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Showing papers by "Oregon State University published in 2004"


Journal ArticleDOI
TL;DR: The key decisions in evaluating collaborative filtering recommender systems are reviewed: the user tasks being evaluated, the types of analysis and datasets being used, the ways in which prediction quality is measured, the evaluation of prediction attributes other than quality, and the user-based evaluation of the system as a whole.
Abstract: Recommender systems have been evaluated in many, often incomparable, ways. In this article, we review the key decisions in evaluating collaborative filtering recommender systems: the user tasks being evaluated, the types of analysis and datasets being used, the ways in which prediction quality is measured, the evaluation of prediction attributes other than quality, and the user-based evaluation of the system as a whole. In addition to reviewing the evaluation strategies used by prior researchers, we present empirical results from the analysis of various accuracy metrics on one content domain where all the tested metrics collapsed roughly into three equivalence classes. Metrics within each equivalency class were strongly correlated, while metrics from different equivalency classes were uncorrelated.

5,686 citations


Journal ArticleDOI
17 Jun 2004-Nature
TL;DR: It is shown that the mammalian SIR2 orthologue, Sirt1 (sirtuin 1), activates a critical component of calorie restriction in mammals; that is, fat mobilization in white adipocytes.
Abstract: Calorie restriction extends lifespan in organisms ranging from yeast to mammals. In yeast, the SIR2 gene mediates the life-extending effects of calorie restriction. Here we show that the mammalian SIR2 orthologue, Sirt1 (sirtuin 1), activates a critical component of calorie restriction in mammals; that is, fat mobilization in white adipocytes. Upon food withdrawal Sirt1 protein binds to and represses genes controlled by the fat regulator PPAR-gamma (peroxisome proliferator-activated receptor-gamma), including genes mediating fat storage. Sirt1 represses PPAR-gamma by docking with its cofactors NCoR (nuclear receptor co-repressor) and SMRT (silencing mediator of retinoid and thyroid hormone receptors). Mobilization of fatty acids from white adipocytes upon fasting is compromised in Sirt1+/- mice. Repression of PPAR-gamma by Sirt1 is also evident in 3T3-L1 adipocytes, where overexpression of Sirt1 attenuates adipogenesis, and RNA interference of Sirt1 enhances it. In differentiated fat cells, upregulation of Sirt1 triggers lipolysis and loss of fat. As a reduction in fat is sufficient to extend murine lifespan, our results provide a possible molecular pathway connecting calorie restriction to life extension in mammals.

1,917 citations


Journal ArticleDOI
TL;DR: Here, three modes of adaptation are identified that plants and animals use to survive floods and/or droughts and the rate of evolution in response to flow regime alteration remains an open question.
Abstract: Floods and droughts are important features of most running water ecosystems, but the alteration of natural flow regimes by recent human activities, such as dam building, raises questions related to both evolution and conservation Among organisms inhabiting running waters, what adaptations exist for surviving floods and droughts? How will the alteration of the frequency, timing and duration of flow extremes affect flood- and drought-adapted organisms? How rapidly can populations evolve in response to altered flow regimes? Here, we identify three modes of adaptation (life history, behavioral and morphological) that plants and animals use to survive floods and/or droughts The mode of adaptation that an organism has determines its vulnerability to different kinds of flow regime alteration The rate of evolution in response to flow regime alteration remains an open question Because humans have now altered the flow regimes of most rivers and many streams, understanding the link between fitness and flow regime is crucial for the effective management and restoration of running water ecosystems

1,593 citations


Journal ArticleDOI
TL;DR: It is concluded that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.
Abstract: Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.

1,571 citations


Journal ArticleDOI
TL;DR: The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding that offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.
Abstract: Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C-X...O-Y interaction (C-X is a carbon-bonded chlorine, bromine, or iodine, and O-Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X...O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl...O, 3.37 A for Br...O, and 3.50 A for I...O) and can conform to the geometry seen in small molecules, with the C-X...O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X...O-Y angle approximately 120 degrees . Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.

