Showing papers by "Oregon State University published in 2005"

Determination of total monomeric anthocyanin pigment content of fruit juices, beverages, natural colorants, and wines by the pH differential method: collaborative study.

Abstract: This collaborative study was conducted to determine the total monomeric anthocyanin concentration by the pH differential method, which is a rapid and simple spectrophotometric method based on the anthocyanin structural transformation that occurs with a change in pH (colored at pH 1.0 and colorless at pH 4.5). Eleven collaborators representing commercial laboratories, academic institutions, and government laboratories participated. Seven Youden pair materials representing fruit juices, beverages, natural colorants, and wines were tested. The repeatability relative standard deviation (RSDr) varied from 1.06 to 4.16%. The reproducibility relative standard deviation (RSDR) ranged from 2.69 to 10.12%. The HorRat values were < or = 1.33 for all materials. The Study Director recommends that the method be adopted Official First Action.

Psychological and physical well-being during unemployment: a meta-analytic study.

Abstract: The authors used theoretical models to organize the diverse unemployment literature, and meta-analytic techniques were used to examine the impact of unemployment on worker well-being across 104 empirical studies with 437 effect sizes. Unemployed individuals had lower psychological and physical well-being than did their employed counterparts. Unemployment duration and sample type (school leaver vs. mature unemployed) moderated the relationship between mental health and unemployment, but the current unemployment rate and the amount of unemployment benefits did not. Within unemployed samples, work-role centrality, coping resources (personal, social, financial, and time structure), cognitive appraisals, and coping strategies displayed stronger relationships with mental health than did human capital or demographic variables. The authors identify gaps in the literature and propose directions for future unemployment research.

Working With Missing Values

Abstract: Less than optimum strategies for missing values can produce biased estimates, distorted statistical power, and invalid conclusions. After reviewing traditional approaches (listwise, pairwise, and mean substitution), selected alternatives are covered including single imputation, multiple imputation, and full information maximum likelihood estimation. The effects of missing values are illustrated for a linear model, and a series of recommendations is provided. When missing values cannot be avoided, multiple imputation and full information methods offer substantial improvements over traditional approaches. Selected results using SPSS, NORM, Stata (mvis/micombine), and Mplus are included as is a table of available software and an appendix with examples of programs for Stata and Mplus.

Loss of foundation species: consequences for the structure and dynamics of forested ecosystems

Abstract: In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short- and long-term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.

Carbon-based ocean productivity and phytoplankton physiology from space

Abstract: carbon(C)andchlorophyll(Chl)biomassandshowthatderivedChl:Cratioscloselyfollow anticipated physiological dependencies on light, nutrients, and temperature. With this new information, global estimates of phytoplankton growth rates (m) and carbon-based NPP are made for the first time. Compared to an earlier chlorophyll-based approach, our carbonbased values are considerably higher in tropical oceans, show greater seasonality at middle and high latitudes, and illustrate important differences in the formation and demise of regional algal blooms. This fusion of emerging concepts from the phycological and remote sensing disciplines has the potential to fundamentally change how we model and observe carbon cycling in the global oceans.

The Varieties of Resource Experience: Natural Resource Export Structures and the Political Economy of Economic Growth

Abstract: Many oil, mineral, and plantation crop-based economies experienced a substantial deceleration in growth following the commodity boom and bust of the 1970s and early 1980s. This article illustrates how countries dependent on point source natural resources (those extracted from a narrow geographic or economic base, such as oil and minerals) and plantation crops are predisposed to heightened economic and social divisions and weakened institutional capacity. This in turn impedes their ability to respond effectively to shocks, which previous studies have shown to be essential for sustaining rising levels of prosperity. Analysis of data on classifications of export structure, controlling for a wide array of other potential determinants of governance, shows that point source and coffee and cocoa exporting countries do relatively poorly across an array of governance indicators. These governance effects are not associated simply with being a natural resource exporter. Countries with natural resource exports that are diffuse relying primarily on livestock and agricultural produce from small family farms do not show the same strong effects and have had more robust growth recoveries.

Combining sources in stable isotope mixing models: alternative methods.

