Science.gov

Sample records for identify active grazers

  1. Reconstructing Grazer Assemblages for Protected Area Restoration

    PubMed Central

    Venter, Jan A.; Prins, Herbert H. T.; Balfour, David A.; Slotow, Rob

    2014-01-01

    Protected area management agencies often struggle to reliably reconstruct grazer assemblages due to a lack of historical distribution data for their regions. Wrong predictions of grazing assemblages could potentially affect biodiversity negatively. The objective of the study was to determine how well grazing herbivores have become established since introduction to the Mkambati Nature Reserve, South Africa, how this was influenced by facilitation and competition, and how indigenous grazer assemblages can best be predicted for effective ecological restoration. Population trends of several grazing species were investigated in in order to determine how well they have become established since introduction. Five different conceivable grazing assemblages reflecting a range of approaches that are commonly encountered during conservation planning and management decision making were assessed. Species packing was used to predict whether facilitation, competition or co-existence were more likely to occur, and the species packing of the different assemblages were assessed using ANCOVA. Reconstructing a species assemblage using biogeographic and biological information provides the opportunity for a grazer assemblage that allows for facilitatory effects, which in turn leads to an ecosystem that is able to maintain its grazer assemblage structure. The strength of this approach lies in the ability to overcome the problem of depauperate grazer assemblages, resulting from a lack of historical data, by using biogeographical and biological processes, to assist in more effectively reconstructing grazer assemblages. Adaptive management of grazer assemblage restoration through reintroduction, using this approach would further mitigate management risks. PMID:24603663

  2. Short-term disturbance of a grazer has long-term effects on bacterial communities--relevance of trophic interactions for recovery from pesticide effects.

    PubMed

    Foit, Kaarina; Chatzinotas, Antonis; Liess, Matthias

    2010-08-15

    Little is known about the transfer of pesticide effects from higher trophic levels to bacterial communities by grazing. We investigated the effects of pulse exposure to the pyrethroid Fenvalerate on a grazer-prey system that comprised populations of Daphnia magna and bacterial communities. We observed the abundance and population size structure of D. magna by image analysis. Aquatic bacteria were monitored with regard to abundance (by cell staining) and community structure (by a 16S ribosomal RNA fingerprinting method). Shortly after exposure (2 days), the abundance of D. magna decreased. In contrast, the abundance of bacteria increased; in particular fast-growing bacteria proliferated, which changed the bacterial community structure. Long after pulse exposure (26 days), the size structure of D. magna was still affected and dominated by a cohort of small individuals. This cohort of small D. magna grazed actively on bacteria, which resulted in low bacterial abundance and low percentage of fast-growing bacteria. We identified grazing pressure as an important mediator for translating long-term pesticide effects from a grazer population on its prey. Hence, bacterial communities are potentially affected throughout the period that their grazers show pesticide effects concerning abundance or population size structure. Owing to interspecific interactions, the recovery of one species can only be assessed by considering its community context. PMID:20554058

  3. Monitoring and Modeling the Impact of Grazers Using Visual, Remote and Traditional Field Techniques

    NASA Astrophysics Data System (ADS)

    Roadknight, C. M.; Marshall, I. W.; Rose, R. J.

    2009-04-01

    The relationship between wild and domestic animals and the landscape they graze upon is important to soil erosion studies because they are a strong influence on vegetation cover (a key control on the rate of overland flow runoff), and also because the grazers contribute directly to sediment transport via carriage and indirectly by exposing fresh soil by trampling and burrowing/excavating. Quantifying the impacts of these effects on soil erosion and their dependence on grazing intensity, in complex semi-natural habitats has proved difficult. This is due to lack of manpower to collect sufficient data and weak standardization of data collection between observers. The advent of cheaper and more sophisticated digital camera technology and GPS tracking devices has lead to an increase in the amount of habitat monitoring information that is being collected. We report on the use of automated trail cameras to continuously capture images of grazer (sheep, rabbits, deer) activity in a variety of habitats at the Moor House nature reserve in northern England. As well as grazer activity these cameras also give valuable information on key climatic soil erosion factors such as snow, rain and wind and plant growth and thus allow the importance of a range of grazer activities and the grazing intensity to be estimated. GPS collars and more well established survey methods (erosion monitoring, dung counting and vegetation surveys) are being used to generate a detailed representation of land usage and plan camera siting. This paper describes the data collection techniques, outlines the quantitative and qualitative data collected and proposes online and offline systems that can reduce the data processing time and increase focus on important subsets in the collected data. We also present a land usage model that estimates grazing intensity, grazer behaviours and their impact on soil coverage at sites where cameras have not been deployed, based on generalising from camera sites to other

  4. Identifying Sexual Harassment: A Classroom Activity

    ERIC Educational Resources Information Center

    Madson, Laura; Shoda, Jennifer

    2002-01-01

    We created a classroom activity to illustrate the complexity involved in identifying sexual harassment. In the activity, students decided whether 6 fictional scenarios constituted sexual harassment. The activity stimulates animated discussion, and evaluation data indicate that it received positive feedback from students and refined students'…

  5. Identifying Crucial Parameter Correlations Maintaining Bursting Activity

    PubMed Central

    Doloc-Mihu, Anca; Calabrese, Ronald L.

    2014-01-01

    Recent experimental and computational studies suggest that linearly correlated sets of parameters (intrinsic and synaptic properties of neurons) allow central pattern-generating networks to produce and maintain their rhythmic activity regardless of changing internal and external conditions. To determine the role of correlated conductances in the robust maintenance of functional bursting activity, we used our existing database of half-center oscillator (HCO) model instances of the leech heartbeat CPG. From the database, we identified functional activity groups of burster (isolated neuron) and half-center oscillator model instances and realistic subgroups of each that showed burst characteristics (principally period and spike frequency) similar to the animal. To find linear correlations among the conductance parameters maintaining functional leech bursting activity, we applied Principal Component Analysis (PCA) to each of these four groups. PCA identified a set of three maximal conductances (leak current, Leak; a persistent K current, K2; and of a persistent Na+ current, P) that correlate linearly for the two groups of burster instances but not for the HCO groups. Visualizations of HCO instances in a reduced space suggested that there might be non-linear relationships between these parameters for these instances. Experimental studies have shown that period is a key attribute influenced by modulatory inputs and temperature variations in heart interneurons. Thus, we explored the sensitivity of period to changes in maximal conductances of Leak, K2, and P, and we found that for our realistic bursters the effect of these parameters on period could not be assessed because when varied individually bursting activity was not maintained. PMID:24945358

  6. Dynamics of a producer-grazer model incorporating the effects of excess food nutrient content on grazer's growth.

    PubMed

    Peace, Angela; Wang, Hao; Kuang, Yang

    2014-09-01

    Modeling under the framework of ecological stoichiometric allows the investigation of the effects of food quality on food web population dynamics. Recent discoveries in ecological stoichiometry suggest that grazer dynamics are affected by insufficient food nutrient content (low phosphorus (P)/carbon (C) ratio) as well as excess food nutrient content (high P:C). This phenomenon is known as the "stoichiometric knife edge." While previous models have captured this phenomenon, they do not explicitly track P in the producer or in the media that supports the producer, which brings questions to the validity of their predictions. Here, we extend a Lotka-Volterra-type stoichiometric model by mechanistically deriving and tracking P in the producer and free P in the environment in order to investigate the growth response of Daphnia to algae of varying P:C ratios. Bifurcation analysis and numerical simulations of the full model, that explicitly tracks phosphorus, lead to quantitative different predictions than previous models that neglect to track free nutrients. The full model shows that the fate of the grazer population can be very sensitive to excess nutrient concentrations. Dynamical free nutrient pool seems to induce extreme grazer population density changes when total nutrient is in an intermediate range. PMID:25124765

  7. Grazer Effects on Stream Primary Production and Nitrate Utilization: Estimating Feedbacks Under Reduced Nitrate Levels at High-Temporal Resolutions from the Patch to Reach-Scale

    NASA Astrophysics Data System (ADS)

    Reijo, C. J.; Cohen, M. J.

    2015-12-01

    While nutrient enrichment is often identified as the leading cause for changes in stream gross primary production (GPP) and shifts in vegetative communities, other factors such as grazers influence overall stream structure and function. Evidence shows that grazers are a top-down control on algae in streams; however, the specific feedbacks between overall stream metabolism, grazer effects, and nutrient cycling have been variable and little is known about these interactions at nutrient levels below ambient. To further our understanding of these linkages, a nutrient depletion chamber was created and paired with high-resolution in situ sensors to estimate stream metabolism and characterize nitrate uptake (UNO3) pathways (i.e. plant uptake and denitrification). The Plexiglas chamber blocks flow and nutrient supply, inserts into upper sediments, allows light in and sediment-water-air interactions to occur. At Gum Slough Springs, FL, nitrate was reduced from ambient levels (1.40 mg N/L) to below regulatory thresholds (ca. 0.20 mg N/L) within one week. Paired chambers with and without the presence of snails (Elimia floridensis) were deployed across submerged aquatic vegetation (SAV; Vallisneria americana) and algae (Lyngbya) substrates. Results show that GPP and UNO3 were higher under SAV (70 g O2/m2/d and 300 mg NO3/m2/d, respectively) and a general lack of nutrient limitation even at low [NO3]. Grazer effects differed by vegetation type as it alleviated the reduction of NO3 levels and GPP under SAV but enhanced the decrease of algal GPP and NO3 levels over time. Continued work includes estimating grazer effects on denitrification, quantifying snail nutrient excretion contributions, and scaling up all estimates from the patch to reach level. Overall, this study will further our understanding of grazer-production-nutrient interactions within stream systems, making it possible to predict changes in feedbacks when one part of the biotic or abiotic ecosystem is altered.

  8. Identifying an active case of tuberculosis.

    PubMed

    Williams, G; Alarcon, E; Jittimanee, S; Walusimbi, M; Sebek, M; Berga, E; Villa, T S

    2008-04-01

    The best practice standards set out in chapter 2 of the Best Practice guide focus on the various aspects of identifying an active case of TB and aim to address some of the challenges associated with case detection. The importance of developing a good relationship with the patient from the start, when he or she is often most vulnerable, is emphasised. The first standard focuses on the assessment of someone who might have TB and the second gives detailed guidance about the collection of sputum for diagnosis. The standards are aimed at the health care worker, who assesses the patient when he or she presents at a health care facility and therefore needs to be familiar with the signs, symptoms and risk factors associated with TB. Having suspected TB, the health care worker then needs to ensure that the correct tests are ordered and procedures are followed so that the best quality samples possible are sent to the laboratory and all documentation is filled out clearly and correctly. The successful implementation of these standards can be measured by the accurate and prompt reporting of results, the registration of every case detected and the continued attendance of every patient who needs treatment. PMID:18371262

  9. Dinosaur coprolites and the early evolution of grasses and grazers.

    PubMed

    Prasad, Vandana; Strömberg, Caroline A E; Alimohammadian, Habib; Sahni, Ashok

    2005-11-18

    Silicified plant tissues (phytoliths) preserved in Late Cretaceous coprolites from India show that at least five taxa from extant grass (Poaceae) subclades were present on the Indian subcontinent during the latest Cretaceous. This taxonomic diversity suggests that crown-group Poaceae had diversified and spread in Gondwana before India became geographically isolated. Other phytoliths extracted from the coprolites (from dicotyledons, conifers, and palms) suggest that the suspected dung producers (titanosaur sauropods) fed indiscriminately on a wide range of plants. These data also make plausible the hypothesis that gondwanatherian mammals with hypsodont cheek teeth were grazers. PMID:16293759

  10. Identifying physical activity gender differences among youth

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physical activity (PA) is an important part of a healthy lifestyle and reduces risk of certain chronic diseases. Many youth do not currently meet PA guidelines; evidence suggests that girls are less active than boys are at all ages. PA differences need to be understood, so that gender-specific inter...

  11. Identifying Diverse Means for Assessing Physical Activity

    ERIC Educational Resources Information Center

    Perlman, Dana J.; Pearson, Phil

    2012-01-01

    Physical inactivity is of concern for the majority of age groups within the United States. Limited engagement in physical activity (PA) has been linked with an increased risk for a host of health problems, including but not limited to heart disease, diabetes and cancer. Benefits of PA are widely documented and accepted yet many people, especially…

  12. Interspecific Competition for Shelters in Territorial and Gregarious Intertidal Grazers: Consequences for Individual Behaviour

    PubMed Central

    Aguilera, Moisés A.; Navarrete, Sergio A.

    2012-01-01

    Experiments have shown that interspecific interactions within consumer guilds can alter patterns of distribution, abundance and size of species. Plastic behavioural responses can be modulated by agonistic interactions. In many cases, consumers compete for space and shelters, and these interactions change the manner in which they exploit food. This study investigates the consequences of competition in the spatial and temporal organization of behaviour of intertidal grazers, which share algal resources and the use of rock crevices while resting, but exhibit different body sizes, spatial behaviour and foraging modes. We evaluate interaction strength between small gregarious Siphonaria lessoni and the larger territorial keyhole limpet Fissurella crassa and between S. lessoni and the medium-size gregarious chiton Chiton granosus. Using field manipulations and artificial arenas in the laboratory, we tested whether the use of crevices, micro-spatial distribution and activity are modified by the density of conspecifics and the presence of heterospecifics. Our results show that small-scale spatial segregation observed in the field between S. lessoni and C. granosus result from species-specific differences in habitat use. In turn, we found evidence that spatial segregation between F. crassa and S. lessoni results from highly asymmetric interference competition in the use of shelters. The presence of F. crassa reduced the use of crevices and growth rates of S. lessoni. Effects on growth rates are assumed to result from exposure to harsh environmental conditions rather than food limitation. Thus, neither gregarious behaviour nor differences in activity were sufficient to prevent competition with the larger grazer. Our study illustrates the importance of competition for shelters, which results in behavioural changes of the smaller-sized species, and how these plastic responses can translate into differences in growth rates. Use of shelters can thus be modulated by environmental

  13. Fungal secondary metabolite dynamics in fungus–grazer interactions: novel insights and unanswered questions

    PubMed Central

    Rohlfs, Marko

    2015-01-01

    In response to fungivore grazing fungi are assumed to have evolved secondary metabolite-based defense mechanisms that harm and repel grazers, and hence provide a benefit to the metabolite producer. However, since research into the ecological meaning of highly diverse fungal secondary metabolites is still in its infancy, many central questions still remain. Which components of the enormous metabolite diversity of fungi act as direct chemical defense mechanisms against grazers? Is the proposed chemical defense of fungi induced by grazer attack? Which role do volatile compounds play in communicating noxiousness to grazers? What is the relative impact of grazers and that of interactions with competing microbes on the evolution of fungal secondary metabolism? Here, I briefly summarize and discuss the results of the very few studies that have tried to tackle some of these questions by (i) using secondary metabolite mutant fungi in controlled experiments with grazers, and by (ii) investigating fungal secondary metabolism as a flexible means to adapt to grazer-rich niches. PMID:25628619

  14. Experimental Removal and Recovery of Subtidal Grazers Highlights the Importance of Functional Redundancy and Temporal Context

    PubMed Central

    Elahi, Robin; Sebens, Kenneth P.