1,421 citations


Journal ArticleDOI
TL;DR: The variability of marine diatom Si:C and Si:N composition ratios was examined to assess their utility as ecological conversion factors and were not statistically different from those calculated for the same species grown under an 18:6 h LD photoperiod.
Abstract: The variability of marine diatom Si:C and Si:N composition ratios was examined to assess their utility as ecological conversion factors. Twenty-seven diatom species grown under an 18:6 h LD cycle and sampled at the end of the light period gave mean ratios, by atoms, of 0.13 ± 0.04 and 1.12 ± 0.33 for Si:C and Si:N ratios, respectively (95% C.I. reported). The mean ratios for 18 species grown under continuous illumination were 0.12 ± 0.03 for Si:C and 0.95 ± 0.23 for Si:N. The mean ratios of the clones grown under constant light were not statistically different from those calculated for the same species grown under an 18:6 h LD photoperiod. The overall mean Si:C and Si:N ratios for the 18:6 h LD and continuous light experiments taken together, weighted by the number of species in each experiment, are 0.13 and 1.05, respectively. The average ratios for the nine nanoplankton species ( 20 μm) had higher mean ratios, Si:C = 0.15 ± 0.04 and Si:N = 1.20 ± 0.37. Time course sampling throughout a 24 h period revealed twofold variations in both ratios for individual species grown on a 14:10 h LD cycle. Changes in irradiance can also produce factor of two variations, both ratios being higher under low light. Comparisons of these data with those from the literature regarding the effects of temperature and nutrient limitation on diatom elemental composition suggest that use of these ratios to convert field estimates of biogenic silica into nitrogen or carbon units, or to estimate silica production from 14C data, should yield results accurate to within a factor of three under most circumstances.

1,247 citations


Journal ArticleDOI
22 Jul 2004-Nature
TL;DR: Using microarray analysis, it is shown that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1).
Abstract: Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.

1,199 citations


Journal ArticleDOI
TL;DR: In this paper, a unified strategy for selecting spatially balanced probability samples of natural resources is presented, which is based on creating a function that maps two-dimensional space into onedimensional space, thereby defining an ordered spatial address.
Abstract: The spatial distribution of a natural resource is an important consideration in designing an efficient survey or monitoring program for the resource. Generally, sample sites that are spatially balanced, that is, more or less evenly dispersed over the extent of the resource, are more efficient than simple random sampling. We review a unified strategy for selecting spatially balanced probability samples of natural resources. The technique is based on creating a function that maps two-dimensional space into one-dimensional space, thereby defining an ordered spatial address. We use a restricted randomization to randomly order the addresses, so that systematic sampling along the randomly ordered linear structure results in a spatially well-balanced random sample. Variable inclusion probability, proportional to an arbitrary positive ancillary variable, is easily accommodated. The basic technique selects points in a two-dimensional continuum, but is also applicable to sampling finite populations or one-dimension...

1,082 citations


Journal ArticleDOI
TL;DR: In this article, a series of case studies are used to develop a more complete understanding of the factors that enable and inhibit efforts at building integration across operations, purchasing and logistics, and the end result of the research is a testable model of how integration can be built across these three key internal supply chain functions.

815 citations


Journal ArticleDOI
13 Feb 2004-Science
TL;DR: Four-year averages of 25-kilometer-resolution measurements of near-surface wind speed and direction over the global ocean from the QuikSCAT satellite radar scatterometer reveal the existence of surprisingly persistent small-scale features in the dynamically and thermodynamically important curl and divergence of the wind stress.
Abstract: Four-year averages of 25-kilometer-resolution measurements of near-surface wind speed and direction over the global ocean from the QuikSCAT satellite radar scatterometer reveal the existence of surprisingly persistent small-scale features in the dynamically and thermodynamically important curl and divergence of the wind stress. Air-sea interaction over sea surface temperature fronts throughout the world ocean is evident in both the curl and divergence fields, as are the influences of islands and coastal mountains. Ocean currents such as the Gulf Stream generate distinctive patterns in the curl field. These previously unresolved features have important implications for oceanographic and air-sea interaction research.

800 citations


Journal ArticleDOI
TL;DR: This study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi and the impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed.
Abstract: Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