Abstract: Stable isotope mixing models are often used to quantify source contributions to a mixture. Examples include pollution source identification; trophic web studies; analysis of water sources for soils, plants; or water bodies, and many others. A common problem is having too many sources to allow a unique solution. We discuss two alternative procedures for addressing this problem. One option is a priori to combine sources with similar signatures so the number of sources is small enough to provide a unique solution. Aggregation should be considered only when isotopic signatures of clustered sources are not significantly different, and sources are related so the combined source group has some functional significance. For example, in a food web analysis, lumping several species within a trophic guild allows more interpretable results than lumping disparate food sources, even if they have similar isotopic signatures. One result of combining mixing model sources is increased uncertainty of the combined end-member isotopic signatures and consequently the source contribution estimates; this effect can be quantified using the IsoError model ( http://www.epa.gov/wed/pages/models/isotopes/isoerror1_04.htm ). As an alternative to lumping sources before a mixing analysis, the IsoSource mixing model ( http://www.epa.gov/wed/pages/models/isosource/isosource.htm ) can be used to find all feasible solutions of source contributions consistent with isotopic mass balance. While ranges of feasible contributions for each individual source can often be quite broad, contributions from functionally related groups of sources can be summed a posteriori, producing a range of solutions for the aggregate source that may be considerably narrower. A paleohuman dietary analysis example illustrates this method, which involves a terrestrial meat food source, a combination of three terrestrial plant foods, and a combination of three marine foods. In this case, a posteriori aggregation of sources allowed strong conclusions about temporal shifts in marine versus terrestrial diets that would not have otherwise been discerned.

Interpreting, measuring, and modeling soil respiration

Abstract: This paper reviews the role of soil respiration in determining ecosystem carbon balance, and the conceptual basis for measuring and modeling soil respiration. We developed it to provide background and context for this special issue on soil respiration and to synthesize the presentations and discussions at the workshop. Soil respiration is the largest component of ecosystem respiration. Because autotrophic and heterotrophic activity belowground is controlled by substrate availability, soil respiration is strongly linked to plant metabolism, photosynthesis and litterfall. This link dominates both base rates and short-term fluctuations in soil respiration and suggests many roles for soil respiration as an indicator of ecosystem metabolism. However, the strong links between above and belowground processes complicate using soil respiration to understand changes in ecosystem carbon storage. Root and associated mycorrhizal respiration produce roughly half of soil respiration, with much of the remainder derived from decomposition of recently produced root and leaf litter. Changes in the carbon stored in the soil generally contribute little to soil respiration, but these changes, together with shifts in plant carbon allocation, determine ecosystem carbon storage belowground and its exchange with the atmosphere. Identifying the small signal from changes in large, slow carbon pools in flux dominated by decomposition of recent material and autotrophic and mycorrhizal respiration is a significant challenge. A mechanistic understanding of the belowground carbon cycle and of the response of different components to the environment will aid in identifying this signal. Our workshop identified information needs to help build that understanding: (1) the mechanisms that control the coupling of canopy and belowground processes; (2) the responses of root and heterotrophic respiration to environment; (3) plant carbon allocation patterns, particularly in different forest developmental stages, and in response to treatments (warming, CO2, nitrogen additions); and (4) coupling measurements of soil respiration with aboveground processes and changes in soil carbon. Multi-factor experiments need to be sufficiently long to allow the systems to adjust to the treatments. New technologies will be necessary to reduce uncertainty in estimates of carbon allocation, soil carbon pool sizes, and different responses of roots and microbes to environmental conditions.

