Total ecosystem carbon stocks at the marine‐terrestrial interface: Blue carbon of the Pacific Northwest Coast,United States

The coastal ecosystems of temperate North America provide a variety of ecosystem services including high rates of carbon sequestration. Yet, little data exist for the carbon stocks of major tidal wetland types in the Pacific Northwest, United States. We quantified the total ecosystem carbon stocks (TECS) in seagrass, emergent marshes, and forested tidal wetlands, occurring along increasing elevation and decreasing salinity gradients. The TECS included the total aboveground carbon stocks and the entire soil profile (to as deep as 3 m). TECS significantly increased along the elevation and salinity gradients: 217 ± 60 Mg C/ha for seagrass (low elevation/high salinity), 417 ± 70 Mg C/ha for low marsh, 551 ± 47 Mg C/ha for high marsh, and 1,064 ± 38 Mg C/ha for tidal forest (high elevation/low salinity). Soil carbon stocks accounted for >98% of TECS in the seagrass and marsh communities and 78% in the tidal forest. Soils in the 0–100 cm portion of the profile accounted for only 48%–53% of the TECS in seagrasses and marshes and 34% of the TECS in tidal forests. Thus, the commonly applied limit defining TECS to a 100 cm depth would greatly underestimate both carbon stocks and potential greenhouse gas emissions from land‐use conversion. The large carbon stocks coupled with other ecosystem services suggest value in the conservation and restoration of temperate zone tidal wetlands through climate change mitigation strategies. However, the findings suggest that long‐term sea‐level rise effects such as tidal inundation and increased porewater salinity will likely decrease ecosystem carbon stocks in the absence of upslope wetland migration buffer zones.     

Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice

Recently, a number of collaborative large-scale mouse mutagenesis programs have been launched. These programs aim for a better understanding of the roles of all individual coding genes and the biological systems in which these genes participate. In international efforts to share phenotypic data among facilities/institutes, it is desirable to integrate information obtained from different phenotypic platforms reliably. Since the definitions of specific phenotypes often depend on a tacit understanding of concepts that tends to vary among different facilities, it is necessary to define phenotypes based on the explicit evidence of assay results. We have developed a website termed PhenoSITE (Phenome Semantics Information with Terminology of Experiments: http://www.gsc.riken.jp/Mouse/), in which we are trying to integrate phenotype-related information using an experimental-evidence-based approach. The site's features include (1) a baseline database for our phenotyping platform; (2) an ontology associating international phenotypic definitions with experimental terminologies used in our phenotyping platform; (3) a database for standardized operation procedures of the phenotyping platform; and (4) a database for mouse mutants using data produced from the large-scale mutagenesis program at RIKEN GSC. We have developed two types of integrated viewers to enhance the accessibility to mutant resource information. One viewer depicts a matrix view of the ontology-based classification and chromosomal location of each gene; the other depicts ontology-mediated integration of experimental protocols, baseline data, and mutant information. These approaches rely entirely upon experiment-based evidence, ensuring the reliability of the integrated data from different phenotyping platforms.     

OmicBrowse: a browser of multidimensional omics annotations

OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species. OmicBrowse integrates multiple data servers into a single omic space through secure peer-to-peer server communications, so that a user can easily obtain an integrated view of distributed data servers, e.g. an integrated view of numerous whole-genome tiling-array data retrieved from a user's in-house private-data server, along with various genomic annotations from public internet servers. OmicBrowse is especially appropriate for positional-cloning purposes. It displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms. We also show that an omic-space chart effectively represents schemes for integrating multiple datasets of multiple species. Availability: OmicBrowse is developed by the Genome-Phenome Superbrain Project and is released as free open-source software under the GNU General Public License at http://omicspace.riken.jp.     

Balancing the Need to Develop Coastal Areas with the Desire for an Ecologically Functioning Coastal Environment: Is Net Ecosystem Improvement Possible?

The global human population is growing exponentially, close to a majority lives and works near the coast, and coastal commerce and development are critical to the economies of many nations. Hence, coastal areas will continue to be a major focus of development and economic activity. People desire the economic advantages provided by coastal development along with the fisheries and social commodities supported by estuarine and coastal ecosystems. Because of these facts, we view the challenge of balancing coastal development with enhancing nearshore marine and estuarine ecosystems (i.e., net ecosystem improvement) as the top priority for coastal researchers in this century. Our restoration research in Pacific Northwest estuaries and participation in nearshore project design and impact mitigation has largely dealt with these competing goals. To this end, we have applied conceptual models, comprehensive assessment methods, and principles of restoration ecology, conservation biology, and adaptive management to incorporate science into decisions about uses of estuarine systems. Case studies of Bainbridge Island and the Columbia River demonstrate the use of objective, defensible methods to prioritize tidally influenced shorelines and habitats (i.e., riparian forests, marshes, unvegetated flats, rocky shores, seagrass meadows, kelp forests) for preservation, conservation, and restoration. Case studies of Clinton, Washington, and Port Townsend, Washington, demonstrate the incorporation of an ecological perspective and technological solutions into design of overwater structures to minimize impacts on nearshore ecosystems. Adaptive management has allowed coastal development and restoration uncertainties to be better evaluated, with the information used to improve management decisions. Although unproven on a large scale, we think these kinds of methods can contribute to the net improvement of already degraded ecosystems. The ingredients include applied science to understand the issues, education, incentives, empirical data, cumulative impact analysis, and an effective adaptive management program. Because the option of net ecosystem improvement is often more costly than alternatives such as no net loss, commitment by the local or regional community to this approach is essential.     