Journal ArticleDOI
TL;DR: Divalent calcium ions greatly enhance natural organic matter fouling by complexation and subsequent formation of intermolecular bridges among organic foulant molecules and a remarkable correlation was obtained between the measured adhesion forces and the fouling and cleaning behavior of the membrane under various solution chemistries.
Abstract: Fouling and subsequent chemical cleaning of nanofiltration (NF) membranes used in water quality control applications are often inevitable. To unravel the mechanisms of organic fouling and chemical cleaning, it is critical to understand the foulant-membrane, foulant-foulant, and foulant-cleaning agent interactions at the molecular level. In this study, the adhesion forces between the foulant and the membrane surface and between the bulk foulant and the fouling layer were determined by atomic force microscopy (AFM). A carboxylate modified AFM colloid probe was used as a surrogate for humic acid, the major organic foulant in natural waters. The interfacial force data were combined with the NF membrane water flux measurements to elucidate the mechanisms of organic fouling and chemical cleaning. A remarkable correlation was obtained between the measured adhesion forces and the fouling and cleaning behavior of the membrane under various solution chemistries. The AFM measurements further confirmed that divalent calcium ions greatly enhance natural organic matter fouling by complexation and subsequent formation of intermolecular bridges among organic foulant molecules. Efficient chemical cleaning was achieved only when the calcium ion bridging was eliminated as a result of the interaction between the chemical cleaning agent and the fouling layer. The cleaning efficiency was highly dependent on solution pH and the concentration of the chemical cleaning agent.

Journal ArticleDOI
01 May 2004-Ecology
TL;DR: It is suggested that progeny from older females can survive under a broader range of environmental conditions compared to progenyFrom younger females, and age truncation commonly induced by fisheries may, therefore, have severe consequences for long-term sustainability of fish populations.
Abstract: Relative body size has long been recognized as a factor influencing repro- ductive success in fishes, but maternal age has only recently been considered. We monitored growth and starvation resistance in larvae from 20 female black rockfish (Sebastes melan- ops), ranging in age from five to 17 years. Larvae from the oldest females in our experiments had growth rates more than three times as fast and survived starvation more than twice as long as larvae from the youngest females. Female age was a far better predictor of larval performance than female size. The apparent underlying mechanism is a greater provisioning of larvae with energy-rich triacylglycerol (TAG) lipids as female age increases. The volume of the oil globule (composed primarily of TAG) present in larvae at parturition increases with maternal age and is correlated with subsequent growth and survival. These results suggest that progeny from older females can survive under a broader range of environmental conditions compared to progeny from younger females. Age truncation commonly induced by fisheries may, therefore, have severe consequences for long-term sustainability of fish populations.

Journal ArticleDOI
TL;DR: The age-related loss in GSH synthesis may be caused by dysregulation of ARE-mediated gene expression, but chemoprotective agents, like LA, can attenuate this loss.
Abstract: Glutathione (GSH) significantly declines in the aging rat liver. Because GSH levels are partly a reflection of its synthetic capacity, we measured the levels and activity of γ-glutamylcysteine ligase (GCL), the rate-controlling enzyme in GSH synthesis. With age, both the catalytic (GCLC) and modulatory (GCLM) subunits of GCL decreased by 47% and 52%, respectively (P < 0.005). Concomitant with lower subunit levels, GCL activity also declined by 53% (P < 0.05). Because nuclear factor erythroid2-related factor 2 (Nrf2) governs basal and inducible GCLC and GCLM expression by means of the antioxidant response element (ARE), we hypothesized that aging results in dysregulation of Nrf2-mediated GCL expression. We observed an ≈50% age-related loss in total (P < 0.001) and nuclear (P < 0.0001) Nrf2 levels, which suggests attenuation in Nrf2-dependent gene transcription. By using gel-shift and supershift assays, a marked reduction in Nrf2/ARE binding in old vs. young rats was noted. To determine whether the constitutive loss of Nrf2 transcriptional activity also affects the inducible nature of Nrf2 nuclear translocation, old rats were treated with (R)-α-lipoic acid (LA; 40 mg/kg i.p. up to 48 h), a disulfide compound shown to induce Nrf2 activation in vitro and improve GSH levels in vivo. LA administration increased nuclear Nrf2 levels in old rats after 12 h. LA also induced Nrf2 binding to the ARE, and, consequently, higher GCLC levels and GCL activity were observed 24 h after LA injection. Thus, the age-related loss in GSH synthesis may be caused by dysregulation of ARE-mediated gene expression, but chemoprotective agents, like LA, can attenuate this loss.