The role of topography on catchment-scale water residence time

Abstract: 624 km 2 ) that represent diverse geologic and geomorphic conditions in the western Cascade Mountains of Oregon Our primary objective was to determine the dominant physical controls on catchment-scale water residence time and specifically test the hypothesis that residence time is related to the size of the basin Residence times were estimated by simple convolution models that described the transfer of precipitation isotopic composition to the stream network We found that base flow mean residence times for exponential distributions ranged from 08 to 33 years Mean residence time showed no correlation to basin area (r 2 < 001) but instead was correlated (r 2 = 091) to catchment terrain indices representing the flow path distance and flow path gradient to the stream network These results illustrate that landscape organization (ie, topography) rather than basin area controls catchment-scale transport Results from this study may provide a framework for describing scale-invariant transport across climatic and geologic conditions, whereby the internal form and structure of the basin defines the first-order control on base flow residence time

Expression of Arabidopsis MIRNA Genes

Abstract: MicroRNAs (miRNAs) are approximately 21-nucleotide noncoding RNAs that regulate target transcripts in plants and animals. In addition to miRNAs, plants contain several classes of endogenous small interfering RNAs (siRNAs) involved in target gene regulation and epigenetic silencing. Small RNA libraries were constructed from wild-type Arabidopsis (Arabidopsis thaliana) and mutant plants (rdr2 and dcl3) that were genetically enriched for miRNAs, and a computational procedure was developed to identify candidate miRNAs. Thirty-eight distinct miRNAs corresponding to 22 families were represented in the libraries. Using a 5' rapid amplification of cDNA ends procedure, the transcription start sites for 63 miRNA primary transcripts from 52 MIRNA loci (99 loci tested) were mapped, revealing features consistent with an RNA polymerase II mechanism of transcription. Ten loci (19%) yielded transcripts from multiple start sites. A canonical TATA box motif was identified upstream of the major start site at 45 (86%) of the mapped MIRNA loci. The 5'-mapping data were combined with miRNA cloning and 3'-PCR data to definitively validate expression of at least 73 MIRNA genes. These data provide a molecular basis to explore regulatory mechanisms of miRNA expression in plants.

Tracking color and pigment changes in anthocyanin products

Abstract: Anthocyanin pigments readily degrade during processing and storage of foodstuffs, which can have a dramatic impact on color quality and may also affect nutritional properties. Total anthocyanin pigment content and indices for polymeric color and browning are easily measured with simple spectrophotometric methods. Once individual pigments are identified, their changes can be monitored by high-performance liquid chromatography (HPLC). Modern color instrumentation has made measurement of CIEL*a*b* indices practical and easy. Indices of lightness (L*), chroma (C*), and hue angle (h°) are particularly useful for tracking color change.

Geochemical mapping of the Mariana arc‐basin system: Implications for the nature and distribution of subduction components

Abstract: A new ICP-MS database for glasses from the Mariana Trough, together with published and new ICP-MS data from the Mariana arc, provides the basis for geochemical mapping of the Mariana arc-basin system. The geochemical maps presented here are based on the graphic representation of spatial variations in geochemical proxies for the principal mantle and subduction components. The focus is on three elements with high and similar partition coefficients but different behavior in subduction systems, namely, Ba, Th, and Nb. Two elements with different partition coefficients, Ta and Yb, are used as normalizing factors. Ratio maps (Ta/Yb, Nb/Ta, Th/Ta, Ba/Ta, Ba/Th) provide the simplest petrogenetic insights, subduction zone addition maps based on deviations from a MORB array provide more quantitative insights, and component maps represent an attempt to isolate the different subduction components. The maps shown here indicate the presence of a variably depleted asthenosphere and three added components: a Nb-Th-Ba component, a Th-Ba deep-subduction component, and a Ba-only shallow-subduction component. The asthenosphere entering the system is enriched relative to N-MORB and appears to be focused at three sites within the Mariana Trough. The Nb-Th-Ba component is present mainly in the north of the arc (the Northern Seamount province and northern Central Island Province), the northern edge of the Mariana Trough, and two locations within the Southern Seamount Province. It has a distinctively high Nb/Ta ratio and a moderate enrichment in Th and Ba relative to Nb. Its composition and distribution indicate that it may not be part of the present subduction system but instead originates in mantle lithosphere previously enriched above the subduction zone by addition of small-degree, subduction-modified mantle melts. The Th-Ba component is present throughout the arc and, in minor amounts, in parts of the back-arc basin. The Ba-only component is mainly present in the central part of the arc and at the edges of the back-arc basin. Overall, the geochemical maps provide a new perspective on the geochemical processes that accompany the evolution of an arc basin system from prerifting lithospheric enrichment, through arc-rifting to arc volcanism and back-arc spreading

Carcinogenic polycyclic aromatic hydrocarbon-DNA adducts and mechanism of action.

