Showing papers by "Oregon State University published in 2012"

DNA methylation arrays as surrogate measures of cell mixture distribution

Abstract: Background: There has been a long-standing need in biomedical research for a method that quantifies the normally mixed composition of leukocytes beyond what is possible by simple histological or flow cytometric assessments. The latter is restricted by the labile nature of protein epitopes, requirements for cell processing, and timely cell analysis. In a diverse array of diseases and following numerous immune-toxic exposures, leukocyte composition will critically inform the underlying immuno-biology to most chronic medical conditions. Emerging research demonstrates that DNA methylation is responsible for cellular differentiation, and when measured in whole peripheral blood, serves to distinguish cancer cases from controls. Results: Here we present a method, similar to regression calibration, for inferring changes in the distribution of white blood cells between different subpopulations (e.g. cases and controls) using DNA methylation signatures, in combination with a previously obtained external validation set consisting of signatures from purified leukocyte samples. We validate the fundamental idea in a cell mixture reconstruction experiment, then demonstrate our method on DNA methylation data sets from several studies, including data from a Head and Neck Squamous Cell Carcinoma (HNSCC) study and an ovarian cancer study. Our method produces results consistent with prior biological findings, thereby validating the approach. Conclusions: Our method, in combination with an appropriate external validation set, promises new opportunities for large-scale immunological studies of both disease states and noxious exposures.

Linking crystallographic model and data quality.

Abstract: In macromolecular x-ray crystallography, refinement R values measure the agreement between observed and calculated data. Analogously, R(merge) values reporting on the agreement between multiple measurements of a given reflection are used to assess data quality. Here, we show that despite their widespread use, R(merge) values are poorly suited for determining the high-resolution limit and that current standard protocols discard much useful data. We introduce a statistic that estimates the correlation of an observed data set with the underlying (not measurable) true signal; this quantity, CC*, provides a single statistically valid guide for deciding which data are useful. CC* also can be used to assess model and data quality on the same scale, and this reveals when data quality is limiting model improvement.

The paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes

Abstract: Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.

Global warming preceded by increasing carbon dioxide concentrations during the last deglaciation

Abstract: The covariation of carbon dioxide (CO2) concentration and temperature in Antarctic ice-core records suggests a close link between CO2 and climate during the Pleistocene ice ages. The role and relative importance of CO2 in producing these climate changes remains unclear, however, in part because the ice-core deuterium record reflects local rather than global temperature. Here we construct a record of global surface temperature from 80 proxy records and show that temperature is correlated with and generally lags CO2 during the last (that is, the most recent) deglaciation. Differences between the respective temperature changes of the Northern Hemisphere and Southern Hemisphere parallel variations in the strength of the Atlantic meridional overturning circulation recorded in marine sediments. These observations, together with transient global climate model simulations, support the conclusion that an antiphased hemispheric temperature response to ocean circulation changes superimposed on globally in-phase warming driven by increasing CO2 concentrations is an explanation for much of the temperature change at the end of the most recent ice age. Understanding the causes of the Pleistocene ice ages has been a significant question in climate dynamics since they were discovered in the mid-nineteenth century. The identification of orbital frequencies

Estimating Global “Blue Carbon” Emissions from Conversion and Degradation of Vegetated Coastal Ecosystems

Abstract: Recent attention has focused on the high rates of annual carbon sequestration in vegetated coastal ecosystems—marshes, mangroves, and seagrasses—that may be lost with habitat destruction (‘conversion’). Relatively unappreciated, however, is that conversion of these coastal ecosystems also impacts very large pools of previously-sequestered carbon. Residing mostly in sediments, this ‘blue carbon’ can be released to the atmosphere when these ecosystems are converted or degraded. Here we provide the first global estimates of this impact and evaluate its economic implications. Combining the best available data on global area, land-use conversion rates, and near-surface carbon stocks in each of the three ecosystems, using an uncertainty-propagation approach, we estimate that 0.15–1.02 Pg (billion tons) of carbon dioxide are being released annually, several times higher than previous estimates that account only for lost sequestration. These emissions are equivalent to 3–19% of those from deforestation globally, and result in economic damages of $US 6–42 billion annually. The largest sources of uncertainty in these estimates stems from limited certitude in global area and rates of landuse conversion, but research is also needed on the fates of ecosystem carbon upon conversion. Currently, carbon emissions from the conversion of vegetated coastal ecosystems are not included in emissions accounting or carbon market protocols, but this analysis suggests they may be disproportionally important to both. Although the relevant science supporting these initial estimates will need to be refined in coming years, it is clear that policies encouraging the sustainable management of coastal ecosystems could significantly reduce carbon emissions from the land-use sector, in addition to sustaining the wellrecognized ecosystem services of coastal habitats.

