprotein Structure and Function

Thesis (Ph.D.)--University of Washington, 2016-06

Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell

Stromules are motile extensions of the plastid envelope membrane, whose roles are not fully understood. They are present on all plastid types but are more common and extensive on non-green plastids that are sparsely distributed within the cell. During tomato fruit ripening, chloroplasts in the mesocarp tissue differentiate into chromoplasts and undergo major shifts in morphology. In order to understand what factors regulate stromule formation, we analysed stromule biogenesis in tobacco hypocotyls and in two distinct plastid populations in tomato mesocarp. We show that increases in stromule length and frequency are correlated with chromoplast differentiation, but only in one plastid population where the plastids are larger and less numerous. We used tobacco hypocotyls to confirm that stromule length increases as plastids become further apart, suggesting that stromules optimise the plastid-cytoplasm contact area. Furthermore, we demonstrate that ectopic chloroplast components decrease stromule formation on tomato fruit chromoplasts, whereas preventing chloroplast development leads to increased numbers of stromules. Inhibition of fruit ripening has a dramatic impact on plastid and stromule morphology, underlining that plastid differentiation status, and not cell type, is a significant factor in determining the extent of plastid stromules. By modifying the plastid surface area, we propose that stromules enhance the specific metabolic activities of plastids. This is an electronic version of an Article published in The Plant Journal, August 2004, Volume 39, pp. 655-667. Copyright 2004 Blackwell Publishing Ltd and The Society for Experimental Biology.

Validation of single photon absorptiometry for on-farm measurement of density and mineral content of tail bone in cattle

A validation study examined the accuracy of a purpose-built single photon absorptiometry (SPA) instrument for making on-farm in vivo measurements of bone mineral density (BMD) in tail bones of cattle. In vivo measurements were made at the proximal end of the ninth coccygeal vertebra (Cy9) in steers of two age groups (each n = 10) in adequate or low phosphorus status. The tails of the steers were then resected and the BMD of the Cy9 bone was measured in the laboratory with SPA on the resected tails and then with established laboratory procedures on defleshed bone. Specific gravity and ash density were measured on the isolated Cy9 vertebrae and on 5-mm2 dorso-ventral cores of bone cut from each defleshed Cy9. Calculated BMD determined by SPA required a measure of tail bone thickness and this was estimated as a fraction of total tail thickness. Actual tail bone thickness was also measured on the isolated Cy9 vertebrae. The accuracy of measurement of BMD by SPA was evaluated by comparison with the ash density of the bone cores measured in the laboratory. In vivo SPA measurements of BMD were closely correlated with laboratory measurements of core ash density (r = 0.92). Ash density and specific gravity of cores, and all SPA measures of BMD, were affected by phosphorus status of the steers, but the effect of steer age was only significant (P < 0.05) for steers in adequate phosphorus status. The accuracy of SPA to determine BMD of tail bone may be improved by reducing error associated with in vivo estimation of tail bone thickness, and also by adjusting for displacement of soft tissue by bone mineral. In conclusion a purpose-built SPA instrument could be used to make on-farm sequential non-invasive in vivo measurements of the BMD of tailbone in cattle with accuracy acceptable for many animal studies.

The effect of neutron irradiation on the density of low-energy excitations in vitreous silica

Systematic low-temperature measurements of the thermal conductivity, specific heat, dielectric constant, and temperature-dependent ultrasound velocity have been made on a single piece of vitreous silica. These measurements were repeated after fast neutron irradiation of the material. It was found that the irradiation produced changes of the same relative magnitude in the low-temperature excess specific heat C , the thermal conductivity K, ex and the anomalous temperature dependence of the ultrasound velocity Deltav/v. A corresponding change in the temperature dependent dielectric constant was not observed. It is therefore likely that K and Deltav/v are determined by the same localized excitations responsible for C , but the temperature dependence of the dielectric constant may have a different, though possibly related, origin. Furthermore, a consistent account for the measured C , K, ex and Deltav/v of unirradiated silica is given by the tunneling-state model with a single, energy-dependent density of states. Changes in these three properties due to irradiation can be explained by altering only the density of tunneling states incorporated in the model.

