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Lyons_Joseph_K_1981.pdf
No full textTime trends in flow and channel characteristics were evaluated for the Middle Fork Willamette (MFW) River, which drains a 668 km2 forested watershed in the Cascade Mountains of western Oregon. Timber
production is the primary land use in the watershed. Analysis of precipitation and peak flow data from 1959 to 1980 suggests that peak flows (greater than 0.15 m3skm2) increased 2% per year as timber harvesting and road building expanded in the basin.
Landslides associated with roads and clearcuts, based on an inventory of aerial photographs dating from 1959 to 1972, were 27 and 23 times more frequent (respectively) than in forested situations. The majority
of landslides appear to have been initiated during the relatively large flood of December 22, 1964. Changes in channel planform morphology from 1936 to 1980 were
documented from aerial photographs. Based on the photographic record, channel width increased prior to 1967 followed by a decreasing trend from 1967 to 1980. Sixty-five channel cross-sectional profiles were surveyed during summer low flows in 1979 and 1980 to provide detailed measurements of existing channel conditions. The presence or absence of aggradational features was noted at each cross section. Regression analysis revealed that significantly greater (c= 0.05) channel
widths were recorded for 62% of the aggraded reaches compared to the dimensions of nonaggraded reaches. The results of the cross-section surveys, combined with the
channel morphology and landslide measurements, suggest three conclusions: (1) major aggradation along the NW River occurred during the 1964 flood, (2) landslides associated with the 1964 flood contributed to the development of aggraded locations along the river, and (3) the
majority of landslides during this period occurred within one geologic zone and were associated with land use activities, thus suggesting management activities, particularly roads, influenced changes in
channel morphology
Managing the Environmental Effects of Fishing, What's Left After Property Rights?
Full text linkCommercial property rights in New Zealand are designed to address utilisation and sustainability issues relating to single-stock management. However, commercial property rights may not provide incentives that address environmental impacts of fishing if these impacts do not affect the value of the property right. But is it really that simple? This paper examines the circumstances under which these property rights also benefit the wider ecosystem, highlights where gaps remain and the subsequent implications for managing environmental impacts. For example, as more species enter a property rights-based system, benefits may accrue through reductions in capacity and effort, reduced discarding and an increase in information about fisheries through improved reporting requirements. These changes contribute towards an ecosystem approach to fisheries management. The additional benefits of the rights-based framework may also affect decisions relating to the use of other management tools. For example, in many states, MPAs are advocated as a key fisheries management tool as well as a reservoir of biodiversity. However, where the majority of mobile species are being managed sustainably through property rights, the role of MPAs, and the areas required to ensure ecosystem function may not need to be as extensive. The property rights system may be less effective where there are limits on the incentives that are connected with property rights, such as protected species bycatch or the effects of fishing on the benthic environment. In these circumstances, targeted spatial management or the extension and adaptation of the property rights framework may be required.Keywords: Environmental Effects, Property Rights, QMS, ITQ, MPAs, New Zealand, QuotaKeywords: Environmental Effects, Property Rights, QMS, ITQ, MPAs, New Zealand, Quot
Ribonucleotide Reductase Association with Mammalian Liver Mitochondria
Full text linkDeoxyribonucleoside triphosphate pools in mammalian mitochondria are highly
asymmetric, and this asymmetry probably contributes toward the elevated
mutation rate for the mitochondrial genome as compared with the nuclear
genome. To understand this asymmetry, we must identify pathways for synthesis
and accumulation of dNTPs within mitochondria. We have identified
ribonucleotide reductase activity specifically associated with mammalian tissue
mitochondria. Examination of immunoprecipitated proteins by mass spectrometry
revealed R1, the large RNR subunit, in purified mitochondria. Significant
enzymatic and immunological activity was seen in rat liver mitochondrial
nucleoids, isolated as described by Wang, Y., and Bogenhagen, D. F. (2006) J.
Biol. Chem. 281, 25791–25802. Moreover, incubation of respiring rat liver
mitochondria with [¹⁴C]cytidine diphosphate leads to acccumulation of
radiolabeled deoxycytidine and thymidine nucleotides within the mitochondria.