Averting biodiversity collapse in tropical forest protected areas

Abstract: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

An index to assess the health and benefits of the global ocean

Abstract: The ocean plays a critical role in supporting human well-being, from providing food, livelihoods and recreational opportunities to regulating the global climate. Sustainable management aimed at maintaining the flow of a broad range of benefits from the ocean requires a comprehensive and quantitative method to measure and monitor the health of coupled human–ocean systems. We created an index comprising ten diverse public goals for a healthy coupled human–ocean system and calculated the index for every coastal country. Globally, the overall index score was 60 out of 100 (range 36–86), with developed countries generally performing better than developing countries, but with notable exceptions. Only 5% of countries scored higher than 70, whereas 32% scored lower than 50. The index provides a powerful tool to raise public awareness, direct resource management, improve policy and prioritize scientific research.

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

Abstract: SUMMARY The symbiosis between cnidarians (e.g., corals or sea anemones) and intracellular dinoflagellate algae of the genus Symbiodinium is of immense ecological importance. In particular, this symbiosis promotes the growth and survival of reef corals in nutrient-poor tropical waters; indeed, coral reefs could not exist without this symbiosis. However, our fundamental understanding of the cnidarian-dinoflagellate symbiosis and of its links to coral calcification remains poor. Here we review what we currently know about the cell biology of cnidarian-dinoflagellate symbiosis. In doing so, we aim to refocus attention on fundamental cellular aspects that have been somewhat neglected since the early to mid-1980s, when a more ecological approach began to dominate. We review the four major processes that we believe underlie the various phases of establishment and persistence in the cnidarian/coral-dinoflagellate symbiosis: (i) recognition and phagocytosis, (ii) regulation of host-symbiont biomass, (iii) metabolic exchange and nutrient trafficking, and (iv) calcification. Where appropriate, we draw upon examples from a range of cnidarian-alga symbioses, including the symbiosis between green Hydra and its intracellular chlorophyte symbiont, which has considerable potential to inform our understanding of the cnidarian-dinoflagellate symbiosis. Ultimately, we provide a comprehensive overview of the history of the field, its current status, and where it should be going in the future.

Tai Chi and Postural Stability in Patients with Parkinson's Disease

Abstract: A B S T R AC T RESULTS The tai chi group performed consistently better than the resistance-training and stretching groups in maximum excursion (between-group difference in the change from baseline, 5.55 percentage points; 95% confidence interval (CI), 1.12 to 9.97; and 11.98 percentage points; 95% CI, 7.21 to 16.74, respectively) and in directional con- trol (10.45 percentage points; 95% CI, 3.89 to 17.00; and 11.38 percentage points; 95% CI, 5.50 to 17.27, respectively). The tai chi group also performed better than the stretching group in all secondary outcomes and outperformed the resistance- training group in stride length and functional reach. Tai chi lowered the incidence of falls as compared with stretching but not as compared with resistance training. The effects of tai chi training were maintained at 3 months after the intervention. No serious adverse events were observed. CONCLUSIONS Tai chi training appears to reduce balance impairments in patients with mild-to- moderate Parkinson's disease, with additional benefits of improved functional capac - ity and reduced falls. (Funded by the National Institute of Neurological Disorders and Stroke; ClinicalTrials.gov number, NCT00611481.)