    2013-01-01

    The extent to which different grazers are functionally redundant has strong implications for the maintenance of community structure and function. Grazing by red urchins (Strongylocentrotus franciscanus) on temperate rocky reefs can initiate a switch from invertebrate or macroalgal dominance to an algal crust state, but can also cause increases in the density of molluscan mesograzers. In this study, we tested the hypothesis that red urchins and lined chitons (Tonicella spp.) are redundant in the maintenance of available space, defined as encrusting algae and bare rock. In a factorial field experiment replicated at three sites, we reduced the densities of urchins and chitons on subtidal rock walls for nine months. The effects of grazers were interpreted in the context of natural temporal variation by monitoring the benthic community one year before, during, and after grazer removal. The removal of each grazer in isolation had no effect on the epilithic community, but the removal of both grazers caused an increase in sessile invertebrates. The increase was due primarily to clonal ascidians, which displayed a large (∼75%) relative increase in response to the removal of both grazers. However, the observed non-additive responses to grazer removal were temporary and smaller than seasonal fluctuations. Our data demonstrate that urchins and chitons can be redundant in the maintenance of available space, and highlight the value of drawing conclusions from experimental manipulations within an extended temporal context. PMID:24250819

  15. Effects of grazer presence on genetic structure of a phenotypically diverse diatom population.

    PubMed

    Sjöqvist, C; Kremp, A; Lindehoff, E; Båmstedt, U; Egardt, J; Gross, S; Jönsson, M; Larsson, H; Pohnert, G; Richter, H; Selander, E; Godhe, A

    2014-01-01

    Studies of predator-prey systems in both aquatic and terrestrial environments have shown that grazers structure the intraspecific diversity of prey species, given that the prey populations are phenotypically variable. Populations of phytoplankton have traditionally considered comprising only low intraspecific variation, hence selective grazing as a potentially structuring factor of both genetic and phenotypic diversity has not been comprehensively studied. In this study, we compared strain specific growth rates, production of polyunsaturated aldehydes, and chain length of the marine diatom Skeletonema marinoi in both grazer and non-grazer conditions by conducting monoclonal experiments. Additionally, a mesocosm experiment was performed with multiclonal experimental S. marinoi populations exposed to grazers at different levels of copepod concentration to test effects of grazer presence on diatom diversity in close to natural conditions. Our results show that distinct genotypes of a geographically restricted population exhibit variable phenotypic traits relevant to grazing interactions such as chain length and growth rates. Grazer presence affected clonal richness and evenness of multiclonal Skeletonema populations in the mesocosms, likely in conjunction with intrinsic interactions among the diatom strains. Only the production of polyunsaturated aldehydes was not affected by grazer presence. Our findings suggest that grazing can be an important factor structuring diatom population diversity in the sea and emphasize the importance of considering clonal differences when characterizing species and their role in nature. PMID:24272280

  16. Climatic warming and the future of bison as grazers

    NASA Astrophysics Data System (ADS)

    Craine, Joseph M.; Towne, E. Gene; Miller, Mary; Fierer, Noah

    2015-11-01

    Climatic warming is likely to exacerbate nutritional stress and reduce weight gain in large mammalian herbivores by reducing plant nutritional quality. Yet accurate predictions of the effects of climatic warming on herbivores are limited by a poor understanding of how herbivore diet varies along climate gradients. We utilized DNA metabarcoding to reconstruct seasonal variation in the diet of North American bison (Bison bison) in two grasslands that differ in mean annual temperature by 6 °C. Here, we show that associated with greater nutritional stress in warmer climates, bison consistently consumed fewer graminoids and more shrubs and forbs, i.e. eudicots. Bison in the warmer grassland consumed a lower proportion of C3 grass, but not a greater proportion of C4 grass. Instead, bison diet in the warmer grassland had a greater proportion of N2-fixing eudicots, regularly comprising >60% of their protein intake in spring and fall. Although bison have been considered strict grazers, as climatic warming reduces grass protein concentrations, bison may have to attempt to compensate by grazing less and browsing more. Promotion of high-protein, palatable eudicots or increasing the protein concentrations of grasses will be critical to minimizing warming-imposed nutritional stress for bison and perhaps other large mammalian herbivores.

  17. Climatic warming and the future of bison as grazers

    PubMed Central

    Craine, Joseph M.; Towne, E. Gene; Miller, Mary; Fierer, Noah

    2015-01-01

    Climatic warming is likely to exacerbate nutritional stress and reduce weight gain in large mammalian herbivores by reducing plant nutritional quality. Yet accurate predictions of the effects of climatic warming on herbivores are limited by a poor understanding of how herbivore diet varies along climate gradients. We utilized DNA metabarcoding to reconstruct seasonal variation in the diet of North American bison (Bison bison) in two grasslands that differ in mean annual temperature by 6 °C. Here, we show that associated with greater nutritional stress in warmer climates, bison consistently consumed fewer graminoids and more shrubs and forbs, i.e. eudicots. Bison in the warmer grassland consumed a lower proportion of C3 grass, but not a greater proportion of C4 grass. Instead, bison diet in the warmer grassland had a greater proportion of N2-fixing eudicots, regularly comprising >60% of their protein intake in spring and fall. Although bison have been considered strict grazers, as climatic warming reduces grass protein concentrations, bison may have to attempt to compensate by grazing less and browsing more. Promotion of high-protein, palatable eudicots or increasing the protein concentrations of grasses will be critical to minimizing warming-imposed nutritional stress for bison and perhaps other large mammalian herbivores. PMID:26567987

  18. Climatic warming and the future of bison as grazers.

    PubMed

    Craine, Joseph M; Towne, E Gene; Miller, Mary; Fierer, Noah

    2015-01-01

    Climatic warming is likely to exacerbate nutritional stress and reduce weight gain in large mammalian herbivores by reducing plant nutritional quality. Yet accurate predictions of the effects of climatic warming on herbivores are limited by a poor understanding of how herbivore diet varies along climate gradients. We utilized DNA metabarcoding to reconstruct seasonal variation in the diet of North American bison (Bison bison) in two grasslands that differ in mean annual temperature by 6 °C. Here, we show that associated with greater nutritional stress in warmer climates, bison consistently consumed fewer graminoids and more shrubs and forbs, i.e. eudicots. Bison in the warmer grassland consumed a lower proportion of C3 grass, but not a greater proportion of C4 grass. Instead, bison diet in the warmer grassland had a greater proportion of N2-fixing eudicots, regularly comprising >60% of their protein intake in spring and fall. Although bison have been considered strict grazers, as climatic warming reduces grass protein concentrations, bison may have to attempt to compensate by grazing less and browsing more. Promotion of high-protein, palatable eudicots or increasing the protein concentrations of grasses will be critical to minimizing warming-imposed nutritional stress for bison and perhaps other large mammalian herbivores. PMID:26567987

  19. Hydrologic drivers and controls of stream biofilm-grazer interactions

    NASA Astrophysics Data System (ADS)

    Ceola, S.; Bertuzzo, E.; Mari, L.; Botter, G.; Hödl, I.; Battin, T. J.; Rinaldo, A.

    2011-12-01

    Understanding the dynamics of fluvial ecosystems linked to hydrology is one of the most important challenges of ecohydrology. In fact, streamflow, which chiefly relies on rainfall, climate, land use and geomorphologic properties, plays a fundamental role in sustaining and regulating fluvial ecosystem integrity. To analyze possible implications of hydrological fluctuations on the biofilm-grazer interaction - a major driver for nutrient cycling and metabolism in streams - we experimented with 36 3-m-long flumes. In particular, two distinct discharge treatments (constant and stochastic discharge regimes) coupled with six different light regimes (from natural light conditions to nearly 70% attenuation) have been performed. To complement and analyze the experimental results, a dynamic model, based on the Rosenzweig-MacArthur predator-prey model, is presented. Several relations between the parameters of the aforementioned model and hydrologic and hydraulic properties, such as streamflow, water depth, flow velocity, shear stress, and light availability will be explored to explain ecohydrologic influences on the basic food-web dynamics.

  20. Ocean acidification and rising temperatures may increase biofilm primary productivity but decrease grazer consumption

    PubMed Central

    Russell, Bayden D.; Connell, Sean D.; Findlay, Helen S.; Tait, Karen; Widdicombe, Stephen; Mieszkowska, Nova

    2013-01-01

    Climate change may cause ecosystems to become trophically restructured as a result of primary producers and consumers responding differently to increasing CO2 and temperature. This study used an integrative approach using a controlled microcosm experiment to investigate the combined effects of CO2 and temperature on key components of the intertidal system in the UK, biofilms and their consumers (Littorina littorea). In addition, to identify whether pre-exposure to experimental conditions can alter experimental outcomes we explicitly tested for differential effects on L. littorea pre-exposed to experimental conditions for two weeks and five months. In contrast to predictions based on metabolic theory, the combination of elevated temperature and CO2 over a five-week period caused a decrease in the amount of primary productivity consumed by grazers, while the abundance of biofilms increased. However, long-term pre-exposure to experimental conditions (five months) altered this effect, with grazing rates in these animals being greater than in animals exposed only for two weeks. We suggest that the structure of future ecosystems may not be predictable using short-term laboratory experiments alone owing to potentially confounding effects of exposure time and effects of being held in an artificial environment over prolonged time periods. A combination of laboratory (physiology responses) and large, long-term experiments (ecosystem responses) may therefore be necessary to adequately predict the complex and interactive effects of climate change as organisms may acclimate to conditions over the longer term. PMID:23980241

  1. Ocean acidification and rising temperatures may increase biofilm primary productivity but decrease grazer consumption.

    PubMed

    Russell, Bayden D; Connell, Sean D; Findlay, Helen S; Tait, Karen; Widdicombe, Stephen; Mieszkowska, Nova

    2013-01-01

    Climate change may cause ecosystems to become trophically restructured as a result of primary producers and consumers responding differently to increasing CO2 and temperature. This study used an integrative approach using a controlled microcosm experiment to investigate the combined effects of CO2 and temperature on key components of the intertidal system in the UK, biofilms and their consumers (Littorina littorea). In addition, to identify whether pre-exposure to experimental conditions can alter experimental outcomes we explicitly tested for differential effects on L. littorea pre-exposed to experimental conditions for two weeks and five months. In contrast to predictions based on metabolic theory, the combination of elevated temperature and CO2 over a five-week period caused a decrease in the amount of primary productivity consumed by grazers, while the abundance of biofilms increased. However, long-term pre-exposure to experimental conditions (five months) altered this effect, with grazing rates in these animals being greater than in animals exposed only for two weeks. We suggest that the structure of future ecosystems may not be predictable using short-term laboratory experiments alone owing to potentially confounding effects of exposure time and effects of being held in an artificial environment over prolonged time periods. A combination of laboratory (physiology responses) and large, long-term experiments (ecosystem responses) may therefore be necessary to adequately predict the complex and interactive effects of climate change as organisms may acclimate to conditions over the longer term. PMID:23980241

  2. Effects of road deicer (NaCl) and amphibian grazers on detritus processing in pond mesocosms.

    PubMed

    Van Meter, Robin J; Swan, Christopher M; Trossen, Carrie A

    2012-10-01

    Road deicers have been identified as potential stressors in aquatic habitats throughout the United States, but we know little regarding associated impacts to ecosystem function. A critical component of ecosystem function that has not previously been evaluated with respect to freshwater salinization is the impact on organic matter breakdown. The purpose of this study was to evaluate cumulative effects of road deicers and tadpole grazers on leaf litter breakdown rate (g d(-1) ) and microbial respiration (mg O(2)  g leaf(-1) h(-1) ). To test this interaction, in May 2008 the authors added dry leaf litter (Quercus spp.) to forty 600-L pond mesocosms and inoculated each with algae and zooplankton. In a full-factorial design, they manipulated a realistic level of road salt (ambient or elevated at 645 mg L(-1) Cl(-) ) and tadpole (Hyla versicolor) presence or absence. The elevated chloride treatment reduced microbial respiration by 24% in the presence of tadpoles. The breakdown of leaf litter by tadpoles occurred 9.7% faster under ambient chloride conditions relative to the elevated chloride treatment. Results of the present study suggest that the microbial community is directly impacted by road deicers and heavy tadpole grazing under ambient conditions limits microbial capacity to process detritus. Road salts and tadpoles interact to limit microbial respiration, but to a lesser extent leaf mass loss rate, thereby potentially restricting energy flow from detrital sources in pond ecosystems. PMID:22821388

  3. Identifying Emotions on the Basis of Neural Activation.

    PubMed

    Kassam, Karim S; Markey, Amanda R; Cherkassky, Vladimir L; Loewenstein, George; Just, Marcel Adam

    2013-01-01

    We attempt to determine the discriminability and organization of neural activation corresponding to the experience of specific emotions. Method actors were asked to self-induce nine emotional states (anger, disgust, envy, fear, happiness, lust, pride, sadness, and shame) while in an fMRI scanner. Using a Gaussian Naïve Bayes pooled variance classifier, we demonstrate the ability to identify specific emotions experienced by an individual at well over chance accuracy on the basis of: 1) neural activation of the same individual in other trials, 2) neural activation of other individuals who experienced similar trials, and 3) neural activation of the same individual to a qualitatively different type of emotion induction. Factor analysis identified valence, arousal, sociality, and lust as dimensions underlying the activation patterns. These results suggest a structure for neural representations of emotion and inform theories of emotional processing. PMID:23840392

  4. Long-Term Climate Sensitivity of Grazer Performance: A Cross-Site Study

    PubMed Central

    Craine, Joseph M.

    2013-01-01

    Climate change will affect grasslands in a number of ways, but the consequences of a warmer, drier world for grazers is uncertain. Predicting future grazer performance is complex since climate change affects both the quantity and quality of forage through a combination of processes that occur over a range of time scales. To better predict the consequences of climate change for grazer performance, a dataset was compiled of over a quarter million bison weights distributed across 22 US herds that span a large range of climates. Patterns of bison body mass among sites, age classes, and sexes were analyzed with respect to differences in geographic patterns of climate and interannual variation in climate. While short-term effects of climate variability are likely to depend on the magnitude and timing of precipitation during the year, grazers will be negatively affected by sustained hotter, drier conditions most likely associated with reductions in forage quality. Short-term, little effect of high temperatures on bison performance is observed, which suggests that the long-term effects of higher temperatures are likely to accrue over time as nitrogen availability in grasslands is reduced and forage quality declines. If relationships observed for bison are general for cattle, the economic consequences of higher temperatures due to decreased weight gain in US cattle could be on the order of US$1B per 1°C increase in temperature. Long-term monitoring of forage quality as well as native and domesticated grazer performance is recommended to better understand climate change effects on grazers. PMID:23840584

  5. Modeling substrate-bacteria-grazer interactions coupled to substrate transport in groundwater

    NASA Astrophysics Data System (ADS)

    Bajracharya, Bijendra M.; Lu, Chuanhe; Cirpka, Olaf A.

    2014-05-01

    Models of microbial dynamics coupled to solute transport in aquifers typically require the introduction of a bacterial capacity term to prevent excessive microbial growth close to substrate-injection boundaries. The factors controlling this carrying capacity, however, are not fully understood. In this study, we propose that grazers or bacteriophages may control the density of bacterial biomass in continuously fed porous media. We conceptualize the flow-through porous medium as a series of retentostats, in which the dissolved substrate is advected with water flow whereas the biomasses of bacteria and grazers are considered essentially immobile. We first model a single retentostat with Monod kinetics of bacterial growth and a second-order grazing law, which shows that the system oscillates but approaches a stable steady state with nonzero concentrations of substrate, bacteria, and grazers. The steady state concentration of the bacteria biomass is independent of the substrate concentration in the inflow. When coupling several retentostats in a series to mimic a groundwater column, the steady state bacteria concentrations thus remain at a constant level over a significant travel distance. The one-dimensional reactive transport model also accounts for substrate dispersion and a random walk of grazers influenced by the bacteria concentration. These dispersive-diffusive terms affect the oscillations until steady state is reached, but hardly the steady state value itself. We conclude that grazing, or infection by bacteriophages, is a possible explanation of the maximum biomass concentration frequently needed in bioreactive transport models. Its value depends on parameters related to the grazers or bacteriophages and is independent of bacterial growth parameters or substrate concentration, provided that there is enough substrate to sustain bacteria and grazers.