Experimental investigation on neural cell survival after dielectrophoretic trapping

Negative dielectrophoretic forces can effectively be used to trap cortical rat neurons. The creation of dielectrophoretic forces requires electric fields of high non-uniformity. High electric field strengths, however, can cause excessive membrane potentials by which cells may unrecoverably be changed or it may lead to cell death. In a previous study it was found that cells trapped at 3 Vtt/14 MHz did not change morphologically as compared to cells that were not exposed to the electric field. This study investigates the viability of fetal cortical rat neurons after being trapped by negative dielectrophoretic forces at frequencies up to 1 MHz. A planar quadrupole micro-electrode structure was used for the creation of a non-uniform electric field. The sinusoidal input signal was varied in amplitude (3 and 5 Vtt) and frequency (10 kHz-1 MHz). The results presented in this paper show that the viability of dielectrophoretically trapped postnatal cortical rat cells was greatly frequency dependent. To preserve viability frequencies above 100 kHz (at 3 Vtt) or 1 MHz (5 Vtt) must be used.     

Reliable expression and purification of highly insoluble transmembrane domains

A general procedure for the reliable preparation of insoluble transmembrane domains has been developed. Improved expression schemes were developed by expressing the transmembrane domains of caveolin proteins 1, 2, and 3 as a fusion to the Trp leader protein. This construct readily formed inclusion bodies during overexpression, allowing high levels of protein to be achieved. Cleavage of the transmembrane domain away from the Trp leader carrier protein was performed with cyanogen bromide. The transmembrane domains were then purified using reverse-phase high-performance liquid chromatography with a C4 column and were eluted with a mixture of 1-butanol and acetic acid. Using this method, the 39-42 amino acid transmembrane domains from caveolin proteins 1, 2, and 3 were successfully purified to homogeneity. Further verification of this method was successfully done with Rfbp(18-51), another insoluble transmembrane domain.     

The effects of livestock grazing on biodiversity are multi‐trophic: a meta‐analysis

Anthropogenic disturbance has generated a significant loss of biodiversity worldwide and grazing by domestic herbivores is a contributing disturbance. Although the effects of grazing on plants are commonly explored, here we address the potential multi‐trophic effects on animal biodiversity (e.g. herbivores, pollinators and predators). We conducted a meta‐analysis on 109 independent studies that tested the response of animals or plants to livestock grazing relative to livestock excluded. Across all animals, livestock exclusion increased abundance and diversity, but these effects were greatest for trophic levels directly dependent on plants, such as herbivores and pollinators. Detritivores were the only trophic level whose abundance decreased with livestock exclusion. We also found that the number of years since livestock was excluded influenced the community and that the effects of grazer exclusion on animal diversity were strongest in temperate climates. These findings synthesise the effects of livestock grazing beyond plants and demonstrate the indirect impacts of livestock grazing on multiple trophic levels in the animal community. We identified the potentially long‐term impacts that livestock grazing can have on lower trophic levels and consequences for biological conservation. We also highlight the potentially inevitable cost to global biodiversity from livestock grazing that must be balanced against socio‐economic benefits.     

Increased bradykinesia in Parkinson’s disease with increased movement complexity: elbow flexion–extension movements

The present research investigates factors contributing to bradykinesia in the control of simple and complex voluntary limb movement in Parkinson’s disease (PD) patients. The functional scheme of the basal ganglia (BG)–thalamocortical circuit was described by a mathematical model based on the mean firing rates of BG nuclei. PD was simulated as a reduction in dopamine levels, and a loss of functional segregation between two competing motor modules. In order to compare model simulations with performed movements, flexion and extension at the elbow joint is taken as a test case. Results indicated that loss of segregation contributed to bradykinesia due to interference between competing modules and a reduced ability to suppress unwanted movements. Additionally, excessive neurotransmitter depletion is predicted as a possible mechanism for the increased difficulty in performing complex movements. The simulation results showed that the model is in qualitative agreement with the results from movement experiments on PD patients and healthy subjects. Furthermore, based on changes in the firing rate of BG nuclei, the model demonstrated that the effective mechanism of Deep Brain Stimulation (DBS) in STN may result from stimulation induced inhibition of STN, partial synaptic failure of efferent projections, or excitation of inhibitory afferent axons even though the underlying methods of action may be quite different for the different mechanisms.