Abstract: Polycyclic aromatic hydrocarbons (PAHs) are a class of widespread environmental carcinogens. Most of our knowledge of their mechanisms of metabolic activation to DNA-binding "ultimate carcinogenic" metabolites has come from analysis of the DNA interaction products formed by these highly reactive intermediates. Studies of their role in forming DNA-binding intermediates identical to those formed in vivo from the PAH itself have also allowed identification of the particular cytochrome P450 enzymes involved in activating various structural classes of carcinogenic PAHs. It has been established that PAHs, after metabolic activation in vivo, are capable of inducing mutations in oncogenes and, by inducing multiple mutations, may result in tumors. PAHs also cause changes in cellular gap-junction communication similar to those caused by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate. Thus, PAHs may also act through a promotional mechanism in addition to serving as tumor initiators. Previous studies on these mechanisms are described and summarized.

Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat.

Abstract: The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.

DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana

Abstract: Arabidopsis thaliana contains four DICER-LIKE (DCL) genes with specialized functions in small RNA biogenesis for RNA interference-related processes. A mutant with defects in DCL4 was identified and analyzed for microRNA- and endogenous, small interfering RNA (siRNA)-related functions. The dcl4-2 mutant contained normal or near-normal levels of microRNAs (21 nt) and heterochromatin-associated siRNAs (24 nt). In contrast, this mutant lacked each of three families of 21-nt trans-acting siRNAs (ta-siRNAs) and possessed elevated levels of ta-siRNA target transcripts. The dcl4-2 mutant resembled an rna-dependent RNA polymerase 6 mutant in that both mutants lacked ta-siRNAs and displayed heterochronic defects in which vegetative phase change was accelerated. Double mutant analyses with dcl2-1, dcl3-1, and dcl4-2 alleles revealed hierarchical redundancy among DCL activities, leading to alternative processing of ta-siRNA precursors in the absence of DCL4. These data support the concept that plants have specialized and compartmentalized DCL functions for biogenesis of distinct small RNA classes.

Marine natural products as anticancer drugs

Abstract: The chemical and biological diversity of the marine environment is immeasurable and therefore is an extraordinary resource for the discovery of new anticancer drugs. Recent technological and methodologic advances in structure elucidation, organic synthesis, and biological assay have resulted in the isolation and clinical evaluation of various novel anticancer agents. These compounds range in structural class from simple linear peptides, such as dolastatin 10, to complex macrocyclic polyethers, such as halichondrin B; equally as diverse are the molecular modes of action by which these molecules impart their biological activity. This review highlights several marine natural products and their synthetic derivatives that are currently undergoing clinical evaluation as anticancer drugs.

Molecular diversity and ecology of microbial plankton

Abstract: The history of microbial evolution in the oceans is probably as old as the history of life itself. In contrast to terrestrial ecosystems, microorganisms are the main form of biomass in the oceans, and form some of the largest populations on the planet. Theory predicts that selection should act more efficiently in large populations. But whether microbial plankton populations harbour organisms that are models of adaptive sophistication remains to be seen. Genome sequence data are piling up, but most of the key microbial plankton clades have no cultivated representatives, and information about their ecological activities is sparse.

Quantitative determination of perfluorochemicals in sediments and domestic sludge.

Abstract: Perfluorochemicals (PFCs) are the subject of increasingly intense environmental research. Despite their detection both in biota and in aqueous systems, little attention has been paid to the possible presence of this class of compounds in solid environmental matrixes. The limited available data indicate that some PFCs such as perfluorooctane sulfonate (PFOS) may strongly sorb to solids, and sewage sludge is widely suspected as a major sink of PFCs entering municipal waste streams. A quantitative analytical method was developed that consists of liquid solvent extraction of the analytes from sediments and sludge, cleanup via solid-phase extraction, and injection of the extracts with internal standards into a high-performance liquid chromatography (HPLC) system coupled to a tandem mass spectrometer (LC/MS/MS). The limits of detections of the method were analyte and matrix dependent, but ranged from 0.7 to 2.2 ng/g and 0.041 to 0.246 ng/g (dry weight) for sludge and sediment, respectively. A demonstration of t...