  6. Identifying Clusters of Active Transportation Using Spatial Scan Statistics

    PubMed Central

    Huang, Lan; Stinchcomb, David G.; Pickle, Linda W.; Dill, Jennifer; Berrigan, David

    2009-01-01

    Background There is an intense interest in the possibility that neighborhood characteristics influence active transportation such as walking or biking. The purpose of this paper is to illustrate how a spatial cluster identification method can evaluate the geographic variation of active transportation and identify neighborhoods with unusually high/low levels of active transportation. Methods Self-reported walking/biking prevalence, demographic characteristics, street connectivity variables, and neighborhood socioeconomic data were collected from respondents to the 2001 California Health Interview Survey (CHIS; N=10,688) in Los Angeles County (LAC) and San Diego County (SDC). Spatial scan statistics were used to identify clusters of high or low prevalence (with and without age-adjustment) and the quantity of time spent walking and biking. The data, a subset from the 2001 CHIS, were analyzed in 2007–2008. Results Geographic clusters of significantly high or low prevalence of walking and biking were detected in LAC and SDC. Structural variables such as street connectivity and shorter block lengths are consistently associated with higher levels of active transportation, but associations between active transportation and socioeconomic variables at the individual and neighborhood levels are mixed. Only one cluster with less time spent walking and biking among walkers/bikers was detected in LAC, and this was of borderline significance. Age-adjustment affects the clustering pattern of walking/biking prevalence in LAC, but not in SDC. Conclusions The use of spatial scan statistics to identify significant clustering of health behaviors such as active transportation adds to the more traditional regression analysis that examines associations between behavior and environmental factors by identifying specific geographic areas with unusual levels of the behavior independent of predefined administrative units. PMID:19589451

  7. Rapid evolution of tolerance to toxic Microcystis in two cladoceran grazers.

    PubMed

    Jiang, Xiaodong; Gao, Han; Zhang, Lihua; Liang, Huishuang; Zhu, Xiao

    2016-01-01

    Evolutionary adaptation could assist organisms to cope with environmental changes, yet few experimental systems allow us to directly track evolutionary trajectory. Using experimental evolution, evolutionary tolerance to Microcystis aeruginosa was investigated in two cladocerans (Daphnia pulex and Simocephalus vetulus) to test the hypothesis that cladoceran grazers rapidly adapt to toxic cyanobacteria. After exposure for either three or six months, both grazers evolved a higher tolerance. The intrinsic rate of population increases in S. vetulus feeding on cyanobacteria was negatively correlated with that on green algae, which suggests that evolutionary adaptation in tolerance would carry a cost in the absence of cyanobacteria. However, the cyanobacterial selection resulted in a general increase in D. pulex when fed both cyanobacteria and green algae. Following a three-month relaxation of selection, S. vetulus in the selection line exhibited reverse evolution back to their original state when their diets were switched back to pure green algae. The present experimental evolution, both forwards and reverse, not only demonstrates the evolutionary responses of cladoceran grazers to toxic cyanobacterial cells in the laboratory, but also indicates that the grazer-cyanobacteria interaction would be an effective system to empirically study rapid evolution to environmental changes. PMID:27122137

  8. Rapid evolution of tolerance to toxic Microcystis in two cladoceran grazers

    PubMed Central

    Jiang, Xiaodong; Gao, Han; Zhang, Lihua; Liang, Huishuang; Zhu, Xiao

    2016-01-01

    Evolutionary adaptation could assist organisms to cope with environmental changes, yet few experimental systems allow us to directly track evolutionary trajectory. Using experimental evolution, evolutionary tolerance to Microcystis aeruginosa was investigated in two cladocerans (Daphnia pulex and Simocephalus vetulus) to test the hypothesis that cladoceran grazers rapidly adapt to toxic cyanobacteria. After exposure for either three or six months, both grazers evolved a higher tolerance. The intrinsic rate of population increases in S. vetulus feeding on cyanobacteria was negatively correlated with that on green algae, which suggests that evolutionary adaptation in tolerance would carry a cost in the absence of cyanobacteria. However, the cyanobacterial selection resulted in a general increase in D. pulex when fed both cyanobacteria and green algae. Following a three-month relaxation of selection, S. vetulus in the selection line exhibited reverse evolution back to their original state when their diets were switched back to pure green algae. The present experimental evolution, both forwards and reverse, not only demonstrates the evolutionary responses of cladoceran grazers to toxic cyanobacterial cells in the laboratory, but also indicates that the grazer-cyanobacteria interaction would be an effective system to empirically study rapid evolution to environmental changes. PMID:27122137

  9. NUTRIENTS, CANOPY COVER, AND GRAZERS: THEIR EFFECTS ON SUMMER PERIPHYTON IN SMALL MIDWESTERN STREAMS

    EPA Science Inventory

    Numerous studies in artificial streams suggest the relationship between nurients and periphyton biomass (AFDM) and chlorophyll a in streams is affected by ambient light, which is influenced by canopy cover, and by grazer densities. To assess the relationships between nutrients a...

  10. Using ILP to Identify Pathway Activation Patterns in Systems Biology

    PubMed Central

    Neaves, Samuel R; Millard, Louise A C; Tsoka, Sophia

    2016-01-01

    We show a logical aggregation method that, combined with propositionalization methods, can construct novel structured biological features from gene expression data. We do this to gain understanding of pathway mechanisms, for instance, those associated with a particular disease. We illustrate this method on the task of distinguishing between two types of lung cancer; Squamous Cell Carcinoma (SCC) and Adenocarcinoma (AC). We identify pathway activation patterns in pathways previously implicated in the development of cancers. Our method identified a model with comparable predictive performance to the winning algorithm of a recent challenge, while providing biologically relevant explanations that may be useful to a biologist. PMID:27478883

  11. Periphyton As A Source Of Bioavailable Cd and Cu To Invertebrate Benthic Grazers

    NASA Astrophysics Data System (ADS)

    Cain, D.; Croteau, M.; Luoma, S. N.

    2009-12-01

    High metal body burdens observed in invertebrate benthic grazers suggest that periphyton is an important source of bioavailable metals. We conducted comparative studies among five species of stream insects (the mayflies Nixe sp., Epeorus albertae, E. longimanus, Serratella tibialis, and Drunella flavilinea) to quantify dietary and dissolved cadmium (Cd) and copper (Cu) bioaccumulation kinetics as a means of characterizing exposure routes. We labeled artificial stream water and benthic diatoms (Nitzschia palea) with enriched stable metal isotopes and determined physiological rate constants representing metal influx from water (ku), food ingestion rate (IR), metal assimilation from food (AE), and elimination of bioaccumulated metal (ke). The ku varied by more than 4-fold and 10-fold for Cu and Cd, respectively, among species. In all species, AEs of both metals from the diatom were equal to or greater than 75%. Assimilation efficiencies did not appear to vary with differences in ingestion rates among or within species. The ke was variable and appeared to be the principal process controlling inter-specific differences in bioaccumulation. Model simulations of bioaccumulation under the laboratory exposures identified food as the primary exposure pathway at dissolved Cd and Cu concentrations less than 0.5 and 5 µg L-1, respectively. To simulate field conditions, we modeled Cu bioaccumulation from water alone using geochemical data from an uncontaminated site and from a moderately Cu-contaminated site within the same river basin and compared the model predictions to observed bioaccumulated Cu. These results also indicated that food was the principal exposure route. At least for the taxa considered in this study, we conclude that consumption of metal-contaminated periphyton can result in high metal body burdens and increased risk of metal toxicity.

  12. Transient dynamics of pelagic producer-grazer systems in a gradient of nutrients and mixing depths.

    PubMed

    Jäger, Christoph G; Diehl, Sebastian; Matauschek, Christian; Klausmeier, Christopher A; Stibor, Herwig

    2008-05-01

    Phytoplankton-grazer dynamics are often characterized by long transients relative to the length of the growing season. Using a phytoplankton-grazer model parameterized for Daphnia pulex with either flexible or fixed algal carbon:nutrient stoichiometry, we explored how nutrient and light supply (the latter by varying depth of the mixed water column) affect the transient dynamics of the system starting from low densities. The system goes through an initial oscillation across nearly the entire light-nutrient supply space. With flexible (but not with fixed) algal stoichiometry, duration of the initial algal peak, timing and duration of the subsequent grazer peak, and timing of the algal minimum are consistently accelerated by nutrient enrichment but decelerated by light enrichment (decreasing mixing depth) over the range of intermediate to shallow mixing depths. These contrasting effects of nutrient vs. light enrichment are consequences of their opposing influences on food quality (algal nutrient content): algal productivity and food quality are positively related along a nutrient gradient but inversely related along a light gradient. Light enrichment therefore slows down grazer growth relative to algal growth, decelerating oscillatory dynamics; nutrient enrichment has opposite effects. We manipulated nutrient supply and mixing depth in a field enclosure experiment. The experimental results were qualitatively much more consistent with the flexible than with the fixed stoichiometry model. Nutrient enrichment increased Daphnia peak biomass, decreased algal minimum biomass, decreased the seston C:P ratio, and accelerated transient oscillatory dynamics. Light enrichment (decreasing mixing depth) produced the opposite patterns, except that Daphnia peak biomass increased monotonously with light enrichment, too. Thus, while the model predicts the possibility of the "paradox of energy enrichment" (a decrease in grazer biomass with light enrichment) at high light and low

  13. Geometric complexity identifies platelet activation in familial hypercholesterolemic patients.

    PubMed

    Bianciardi, Giorgio; Aglianò, Margherita; Volpi, Nila; Stefanutti, Claudia

    2015-06-01

    Familial hypercholesterolemia (FH), a genetic disease, is associated with a severe incidence of athero-thrombotic events, related, also, to platelet hyperreactivity. A plethora of methods have been proposed to identify those activated circulating platelets, none of these has proved really effective. We need efficient methods to identify the circulating platelet status in order to follow the patients after therapeutic procedures. We propose the use of computerized fractal analysis for an objective characterization of the complexity of circulating platelet shapes observed by means of transmission electron microscopy in order to characterize the in vivo hyperactivated platelets of familial hypercholesterolemic patients, distinguishing them from the in vivo resting platelets of healthy individuals. Platelet boundaries were extracted by means of automatically image analysis. Geometric complexity (fractal dimension, D) by box counting was automatically calculated. The platelet boundary observed by electron microscopy is fractal, the shape of the circulating platelets is more complex in FH (n = 6) than healthy subjects (n = 5, P < 0.01), with 100% correct classification in selected individuals. In vitro activated platelets from healthy subjects show an analogous increase of D. The observed high D in the platelet boundary in FH originates from the in vivo platelet activation. Computerized fractal analysis of platelet shape observed by transmission electron microscopy can provide accurate, quantitative data to study platelet activation in familial hypercholesterolemia and after administration of drugs or other therapeutic procedures. PMID:25877374

  14. Body size and the division of niche space: food and predation differentially shape the distribution of Serengeti grazers.

    PubMed

    Hopcraft, J Grant C; Anderson, T Michael; Pérez-Vila, Saleta; Mayemba, Emilian; Olff, Han

    2012-01-01

    1. Theory predicts that small grazers are regulated by the digestive quality of grass, while large grazers extract sufficient nutrients from low-quality forage and are regulated by its abundance instead. In addition, predation potentially affects populations of small grazers more than large grazers, because predators have difficulty capturing and handling large prey. 2. We analyse the spatial distribution of five grazer species of different body size in relation to gradients of food availability and predation risk. Specifically, we investigate how the quality of grass, the abundance of grass biomass and the associated risks of predation affect the habitat use of small, intermediate and large savanna grazers at a landscape level. 3. Resource selection functions of five mammalian grazer species surveyed over a 21-year period in Serengeti are calculated using logistic regressions. Variables included in the analyses are grass nitrogen, rainfall, topographic wetness index, woody cover, drainage lines, landscape curvature, water and human habitation. Structural equation modelling (SEM) is used to aggregate predictor variables into 'composites' representing food quality, food abundance and predation risk. Subsequently, SEM is used to investigate species' habitat use, defined as their recurrence in 5 × 5 km cells across repeated censuses. 4. The distribution of small grazers is constrained by predation and food quality, whereas the distribution of large grazers is relatively unconstrained. The distribution of the largest grazer (African buffalo) is primarily associated with forage abundance but not predation risk, while the distributions of the smallest grazers (Thomson's gazelle and Grant's gazelle) are associated with high grass quality and negatively with the risk of predation. The distributions of intermediate sized grazers (Coke's hartebeest and topi) suggest they optimize access to grass biomass of sufficient quality in relatively predator-safe areas. 5. The results

  15. Descriptive Study of Activities Identified by Principals as Parental Involvement Activities through Survey Research

    ERIC Educational Resources Information Center

    Anderson, Melinda

    2009-01-01

    This study was designed to identify parental involvement activities used by successful schools. Participating schools were identified as successful by an Academic Excellence Indicator System (AEIS) rating of recognized or exemplary. Using survey methods, data was collected from the principals of the schools about parental involvement activities on…

  16. Diverse protist grazers select for virulence-related traits in Legionella

    PubMed Central

    Amaro, Francisco; Wang, Wen; Gilbert, Jack A; Roger Anderson, O; Shuman, Howard A

    2015-01-01

    It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as ‘food poisoning'. PMID:25575308

  17. Predator diversity stabilizes and strengthens trophic control of a keystone grazer.

    PubMed

    Griffin, John N; Silliman, Brian R

    2011-02-23

    Despite the global vulnerability of predators to extinction, and the critical functional role they play in many ecosystems, there have been few realistic tests of the consequences of predator species deletion (conversely, predator diversity) in natural ecosystems. We performed a four-month field experiment in a southeastern United States salt marsh to test the role of predatory crab diversity in regulating populations of a keystone grazer that can decimate marsh vegetation at high densities. Our results revealed that a combination of this system's two resident predator species, in comparison to individual species, both stabilize and strengthen predation rates on the potent grazer. Monthly monitoring of predation rates from intense, hot summer months into the cooler autumn indicate this diversity benefit arises from predators responding differentially to changing environmental conditions across seasons. This study provides some of the first experimental field support for the insurance hypothesis from marine ecosystems, suggests that predator temporal complementarity may be more common than currently perceived, and argues for conservation of predator diversity to ensure reliable and effective control of potentially habitat-destroying grazers. PMID:20739314

  18. Biased and unbiased strategies to identify biologically active small molecules.

    PubMed

    Abet, Valentina; Mariani, Angelica; Truscott, Fiona R; Britton, Sébastien; Rodriguez, Raphaël

    2014-08-15

    Small molecules are central players in chemical biology studies. They promote the perturbation of cellular processes underlying diseases and enable the identification of biological targets that can be validated for therapeutic intervention. Small molecules have been shown to accurately tune a single function of pluripotent proteins in a reversible manner with exceptional temporal resolution. The identification of molecular probes and drugs remains a worthy challenge that can be addressed by the use of biased and unbiased strategies. Hypothesis-driven methodologies employs a known biological target to synthesize complementary hits while discovery-driven strategies offer the additional means of identifying previously unanticipated biological targets. This review article provides a general overview of recent synthetic frameworks that gave rise to an impressive arsenal of biologically active small molecules with unprecedented cellular mechanisms. PMID:24811300