Journal ArticleDOI
TL;DR: Recent research suggesting that an old-growth age structure, combined with a broad spatial distribution of spawning and recruitment, is at least as important as spawning biomass in maintaining long-term sustainable population levels is summarized.
Abstract: Numerous groundfish stocks in both the Atlantic and Pacific are considered overfished, resulting in large-scale fishery closures. Fishing, in addition to simply removing biomass, also truncates the age and size structure of fish populations and often results in localized depletions. We summarize recent research suggesting that an old-growth age structure, combined with a broad spatial distribution of spawning and recruitment, is at least as important as spawning biomass in maintaining long-term sustainable population levels. In particular, there is evidence that older, larger female rockfishes produce larvae that withstand starvation longer and grow faster than the offspring of younger fish, that stocks may actually consist of several reproductively isolated units, and that recruitment may come from only a small and different fraction of the spawning population each year. None of these phenomena is accounted for in current management programs. We examine alternative management measures that addre...

Journal ArticleDOI
16 Apr 2004-Science
TL;DR: Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean, demonstrating iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.
Abstract: The availability of iron is known to exert a controlling influence on biological productivity in surface waters over large areas of the ocean and may have been an important factor in the variation of the concentration of atmospheric carbon dioxide over glacial cycles. The effect of iron in the Southern Ocean is particularly important because of its large area and abundant nitrate, yet iron-enhanced growth of phytoplankton may be differentially expressed between waters with high silicic acid in the south and low silicic acid in the north, where diatom growth may be limited by both silicic acid and iron. Two mesoscale experiments, designed to investigate the effects of iron enrichment in regions with high and low concentrations of silicic acid, were performed in the Southern Ocean. These experiments demonstrate iron's pivotal role in controlling carbon uptake and regulating atmospheric partial pressure of carbon dioxide.

Journal ArticleDOI
TL;DR: Evidence is provided that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences, and a model for miRNA evolution is proposed that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.
Abstract: MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA‐generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.

Journal ArticleDOI
TL;DR: Biological activities suggest that prenylflavonoids from hops have potential for application in cancer prevention programs and in prevention or treatment of (post-)menopausal 'hot flashes' and osteoporosis.

Journal ArticleDOI
TL;DR: Three unrelated suppressors from multiple viruses were shown to inhibit microRNA (miRNA) activities and trigger an overlapping series of severe developmental defects in transgenic Arabidopsis thaliana, suggesting that interference with miRNA-directed processes may be a general feature contributing to pathogenicity of many viruses.
Abstract: RNA silencing suppressors from different plant viruses are structurally diverse. In addition to inhibiting the antiviral silencing response to condition susceptibility, many suppressors are pathogenicity factors that cause disease or developmental abnormalities. Here, unrelated suppressors from multiple viruses were shown to inhibit microRNA (miRNA) activities and trigger an overlapping series of severe developmental defects in transgenic Arabidopsis thaliana. This suggests that interference with miRNA-directed processes may be a general feature contributing to pathogenicity of many viruses. A normally labile intermediate in the miRNA biogenesis/RNA-induced silencing complex (RISC) assembly pathway, miRNA*, accumulated specifically in the presence of suppressors (P1/HC-Pro, p21, or p19) that inhibited miRNA-guided cleavage of target mRNAs. Both p21 and p19, but not P1/HC-Pro, interacted with miRNA/miRNA* complexes and hairpin RNA-derived short interfering RNAs (siRNAs) in vivo. In addition, p21 bound to synthetic miRNA/miRNA* and siRNA duplexes in vitro. We propose that several different suppressors act by distinct mechanisms to inhibit the incorporation of small RNAs into active RISCs.

Journal ArticleDOI
TL;DR: Even though SeMCYS was shown to be the most effective seleno-compound in the reduction of mammary tumours, it may not be the best choice for reduction of colon tumours because several mechanisms have been proposed on the mechanism whereby Se reduces tumours.
Abstract: Selenomethionine (Semet) is the major seleno-compound in cereal grains and enriched yeast whereas Se-methylselenocysteine (SeMCYS) is the major seleno-compound in Se-accumulator plants and some plants of economic importance such as garlic and broccoli exposed to excess Se. Animals can metabolize both Semet and SeMCYS. Epidemiological studies have indicated an inverse relationship between Se intake and the incidence of certain cancers. Blood or plasma levels of Se are usually lower in patients with cancer than those without this disorder, but inconsistent results have been found with toenail-Se values and the incidence of cancer. There have been eight trials with human subjects conducted on the influence of Se on cancer incidence or biomarkers, and except for one, all have shown a positive benefit of Se on cancer reduction or biomarkers of this disorder. This is consistent with about 100 small-animal studies where Se has been shown to reduce the incidence of tumours in most of these trials. Se-enriched yeast is the major form of Se used in trials with human subjects. In the mammary-tumour model, SeMCYS has been shown to be the most effective seleno-compound identified so far in reduction of tumours. Several mechanisms have been proposed on the mechanism whereby Se reduces tumours. Even though SeMCYS was shown to be the most effective seleno-compound in the reduction of mammary tumours, it may not be the most effective seleno-compound for reduction of colon tumours.