Sexual assault education programs: a meta‐analytic examination of their effectiveness

Abstract: Meta-analyses of the effectiveness of college sexual assault education programs on seven outcome measure categories were conducted using 69 studies that involved 102 treatment interventions and 18,172 participants. Five of the outcome categories had significant average effect sizes (i.e., rape attitudes, rape-related attitudes, rape knowledge, behavioral intent, and incidence of sexual assault), while the outcome areas of rape empathy and rape awareness behaviors did not have average effect sizes that differed from zero. A significant finding of this study is that longer interventions are more effective than brief interventions in altering both rape attitudes and rape-related attitudes. Moderator analyses also suggest that the content of programming, type of presenter, gender of the audience, and type of audience may also be associated with greater program effectiveness. Implications for research and practice are discussed.

Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests.

Abstract: Phytophthora ramorum, causal agent of sudden oak death, is an emerging plant pathogen first observed in North America associated with mortality of tanoak (Lithocarpus densiflorus) and coast live oak (Quercus agrifolia) in coastal forests of California during the mid-1990s. The pathogen is now known to occur in North America and Europe and have a host range of over 40 plant genera. Sudden oak death has become an example of unintended linkages between the horticultural industry and potential impacts on forest ecosystems. This paper examines the biology and ecology of P. ramorum in California and Oregon forests as well discussing research on the pathogen in a broader management context.

A meta-analytic review of behavior modeling training.

Abstract: A meta-analysis of 117 studies evaluated the effects of behavior modeling training (BMT) on 6 training outcomes, across characteristics of training design. BMT effects were largest for learning outcomes, smaller for job behavior, and smaller still for results outcomes. Although BMT effects on declarative knowledge decayed over time, training effects on skills and job behavior remained stable or even increased. Skill development was greatest when learning points were used and presented as rule codes and when training time was longest. Transfer was greatest when mixed (negative and positive) models were presented, when practice included trainee-generated scenarios, when trainees were instructed to set goals, when trainees' superiors were also trained, and when rewards and sanctions were instituted in trainees' work environments.

Phylogeny and classification of Pinus

Abstract: We used chloroplast DNA sequences from matK and rbcL to infer the phylogeny for 101 of the approximately 111 species of Pinus (Pinaceae). At the level of subsection and above, the cpDNA tree is congruent with phylogenies based on nuclear DNA with one notable exception: cpDNA sequences from subsect. Contortae are sister to all other North American hard pines rather than occupying a more derived position in the same clade. We used the cpDNA tree plus evidence from nuclear ribosomal DNA and morphology to propose a new classification for the genus. The molecular phylogenies are symmetrical at the deepest branches of the genus, allowing for the delineation of two subgenera, each with two sections that form sister groups. Within sections, clades were slightly asymmetric and sometimes ambiguously resolved. To accomodate ambiguity in some interrelationships, avoid the creation of new ranks, and retain traditional names, we recognised up to three monophyletic subsections per section. Subgenus Pinus (the diploxylon, or hard pines) is divided into the predominantly Eurasian and Mediterranean section Pinus, composed of subsections Pinus and Pinaster, and the strictly North American section Trifoliae, composed of subsections Australes, Ponderosae, and Contortae. Subgenus Strobus (the haploxylon, or soft pines) is divided into the strictly North American section Parrya, composed of subsections Cembroides, Nelsoniae, and Balfourianae, and the Eurasian and North American section Quinquefoliae, composed of subsections Gerardianae, Krempfianae, and Strobus. Mapping of ten morphological and distributional characters indicates that two were diagnostic for infrageneric taxa: the number of vascular bundles per leaf distinguishes subgenus Pinus from subgenus Strobus, and a terminal-positioned umbo on the ovulate cone scale is diagnostic of subsect. Strobus.