Comparable results were seen with [¹⁴C]guanosine diphosphate. Ribonucleotide
reduction within the mitochondrion, as well as outside the organelle, needs to be
considered as a possibly significant contributor to mitochondrial dNTP pools.This research was originally published in the Journal of Biological Chemistry. Chimploy, K., Song, S., Wheeler, L. J., & Mathews, C. K. Ribonucleotide reductase association with mammalian liver mitochondria. 2013. 288(18), 13145-13155. © the American Society for Biochemistry and Molecular Biology. This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Society for Biochemistry and Molecular Biology and can be found at: http://www.jbc.org/.Keywords: deoxyribonucleotide metabolism, ribonucleotide reductase, mitochondria, nucleotide pool asymmetryKeywords: deoxyribonucleotide metabolism, ribonucleotide reductase, mitochondria, nucleotide pool asymmetr
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Full text linkBackground: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great
“Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom
phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more
generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard
names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch
lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become
a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact
through clearly defined interfaces.
Results: With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies
(HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012.
During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations,
documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proofof-
concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing,
finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an
innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to
nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a
website (www.phylotastic.org), and a server image.
Conclusions: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in
the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3
end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential
for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of
phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation
in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality
assessment.Keywords: Web services, Taxonomy, Data reuse, Phylogeny, Tree of life, HackathonKeywords: Web services, Taxonomy, Data reuse, Phylogeny, Tree of life, Hackatho
OMalleyFigure2.tif
No full textSubmarine volcanic eruptions can result in both real and apparent changes in marine algal communities, e.g., increases in phytoplankton biomass and/or growth rates that can cover thousands of square kilometers. Satellite ocean color monitoring detects these changes as increases in chlorophyll and particulate backscattering. Detailed, high resolution analysis is needed to separate the optical effects of volcanic products from the response of the marine algal community. It is possible to calculate an index, which maps the magnitude of improbable change (relative to long term average conditions) following known volcanic eruptions by using low resolution, initial estimates of chlorophyll and backscatter along with an archived history of satellite data. We apply multivariate probability analysis to changes in global satellite ocean chlorophyll and particulate backscatter data to create a new metric for observing apparent biological responses to submarine eruptions. Several examples are shown, illustrating the sensitivity of our improbability mapping index to known submarine volcanic events, yielding a potentially robust method for the detection of new events in remote locations
RuggieroPeterCEOASForecastingResponeEarths.pdf
No full textIn the future, Earth will be warmer, precipitation events will be more extreme, global mean sea level will rise, and many arid and semiarid regions will be drier. Human modifications of landscapes will also occur at an accelerated rate as developed areas increase in size and population density. We now have gridded global forecasts, being continually improved, of the climatic and land use changes (C&LUC) that are likely to occur in the coming decades. However, besides a few exceptions, consensus forecasts do not exist for how these C&LUC will likely impact Earth-surface processes and hazards. In some cases, we have the tools to forecast the geomorphic responses to likely future C&LUC. Fully exploiting these models and utilizing these tools will require close collaboration among Earth-surface scientists and Earth-system modelers. This