Modeling the effects of doliolids on the plankton community structure of the southeastern US continental shelf

A model of the lower trophic levels that consists of a system of coupled ordinary differential equations was developed to investigate the time-dependent behavior of doliolid populations associated with upwelling features on the outer southeastern US continental shelf. Model equations describe the interactions of doliolids with two phytoplankton size fractions, five copepod developmental states and detrital pool. Additional equations describe nitrate and ammonia. Model dynamics are based primarily upon data obtained from field and laboratory experiments for southeastern US continental shelf plankton populations. Variations on a reference simulation, which represents average upwelling conditions without doliolids, were carried out to determine the effect of inclusion of doliolids, temperature and nutrient variations, and variations in ambient food concentrations on the basic plankton community structure. These simulations provide a measure of the role of environmental versus biological interactions in structuring the planktonic food web on the southeastern US continental shelf. Simulations show that he copepod population is significantly reduce when doliolids are present. This happens primarily as a result of direct predation of the doliolids on copepod eggs and juveniles as opposed to an increase in competition for phytoplankton, the primary food source. Additional simulations show that the cooler temperatures associated with the newly upwelled water temporarily decrease the growth rates of doliolids and copepods, bestowing an event greater advantage on the rapidly reproducing doliolids.      

Diurnal regulation of Hsp70s in leaf tissue

Steady-state mRNA levels for three Hsp70s were found to be regulated by a distinctive light/dark mechanism in spinach leaves. Messenger RNAs for the chloroplast stromal and two cytosolic forms displayed a diurnal expression pattern under isothermal conditions that appeared to be independent of circadian control. While protein blot data showed relatively constant Hsp70 protein levels, the higher Hsp70 mRNA levels in the light paralleled the diurnal cycle of total cell protein synthesis. Fractionation studies showed that the major cytosolic Hsp70 cognate group was associated with polysomes. Therefore, the variation of Hsp70 mRNAs is consistent with the diurnal metabolic activity of plant photosynthetic cells in which the demand of protein biogenesis for chaperone function and tissue temperature are highest during the day.     

Tumor necrosis factor-alpha-converting enzyme mediates the inducible cleavage of fractalkine

Fractalkine (FK, CX3CL1) is a novel multidomain protein expressed on the surface of endothelial cells. As a full-length transmembrane protein, FK binds cells expressing CX3CR1, its cognate receptor, with high affinity. Proteolytic cleavage of FK releases a soluble form that is a potent chemoattractant for monocytes, T cells, and natural killer cells. Activation of protein kinase C dramatically increases the rate of this cleavage. Regulation of FK cleavage is critical for maintaining the balance between the immobilized and soluble forms, but the protease responsible has not been identified. Here we report that tumor necrosis factor-alpha-converting enzyme (TACE) is primarily responsible for the inducible cleavage of FK. After transfection into host cells, the proteolytic cleavage of FK was blocked by TACE-specific inhibitors and was not detected in cells genetically altered to remove TACE activity. In contrast, the constitutive cleavage of FK was not mediated by TACE and proceeded normally in TACE-null fibroblasts. We conclude that TACE is primarily responsible for the inducible cleavage of FK. These studies identify a potentially important link between local generation of potent cytokines and control of the balance between the cell adhesion and chemotactic properties of FK.     

Infectious diseases in wild animals in Utah. VI. Experimental infection of birds with Rickettsia rickettsii

Lundgren, D. L. (University of Utah, Salt Lake City), B. D. Thorpe, and C. D. Haskell. Infectious diseases in wild animals in Utah. VI. Experimental infection of birds with Rickettsia rickettsii. J. Bacteriol. 91:963-966. 1966.-Chickens, pigeons, pheasants, sparrow hawks, red-tailed hawks, ravens, magpies, and a marsh hawk were inoculated with Rickettsia rickettsii, the etiological agent of Rocky Mountain spotted fever. The development and persistence of complement-fixing (CF) antibodies and rickettsemias were tested for in these birds. Rickettsiae were recovered from the blood of a number of birds up to the 16th day after inoculation, whereas only the pigeon was found to develop high CF antibody titers. It was concluded that certain species of birds have the potential of contributing to the dissemination of R. rickettsii in nature, and that the CF test is generally unsuitable for serological diagnosis of this organism in birds.     

Marine Vibrios Associated with Bacillary Necrosis, a Disease of Larval and Juvenile Bivalve Mollusks

The etiological agents of bacillary necrosis, a disease of larval and juvenile bivalve mollusks, are designated members of the genus Vibrio.     