Journal ArticleDOI
27 Feb 2004-Science
TL;DR: Maintenance DNA methyltransferases propagate pre-existing DNA methylation in the CG sequence context by methylating hemi-methylated sites after DNA replication.
Abstract: Cytosine DNA methylation silences harmful DNAs such as transposons and retroviruses ([ 1 ][1]). Maintenance DNA methyltransferases propagate pre-existing DNA methylation in the CG sequence context by methylating hemi-methylated sites after DNA replication. Much less is understood about how invasive

Journal ArticleDOI
TL;DR: The results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression and facilitate statistical and graphical evaluation of gene expression stability.
Abstract: Background Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed.

Journal ArticleDOI
TL;DR: In this paper, the rare earth elements (REEs) were measured in pore waters of the upper ∼25 cm of sediment from one site off Peru and three sites on the California margin.

Journal ArticleDOI
TL;DR: A particularly reactive and versatile reversibly oxidized form of cysteine, the sulfenic acid (Cys-SOH), has important roles as a catalytic center in enzymes and as a sensor of oxidative and nitrosative stress in enzyme and transcriptional regulators.
Abstract: Reactive (low pKa) cysteine residues in proteins are critical components in redox signaling. A particularly reactive and versatile reversibly oxidized form of cysteine, the sulfenic acid (Cys-SOH), has important roles as a catalytic center in enzymes and as a sensor of oxidative and nitrosative stress in enzymes and transcriptional regulators. Depending on environment, sometimes the sulfenic acid provides a metastable oxidized form, and other times it is a fleeting intermediate giving rise to more stable disulfide, sulfinic acid, or sulfenyl-amide forms.

Journal ArticleDOI
TL;DR: This work suggests an alternative approach which allows us to explicitly model a joint environmental technology and gauge performance in terms of increased good output and decreased undesirable output by adopting a directional distance function which may be estimated using the usual linear programming techniques employed in DEA.

Journal ArticleDOI
17 Jun 2004-Nature
TL;DR: The unprecedented development of severe inner-shelf (<70 m) hypoxia and resultant mass die-offs of fish and invertebrates within the California Current System is reported, highlighting the sensitivity of inner- shelf ecosystems to variation in ocean conditions, and the potential impacts of climate change on marine communities.
Abstract: Seasonal development of dissolved-oxygen deficits (hypoxia) represents an acute system-level perturbation to ecological dynamics and fishery sustainability in coastal ecosystems around the globe1,2,3. Whereas anthropogenic nutrient loading has increased the frequency and severity of hypoxia in estuaries and semi-enclosed seas3,4, the occurrence of hypoxia in open-coast upwelling systems reflects ocean conditions that control the delivery of oxygen-poor and nutrient-rich deep water onto continental shelves1. Upwelling systems support a large proportion of the world's fisheries5, therefore understanding the links between changes in ocean climate, upwelling-driven hypoxia and ecological perturbations is critical. Here we report on the unprecedented development of severe inner-shelf (<70 m) hypoxia and resultant mass die-offs of fish and invertebrates within the California Current System. In 2002, cross-shelf transects revealed the development of abnormally low dissolved-oxygen levels as a response to anomalously strong flow of subarctic water into the California Current System. Our findings highlight the sensitivity of inner-shelf ecosystems to variation in ocean conditions, and the potential impacts of climate change on marine communities.