Computational recipes for electromagnetic inverse problems

Abstract: SUMMARY The Jacobian of the non-linear mapping from model parameters to observations is a key component in all gradient-based inversion methods, including variants on Gauss–Newton and non-linear conjugate gradients. Here, we develop a general mathematical framework for Jacobian computations arising in electromagnetic (EM) geophysical inverse problems. Our analysis, which is based on the discrete formulation of the forward problem, divides computations into components (data functionals, forward and adjoint solvers, model parameter mappings), and clarifies dependencies among these elements within realistic numerical inversion codes. To be concrete, we focus much of the specific discussion on 2-D and 3-D magnetotelluric (MT) inverse problems, but our analysis is applicable to a wide range of active and passive source EM methods. The general theory developed here provides the basis for development of a modular system of computer codes for inversion of EM geophysical data, which we summarize at the end of the paper.

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

Abstract: We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades, which was reinforced by high levels of synteny, size of core genomes, and relatedness of orthologous genes between strains within a sub-clade. The heterogeneity of the P. fluorescens group was reflected in the large size of its pan-genome, which makes up approximately 54% of the pan-genome of the genus as a whole, and a core genome representing only 45–52% of the genome of any individual strain. We discovered genes for traits that were not known previously in the strains, including genes for the biosynthesis of the siderophores achromobactin and pseudomonine and the antibiotic 2-hexyl-5-propyl-alkylresorcinol; novel bacteriocins; type II, III, and VI secretion systems; and insect toxins. Certain gene clusters, such as those for two type III secretion systems, are present only in specific sub-clades, suggesting vertical inheritance. Almost all of the genes associated with multitrophic interactions map to genomic regions present in only a subset of the strains or unique to a specific strain. To explore the evolutionary origin of these genes, we mapped their distributions relative to the locations of mobile genetic elements and repetitive extragenic palindromic (REP) elements in each genome. The mobile genetic elements and many strain-specific genes fall into regions devoid of REP elements (i.e., REP deserts) and regions displaying atypical tri-nucleotide composition, possibly indicating relatively recent acquisition of these loci. Collectively, the results of this study highlight the enormous heterogeneity of the P. fluorescens group and the importance of the variable genome in tailoring individual strains to their specific lifestyles and functional repertoire.

2b-RAD: a simple and flexible method for genome-wide genotyping

Abstract: Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing. We describe 2b-RAD, a streamlined restriction site–associated DNA (RAD) genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Well-studied accessions of Arabidopsis thaliana were genotyped to validate the method's accuracy and to demonstrate fine-tuning of marker density as needed. The simplicity of the 2b-RAD protocol makes it particularly suitable for high-throughput genotyping as required for linkage mapping and profiling genetic variation in natural populations.

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Abstract: The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

Abstract:  Premise of the study: Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters Here we describe a genome skimming (shallow sequencing) approach for plant systematics  Methods: Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae)  Key results: Paired-end reads performed better than single-end reads Minimum sequencing depths for high quality rDNA and plastome assemblies were 40 × and 30 × , respectively Divergence from the reference signifi cantly affected plastome assembly, but relatively similar references are available for most seed plants Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths Nearly 160 000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC  Conclusions: Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be effi ciently obtained for molecular phylogenetics studies

A realignment of marine biogeographic provinces with particular reference to fish distributions

Abstract: Marine provinces, founded on contrasting floras or faunas, have been recognized for more than 150 years but were not consistently defined by endemism until 1974. At that time, provinces were based on at least a 10% endemism and nested within biogeographic regions that covered large geographic areas with contrasting biotic characteristics. Over time, some minor adjustments were made but the overall arrangement remained essentially unaltered. In many provinces, data on endemism were still not available, or were available only for the most widely studied vertebrates (fishes), a problem that is ongoing. In this report we propose a realignment for three reasons. First, recent works have provided new information to modify or redefine the various divisions and to describe new ones, including the Mid-Atlantic Ridge, Southern Ocean, Tropical East Pacific and Northeast Pacific. Second, phylogeographic studies have demonstrated genetic subdivisions within and between species that generally corroborated provinces based on taxonomic partitions, with a notable exception at the Indian–Pacific oceanic boundary. Third, the original separation of the warm-temperate provinces from the adjoining tropical ones has distracted from their close phylogenetic relationships. Here we propose uniting warm-temperate and tropical regions into a single warm region within each ocean basin, while still recognizing provinces within the warm-temperate and tropical zones. These biogeographic subdivisions are based primarily on fish distribution but utilize other marine groups for comparison. They are intended to demonstrate the evolutionary relationships of the living marine biota, and to serve as a framework for the establishment of smaller ecological units in a conservation context.