paper assesses the state-of-the-art tools and data that are being used or could be used to forecast changes in the state of Earth's surface as a result of likely future C&LUC. We also propose strategies for filling key knowledge gaps, emphasizing where additional basic research and/or collaboration across disciplines are necessary. The main body of the paper addresses cross-cutting issues, including the importance of nonlinear/threshold-dominated interactions among topography, vegetation, and sediment transport, as well as the importance of alternate stable states and extreme, rare events for understanding and forecasting Earth-surface response to C&LUC. Five supplements delve into different scales or process zones (global-scale assessments and fluvial, aeolian, glacial/periglacial, and coastal process zones) in detail.Keywords: forecasting, global change, Earth-surface processesKeywords: forecasting, global change, Earth-surface processe
HoEmilyPublicHealthHumanSciencesPhytochemicalsFromCruciferous.pdf
No full textEpidemiological evidence has demonstrated a reduced risk of prostate cancer associated with cruciferous vegetable intake. Follow-up studies have attributed this protective activity to the metabolic products of glucosinolates, a class of secondary metabolites produced by crucifers. The metabolic products of glucoraphanin and glucobrassicin, sulforaphane and indole-3-carbinol respectively, have been the subject of intense investigation by cancer researchers. Sulforaphane and indole-3-carbinol inhibit prostate cancer by both blocking initiation and suppressing prostate cancer progression in vitro and in vivo. Research has largely focused on the anti-initiation and cytoprotective effects of sulforaphane and indole-3-carbinol through induction of Phase I and Phase II detoxification pathways. With regards to suppressive activity, research has focused on the ability of sulforaphane and indole-3-carbinol to antagonize cell signaling pathways known to be dysregulated in prostate cancer. More recent investigations have characterized the ability of sulforaphane and indole-3-carbinol derivatives to modulate the activity of enzymes controlling the epigenetic status of prostate cancer cells. In this review we will summarize the well-established, “classic” non-epigenetic targets of sulforaphane and indole-3-carbinol, and highlight more recent evidence supporting these phytochemicals as epigenetic modulators for prostate cancer chemoprevention.Keywords: prostate cancer, I3C, epigenetic, sulforaphaneKeywords: prostate cancer, I3C, epigenetic, sulforaphaneKeywords: prostate cancer, I3C, epigenetic, sulforaphaneKeywords: prostate cancer, I3C, epigenetic, sulforaphan
RingoChrisCropSoilScienceNewApproachEvaluate.pdf
No full textWidespread habitat degradation and uncharacteristic fire, insect, and disease outbreaks in forests across
the western United States have led to highly publicized calls to increase the pace and scale of forest restoration.
Despite these calls, we frequently lack a comprehensive understanding of forest restoration
needs. In this study we demonstrate a new approach for evaluating where, how much, and what types
of restoration are needed to move present day landscape scale forest structure towards a Natural Range
of Variability (NRV) across eastern Washington, eastern Oregon, and southwestern Oregon. Our approach
builds on the conceptual framework of the LANDFIRE and Fire Regime Condition Class programs.
Washington–Oregon specific datasets are used to assess the need for changes to current forest structure
resulting from disturbance and/or succession at watershed and regional scales.
Across our analysis region we found that changes in current structure would be needed on an
estimated 4.7 million+ ha (40% of all coniferous forests) in order to restore forest structure approximating
NRV at the landscape scale. Both the overall level and the type of restoration need varied greatly between
forested biophysical settings. Regional restoration needs were dominated by the estimated 3.8+ million
ha in need of thinning and/or low severity fire in forests that were historically maintained by frequent
low or mixed severity fire (historical Fire Regime Group I and III biophysical settings). However, disturbance
alone cannot restore NRV forest structure. We found that time to transition into later development
structural classes through successional processes was required on approximately 3.2 million ha (over 25%
of all coniferous forests). On an estimated 2.3 million ha we identified that disturbance followed by succession
was required to restore NRV forest structure.