  19. How Can We Identify Ictal and Interictal Abnormal Activity?

    PubMed Central

    Fisher, Robert S.; Scharfman, Helen E.; deCurtis, Marco

    2015-01-01

    The International League Against Epilepsy (ILAE) defined a seizure as “a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain.” This definition has been used since the era of Hughlings Jackson, and does not take into account subsequent advances made in epilepsy and neuroscience research. The clinical diagnosis of a seizure is empirical, based upon constellations of certain signs and symptoms, while simultaneously ruling out a list of potential imitators of seizures. Seizures should be delimited in time, but the borders of ictal (during a seizure), interictal (between seizures) and postictal (after a seizure) often are indistinct. EEG recording is potentially very helpful for confirmation, classification and localization. About a half-dozen common EEG patterns are encountered during seizures. Clinicians rely on researchers to answer such questions as why seizures start, spread and stop, whether seizures involve increased synchrony, the extent to which extra-cortical structures are involved, and how to identify the seizure network and at what points interventions are likely to be helpful. Basic scientists have different challenges in use of the word ‘seizure,’ such as distinguishing seizures from normal behavior, which would seem easy but can be very difficult because some rodents have EEG activity during normal behavior that resembles spike-wave discharge or bursts of rhythmic spiking. It is also important to define when a seizure begins and stops so that seizures can be quantified accurately for pre-clinical studies. When asking what causes seizures, the transition to a seizure and differentiating the pre-ictal, ictal and post-ictal state is also important because what occurs before a seizure could be causal and may warrant further investigation for that reason. These and other issues are discussed by three epilepsy researchers with clinical and basic science expertise. PMID:25012363

  20. Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters

    PubMed Central

    Unrein, Fernando; Gasol, Josep M; Not, Fabrice; Forn, Irene; Massana, Ramon

    2014-01-01

    Grazing rate estimates indicate that approximately half of the bacterivory in oligotrophic oceans is due to mixotrophic flagellates (MFs). However, most estimations have considered algae as a single group. Here we aimed at opening the black-box of the phytoflagellates (PFs) <20 μm. Haptophytes, chlorophytes, cryptophytes and pigmented dinoflagellates were identified using fluorescent in situ hybridization or by standard 4′,6-diamidino-2-phenylindole staining. Their fluctuations in abundance, cell size, biomass and bacterivory rates were measured through an annual cycle in an oligotrophic coastal system. On average, we were able to assign to these groups: 37% of the total pico-PFs and 65% of the nano-PFs composition. Chlorophytes were mostly picoplanktonic and they never ingested fluorescently labeled bacteria. About 50% of the PF <20 μm biomass was represented by mixotrophic algae. Pigmented dinoflagellates were the least abundant group with little impact on bacterioplankton. Cryptophytes were quantitatively important during the coldest periods and explained about 4% of total bacterivory. Haptophytes were the most important mixotrophic group: (i) they were mostly represented by cells 3–5 μm in size present year-round; (ii) cell-specific grazing rates were comparable to those of other bacterivorous non-photosynthetic organisms, regardless of the in situ nutrient availability conditions; (iii) these organisms could acquire a significant portion of their carbon by ingesting bacteria; and (iv) haptophytes explained on average 40% of the bacterivory exerted by MFs and were responsible for 9–27% of total bacterivory at this site. Our results, when considered alongside the widespread distribution of haptophytes in the ocean, indicate that they have a key role as bacterivores in marine ecosystems. PMID:23924785

  1. Functional and ecological consequences of saprotrophic fungus–grazer interactions

    PubMed Central

    Crowther, Thomas W; Boddy, Lynne; Hefin Jones, T

    2012-01-01

    Saprotrophic fungi are key regulators of nutrient cycling in terrestrial ecosystems. They are the primary agents of plant litter decomposition and their hyphal networks, which grow throughout the soil–litter interface, represent highly dynamic channels through which nutrients are readily distributed. By ingesting hyphae and dispersing spores, soil invertebrates, including Arthropoda, Oligochaetae and Nematoda, influence fungal-mediated nutrient distribution within soil. Fungal physiological responses to grazing include changes to hydrolytic enzyme production and respiration rates. These directly affect nutrient mineralisation and the flux of CO2 between terrestrial and atmospheric pools. Preferential grazing may also exert selective pressures on saprotrophic communities, driving shifts in fungal succession and community composition. These functional and ecological consequences of grazing are intrinsically linked, and influenced by invertebrate grazing intensity. High-intensity grazing often reduces fungal growth and activity, whereas low-intensity grazing can have stimulatory effects. Grazing intensity is directly related to invertebrate abundance, and varies dramatically between species and functional groups. Invertebrate diversity and community composition, therefore, represent key factors determining the functioning of saprotrophic fungal communities and the services they provide. PMID:22717883

  2. Activation tag screening to identify novel genes for trichothecene resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of our research is to identify plant genes which enhance trichothecene resistance and, ultimately, Fusarium Head Blight resistance in wheat and barley. We are taking a two pronged approach using Arabidopsis to identify plant genes which confer resistance to trichothecenes. The first approac...

  3. Management Development Program. Preliminary Organizing Structure for Identifying Educational Activities.

    ERIC Educational Resources Information Center

    Cloud, Sherrill

    The Management Development Program, which was designed to address the needs of executive-level administrators of higher education, is described. The program was developed by the National Center for Higher Education Management Systems (NCHEMS). Seven limitations of executive-level administrators are identified, along with the capabilities of NCHEMS…

  4. Using perturbations to identify the brain circuits underlying active vision

    PubMed Central

    Wurtz, Robert H.

    2015-01-01

    The visual and oculomotor systems in the brain have been studied extensively in the primate. Together, they can be regarded as a single brain system that underlies active vision—the normal vision that begins with visual processing in the retina and extends through the brain to the generation of eye movement by the brainstem. The system is probably one of the most thoroughly studied brain systems in the primate, and it offers an ideal opportunity to evaluate the advantages and disadvantages of the series of perturbation techniques that have been used to study it. The perturbations have been critical in moving from correlations between neuronal activity and behaviour closer to a causal relation between neuronal activity and behaviour. The same perturbation techniques have also been used to tease out neuronal circuits that are related to active vision that in turn are driving behaviour. The evolution of perturbation techniques includes ablation of both cortical and subcortical targets, punctate chemical lesions, reversible inactivations, electrical stimulation, and finally the expanding optogenetic techniques. The evolution of perturbation techniques has supported progressively stronger conclusions about what neuronal circuits in the brain underlie active vision and how the circuits themselves might be organized. PMID:26240420

  5. Activation Tagging Identifies a Conserved MYB Regulator of Phenylpropanoid Biosynthesis

    PubMed Central

    Borevitz, Justin O.; Xia, Yiji; Blount, Jack; Dixon, Richard A.; Lamb, Chris

    2000-01-01

    Plants produce a wide array of natural products, many of which are likely to be useful bioactive structures. Unfortunately, these complex natural products usually occur at very low abundance and with restricted tissue distribution, thereby hindering their evaluation. Here, we report a novel approach for enhancing the accumulation of natural products based on activation tagging by Agrobacterium-mediated transformation with a T-DNA that carries cauliflower mosaic virus 35S enhancer sequences at its right border. Among ∼5000 Arabidopsis activation-tagged lines, we found a plant that exhibited intense purple pigmentation in many vegetative organs throughout development. This upregulation of pigmentation reflected a dominant mutation that resulted in massive activation of phenylpropanoid biosynthetic genes and enhanced accumulation of lignin, hydroxycinnamic acid esters, and flavonoids, including various anthocyanins that were responsible for the purple color. These phenotypes, caused by insertion of the viral enhancer sequences adjacent to an MYB transcription factor gene, indicate that activation tagging can overcome the stringent genetic controls regulating the accumulation of specific natural products during plant development. Our findings suggest a functional genomics approach to the biotechnological evaluation of phytochemical biodiversity through the generation of massively enriched tissue sources for drug screening and for isolating underlying regulatory and biosynthetic genes. PMID:11148285

  6. Loss of a large grazer impacts savanna grassland plant communities similarly in North America and South Africa.

    PubMed

    Eby, Stephanie; Burkepile, Deron E; Fynn, Richard W S; Burns, Catherine E; Govender, Navashni; Hagenah, Nicole; Koerner, Sally E; Matchett, Katherine J; Thompson, Dave I; Wilcox, Kevin R; Collins, Scott L; Kirkman, Kevin P; Knapp, Alan K; Smith, Melinda D

    2014-05-01

    Large herbivore grazing is a widespread disturbance in mesic savanna grasslands which increases herbaceous plant community richness and diversity. However, humans are modifying the impacts of grazing on these ecosystems by removing grazers. A more general understanding of how grazer loss will impact these ecosystems is hampered by differences in the diversity of large herbivore assemblages among savanna grasslands, which can affect the way that grazing influences plant communities. To avoid this we used two unique enclosures each containing a single, functionally similar large herbivore species. Specifically, we studied a bison (Bos bison) enclosure at Konza Prairie Biological Station, USA and an African buffalo (Syncerus caffer) enclosure in Kruger National Park, South Africa. Within these enclosures we erected exclosures in annually burned and unburned sites to determine how grazer loss would impact herbaceous plant communities, while controlling for potential fire-grazing interactions. At both sites, removal of the only grazer decreased grass and forb richness, evenness and diversity, over time. However, in Kruger these changes only occurred with burning. At both sites, changes in plant communities were driven by increased dominance with herbivore exclusion. At Konza, this was caused by increased abundance of one grass species, Andropogon gerardii, while at Kruger, three grasses, Themeda triandra, Panicum coloratum, and Digitaria eriantha increased in abundance. PMID:24554031

  7. Identifying the Main Driver of Active Region Outflows

    NASA Astrophysics Data System (ADS)

    Baker, D.; van Driel-Gesztelyi, L.; Mandrini, C. H.; Démoulin, P.; Murray, M. J.

    2012-08-01

    Hinode's EUV Imaging Spectrometer (EIS) has discovered ubiquitous outflows of a few to 50 km s-1 from active regions (ARs). The characteristics of these outflows are very curious in that they are most prominent at the AR boundary and appear over monopolar magnetic areas. They are linked to strong non-thermal line broadening and are stronger in hotter EUV lines. The outflows persist for at least several days. Whereas red-shifted down flows observed in AR closed loops are well understood, to date there is no general consensus for the mechanism(s) driving blue-shifted AR-related outflows. We use Hinode EIS and X-Ray Telescope observations of AR 10942 coupled with magnetic modeling to demonstrate for the first time that the outflows originate from specific locations of the magnetic topology where field lines display strong gradients of magnetic connectivity, namely quasi-separatrix layers (QSLs), or in the limit of infinitely thin QSLs, separatrices. The strongest AR outflows were found to be in the vicinity of QSL sections located over areas of strong magnetic field. We argue that magnetic reconnection at QSLs, separating closed field lines of the AR and either large-scale externally connected or ‘open’ field lines, is a viable mechanism for driving AR outflows which are potentially sources of the slow solar wind. In fact, magnetic reconnection along QSLs (including separatricies) is the first theory to explain the most puzzling characteristics of the outflows, namely their occurrence over monopolar areas at the periphery of ARs and their longevity.

  8. Multivariate statistical analysis of stream-sediment geochemistry in the Grazer Paläozoikum, Austria

    USGS Publications Warehouse

    Weber, L.; Davis, J.C.

    1990-01-01

    The Austrian reconnaissance study of stream-sediment composition — more than 30000 clay-fraction samples collected over an area of 40000 km2 — is summarized in an atlas of regional maps that show the distributions of 35 elements. These maps, rich in information, reveal complicated patterns of element abundance that are difficult to compare on more than a small number of maps at one time. In such a study, multivariate procedures such as simultaneous R-Q mode components analysis may be helpful. They can compress a large number of variables into a much smaller number of independent linear combinations. These composite variables may be mapped and relationships sought between them and geological properties. As an example, R-Q mode components analysis is applied here to the Grazer Paläozoikum, a tectonic unit northeast of the city of Graz, which is composed of diverse lithologies and contains many mineral deposits.

  9. Genotype × genotype interactions between the toxic cyanobacterium Microcystis and its grazer, the waterflea Daphnia

    PubMed Central

    Lemaire, Veerle; Brusciotti, Silvia; van Gremberghe, Ineke; Vyverman, Wim; Vanoverbeke, Joost; De Meester, Luc

    2012-01-01

    Toxic algal blooms are an important problem worldwide. The literature on toxic cyanobacteria blooms in inland waters reports widely divergent results on whether zooplankton can control cyanobacteria blooms or cyanobacteria suppress zooplankton by their toxins. Here we test whether this may be due to genotype × genotype interactions, in which interactions between the large-bodied and efficient grazer Daphnia and the widespread cyanobacterium Microcystis are not only dependent on Microcystis strain or Daphnia genotype but are specific to genotype × genotype combinations. We show that genotype × genotype interactions are important in explaining mortality in short-time exposures of Daphnia to Microcystis. These genotype × genotype interactions may result in local coadaptation and a geographic mosaic of coevolution. Genotype × genotype interactions can explain why the literature on zooplankton–cyanobacteria interactions is seemingly inconsistent, and provide hope that zooplankton can contribute to the suppression of cyanobacteria blooms in restoration projects. PMID:25568039

  10. Grazer traits, competition, and carbon sources to a headwater-stream food web.

    PubMed

    McNeely, Camille; Finlay, Jacques C; Power, Mary E

    2007-02-01

    We investigated the effect of grazing by a dominant invertebrate grazer (the caddisfly Glossosoma penitum) on the energy sources used by other consumers in a headwater-stream food web. Stable isotope studies in small, forested streams in northern California have shown that G. penitum larvae derive most of their carbon from algae, despite low algal standing crops. We hypothesized that the caddisfly competes with other primary consumers (including mayflies) for algal food and increases their reliance on terrestrial detritus. Because Glossosoma are abundant and defended from predators by stone cases, their consumption of algal energy may reduce its transfer up the food chain. We removed Glossosoma (natural densities >1000 caddisflies/m2) from five approximately 4 m2) stream sections during the summer of 2000 and measured responses of algae, invertebrate primary consumers, and invertebrate predators. The treatment reduced Glossosoma biomass by 80-90%. We observed a doubling in chlorophyll a per area in sections with reduced Glossosoma abundance and aggregative increases in the biomass of undefended primary consumers. Heptageniid mayfly larvae consumed more algae (as measured by stable carbon isotope ratios and gut content analysis) in caddisfly removal plots at the end of the 60-day experiment, although not after one month. We did not see isotopic evidence of increased algal carbon in invertebrate predators, however. Patterns of caddisfly and mayfly diets in the surrounding watershed suggested that mayfly diets are variable and include algae and detrital carbon in variable proportions, but scraping caddisflies consume primarily algae. Caddisfly and mayfly diets are more similar in larger, more productive streams where the mayflies assimilate more algae. Isotopic analysis, in combination with measurements of macroinvertebrate abundance and biomass in unmanipulated plots, suggested that a substantial portion of the invertebrate community (>50% of biomass) was supported

  11. Using Indices of Fidelity to Intervention Core Components to Identify Program Active Ingredients

    ERIC Educational Resources Information Center

    Abry, Tashia; Hulleman, Chris S.; Rimm-Kaufman, Sara E.