Live plant imports: the major pathway for forest insect and pathogen invasions of the US

Abstract: Trade in live plants has been recognized worldwide as an important invasion pathway for non-native plant pests. Such pests can have severe economic and ecological consequences. Nearly 70% of damaging forest insects and pathogens established in the US between 1860 and 2006 most likely entered on imported live plants. The current regulation of plant imports is outdated and needs to balance the impacts of pest damage, the expense of mitigation efforts, and the benefits of live plant importation. To inform these discussions, we document large increases in the volume and value of plant imports over the past five decades and explain recent and proposed changes to plant import regulations. Two data sources were used to estimate the infestation rate of regulated pests in live plant shipments entering the US, thus allowing evaluation of the efficacy of the current port inspection process.

The Pacific oyster, Crassostrea gigas, shows negative correlation to naturally elevated carbon dioxide levels: Implications for near-term ocean acidification effects

Abstract: We report results from an oyster hatchery on the Oregon coast, where intake waters experienced variable carbonate chemistry (aragonite saturation state , 0.8 to . 3.2; pH , 7.6 to . 8.2) in the early summer of 2009. Both larval production and midstage growth (, 120 to , 150 mm) of the oyster Crassostrea gigas were significantly negatively correlated with the aragonite saturation state of waters in which larval oysters were spawned and reared for the first 48 h of life. The effects of the initial spawning conditions did not have a significant effect on early-stage growth (growth from D-hinge stage to , 120 mm), suggesting a delayed effect of water chemistry on larval development.

Self‐regulation in early childhood: Improving conceptual clarity and developing ecologically valid measures.

Abstract: — Children’s ability to direct their attention and behavior to learning tasks provides a foundation for healthy social and academic development in early schooling. Although an explosion of research on this topic has occurred in recent years, the field has been hindered by a lack of conceptual clarity, as well as debate over underlying components and their significance in predicting school success. In addition, few measures tap these skills as children move into formal schooling. This article describes the aspects of self-regulation that are most important for early school success. It then discusses methodological challenges in reliably and validly assessing these skills in young children and describes recent advances in direct measures of self-regulation that are reliable and ecologically valid and that predict children’s school success. It concludes by summarizing critical issues in the study of self-regulation in school contexts and discussing next steps.

Global climate evolution during the last deglaciation

Abstract: Deciphering the evolution of global climate from the end of the Last Glacial Maximum approximately 19 ka to the early Holocene 11 ka presents an outstanding opportunity for understanding the transient response of Earth’s climate system to external and internal forcings. During this interval of global warming, the decay of ice sheets caused global mean sea level to rise by approximately 80 m; terrestrial and marine ecosystems experienced large disturbances and range shifts; perturbations to the carbon cycle resulted in a net release of the greenhouse gases CO2 and CH4 to the atmosphere; and changes in atmosphere and ocean circulation affected the global distribution and fluxes of water and heat. Here we summarize a major effort by the paleoclimate research community to characterize these changes through the development of well-dated, high-resolution records of the deep and intermediate ocean as well as surface climate. Our synthesis indicates that the superposition of two modes explains much of the variability in regional and global climate during the last deglaciation, with a strong association between the first mode and variations in greenhouse gases, and between the second mode and variations in the Atlantic meridional overturning circulation.