Journal ArticleDOI
TL;DR: Findings suggest that SFN may be effective as a tumor-suppressing agent and as a chemotherapeutic agent, alone or in combination with other HDAC inhibitors currently undergoing clinical trials.
Abstract: Sulforaphane (SFN), a compound found at high levels in broccoli and broccoli sprouts, is a potent inducer of phase 2 detoxification enzymes and inhibits tumorigenesis in animal models. SFN also has a marked effect on cell cycle checkpoint controls and cell survival and/or apoptosis in various cancer cells, through mechanisms that are poorly understood. We tested the hypothesis that SFN acts as an inhibitor of histone deacetylase (HDAC). In human embryonic kidney 293 cells, SFN dose-dependently increased the activity of a beta-catenin-responsive reporter (TOPflash), without altering beta-catenin or HDAC protein levels. Cytoplasmic and nuclear extracts from these cells had diminished HDAC activity, and both global and localized histone acetylation was increased, compared with untreated controls. Studies with SFN and with media from SFN-treated cells indicated that the parent compound was not responsible for the inhibition of HDAC, and this was confirmed using an inhibitor of glutathione S-transferase, which blocked the first step in the metabolism of SFN, via the mercapturic acid pathway. Whereas SFN and its glutathione conjugate (SFN-GSH) had little or no effect, the two major metabolites SFN-cysteine and SFN-N-acetylcysteine were effective HDAC inhibitors in vitro. Finally, several of these findings were recapitulated in HCT116 human colorectal cancer cells: SFN dose-dependently increased TOPflash reporter activity and inhibited HDAC activity, there was an increase in acetylated histones and in p21(Cip1/Waf1), and chromatin immunoprecipitation assays revealed an increase in acetylated histones bound to the P21 promoter. Collectively, these findings suggest that SFN may be effective as a tumor-suppressing agent and as a chemotherapeutic agent, alone or in combination with other HDAC inhibitors currently undergoing clinical trials.

Journal ArticleDOI
TL;DR: An inversion algorithm is provided (with proof) when the mean values are known for all spheres centered on the boundary of D, with radii in the interval [0, diam(D)/2].
Abstract: Suppose D is a bounded, connected, open set in Rn and f is a smooth function on Rn with support in $\overD$. We study the recovery of f from the mean values of f over spheres centered on a part or the whole boundary of D. For strictly convex $\overline{D}$, we prove uniqueness when the centers are restricted to an open subset of the boundary. We provide an inversion algorithm (with proof) when the mean values are known for all spheres centered on the boundary of D, with radii in the interval [0, diam(D)/2]. We also give an inversion formula when D is a ball in Rn, $n \geq 3$ and odd, and the mean values are known for all spheres centered on the boundary.

Journal ArticleDOI
14 Feb 2004-Zootaxa
TL;DR: This updated catalog of Moraes et al. (1986) includes references to descriptions and redescriptions of species, synonymies and recorded world distributions of mite pests.
Abstract: Mites of the family Phytoseiidae are the most common predators of phytophagous mites on most plant species. Some species are widely studied and used for the biological control of mite pests. Many new species continue to be discovered as collections are intensified in certain regions or habitats, e.g. in Africa, Asia, Central and South America. The last catalog of Moraes et al. (1986) included about 1500 described species. This updated catalog includes almost 2250 species. As in the last catalog, it includes references to descriptions and redescriptions of species, synonymies and recorded world distributions.

Journal ArticleDOI
TL;DR: Future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.
Abstract: The microbial communities associated with electrodes from underwater fuel cells harvesting electricity from five different aquatic sediments were investigated. Three fuel cells were constructed with marine, salt-marsh, or freshwater sediments incubated in the laboratory. Fuel cells were also deployed in the field in salt marsh sediments in New Jersey and estuarine sediments in Oregon, USA. All of the sediments produced comparable amounts of power. Analysis of 16S rRNA gene sequences after 3-7 months of incubation demonstrated that all of the energy-harvesting anodes were highly enriched in microorganisms in the delta-Proteobacteria when compared with control electrodes not connected to a cathode. Geobacteraceae accounted for the majority of delta-Proteobacterial sequences or all of the energy-harvesting anodes, except the one deployed at the Oregon estuarine site. Quantitative PCR analysis of 16S rRNA genes and culturing studies indicated that Geobacteraceae were 100-fold more abundant on the marine-deployed anodes versus controls. Sequences most similar to microorganisms in the family Desulfobulbaceae predominated on the anode deployed in the estuarine sediments, and a significant proportion of the sequences recovered from the freshwater anodes were closely related to the Fe(III)-reducing isolate, Geothrix fermentans. There was also a specific enrichment of microorganisms on energy harvesting cathodes, but the enriched populations varied with the sediment/water source. Thus, future studies designed to help optimize the harvesting of electricity from aquatic sediments or waste organic matter should focus on the electrode interactions of these microorganisms which are most competitive in colonizing anodes and cathodes.