    2015-01-01

    Identifying the active ingredients of an intervention--intervention-specific components serving as key levers of change--is crucial for unpacking the intervention black box. Measures of intervention fidelity can be used to identify specific active ingredients, yet such applications are rare. We illustrate how fidelity measures can be used to…

  12. A modified reverse one-hybrid screen identifies transcriptional activation in Phyochrome-Interacting Factor 3

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Transcriptional activation domains (TAD) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput...

  13. Use of component analyses to identify active variables in treatment packages for children with feeding disorders.

    PubMed Central

    Cooper, L J; Wacker, D P; McComas, J J; Brown, K; Peck, S M; Richman, D; Drew, J; Frischmeyer, P; Millard, T

    1995-01-01

    We evaluated the separate components in treatment packages for food refusal of 4 young children. First, treatment packages were implemented until food acceptance improved. Next, a component analysis was conducted within a multielement or reversal design to identify the active components that facilitated food acceptance. The results indicated that escape extinction was always identified as an active variable when assessed; however, other variables, including positive reinforcement and noncontingent play, were also identified as active variables for 2 of the children. The results suggest that the component analysis was useful for identifying variables that affected food acceptance. PMID:7601802

  14. Community context mediates the top-down vs. bottom-up effects of grazers on rocky shores.

    PubMed

    Bracken, Matthew E S; Dolecal, Renee E; Long, Jeremy D

    2014-06-01

    Interactions between grazers and autotrophs are complex, including both top-down consumptive and bottom-up facilitative effects of grazers. Thus, in addition to consuming autotrophs, herbivores can also enhance autotroph biomass by recycling limiting nutrients, thereby increasing nutrient availability. Here, we evaluated these consumptive and facilitative interactions between snails (Littorina littorea) and seaweeds (Fucus vesiculosus and Ulva lactuca) on a rocky shore. We partitioned herbivores' total effects on seaweeds into their consumptive and facilitative effects and evaluated how community context (the presence of another seaweed species) modified the effects of Littorina on a focal seaweed species. Ulva, the more palatable species, enhanced the facilitative effects of Littorina on Fucus. Ulva did not modify the consumptive effect of Littorina on Fucus. Taken together, the consumptive and facilitative effects of snails on Fucus in the presence of Ulva balanced each other, resulting in no net effect of Littorina on Fucus. In contrast, the only effect of Fucus on Ulva was to enhance consumptive effects of Littorina on Ulva. Our results highlight the necessity of considering both consumptive and facilitative effects of herbivores on multiple autotroph species in order to gain a mechanistic understanding of grazers' top-down and bottom-up roles in structuring communities. PMID:25039210

  15. Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments.

    PubMed

    Pradeep Ram, A S; Colombet, Jonathan; Perriere, Fanny; Thouvenot, Antoine; Sime-Ngando, Telesphore

    2015-02-01

    In aquatic systems, limited data exists on the impact of mortality forces such as viral lysis and flagellate grazing when seeking to explain factors regulating prokaryotic metabolism. We explored the relative influence of top-down factors (viral lysis and heterotrophic nanoflagellate grazing) on prokaryotic mortality and their subsequent impact on their community metabolism in the euphotic zone of 21 temperate freshwater lakes located in the French Massif Central. Prokaryotic growth efficiency (PGE, index of prokaryotic community metabolism) determined from prokaryotic production and respiration measurements varied from 5 to 74% across the lakes. Viral and potential grazer-induced mortality of prokaryotes had contrasting impact on PGE. Potential flagellate grazing was found to enhance PGE whereas viral lysis had antagonistic impacts on PGE. The average PGE value in the grazing and viral lysis dominated lake water samples was 35.4% (±15.2%) and 17.2% (±8.1%), respectively. Selective viral lysis or flagellate grazing on prokaryotes together with the nature of contrasted substrates released through mortality processes can perhaps explain for the observed variation and differences in PGE among the studied lakes. The influences of such specific top-down processes on PGE can have strong implications on the carbon and nutrient fluxes in freshwater pelagic environments. PMID:25764557

  16. Grazer-induced morphological defense in Scenedesmus obliquus is affected by competition against Microcystis aeruginosa

    PubMed Central

    Zhu, Xuexia; Wang, Jun; Lu, Yichun; Chen, Qinwen; Yang, Zhou

    2015-01-01

    The green alga Scenedesmus is known for its phenotypic plasticity in response to grazing risk. However, the benefits of colony formation induced by infochemicals from zooplankton should come with costs. That is, a tradeoff in benefit-to-cost ratios is likely under complex environmental conditions. In this study, we hypothesized that the coexistence of Scenedesmus and its competitors decreases the formation of anti-grazer colonies in Scenedesmus. Results demonstrated that the presence of a competitor Microcystis aeruginosa inhibited inducible defensive colony formation of Scenedesmus obliquus, and the established defensive colonies negatively affected the competitive ability of S. obliquus. The proportion of induced defensive colonies in cultures was dependent on the relative abundance of competitors. Under low competition intensity, large amount of eight-celled colonies were formed but at the cost of decreased competitive inhibition on M. aeruginosa. By contrast, defensive colony formation of S. obliquus slacked in the presence of high competition intensity to maintain a high displacement rate (competitive ability). In conclusion, S. obliquus exhibited different responses to potential grazing pressure under different intensities of competition, i.e., Scenedesmus morphological response to grazing infochemicals was affected by competition against Microcystis. PMID:26224387

  17. Introduced grazers can restrict potential soil carbon sequestration through impacts on plant community composition.

    PubMed

    Bagchi, Sumanta; Ritchie, Mark E

    2010-08-01

    Grazing occurs over a third of the earth's land surface and may potentially influence the storage of 10(9) Mg year(-1) of greenhouse gases as soil C. Displacement of native herbivores by high densities of livestock has often led to overgrazing and soil C loss. However, it remains unknown whether matching livestock densities to those of native herbivores can yield equivalent soil C sequestration. In the Trans-Himalayas we found that, despite comparable grazing intensities, watersheds converted to pastoralism had 49% lower soil C than watersheds which retain native herbivores. Experimental grazer-exclusion within each watershed type, show that this difference appears to be driven by indirect effects of livestock diet selection, leading to vegetation shifts that lower plant production and reduce likely soil C inputs from vegetation by c. 25 gC m(-2) year(-1). Our results suggest that while accounting for direct impacts (stocking density) is a major step, managing indirect impacts on vegetation composition are equally important in influencing soil C sequestration in grazing ecosystems. PMID:20482575

  18. Decoupling of nutrient and grazer impacts on a benthic estuarine diatom assemblage

    PubMed Central

    Armitage, Anna R.; Gonzalez, Vanessa L.; Fong, Peggy

    2014-01-01

    Strong interactions between top-down (consumptive) and bottom-up (resource supply) trophic factors occur in many aquatic communities, but these forces can act independently in some microphytobenthic communities. Within benthic estuarine diatom assemblages, the dynamics of these interactions and how they vary with abiotic environmental conditions are not well understood. We conducted a field experiment at two sites with varying habitat characteristics to investigate the interactive effects of grazers and nutrients on benthic estuarine diatoms. We crossed snail (Cerithidea californica) and nutrient (nitrogen and phosphorus) addition treatments in enclosures on a restored tidal sandflat and a reference tidal mudflat in Mugu Lagoon, southern California. We repeated the study in summer 2000 and spring 2001 to assess temporal variation in the interactions. Snails caused a large decrease in diatom relative abundance and biomass (estimated as surface area); nutrients increased diatom abundance but did not alter diatom biomass. Snails and nutrients both reduced average diatom length, although the nutrient effect was weaker and temporally variable, occurring in the reference mudflat in the spring. There were few interactions between snail and nutrient addition treatments, suggesting that links between top-down and bottom-up forces on the diatom community were weak. There were no consistent differences in diatom assemblage characteristics between the two study sites, despite marked differences in sediment grain size and other abiotic characteristics between the sites. The strong diatom response to herbivores and weaker responses to enrichment differed from the previous studies where cyanobacteria increased in response to nutrient enrichment, further dissolving the “black box” perception of microphytobenthic communities. PMID:25568503

  19. Plant Trait Assembly Affects Superiority of Grazer's Foraging Strategies in Species-Rich Grasslands

    PubMed Central

    Mládek, Jan; Mládková, Pavla; Hejcmanová, Pavla; Dvorský, Miroslav; Pavlu, Vilém; De Bello, Francesco; Duchoslav, Martin; Hejcman, Michal; Pakeman, Robin J.

    2013-01-01

    Background Current plant – herbivore interaction models and experiments with mammalian herbivores grazing plant monocultures show the superiority of a maximizing forage quality strategy (MFQ) over a maximizing intake strategy (MI). However, there is a lack of evidence whether grazers comply with the model predictions under field conditions. Methodology/Findings We assessed diet selection of sheep (Ovis aries) using plant functional traits in productive mesic vs. low-productivity dry species-rich grasslands dominated by resource-exploitative vs. resource-conservative species respectively. Each grassland type was studied in two replicates for two years. We investigated the first grazing cycle in a set of 288 plots with a diameter of 30 cm, i.e. the size of sheep feeding station. In mesic grasslands, high plot defoliation was associated with community weighted means of leaf traits referring to high forage quality, i.e. low leaf dry matter content (LDMC) and high specific leaf area (SLA), with a high proportion of legumes and the most with high community weighted mean of forage indicator value. In contrast in dry grasslands, high community weighted mean of canopy height, an estimate of forage quantity, was the best predictor of plot defoliation. Similar differences in selection on forage quality vs. quantity were detected within plots. Sheep selected plants with higher forage indicator values than the plot specific community weighted mean of forage indicator value in mesic grasslands whereas taller plants were selected in dry grasslands. However, at this scale sheep avoided legumes and plants with higher SLA, preferred plants with higher LDMC while grazing plants with higher forage indicator values in mesic grasslands. Conclusions Our findings indicate that MFQ appears superior over MI only in habitats with a predominance of resource-exploitative species. Furthermore, plant functional traits (LDMC, SLA, nitrogen fixer) seem to be helpful correlates of forage quality

  20. Functional Brain Activation Differences in Stuttering Identified with a Rapid fMRI Sequence

    ERIC Educational Resources Information Center

    Loucks, Torrey; Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

    2011-01-01

    The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech…

  1. Identifying Facilitators and Barriers to Physical Activity for Adults with Down Syndrome

    ERIC Educational Resources Information Center

    Mahy, J.; Shields, N.; Taylor, N. F.; Dodd, K. J.

    2010-01-01

    Background: Adults with Down syndrome are typically sedentary, and many do not participate in the recommended levels of physical activity per week. The aim of this study was to identify the facilitators and barriers to physical activity for this group. Method: Semi-structured interviews were conducted to elicit the views of adults with Down…

  2. Bayesian Modeling of the Effects of Extreme Flooding and the Grazer Community on Algal Biomass Dynamics in a Monsoonal Taiwan Stream.

    PubMed

    Chiu, Ming-Chih; Kuo, Mei-Hwa; Chang, Hao-Yen; Lin, Hsing-Juh

    2016-08-01

    The effects of grazing and climate change on primary production have been studied widely, but seldom with mechanistic models. We used a Bayesian model to examine the effects of extreme weather and the invertebrate grazer community on epilithic algal biomass dynamics over 10 years (from January 2004 to August 2013). Algal biomass and the invertebrate grazer community were monitored in the upstream drainage of the Dajia River in Taiwan, where extreme floods have been becoming more frequent. The biomass of epilithic algae changed, both seasonally and annually, and extreme flooding changed the growth and resistance to flow detachment of the algae. Invertebrate grazing pressure changes with the structure of the invertebrate grazer community, which, in turn, is affected by the flow regime. Invertebrate grazer community structure and extreme flooding both affected the dynamics of epilithic algae, but in different ways. Awareness of the interactions between algal communities and grazers/abiotic factors can help with the design of future studies and could facilitate the development of management programs for stream ecosystems. PMID:27273089

  3. High Throughput Screening Identifies Novel Lead Compounds with Activity against Larval, Juvenile and Adult Schistosoma mansoni.

    PubMed

    Mansour, Nuha R; Paveley, Ross; Gardner, J Mark F; Bell, Andrew S; Parkinson, Tanya; Bickle, Quentin

    2016-04-01

    An estimated 600 million people are affected by the helminth disease schistosomiasis caused by parasites of the genus Schistosoma. There is currently only one drug recommended for treating schistosomiasis, praziquantel (PZQ), which is effective against adult worms but not against the juvenile stage. In an attempt to identify improved drugs for treating the disease, we have carried out high throughput screening of a number of small molecule libraries with the aim of identifying lead compounds with balanced activity against all life stages of Schistosoma. A total of almost 300,000 compounds were screened using a high throughput assay based on motility of worm larvae and image analysis of assay plates. Hits were screened against juvenile and adult worms to identify broadly active compounds and against a mammalian cell line to assess cytotoxicity. A number of compounds were identified as promising leads for further chemical optimization. PMID:27128493

  4. High Throughput Screening Identifies Novel Lead Compounds with Activity against Larval, Juvenile and Adult Schistosoma mansoni

    PubMed Central

    Gardner, J. Mark F.; Bell, Andrew S.; Parkinson, Tanya; Bickle, Quentin

    2016-01-01

    An estimated 600 million people are affected by the helminth disease schistosomiasis caused by parasites of the genus Schistosoma. There is currently only one drug recommended for treating schistosomiasis, praziquantel (PZQ), which is effective against adult worms but not against the juvenile stage. In an attempt to identify improved drugs for treating the disease, we have carried out high throughput screening of a number of small molecule libraries with the aim of identifying lead compounds with balanced activity against all life stages of Schistosoma. A total of almost 300,000 compounds were screened using a high throughput assay based on motility of worm larvae and image analysis of assay plates. Hits were screened against juvenile and adult worms to identify broadly active compounds and against a mammalian cell line to assess cytotoxicity. A number of compounds were identified as promising leads for further chemical optimization. PMID:27128493

  5. Identifying predictors of activity based anorexia susceptibility in diverse genetic rodent populations.

    PubMed

    Pjetri, Eneda; de Haas, Ria; de Jong, Simone; Gelegen, Cigdem; Oppelaar, Hugo; Verhagen, Linda A W; Eijkemans, Marinus J C; Adan, Roger A; Olivier, Berend; Kas, Martien J

    2012-01-01

    Animal studies are very useful in detection of early disease indicators and in unravelling the pathophysiological processes underlying core psychiatric disorder phenotypes. Early indicators are critical for preventive and efficient treatment of progressive psychiatric disorders like anorexia nervosa. Comparable to physical hyperactivity observed in anorexia nervosa patients, in the activity-based anorexia rodent model, mice and rats express paradoxical high voluntary wheel running activity levels when food restricted. Eleven inbred mouse strains and outbred Wistar WU rats were exposed to the activity-based anorexia model in search of identifying susceptibility predictors. Body weight, food intake and wheel running activity levels of each individual mouse and rat were measured. Mouse strains and rats with high wheel running activity levels during food restriction exhibited accelerated body weight loss. Linear mixed models for repeated measures analysis showed that baseline wheel running activity levels preceding the scheduled food restriction phase strongly predicted activity-based anorexia susceptibility (mice: Beta  =  -0.0158 (±0.003 SE), P<0.0001; rats: Beta  =  -0.0242 (±0.004 SE), P<0.0001) compared to other baseline parameters. These results suggest that physical activity levels play an important role in activity-based anorexia susceptibility in different rodent species with genetically diverse background. These findings support previous retrospective studies on physical activity levels in anorexia nervosa patients and indicate that pre-morbid physical activity levels could reflect an early indicator for disease severity. PMID:23226287

  6. Identifying the Common Characteristics of Comprehensive School Physical Activity Programs in Louisiana

    ERIC Educational Resources Information Center

    Deslatte, Kyrie'; Carson, Russell L.