Adjustment of juvenile tuatara to a cooler,southern climate: operative temperatures,emergence behaviour and growth rate

Translocations for conservation often involve species limited to relict distributions. However, uncertainty can exist regarding the ability of source individuals to acclimatise following a shift to a distant location. We investigated the ability of captive-reared juvenile tuatara (Sphenodon punctatus) of Cook Strait stock (41°S) to adjust to outdoor, predator-protected pens within Orokonui Ecosanctuary (45 °S). We examined potential basking and within burrow temperatures, the influence of temperature on emergence, and growth rates in comparison with other locations. Tuatara at Orokonui reached their preferred temperature when basking over summer, and burrows provided protection from freezing over winter. Emergence was temperature-dependent and essentially ceased during winter. Growth rates of Orokonui-held juveniles were within the range for four other captive-rearing facilities and faster than for wild juveniles from a Cook Strait population. As all Orokonui-held juveniles have survived and grown we conclude that the climate at this southern location is suitable to consider a free-release.     

Impact of variance components on reliability of absolute quantification using digital PCR

Background

Digital polymerase chain reaction (dPCR) is an increasingly popular technology for detecting and quantifying target nucleic acids. Its advertised strength is high precision absolute quantification without needing reference curves. The standard data analytic approach follows a seemingly straightforward theoretical framework but ignores sources of variation in the data generating process. These stem from both technical and biological factors, where we distinguish features that are 1) hard-wired in the equipment, 2) user-dependent and 3) provided by manufacturers but may be adapted by the user. The impact of the corresponding variance components on the accuracy and precision of target concentration estimators presented in the literature is studied through simulation.

Results

We reveal how system-specific technical factors influence accuracy as well as precision of concentration estimates. We find that a well-chosen sample dilution level and modifiable settings such as the fluorescence cut-off for target copy detection have a substantial impact on reliability and can be adapted to the sample analysed in ways that matter. User-dependent technical variation, including pipette inaccuracy and specific sources of sample heterogeneity, leads to a steep increase in uncertainty of estimated concentrations. Users can discover this through replicate experiments and derived variance estimation. Finally, the detection performance can be improved by optimizing the fluorescence intensity cut point as suboptimal thresholds reduce the accuracy of concentration estimates considerably.

Conclusions

Like any other technology, dPCR is subject to variation induced by natural perturbations, systematic settings as well as user-dependent protocols. Corresponding uncertainty may be controlled with an adapted experimental design. Our findings point to modifiable key sources of uncertainty that form an important starting point for the development of guidelines on dPCR design and data analysis with correct precision bounds. Besides clever choices of sample dilution levels, experiment-specific tuning of machine settings can greatly improve results. Well-chosen data-driven fluorescence intensity thresholds in particular result in major improvements in target presence detection. We call on manufacturers to provide sufficiently detailed output data that allows users to maximize the potential of the method in their setting and obtain high precision and accuracy for their experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-283) contains supplementary material, which is available to authorized users.     

Variation in Soil Temperature,Moisture, and Plant Growth with the Addition of Downed Woody Material on Lakeshore Restoration Sites

Downed woody material (DWM) is an important ecosystem component that performs many critical functions including influencing soil temperature and moisture, which affects plant growth and survival. Residential development along lakeshores has increased dramatically in recent decades in the northern Great Lakes region. Such development often leads to reductions in terrestrial and aquatic woody material. Although lakeshore restoration projects have occurred in the past few years in the region, there has been little effort to evaluate success. In 2007, a collaborative lakeshore restoration research project began on two lakes in Vilas County, Wisconsin. We investigated the benefits of the addition of DWM as part of these restoration projects. We randomly assigned three coverage treatments (0, 25, and 50%) of DWM on 3 × 3–m experimental plots (n = 10 per treatment) and monitored soil temperature and volumetric soil water content at a depth of 10 cm. All plots were planted with two native shrub species and five native understory herbaceous species. Mean maximum soil temperature, mean difference in daily high and low soil temperature, and percent change in soil moisture content were significantly lower in the 25 and 50% DWM plots. Plant canopy volume growth for snowberry (Symphoricarpos albus) and Barren strawberry (Waldstenia fragaroides) was significantly greater in the 25 and 50% DWM plots. We conclude that the addition of DWM had a significant positive effect on regulating soil temperature extremes, soil moisture, and plant volume growth for two species of native plants used for restoration projects.