Biochemical studies of postsynaptic density signaling proteins with a focus on synaptic GTPase activating protein and PDZ domains

Memory storage in the brain involves adjustment of the strength of existing synapses and formation of new neural networks. A key process underlying memory formation is synaptic plasticity, the ability of excitatory synapses to strengthen or weaken their connections in response to patterns of activity between their connected neurons. Synaptic plasticity is governed by the precise pattern of Ca²⁺ influx through postsynaptic N-methyl-D-aspartate-type glutamate receptors (NMDARs), which can lead to the activation of the small GTPases Ras and Rap. Differential activation of Ras and Rap acts to modulate synaptic strength by promoting the insertion or removal of 2-amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propanoic acid receptors (AMPARs) from the synapse. Synaptic GTPase activating protein (synGAP) regulates AMPAR levels by catalyzing the inactivation of GTP-bound (active) Ras or Rap. synGAP is positioned in close proximity to the cytoplasmic tail regions of the NMDAR through its association with the PDZ domains of PSD-95. SynGAP’s activity is regulated by the prominent postsynaptic protein kinase, Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) and cyclin-dependent kinase 5 (CDK5), a known binding partner of CaMKII. Modulation of synGAP’s activity by phosphorylation may alter the ratio of active Ras to Rap in spines, thus pushing the spine towards the insertion or removal of AMPARs, subsequently strengthening or weakening the synapse. To date, all biochemical studies of the regulation of synGAP activity by protein kinases have utilized impure preparations of membrane bound synGAP. Here we have clarified the effects of phosphorylation of synGAP on its Ras and Rap GAP activities by preparing and utilizing purified, soluble recombinant synGAP, Ras, Rap, CaMKII, CDK5, PLK2, and CaM. Using mass spectrometry, we have confirmed the presence of previously identified CaMKII and CDK5 sites in synGAP, and have identified novel sites of phosphorylation by CaMKII, CDK5, and PLK2. We have shown that the net effect of phosphorylation of synGAP by CaMKII, CDK5, and PLK2 is an increase in its GAP activity toward HRas and Rap1. In contrast, there is no effect on its GAP activity toward Rap2. Additionally, by assaying the GAP activity of phosphomimetic synGAP mutants, we have been able to hypothesize the effects of CDK5 phosphorylation at specific sites in synGAP. In the course of this work, we also found, unexpectedly, that synGAP is itself a Ca²⁺/CaM binding protein. While Ca²⁺/CaM binding does not directly affect synGAP activity, it causes a conformational change in synGAP that increases the rate of its phosphorylation and exposes additional phosphorylation sites that are inaccessible in the absence of Ca²⁺/CaM.

The postsynaptic density (PSD) is an electron-dense region in excitatory postsynaptic neurons that contains a high concentration of glutamate receptors, cytoskeletal proteins, and associated signaling enzymes. Within the PSD, three major classes of scaffolding molecules function to organize signaling enzymes and glutamate receptors. PDZ domains present in the Shank and PSD-95 scaffolds families serve to physically link AMPARs and NMDARs to signaling molecules in the PSD. Because of the specificity and high affinity of PDZ domains for their ligands, I reasoned that these interacting pairs could provide the core components of an affinity chromatography system, including affinity resins, affinity tags, and elution agents. I show that affinity columns containing the PDZ domains of PSD-95 can be used to purify active PDZ domain-binding proteins to very high purity in a single step. Five heterologously expressed neuronal proteins containing endogenous PDZ domain ligands (NMDAR GluN2B subunit Tail, synGAP, neuronal nitric oxide synthase PDZ domain, cysteine rich interactor of PDZ three and cypin) were purified using PDZ domain resin, with synthetic peptides having the sequences of cognate PDZ domain ligands used as elution agents. I also show that conjugation of PDZ domain-related affinity tags to Proteins Of Interest (POIs) that do not contain endogenous PDZ domains or ligands does not alter protein activity and enables purification of the POIs on PDZ domain-related affinity resins.