    2014-01-01

    The purpose of this project was to (a) determine the common characteristics of current comprehensive school physical activity programs (CSPAP) in Louisiana and (b) identify strategies for implementing a CSPAP. Four individuals (i.e., one physical education teacher, one principal, and two classroom teachers) were recruited from three public schools…

  7. Use of Bromodeoxyuridine Immunocapture To Identify Active Bacteria Associated with Arbuscular Mycorrhizal Hyphae

    PubMed Central

    Artursson, Veronica; Jansson, Janet K.

    2003-01-01

    Arbuscular mycorrhizae are beneficial for crops grown under low-till management systems. Increasingly, it is becoming apparent that bacteria associated with mycorrhizae can enhance the beneficial relationship between mycorrhizae and plants. However, it has been difficult to study these relationships by conventional techniques. In this study actively growing bacteria were identified in soil from an undisturbed fallow field known to contain arbuscular mycorrhizae by using molecular tools to eliminate the need for cultivation. A thymidine analog, bromodeoxyuridine (BrdU), was added to the soil and incubated for 2 days. DNA was extracted, and the newly synthesized DNA was isolated by immunocapture of the BrdU-containing DNA. The active bacteria in the community were identified by 16S rRNA gene PCR amplification and DNA sequence analysis. Based on 16S rRNA gene sequence information, a selective medium was chosen to isolate the corresponding active bacteria. Bacillus cereus strain VA1, one of the bacteria identified by the BrdU method, was isolated from the soil and tagged with green fluorescent protein. By using confocal microscopy, this bacterium was shown to clearly attach to arbuscular mycorrhizal hyphae. This study was the first to use this combination of molecular and traditional approaches to isolate, identify, and visualize a specific bacterium that is active in fallow soil and associates with arbuscular mycorrhizal hyphae. PMID:14532082

  8. Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism

    PubMed Central

    Gut, Philipp; Baeza-Raja, Bernat; Andersson, Olov; Hasenkamp, Laura; Hsiao, Joseph; Hesselson, Daniel; Akassoglou, Katerina; Verdin, Eric; Hirschey, Matthew D.; Stainier, Didier Y.R.

    2012-01-01

    Improving the control of energy homeostasis can lower cardiovascular risk in metabolically compromised individuals. To identify new regulators of whole-body energy control, we conducted a high-throughput screen in transgenic reporter zebrafish for small molecules that modulate the expression of the fasting-inducible gluconeogenic gene pck1. We show that this in vivo strategy identified several drugs that impact gluconeogenesis in humans, as well as metabolically uncharacterized compounds. Most notably, we find that the Translocator Protein (TSPO) ligands PK 11195 and Ro5-4864 are glucose lowering agents despite a strong inductive effect on pck1 expression. We show that these drugs are activators of a fasting-like energy state, and importantly that they protect high-fat diet induced obese mice from hepatosteatosis and glucose intolerance, two pathological manifestations of metabolic dysregulation. Thus, using a whole-organism screening strategy, this study has identified new small molecule activators of fasting metabolism. PMID:23201900

  9. A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity

    PubMed Central

    2016-01-01

    Recent outbreaks of highly pathogenic and occasional drug-resistant influenza strains have highlighted the need to develop novel anti-influenza therapeutics. Here, we report computational and experimental efforts to identify influenza neuraminidase inhibitors from among the 3000 natural compounds in the Malaysian-Plants Natural-Product (NADI) database. These 3000 compounds were first docked into the neuraminidase active site. The five plants with the largest number of top predicted ligands were selected for experimental evaluation. Twelve specific compounds isolated from these five plants were shown to inhibit neuraminidase, including two compounds with IC50 values less than 92 μM. Furthermore, four of the 12 isolated compounds had also been identified in the top 100 compounds from the virtual screen. Together, these results suggest an effective new approach for identifying bioactive plant species that will further the identification of new pharmacologically active compounds from diverse natural-product resources. PMID:25555059

  10. A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity.

    PubMed

    Ikram, Nur Kusaira Khairul; Durrant, Jacob D; Muchtaridi, Muchtaridi; Zalaludin, Ayunni Salihah; Purwitasari, Neny; Mohamed, Nornisah; Rahim, Aisyah Saad Abdul; Lam, Chan Kit; Normi, Yahaya M; Rahman, Noorsaadah Abd; Amaro, Rommie E; Wahab, Habibah A

    2015-02-23

    Recent outbreaks of highly pathogenic and occasional drug-resistant influenza strains have highlighted the need to develop novel anti-influenza therapeutics. Here, we report computational and experimental efforts to identify influenza neuraminidase inhibitors from among the 3000 natural compounds in the Malaysian-Plants Natural-Product (NADI) database. These 3000 compounds were first docked into the neuraminidase active site. The five plants with the largest number of top predicted ligands were selected for experimental evaluation. Twelve specific compounds isolated from these five plants were shown to inhibit neuraminidase, including two compounds with IC50 values less than 92 μM. Furthermore, four of the 12 isolated compounds had also been identified in the top 100 compounds from the virtual screen. Together, these results suggest an effective new approach for identifying bioactive plant species that will further the identification of new pharmacologically active compounds from diverse natural-product resources. PMID:25555059

  11. Identifying the functional contribution of the defatty-acylase activity of SIRT6.

    PubMed

    Zhang, Xiaoyu; Khan, Saba; Jiang, Hong; Antonyak, Marc A; Chen, Xiao; Spiegelman, Nicole A; Shrimp, Jonathan H; Cerione, Richard A; Lin, Hening

    2016-08-01

    Mammalian sirtuin 6 (SIRT6) exhibits many pivotal functions and multiple enzymatic activities, but the contribution of each activity to the various functions is unclear. We identified a SIRT6 mutant (G60A) that possesses efficient defatty-acylase activity but has substantially decreased deacetylase activity in vitro and no detectable deacetylase activity in cells. The G60A mutant has a decreased ability to bind NAD(+), but the presence of fatty-acyl lysine peptides restores NAD(+) binding, explaining the retention of the defatty-acylase activity. Using this mutant, we found that the defatty-acylase activity of SIRT6 regulates the secretion of numerous proteins. Notably, many ribosomal proteins were secreted via exosomes from Sirt6 knockout mouse embryonic fibroblasts, and these exosomes increased NIH 3T3 cell proliferation compared with control exosomes. Our data indicate that distinct activities of SIRT6 regulate different pathways and that the G60A mutant is a useful tool to study the contribution of defatty-acylase activity to SIRT6's various functions. PMID:27322069

  12. Identifying combinations of risk and protective factors predicting physical activity change in high school students.

    PubMed

    Dunton, Genevieve Fridlund; Atienza, Audie A; Tscherne, James; Rodriguez, Daniel

    2011-02-01

    Research sought to identify combinations of risk and protective factors predicting change in physical activity (PA) over one year in high school students. Adolescents (N = 344; M = 15.7 years) participated in a longitudinal study with assessment of demographics, substance use/smoking exposure, height and weight, psychological factors, and PA in 10th and 11th grade. PA participation in 11th grade was greatest for adolescents who engaged in PA and had high sports competence (78%), and least for adolescents who did not engage in or enjoy PA (13%) in 10th grade. Identifying adolescent subgroups at risk for decreasing PA can inform the development of tailored interventions. PMID:21467595

  13. A high-content screening assay in transgenic zebrafish identifies two novel activators of fgf signaling.

    PubMed

    Saydmohammed, Manush; Vollmer, Laura L; Onuoha, Ezenwa Obi; Vogt, Andreas; Tsang, Michael

    2011-09-01

    Zebrafish have become an invaluable vertebrate animal model to interrogate small molecule libraries for modulators of complex biological pathways and phenotypes. We have recently described the implementation of a quantitative, high-content imaging assay in multi-well plates to analyze the effects of small molecules on Fibroblast Growth Factor (FGF) signaling in vivo. Here we have evaluated the capability of the assay to identify compounds that hyperactivate FGF signaling from a test cassette of agents with known biological activities. Using a transgenic zebrafish reporter line for FGF activity, we screened 1040 compounds from an annotated library of known bioactive agents, including FDA-approved drugs. The assay identified two molecules, 8-hydroxyquinoline sulfate and pyrithione zinc, that enhanced FGF signaling in specific areas of the brain. Subsequent studies revealed that both compounds specifically expanded FGF target gene expression. Furthermore, treatment of early stage embryos with either compound resulted in dorsalized phenotypes characteristic of hyperactivation of FGF signaling in early development. Documented activities for both agents included activation of extracellular signal-related kinase (ERK), consistent with FGF hyperactivation. To conclude, we demonstrate the power of automated quantitative high-content imaging to identify small molecule modulators of FGF. PMID:21932436

  14. Machine learning models identify molecules active against the Ebola virus in vitro

    PubMed Central

    Ekins, Sean; Freundlich, Joel S.; Clark, Alex M.; Anantpadma, Manu; Davey, Robert A.; Madrid, Peter

    2016-01-01

    The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC 50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in vitro. PMID:26834994

  15. Machine learning models identify molecules active against the Ebola virus in vitro.

    PubMed

    Ekins, Sean; Freundlich, Joel S; Clark, Alex M; Anantpadma, Manu; Davey, Robert A; Madrid, Peter

    2015-01-01

    The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC 50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in vitro. PMID:26834994

  16. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential.

    PubMed

    Chauhan, Santosh; Ahmed, Zahra; Bradfute, Steven B; Arko-Mensah, John; Mandell, Michael A; Won Choi, Seong; Kimura, Tomonori; Blanchet, Fabien; Waller, Anna; Mudd, Michal H; Jiang, Shanya; Sklar, Larry; Timmins, Graham S; Maphis, Nicole; Bhaskar, Kiran; Piguet, Vincent; Deretic, Vojo

    2015-01-01

    Autophagy is a conserved homeostatic process active in all human cells and affecting a spectrum of diseases. Here we use a pharmaceutical screen to discover new mechanisms for activation of autophagy. We identify a subset of pharmaceuticals inducing autophagic flux with effects in diverse cellular systems modelling specific stages of several human diseases such as HIV transmission and hyperphosphorylated tau accumulation in Alzheimer's disease. One drug, flubendazole, is a potent inducer of autophagy initiation and flux by affecting acetylated and dynamic microtubules in a reciprocal way. Disruption of dynamic microtubules by flubendazole results in mTOR deactivation and dissociation from lysosomes leading to TFEB (transcription factor EB) nuclear translocation and activation of autophagy. By inducing microtubule acetylation, flubendazole activates JNK1 leading to Bcl-2 phosphorylation, causing release of Beclin1 from Bcl-2-Beclin1 complexes for autophagy induction, thus uncovering a new approach to inducing autophagic flux that may be applicable in disease treatment. PMID:26503418

  17. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential

    PubMed Central

    Chauhan, Santosh; Ahmed, Zahra; Bradfute, Steven B.; Arko-Mensah, John; Mandell, Michael A.; Won Choi, Seong; Kimura, Tomonori; Blanchet, Fabien; Waller, Anna; Mudd, Michal H.; Jiang, Shanya; Sklar, Larry; Timmins, Graham S.; Maphis, Nicole; Bhaskar, Kiran; Piguet, Vincent; Deretic, Vojo

    2015-01-01

    Autophagy is a conserved homeostatic process active in all human cells and affecting a spectrum of diseases. Here we use a pharmaceutical screen to discover new mechanisms for activation of autophagy. We identify a subset of pharmaceuticals inducing autophagic flux with effects in diverse cellular systems modelling specific stages of several human diseases such as HIV transmission and hyperphosphorylated tau accumulation in Alzheimer's disease. One drug, flubendazole, is a potent inducer of autophagy initiation and flux by affecting acetylated and dynamic microtubules in a reciprocal way. Disruption of dynamic microtubules by flubendazole results in mTOR deactivation and dissociation from lysosomes leading to TFEB (transcription factor EB) nuclear translocation and activation of autophagy. By inducing microtubule acetylation, flubendazole activates JNK1 leading to Bcl-2 phosphorylation, causing release of Beclin1 from Bcl-2-Beclin1 complexes for autophagy induction, thus uncovering a new approach to inducing autophagic flux that may be applicable in disease treatment. PMID:26503418

  18. A novel pattern mining approach for identifying cognitive activity in EEG based functional brain networks.

    PubMed

    Thilaga, M; Vijayalakshmi, R; Nadarajan, R; Nandagopal, D

    2016-06-01

    The complex nature of neuronal interactions of the human brain has posed many challenges to the research community. To explore the underlying mechanisms of neuronal activity of cohesive brain regions during different cognitive activities, many innovative mathematical and computational models are required. This paper presents a novel Common Functional Pattern Mining approach to demonstrate the similar patterns of interactions due to common behavior of certain brain regions. The electrode sites of EEG-based functional brain network are modeled as a set of transactions and node-based complex network measures as itemsets. These itemsets are transformed into a graph data structure called Functional Pattern Graph. By mining this Functional Pattern Graph, the common functional patterns due to specific brain functioning can be identified. The empirical analyses show the efficiency of the proposed approach in identifying the extent to which the electrode sites (transactions) are similar during various cognitive load states. PMID:27401999

  19. Identifying Activity Levels and Steps in People with Stroke using a Novel Shoe-Based Sensor

    PubMed Central

    Fulk, George D.; Edgar, S. Ryan; Bierwirth, Rebecca; Hart, Phil; Lopez-Meyer, Paulo; Sazonov, Edward

    2012-01-01

    Background/Purpose Advances in sensory technologies provides a method to accurately assess activity levels of people with stroke in their community. This information could be used to determine the effectiveness of rehabilitation interventions as well as provide behavioral enhancing feedback. The purpose of this study was to assess the accuracy of a novel shoe-based sensor system (SmartShoe) to identify different functional postures and steps in people with stroke. The SmartShoe system consists of five force sensitive resistors built into a flexible insole and an accelerometer on the back of the shoe. Pressure and acceleration data are sent via Bluetooth to a smart phone. Methods Participants with stroke wore the SmartShoe while they performed activities of daily living (ADL) in sitting, standing and walking. Data from four participants were used to develop a multi-layer perceptron artificial neural network (ANN) to identify sitting, standing, and walking. A signal-processing algorithm used data from the pressure sensors to estimate number of steps taken while walking. The accuracy, precision and recall of the ANN for identifying the three functional postures were calculated using data from a different set of participants. Agreement between steps identified by SmartShoe and actual steps taken was analyzed using the Bland Altman method. Results The SmartShoe was able to accurately identify sitting, standing and walking. Accuracy, precision and recall were all greater than 95%. The mean difference between steps identified by SmartShoe and actual steps was less than 1 step. Discussion The SmartShoe was able to accurately identify different functional postures using a unique combination of pressure and acceleration data in people with stroke as they performed different ADLs. There was a strong level of agreement between actual steps taken and steps identified using the SmartShoe. Further study is needed to determine if the SmartShoe could be used to provide valid

  20. Emodin is identified as the active component of ether extracts from Rhizoma Polygoni Cuspidati, for anti-MRSA activity.