The results of this study are intended to facilitate the ability of local land managers to incorporate
regional scale, multi-ownership context into local forest management and restoration. Meeting the
region-wide restoration needs identified in this study will require a substantial increase in the pace
and scale of restoration treatments and coordination amongst governments, agencies, and landowners.Keywords: Fire Regime Condition Class, Landfire, Natural range of variation, Pacific Northwest, Ecological restoration, Gradient nearest neighborKeywords: Fire Regime Condition Class, Landfire, Natural range of variation, Pacific Northwest, Ecological restoration, Gradient nearest neighbo
Cerón-SouzaIvaniaBotanyPlantPathContrastingDemographicHistoryAppendixS4.xlsx
No full textComparative phylogeography offers a unique opportunity to understand the interplay between past environmental events and life-history traits on diversification of unrelated but co-distributed species. Here, we examined the effects of the quaternary climate fluctuations and palaeomarine currents and present-day marine currents on the extant patterns of genetic diversity in the two most conspicuous mangrove species of the Neotropics. The black (Avicennia germinans, Avicenniaceae) and the red (Rhizophora mangle, Rhizophoraceae) mangroves have similar geographic ranges but are very distantly related and show striking differences on their life-history traits. We sampled 18 Atlantic and 26 Pacific locations for A. germinans (N = 292) and R. mangle (N = 422). We performed coalescence simulations using microsatellite diversity to test for evidence of population change associated with quaternary climate fluctuations. In addition, we examined whether patterns of genetic variation were consistent with the directions of major marine (historical and present day) currents in the region. Our demographic analysis was grounded within a phylogeographic framework provided by the sequence analysis of two chloroplasts and one flanking microsatellite region in a subsample of individuals. The two mangrove species shared similar biogeographic histories including: (1) strong genetic breaks between Atlantic and Pacific ocean basins associated with the final closure of the Central American Isthmus (CAI), (2) evidence for simultaneous population declines between the mid-Pleistocene and early Holocene, (3) asymmetric historical migration with higher gene flow from the Atlantic to the Pacific oceans following the direction of the palaeomarine current, and (4) contemporary gene flow between West Africa and South America following the major Atlantic Ocean currents. Despite the remarkable differences in life-history traits of mangrove species, which should have had a strong influence on seed dispersal capability and, thus, population connectivity, we found that vicariant events, climate fluctuations and marine currents have shaped the distribution of genetic diversity in strikingly similar ways.Keywords: climate change, comparative phylogeography, Avicennia germinans, Neotropics, last glacial maximum, population genetic structure, mangroves, bottleneck, Rhizophora mangle, gene flowKeywords: climate change, comparative phylogeography, Avicennia germinans, Neotropics, last glacial maximum, population genetic structure, mangroves, bottleneck, Rhizophora mangle, gene flo
Heat transfer predictions for aquaculture facilities
Full text linkRecycling of water in aquaculture facilities is used to minimize the amount of energy or tempered water required to control water temperatures. The rate of heat exchange between the water and the environment can be an important variable in the design, management, and economic analysis of a recycle system. A review of heat transfer relationships is presented in this thesis. Combined use of these relationships for predicting the rate of heat transfer from the water in an aquaculture facility is also presented. A comprehensive model is developed from the heat transfer relationships to simulate the primary locations of heat exchange in a salmon production facility. These locations are identified as the air-water interfaces, the soil-wall-water interfaces, the air-wall-water interfaces, the pipes and the aeration processes. The transfer rates are based on the climatic data and physical parameters of the facility. The model is used to compare predicted and measured rates of heat exchange for a heated water raceway at the Oregon Aqua-Foods Facility in Springfield, Oregon. The model is also used with a hypothetical raceway and recycle system to determine the relative importance of the different locations of heat exchange and to simulate operational heating costs for relative economic ranking of different operating conditions and design strategies. A comparison is lade between predictions based on three-hour data and average daily data. The sensitivity of the predicted net heat transfer rates to the flowrate, soil and wall thermal conductivities, and the thermal convection coefficient between the water and wall is also investigated. The comparison of the predicted and measured rates of heat transfer indicates that close estimates of the net heat exchange fro. a raceway can be predicted by the model. Comparisons of daily heat exchange predictions from the three-hour and average, daily data showed that the daily data are adequate for estimates, but that three-hour data should be used when more precise estimates are needed (i.e. for sizing heating units). The predicted net heat transfer rates were not significantly affected by the changes in the flowrate, soil and wall thermal conductivities, and the water-to-wall thermal convection coefficient. The air-water interface was found to be the primary location of heat exchange for the specific conditions analyzed and it was concluded that order of magnitude estimates of net heat exchange could be obtained by analyzing the air-water interface and neglecting all other locations. The simulated operational heating costs for the hypothetical system showed a high dependence on ambient and culture water temperatures, and the degree of recycling. Covering open water surfaces during cold temperature months showed a substantial reduction in the heating costs. Economic simulations demonstrated the value of the model for comparing the relative economics of' alternative production strategies