Evapotranspiration: A process driving mass transport and energy exchange in the soil‐plant‐atmosphere‐climate system

Abstract: [1] The role of evapotranspiration (ET) in the global, continental, regional, and local water cycles is reviewed. Elevated atmospheric CO2, air temperature, vapor pressure deficit (D), turbulent transport, radiative transfer, and reduced soil moisture all impact biotic and abiotic processes controlling ET that must be extrapolated to large scales. Suggesting a blueprint to achieve this link is the main compass of this review. Leaf-scale transpiration (fe) as governed by the plant biochemical demand for CO2 is first considered. When this biochemical demand is combined with mass transfer formulations, the problem remains mathematically intractable, requiring additional assumptions. A mathematical “closure” that assumes stomatal aperture is autonomously regulated so as to maximize the leaf carbon gain while minimizing water loss is proposed, which leads to analytical expressions for leaf-scale transpiration. This formulation predicts well the effects of elevated atmospheric CO2 and increases in D on fe. The case of soil moisture stress is then considered using extensive gas exchange measurements collected in drought studies. Upscaling the fe to the canopy is then discussed at multiple time scales. The impact of limited soil water availability within the rooting zone on the upscaled ET as well as some plant strategies to cope with prolonged soil moisture stress are briefly presented. Moving further up in direction and scale, the soil-plant system is then embedded within the atmospheric boundary layer, where the influence of soil moisture on rainfall is outlined. The review concludes by discussing outstanding challenges and how to tackle them by means of novel theoretical, numerical, and experimental approaches.

Genetic adaptation to captivity can occur in a single generation

Abstract: Captive breeding programs are widely used for the conservation and restoration of threatened and endangered species. Nevertheless, captive-born individuals frequently have reduced fitness when reintroduced into the wild. The mechanism for these fitness declines has remained elusive, but hypotheses include environmental effects of captive rearing, inbreeding among close relatives, relaxed natural selection, and unintentional domestication selection (adaptation to captivity). We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.

Identification of Novel Fluorochemicals in Aqueous Film-Forming Foams Used by the US Military

Abstract: Aqueous film-forming foams (AFFFs) are a vital tool to fight large hydrocarbon fires and can be used by public, commercial, and military firefighting organizations. In order to possess these superior firefighting capabilities, AFFFs contain fluorochemical surfactants, of which many of the chemical identities are listed as proprietary. Large-scale controlled (e.g., training activities) and uncontrolled releases of AFFF have resulted in contamination of groundwater. Information on the composition of AFFF formulations is needed to fully define the extent of groundwater contamination, and the first step is to fully define the fluorochemical composition of AFFFs used by the US military. Fast atom bombardment mass spectrometry (FAB-MS) and high resolution quadrupole-time-of-flight mass spectrometry (QTOF-MS) were combined to elucidate chemical formulas for the fluorochemicals in AFFF mixtures, and, along with patent-based information, structures were assigned. Sample collection and analysis was focused on AFFFs...

Microbial oceanography of anoxic oxygen minimum zones

Abstract: Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N2) and nitrous oxide (N2O) gases. Anaerobic microbial processes, including the two pathways of N2 production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two “end points” represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

A Survey on Energy-Efficient Routing Techniques with QoS Assurances for Wireless Multimedia Sensor Networks

Abstract: The recent technological advances in micro electro-mechanical systems have promoted the development of a powerful class of sensor-based distributed intelligent systems capable of ubiquitously retrieving multimedia information, namely Wireless Multimedia Sensor Networks (WMSNs). WMSNs are gaining more popularity day by day as they are envisioned to support a large number of both non-real time and real-time multimedia applications. However, satisfying the stringent quality of service (QoS) requirements of multimedia transmission in a resource-constrained sensor network environment places new challenges to routing. As an outcome, optimal energy and application-specific QoS aware routing for WMSNs has gained considerable research attention recently. In this paper, current state-of-the-art in energy-efficient routing techniques for WMSNs is surveyed together with the highlights of the performance issues of each strategy. We outline the design challenges of routing protocols for WMSNs followed by the limitations of current techniques designed for non-multimedia data transmission. Further, a classification of recent routing protocols for WMSNs and a discussion of possible future research trends are presented.