    PubMed

    Cao, Feng; Peng, Wei; Li, Xiaoli; Liu, Ming; Li, Bin; Qin, Rongxin; Jiang, Weiwei; Cen, Yanyan; Pan, Xichun; Yan, Zifei; Xiao, Kangkang; Zhou, Hong

    2015-06-01

    This study investigated the anti-methicillin-resistant Staphylococcus aureus (anti-MRSA) activity and chemical compositions of ether extracts from Rhizoma Polygoni Cuspidati (ET-RPC). Significant anti-MRSA activities of ET-RPC against MRSA252 and MRSA clinical strains were tested in in vitro antibacterial experiments, such as inhibition zone diameter test, minimal inhibitory concentration test, and dynamic bacterial growth assay. Subsequently, 7 major compounds of ET-RPC were purified and identified as polydatin, resveratrol-4-O-d-(6'-galloyl)-glucopyranoside, resveratrol, torachryson-8-O-glucoside, emodin-8-O-glucoside, 6-hydroxy-emodin, and emodin using liquid chromatography - electrospray ionization - tandem mass spectrometry. After investigation of anti-MRSA activities of the 7 major compounds, only emodin had significant anti-MRSA activity. Further, transmission electron microscopy was used to observe morphological changes in the cell wall of MRSA252, and the result revealed that emodin could damage the integrity of cell wall, leading to loss of intracellular components. In summary, our results showed ET-RPC could significantly inhibit bacterial growth of MRSA strains. Emodin was identified as the major compound with anti-MRSA activity; this activity was related to destruction of the integrity of the cell wall and cell membrane. PMID:25966789

  1. Activity-based protein profiling identifies a host enzyme, carboxylesterase 1, which is differentially active during hepatitis C virus replication.

    PubMed

    Blais, David R; Lyn, Rodney K; Joyce, Michael A; Rouleau, Yanouchka; Steenbergen, Rineke; Barsby, Nicola; Zhu, Lin-Fu; Pegoraro, Adrian F; Stolow, Albert; Tyrrell, David L; Pezacki, John Paul

    2010-08-13

    Hepatitis C virus (HCV) relies on many interactions with host cell proteins for propagation. Successful HCV infection also requires enzymatic activity of host cell enzymes for key post-translational modifications. To identify such enzymes, we have applied activity-based protein profiling to examine the activity of serine hydrolases during HCV replication. Profiling of hydrolases in Huh7 cells replicating HCV identified CES1 (carboxylesterase 1) as a differentially active enzyme. CES1 is an endogenous liver protein involved in processing of triglycerides and cholesterol. We observe that CES1 expression and activity were altered in the presence of HCV. The knockdown of CES1 with siRNA resulted in lower levels of HCV replication, and up-regulation of CES1 was observed to favor HCV propagation, implying an important role for this host cell protein. Experiments in HCV JFH1-infected cells suggest that CES1 facilitates HCV release because less intracellular HCV core protein was observed, whereas HCV titers remained high. CES1 activity was observed to increase the size and density of lipid droplets, which are necessary for the maturation of very low density lipoproteins, one of the likely vehicles for HCV release. In transgenic mice containing human-mouse chimeric livers, HCV infection also correlates with higher levels of endogenous CES1, providing further evidence that CES1 has an important role in HCV propagation. PMID:20530478

  2. Multiscale responses of soil stability and invasive plants to removal of non-native grazers from an arid conservation reserve

    USGS Publications Warehouse

    Beever, E.A.; Huso, M.; Pyke, D.A.

    2006-01-01

    Disturbances and ecosystem recovery from disturbance both involve numerous processes that operate on multiple spatial and temporal scales. Few studies have investigated how gradients of disturbance intensity and ecosystem responses are distributed across multiple spatial resolutions and also how this relationship changes through time during recovery. We investigated how cover of non-native species and soil-aggregate stability (a measure of vulnerability to erosion by water) in surface and subsurface soils varied spatially during grazing by burros and cattle and whether patterns in these variables changed after grazer removal from Mojave National Preserve, California, USA. We compared distance from water and number of ungulate defecations - metrics of longer-term and recent grazing intensity, respectively, - as predictors of our response variables. We used information-theoretic analyses to compare hierarchical linear models that accounted for important covariates and allowed for interannual variation in the disturbance-response relationship at local and landscape scales. Soil stability was greater under perennial vegetation than in bare interspaces, and surface soil stability decreased with increasing numbers of ungulate defecations. Stability of surface samples was more affected by time since removal of grazers than was stability of subsurface samples, and subsurface soil stability in bare spaces was not related to grazing intensity, time since removal, or any of our other predictors. In the high rainfall year (2003) after cattle had been removed for 1-2 years, cover of all non-native plants averaged nine times higher than in the low-rainfall year (2002). Given the heterogeneity in distribution of large-herbivore impacts that we observed at several resolutions, hierarchical analyses provided a more complete understanding of the spatial and temporal complexities of disturbance and recovery processes in arid ecosystems. ?? 2006 Blackwell Publishing Ltd.

  3. ModuleBlast: identifying activated sub-networks within and across species

    PubMed Central

    Zinman, Guy E.; Naiman, Shoshana; O'Dee, Dawn M.; Kumar, Nishant; Nau, Gerard J.; Cohen, Haim Y.; Bar-Joseph, Ziv

    2015-01-01

    Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFκB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein. PMID:25428368

  4. Tumor cell-specific bioluminescence platform to identify stroma-induced changes to anticancer drug activity.

    PubMed

    McMillin, Douglas W; Delmore, Jake; Weisberg, Ellen; Negri, Joseph M; Geer, D Corey; Klippel, Steffen; Mitsiades, Nicholas; Schlossman, Robert L; Munshi, Nikhil C; Kung, Andrew L; Griffin, James D; Richardson, Paul G; Anderson, Kenneth C; Mitsiades, Constantine S

    2010-04-01

    Conventional anticancer drug screening is typically performed in the absence of accessory cells of the tumor microenvironment, which can profoundly alter antitumor drug activity. To address this limitation, we developed the tumor cell-specific in vitro bioluminescence imaging (CS-BLI) assay. Tumor cells (for example, myeloma, leukemia and solid tumors) stably expressing luciferase are cultured with nonmalignant accessory cells (for example, stromal cells) for selective quantification of tumor cell viability, in presence versus absence of stromal cells or drug treatment. CS-BLI is high-throughput scalable and identifies stroma-induced chemoresistance in diverse malignancies, including imatinib resistance in leukemic cells. A stroma-induced signature in tumor cells correlates with adverse clinical prognosis and includes signatures for activated Akt, Ras, NF-kappaB, HIF-1alpha, myc, hTERT and IRF4; for biological aggressiveness; and for self-renewal. Unlike conventional screening, CS-BLI can also identify agents with increased activity against tumor cells interacting with stroma. One such compound, reversine, shows more potent activity in an orthotopic model of diffuse myeloma bone lesions than in conventional subcutaneous xenografts. Use of CS-BLI, therefore, enables refined screening of candidate anticancer agents to enrich preclinical pipelines with potential therapeutics that overcome stroma-mediated drug resistance and can act in a synthetic lethal manner in the context of tumor-stroma interactions. PMID:20228816

  5. Significant Centers of Tectonic Activity as Identified by Wrinkle Ridges for the Western Hemisphere of Mars

    NASA Technical Reports Server (NTRS)

    Anderson, R.C.; Haldemann, A. F. C.; Golombek, M. P.; Franklin, B. J.; Dohm, J. M.; Lias, J.

    2000-01-01

    The western hemisphere region of Mars has been the site of numerous scientific investigations regarding its tectonic evolution. For this region of Mars, the dominant tectonic region is the Tharsis province. Tharsis is characterized by an enormous system of radiating grabens and a circumferential system of wrinkle ridges. Past investigations of grabens associated with Tharsis have identified specific centers of tectonic activity. A recent structural analysis of the western hemisphere region of Mars which includes the Tharsis region, utilized 25,000 structures to determine the history of local and regional centers of tectonic activity based primarily on the spatial and temporal relationships of extensional features. This investigation revealed that Tharsis is more structurally complex (heterogeneous) than has been previously identified: it consists of numerous regional and local centers of tectonic activity (some are more dominant and/or more long lived than others). Here we use the same approach as Anderson et al. to determine whether the centers of tectonic activity that formed the extensional features also contributed to wrinkle ridge (compressional) formation.

  6. ModuleBlast: identifying activated sub-networks within and across species.

    PubMed

    Zinman, Guy E; Naiman, Shoshana; O'Dee, Dawn M; Kumar, Nishant; Nau, Gerard J; Cohen, Haim Y; Bar-Joseph, Ziv

    2015-02-18

    Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFκB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein. PMID:25428368

  7. Validation of mercury tip-switch and accelerometer activity sensors for identifying resting and active behavior in bears

    USGS Publications Warehouse

    Jasmine Ware; Rode, Karyn D.; Pagano, Anthony M.; Bromaghin, Jeffrey; Charles T Robbins; Joy Erlenbach; Shannon Jensen; Amy Cutting; Nicole Nicassio-Hiskey; Amy Hash; Owen, Megan A.; Heiko Jansen

    2015-01-01

    Activity sensors are often included in wildlife transmitters and can provide information on the behavior and activity patterns of animals remotely. However, interpreting activity-sensor data relative to animal behavior can be difficult if animals cannot be continuously observed. In this study, we examined the performance of a mercury tip-switch and a tri-axial accelerometer housed in collars to determine whether sensor data can be accurately classified as resting and active behaviors and whether data are comparable for the 2 sensor types. Five captive bears (3 polar [Ursus maritimus] and 2 brown [U. arctos horribilis]) were fitted with a collar specially designed to internally house the sensors. The bears’ behaviors were recorded, classified, and then compared with sensor readings. A separate tri-axial accelerometer that sampled continuously at a higher frequency and provided raw acceleration values from 3 axes was also mounted on the collar to compare with the lower resolution sensors. Both accelerometers more accurately identified resting and active behaviors at time intervals ranging from 1 minute to 1 hour (≥91.1% accuracy) compared with the mercury tip-switch (range = 75.5–86.3%). However, mercury tip-switch accuracy improved when sampled at longer intervals (e.g., 30–60 min). Data from the lower resolution accelerometer, but not the mercury tip-switch, accurately predicted the percentage of time spent resting during an hour. Although the number of bears available for this study was small, our results suggest that these activity sensors can remotely identify resting versus active behaviors across most time intervals. We recommend that investigators consider both study objectives and the variation in accuracy of classifying resting and active behaviors reported here when determining sampling interval.

  8. CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil.

    PubMed

    Almqvist, Helena; Axelsson, Hanna; Jafari, Rozbeh; Dan, Chen; Mateus, André; Haraldsson, Martin; Larsson, Andreas; Martinez Molina, Daniel; Artursson, Per; Lundbäck, Thomas; Nordlund, Pär

    2016-01-01

    Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery. PMID:27010513

  9. CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

    NASA Astrophysics Data System (ADS)

    Almqvist, Helena; Axelsson, Hanna; Jafari, Rozbeh; Dan, Chen; Mateus, André; Haraldsson, Martin; Larsson, Andreas; Molina, Daniel Martinez; Artursson, Per; Lundbäck, Thomas; Nordlund, Pär

    2016-03-01

    Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery.

  10. CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil

    PubMed Central

    Almqvist, Helena; Axelsson, Hanna; Jafari, Rozbeh; Dan, Chen; Mateus, André; Haraldsson, Martin; Larsson, Andreas; Molina, Daniel Martinez; Artursson, Per; Lundbäck, Thomas; Nordlund, Pär

    2016-01-01

    Target engagement is a critical factor for therapeutic efficacy. Assessment of compound binding to native target proteins in live cells is therefore highly desirable in all stages of drug discovery. We report here the first compound library screen based on biophysical measurements of intracellular target binding, exemplified by human thymidylate synthase (TS). The screen selected accurately for all the tested known drugs acting on TS. We also identified TS inhibitors with novel chemistry and marketed drugs that were not previously known to target TS, including the DNA methyltransferase inhibitor decitabine. By following the cellular uptake and enzymatic conversion of known drugs we correlated the appearance of active metabolites over time with intracellular target engagement. These data distinguished a much slower activation of 5-fluorouracil when compared with nucleoside-based drugs. The approach establishes efficient means to associate drug uptake and activation with target binding during drug discovery. PMID:27010513

  11. Improving assessment of daily energy expenditure by identifying types of physical activity with a single accelerometer.

    PubMed

    Bonomi, A G; Plasqui, G; Goris, A H C; Westerterp, K R

    2009-09-01

    Accelerometers are often used to quantify the acceleration of the body in arbitrary units (counts) to measure physical activity (PA) and to estimate energy expenditure. The present study investigated whether the identification of types of PA with one accelerometer could improve the estimation of energy expenditure compared with activity counts. Total energy expenditure (TEE) of 15 subjects was measured with the use of double-labeled water. The physical activity level (PAL) was derived by dividing TEE by sleeping metabolic rate. Simultaneously, PA was measured with one accelerometer. Accelerometer output was processed to calculate activity counts per day (AC(D)) and to determine the daily duration of six types of common activities identified with a classification tree model. A daily metabolic value (MET(D)) was calculated as mean of the MET compendium value of each activity type weighed by the daily duration. TEE was predicted by AC(D) and body weight and by AC(D) and fat-free mass, with a standard error of estimate (SEE) of 1.47 MJ/day, and 1.2 MJ/day, respectively. The replacement in these models of AC(D) with MET(D) increased the explained variation in TEE by 9%, decreasing SEE by 0.14 MJ/day and 0.18 MJ/day, respectively. The correlation between PAL and MET(D) (R(2) = 51%) was higher than that between PAL and AC(D) (R(2) = 46%). We conclude that identification of activity types combined with MET intensity values improves the assessment of energy expenditure compared with activity counts. Future studies could develop models to objectively assess activity type and intensity to further increase accuracy of the energy expenditure estimation. PMID:19556460

  12. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.

    PubMed

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C; Hanson, Buck T; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M; Fowler, Patrick W; Huang, Wei E; Wagner, Michael

    2015-01-13

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  13. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells

    PubMed Central

    Berry, David; Mader, Esther; Lee, Tae Kwon; Woebken, Dagmar; Wang, Yun; Zhu, Di; Palatinszky, Marton; Schintlmeister, Arno; Schmid, Markus C.; Hanson, Buck T.; Shterzer, Naama; Mizrahi, Itzhak; Rauch, Isabella; Decker, Thomas; Bocklitz, Thomas; Popp, Jürgen; Gibson, Christopher M.; Fowler, Patrick W.; Huang, Wei E.; Wagner, Michael

    2015-01-01

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics. PMID:25550518

  14. Potent Plasmodium falciparum gametocytocidal activity of diaminonaphthoquinones, lead antimalarial chemotypes identified in an antimalarial compound screen.