Whole body vibration treatments in postmenopausal women can improve bone mineral density:results of a stimulus focussed meta-analysis

Whole body vibration treatment is a non-pharmacological intervention intended to stimulate muscular response and increase bone mineral density, particularly for postmenopausal women. The literature related to this topic is controversial, heterogeneous, and unclear despite the prospect of a major clinical effect. The aim of this study was to identify and systematically review the literature to assess the effect of whole body vibration treatments on bone mineral density (BMD) in postmenopausal women with a specific focus on the experimental factors that influence the stimulus. Nine studies fulfilled the inclusion criteria, including 527 postmenopausal women and different vibration delivery designs. Cumulative dose, amplitudes and frequency of treatments as well as subject posture during treatment vary widely among studies. Some of the studies included an associated exercise training regime. Both randomized and controlled clinical trials were included. Whole body vibration was shown to produce significant BMD improvements on the hip and spine when compared to no intervention. Conversely, treatment associated with exercise training resulted in negligible outcomes when compared to exercise training or to placebo. Moreover, side-alternating platforms were more effective in improving BMD values than synchronous platforms and mechanical oscillations of magnitude higher than 3 g and/or frequency lower than 25 Hz were also found to be effective. Treatments with a cumulative dose over 1000 minutes in the follow-up period were correlated to positive outcomes. Our conclusion is that whole body vibration treatments in elderly women can reduce BMD decline.However, many factors (e.g. amplitude, frequency and subject posture) affect the capacity of the vibrations to propagate to the target site; the adequate level of stimulation required to produce these effects has not yet been defined. Further biomechanical analyses to predict the propagation of the vibration waves along the body and assess the stimulation levels are required.

Physical therapy for urinary incontinence in postmenopausal women with osteoporosis or low bone density : a randomized controlled trial

Objective: To assess the effectiveness of 12 weekly physical therapy sessions for urinary incontinence (UI) compared with a control intervention, for reducing the number of UI episodes measured with the 7-day bladder diary, at 3 months and 1 year postrandomization. Methods: A single parallel-group randomized controlled trial was conducted at one outpatient public health center, in postmenopausal women aged 55 years and over with osteoporosis or low bone density and UI. Women were randomized to physical therapy (PT) for UI or osteoporosis education. The primary outcome measure was number of leakage episodes on the 7-day bladder diary, assessed at baseline, after treatment and at 1 year. The secondary outcome measures included the pad test and disease-specific quality of life and self-efficacy questionnaires assessed at the same timepoints. Results: Forty-eight women participated (24 per group). Two participants dropped out of each group and one participant was deceased before 3-month follow-up. Intention-to-treat analysis was undertaken. At 3 months and 1 year, there was a statistically significant difference in the number of leakage episodes on the 7-day bladder diary (3 mo: P = 0.04; 1 y: P = 0.01) in favor of the PT group. The effect size was 0.34 at 1 year. There were no harms reported. Conclusions: After a 12-week course of PT once per week for UI, PT group participants had a 75% reduction in weekly median number of leakage episodes, whereas the control group's condition had no improvement. At 1 year, the PT group participants maintained this improvement, whereas the control group's incontinence worsened.

Physical therapy for urinary incontinence in postmenopausal women with osteoporosis or low bone density : a randomized controlled trial

Objective: To assess the effectiveness of 12 weekly physical therapy sessions for urinary incontinence (UI) compared with a control intervention, for reducing the number of UI episodes measured with the 7-day bladder diary, at 3 months and 1 year postrandomization. Methods: A single parallel-group randomized controlled trial was conducted at one outpatient public health center, in postmenopausal women aged 55 years and over with osteoporosis or low bone density and UI. Women were randomized to physical therapy (PT) for UI or osteoporosis education. The primary outcome measure was number of leakage episodes on the 7-day bladder diary, assessed at baseline, after treatment and at 1 year. The secondary outcome measures included the pad test and disease-specific quality of life and self-efficacy questionnaires assessed at the same timepoints. Results: Forty-eight women participated (24 per group). Two participants dropped out of each group and one participant was deceased before 3-month follow-up. Intention-to-treat analysis was undertaken. At 3 months and 1 year, there was a statistically significant difference in the number of leakage episodes on the 7-day bladder diary (3 mo: P = 0.04; 1 y: P = 0.01) in favor of the PT group. The effect size was 0.34 at 1 year. There were no harms reported. Conclusions: After a 12-week course of PT once per week for UI, PT group participants had a 75% reduction in weekly median number of leakage episodes, whereas the control group's condition had no improvement. At 1 year, the PT group participants maintained this improvement, whereas the control group's incontinence worsened.