Data-intensive science applied to broad-scale citizen science

Abstract: Identifying ecological patterns across broad spatial and temporal extents requires novel approaches and methods for acquiring, integrating and modeling massive quantities of diverse data. For example, a growing number of research projects engage continent-wide networks of volunteers (‘citizen-scientists') to collect species occurrence data. Although these data are information rich, they present numerous challenges in project design, implementation and analysis, which include: developing data collection tools that maximize data quantity while maintaining high standards of data quality, and applying new analytical and visualization techniques that can accurately reveal patterns in these data. Here, we describe how advances in data-intensive science provide accurate estimates in species distributions at continental scales by identifying complex environmental associations.

More than a meal… integrating non-feeding interactions into food webs.

Abstract: Organisms eating each other are only one of many types of well documented and important interactions among species. Other such types include habitat modification, predator interference and facilitation. However, ecological network research has been typically limited to either pure food webs or to networks of only a few (<3) interaction types. The great diversity of non-trophic interactions observed in nature has been poorly addressed by ecologists and largely excluded from network theory. Herein, we propose a conceptual framework that organises this diversity into three main functional classes defined by how they modify specific parameters in a dynamic food web model. This approach provides a path forward for incorporating non-trophic interactions in traditional food web models and offers a new perspective on tackling ecological complexity that should stimulate both theoretical and empirical approaches to understanding the patterns and dynamics of diverse species interactions in nature.

PEST STATUS OF THE BROWN MARMORATED STINK BUG, HALyOMORPHA HALyS IN THE USA

Abstract: Since its initial discovery in Allentown, PA, USA, the brown marmorated stink bug (BMSB), Halyomorpha halys (Heteroptera: Pentatomidae) has now officially has been detected in 38 states and the District of Columbia in the USA. Isolated populations also exist in Switzerland and Canada. This Asian species quickly became a major nuisance pest in the mid-Atlantic USA region due to its overwintering behavior of entering structures. BMSB has an extremely wide host range in both its native home and invaded countries where it feeds on numerous tree fruits, vegetables, field crops, ornamental plants, and native vegetation. In 2010, populations exploded causing severe crop losses to apples, peaches, sweet corn, peppers, tomatoes and row crops such as field corn and soybeans in several midAtlantic states. Damaging populations were detected in vineyards, small fruit and ornamentals. Researchers are collaborating to develop management solutions that will complement current integrated pest management programs. This article summarizes the current pest status and strategies being developed to manage BMSB in the USA.

Impact of the Deepwater Horizon oil spill on bioavailable polycyclic aromatic hydrocarbons in Gulf of Mexico coastal waters

Abstract: An estimated 4.1 million barrels of oil and 2.1 million gallons of dispersants were released into the Gulf of Mexico during the Deepwater Horizon oil spill. There is a continued need for information about the impacts and long-term effects of the disaster on the Gulf of Mexico. The objectives of this study were to assess bioavailable polycyclic aromatic hydrocarbons (PAHs) in the coastal waters of four Gulf Coast states that were impacted by the spill. For over a year, beginning in May 2010, passive sampling devices were used to monitor the bioavailable concentration of PAHs. Prior to shoreline oiling, baseline data were obtained at all the study sites, allowing for direct before and after comparisons of PAH contamination. Significant increases in bioavailable PAHs were seen following the oil spill, however, preoiling levels were observed at all sites by March 2011. A return to elevated PAH concentrations, accompanied by a chemical fingerprint similar to that observed while the site was being impacted by the spill, was observed in Alabama in summer 2011. Chemical forensic modeling demonstrated that elevated PAH concentrations are associated with distinctive chemical profiles.

Detection of apoptosis by TUNEL assay.

Abstract: Terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) assay has been designed to detect apoptotic cells that undergo extensive DNA degradation during the late stages of apoptosis. The method is based on the ability of TdT to label blunt ends of double-stranded DNA breaks independent of a template. This chapter describes an assay for detection of apoptotic cells during mouse odontogenesis using a colorimetric TUNEL system.