    PubMed

    Tanaka, Takeshi Q; Guiguemde, W Armand; Barnett, David S; Maron, Maxim I; Min, Jaeki; Connelly, Michele C; Suryadevara, Praveen Kumar; Guy, R Kiplin; Williamson, Kim C

    2015-03-01

    Forty percent of the world's population is threatened by malaria, which is caused by Plasmodium parasites and results in an estimated 200 million clinical cases and 650,000 deaths each year. Drug resistance has been reported for all commonly used antimalarials and has prompted screens to identify new drug candidates. However, many of these new candidates have not been evaluated against the parasite stage responsible for transmission, gametocytes. If Plasmodium falciparum gametocytes are not eliminated, patients continue to spread malaria for weeks after asexual parasite clearance. Asymptomatic individuals can also harbor gametocyte burdens sufficient for transmission, and a safe, effective gametocytocidal agent could also be used in community-wide malaria control programs. Here, we identify 15 small molecules with nanomolar activity against late-stage gametocytes. Fourteen are diaminonaphthoquinones (DANQs), and one is a 2-imino-benzo[d]imidazole (IBI). One of the DANQs identified, SJ000030570, is a lead antimalarial candidate. In contrast, 94% of the 650 compounds tested are inactive against late-stage gametocytes. Consistent with the ineffectiveness of most approved antimalarials against gametocytes, of the 19 novel compounds with activity against known anti-asexual-stage targets, only 3 had any strong effect on gametocyte viability. These data demonstrate the distinct biology of the transmission stages and emphasize the importance of screening for gametocytocidal activity. The potent gametocytocidal activity of DANQ and IBI coupled with their efficacy against asexual parasites provides leads for the development of antimalarials with the potential to prevent both the symptoms and the spread of malaria. PMID:25512421

  15. Potent Plasmodium falciparum Gametocytocidal Activity of Diaminonaphthoquinones, Lead Antimalarial Chemotypes Identified in an Antimalarial Compound Screen

    PubMed Central

    Tanaka, Takeshi Q; Guiguemde, W. Armand; Barnett, David S.; Maron, Maxim I.; Min, Jaeki; Connelly, Michele C.; Suryadevara, Praveen Kumar; Guy, R. Kiplin

    2014-01-01

    Forty percent of the world's population is threatened by malaria, which is caused by Plasmodium parasites and results in an estimated 200 million clinical cases and 650,000 deaths each year. Drug resistance has been reported for all commonly used antimalarials and has prompted screens to identify new drug candidates. However, many of these new candidates have not been evaluated against the parasite stage responsible for transmission, gametocytes. If Plasmodium falciparum gametocytes are not eliminated, patients continue to spread malaria for weeks after asexual parasite clearance. Asymptomatic individuals can also harbor gametocyte burdens sufficient for transmission, and a safe, effective gametocytocidal agent could also be used in community-wide malaria control programs. Here, we identify 15 small molecules with nanomolar activity against late-stage gametocytes. Fourteen are diaminonaphthoquinones (DANQs), and one is a 2-imino-benzo[d]imidazole (IBI). One of the DANQs identified, SJ000030570, is a lead antimalarial candidate. In contrast, 94% of the 650 compounds tested are inactive against late-stage gametocytes. Consistent with the ineffectiveness of most approved antimalarials against gametocytes, of the 19 novel compounds with activity against known anti-asexual-stage targets, only 3 had any strong effect on gametocyte viability. These data demonstrate the distinct biology of the transmission stages and emphasize the importance of screening for gametocytocidal activity. The potent gametocytocidal activity of DANQ and IBI coupled with their efficacy against asexual parasites provides leads for the development of antimalarials with the potential to prevent both the symptoms and the spread of malaria. PMID:25512421

  16. Calcium Imaging of Neuronal Activity in Drosophila Can Identify Anticonvulsive Compounds

    PubMed Central

    Streit, Anne K.; Fan, Yuen Ngan; Masullo, Laura; Baines, Richard A.

    2016-01-01

    Although there are now a number of antiepileptic drugs (AEDs) available, approximately one-third of epilepsy patients respond poorly to drug intervention. The reasons for this are complex, but are probably reflective of the increasing number of identified mutations that predispose individuals to this disease. Thus, there is a clear requirement for the development of novel treatments to address this unmet clinical need. The existence of gene mutations that mimic a seizure-like behaviour in the fruit fly, Drosophila melanogaster, offers the possibility to exploit the powerful genetics of this insect to identify novel cellular targets to facilitate design of more effective AEDs. In this study we use neuronal expression of GCaMP, a potent calcium reporter, to image neuronal activity using a non-invasive and rapid method. Expression in motoneurons in the isolated CNS of third instar larvae shows waves of calcium-activity that pass between segments of the ventral nerve cord. Time between calcium peaks, in the same neurons, between adjacent segments usually show a temporal separation of greater than 200 ms. Exposure to proconvulsants (picrotoxin or 4-aminopyridine) reduces separation to below 200 ms showing increased synchrony of activity across adjacent segments. Increased synchrony, characteristic of epilepsy, is similarly observed in genetic seizure mutants: bangsenseless1 (bss1) and paralyticK1270T (paraK1270T). Exposure of bss1 to clinically-used antiepileptic drugs (phenytoin or gabapentin) significantly reduces synchrony. In this study we use the measure of synchronicity to evaluate the effectiveness of known and novel anticonvulsive compounds (antipain, isethionate, etopiside rapamycin and dipyramidole) to reduce seizure-like CNS activity. We further show that such compounds also reduce the Drosophila voltage-gated persistent Na+ current (INaP) in an identified motoneuron (aCC). Our combined assays provide a rapid and reliable method to screen unknown compounds

  17. Transposon activation mutagenesis as a screening tool for identifying resistance to cancer therapeutics

    PubMed Central

    2013-01-01

    Background The development of resistance to chemotherapies represents a significant barrier to successful cancer treatment. Resistance mechanisms are complex, can involve diverse and often unexpected cellular processes, and can vary with both the underlying genetic lesion and the origin or type of tumor. For these reasons developing experimental strategies that could be used to understand, identify and predict mechanisms of resistance in different malignant cells would be a major advance. Methods Here we describe a gain-of-function forward genetic approach for identifying mechanisms of resistance. This approach uses a modified piggyBac transposon to generate libraries of mutagenized cells, each containing transposon insertions that randomly activate nearby gene expression. Genes of interest are identified using next-gen high-throughput sequencing and barcode multiplexing is used to reduce experimental cost. Results Using this approach we successfully identify genes involved in paclitaxel resistance in a variety of cancer cell lines, including the multidrug transporter ABCB1, a previously identified major paclitaxel resistance gene. Analysis of co-occurring transposons integration sites in single cell clone allows for the identification of genes that might act cooperatively to produce drug resistance a level of information not accessible using RNAi or ORF expression screening approaches. Conclusion We have developed a powerful pipeline to systematically discover drug resistance in mammalian cells in vitro. This cost-effective approach can be readily applied to different cell lines, to identify canonical or context specific resistance mechanisms. Its ability to probe complex genetic context and non-coding genomic elements as well as cooperative resistance events makes it a good complement to RNAi or ORF expression based screens. PMID:23442791

  18. Identifying induced seismicity in active tectonic regions: A case study of the San Joaquin Basin, California

    NASA Astrophysics Data System (ADS)

    Aminzadeh, F.; Göbel, T.

    2013-12-01

    Understanding the connection between petroleum-industry activities, and seismic event occurrences is essential to monitor, quantify, and mitigate seismic risk. While many studies identified anthropogenically-induced seismicity in intraplate regions where background seismicity rates are generally low, little is known about how to distinguish naturally occurring from induced seismicity in active tectonic regions. Further, it is not clear how different oil and gas operational parameters impact the frequency and magnitude of the induced seismic events. Here, we examine variations in frequency-size and spatial distributions of seismicity within the Southern Joaquin basin, an area of both active petroleum production and active fault systems. We analyze a newly available, high-quality, relocated earthquake catalog (Hauksson et al. 2012). This catalog includes many seismic events with magnitudes up to M = 4.5 within the study area. We start by analyzing the overall quality and consistence of the seismic catalog, focusing on temporal variations in seismicity rates and catalog completeness which could indicate variations in network sensitivity. This catalog provides relatively homogeneous earthquake recordings after 1981, enabling us to compare seismicity rates before and after the beginning of more pervasive petroleum-industry activities, for example, hydraulic-fracturing and waste-water disposals. We conduct a limited study of waste-water disposal wells to establish a correlation between seismicity statistics (i.e. rate changes, fractal dimension, b-value) within specific regions and anthropogenic influences. We then perform a regional study, to investigate spatial variations in seismicity statistics which are then correlated to oil field locations and well densities. In order to distinguish, predominantly natural seismicity from induced seismicity, we perform a spatial mapping of b-values and fractal dimensions of earthquake hypocenters. Seismic events in the proximity to

  19. Identifying active methane-oxidizers in thawed Arctic permafrost by proteomics

    NASA Astrophysics Data System (ADS)

    Lau, C. M.; Stackhouse, B. T.; Chourey, K.; Hettich, R. L.; Vishnivetskaya, T. A.; Pfiffner, S. M.; Layton, A. C.; Mykytczuk, N. C.; Whyte, L.; Onstott, T. C.

    2012-12-01

    The rate of CH4 release from thawing permafrost in the Arctic has been regarded as one of the determining factors on future global climate. It is uncertain how indigenous microorganisms would interact with such changing environmental conditions and hence their impact on the fate of carbon compounds that are sequestered in the cryosol. Multitudinous studies of pristine surface cryosol (top 5 cm) and microcosm experiments have provided growing evidence of effective methanotrophy. Cryosol samples corresponding to active layer were sampled from a sparsely vegetated, ice-wedge polygon at the McGill Arctic Research Station at Axel Heiberg Island, Nunavut, Canada (N79°24, W90°45) before the onset of annual thaw. Pyrosequencing of 16S rRNA gene indicated the occurrence of methanotroph-containing bacterial families as minor components (~5%) in pristine cryosol including Bradyrhizobiaceae, Methylobacteriaceae and Methylocystaceae within alpha-Proteobacteria, and Methylacidiphilaceae within Verrucomicrobia. The potential of methanotrophy is supported by preliminary analysis of metagenome data, which indicated putative methane monooxygenase gene sequences relating to Bradyrhizobium sp. and Pseudonocardia sp. are present. Proteome profiling in general yielded minute traces of proteins, which likely hints at dormant nature of the soil microbial consortia. The lack of specific protein database for permafrost posted additional challenge to protein identification. Only 35 proteins could be identified in the pristine cryosol and of which 60% belonged to Shewanella sp. Most of the identified proteins are known to be involved in energy metabolism or post-translational modification of proteins. Microcosms amended with sodium acetate exhibited a net methane consumption of ~65 ngC-CH4 per gram (fresh weight) of soil over 16 days of aerobic incubation at room temperature. The pH in microcosm materials remained acidic (decreased from initial 4.7 to 4.5). Protein extraction and

  20. Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers

    PubMed Central

    Rousseaux, Sophie; Debernardi, Alexandra; Jacquiau, Baptiste; Vitte, Anne-Laure; Vesin, Aurélien; Nagy-Mignotte, Hélène; Moro-Sibilot, Denis; Brichon, Pierre-Yves; Lantuejoul, Sylvie; Hainaut, Pierre; Laffaire, Julien; de Reyniès, Aurélien; Beer, David G.; Timsit, Jean-François; Brambilla, Christian; Brambilla, Elisabeth; Khochbin, Saadi

    2016-01-01

    Activation of normally silent tissue-specific genes and the resulting cell “identity crisis” are the unexplored consequences of malignant epigenetic reprogramming. We designed a strategy for investigating this reprogramming, which consisted of identifying a large number of tissue-restricted genes that are epigenetically silenced in normal somatic cells and then detecting their expression in cancer. This approach led to the demonstration that large-scale “off-context” gene activations systematically occur in a variety of cancer types. In our series of 293 lung tumors, we identified an ectopic gene expression signature associated with a subset of highly aggressive tumors, which predicted poor prognosis independently of the TNM (tumor size, node positivity, and metastasis) stage or histological subtype. The ability to isolate these tumors allowed us to reveal their common molecular features characterized by the acquisition of embryonic stem cell/germ cell gene expression profiles and the down-regulation of immune response genes. The methodical recognition of ectopic gene activations in cancer cells could serve as a basis for gene signature–guided tumor stratification, as well as for the discovery of oncogenic mechanisms, and expand the understanding of the biology of very aggressive tumors. PMID:23698379

  1. Transcriptional Responses to Estrogen and Progesterone in Mammary Gland Identify Networks Regulating p53 Activity

    PubMed Central

    Lu, Shaolei; Becker, Klaus A.; Hagen, Mary J.; Yan, Haoheng; Roberts, Amy L.; Mathews, Lesley A.; Schneider, Sallie S.; Siegelmann, Hava T.; MacBeth, Kyle J.; Tirrell, Stephen M.; Blanchard, Jeffrey L.; Jerry, D. Joseph

    2008-01-01

    Estrogen and progestins are essential for mammary growth and differentiation but also enhance the activity of the p53 tumor suppressor protein in the mammary epithelium. However, the pathways by which these hormones regulate p53 activity are unknown. Microarrays were used to profile the transcriptional changes within the mammary gland after administration of either vehicle, 17β-estradiol (E), or progesterone (P) individually and combined (EP). Treatment with EP yielded 1182 unique genes that were differentially expressed compared to the vehicle-treated group. Although 30% of genes were responsive to either E or P individually, combined treatment with both EP had a synergistic effect accounting for 60% of the differentially regulated genes. Analysis of protein-protein interactions identified p53, RelA, Snw1, and Igfals as common targets of genes regulated by EP. RelA and p53 form hubs within a network connected by genes that are regulated by EP and that may coordinate the competing functions of RelA and p53 in proliferation and survival of cells. Induction of early growth response 1 (Egr1) and Stratifin (Sfn) (also known as 14–3-3σ) by EP was confirmed by reverse transcription-quantitative PCR and shown to be p53 independent. In luciferase reporter assays, Egr1 was shown to enhance transcriptional activation by p53 and inhibit nuclear factor κB activity. These results identify a gene expression network that provides redundant activation of RelA to support proliferation as well as sensitize p53 to ensure proper surveillance and integration of their competing functions through factors such as Egr1, which both enhance p53 and inhibit RelA. PMID:18556351

  2. Comprehensive profiling analysis of actively resorbing osteoclasts identifies critical signaling pathways regulated by bone substrate

    PubMed Central

    Purdue, P. Edward; Crotti, Tania N.; Shen, Zhenxin; Swantek, Jennifer; Li, Jun; Hill, Jonathan; Hanidu, Adedayo; Dimock, Janice; Nabozny, Gerald; Goldring, Steven R.; McHugh, Kevin P.

    2014-01-01

    As the only cells capable of efficiently resorbing bone, osteoclasts are central mediators of both normal bone remodeling and pathologies associates with excessive bone resorption. However, despite the clear evidence of interplay between osteoclasts and the bone surface in vivo, the role of the bone substrate in regulating osteoclast differentiation and activation at a molecular level has not been fully defined. Here, we present the first comprehensive expression profiles of osteoclasts differentiated on authentic resorbable bone substrates. This analysis has identified numerous critical pathways coordinately regulated by osteoclastogenic cytokines and bone substrate, including the transition from proliferation to differentiation, and sphingosine-1-phosphate signaling. Whilst, as expected, much of this program is dependent upon integrin beta 3, the pre-eminent mediator of osteoclast-bone interaction, a surprisingly significant portion of the bone substrate regulated expression signature is independent of this receptor. Together, these findings identify an important hitherto underappreciated role for bone substrate in osteoclastogenesis. PMID:25534583

  3. Screening of Pharmacologically Active Small Molecule Compounds Identifies Antifungal Agents Against Candida Biofilms

    PubMed Central

    Watamoto, Takao; Egusa, Hiroshi; Sawase, Takashi; Yatani, Hirofumi

    2015-01-01

    Candida species have emerged as important and common opportunistic human pathogens, particularly in immunocompromised individuals. The current antifungal therapies either have toxic side effects or are insufficiently effect. The aim of this study is develop new small-molecule antifungal compounds by library screening methods using Candida albicans, and to evaluate their antifungal effects on Candida biofilms and cytotoxic effects on human cells. Wild-type C. albicans strain SC5314 was used in library screening. To identify antifungal compounds, we screened a small-molecule library of 1,280 pharmacologically active compounds (LOPAC1280TM) using an antifungal susceptibility test (AST). To investigate the antifungal effects of the hit compounds, ASTs were conducted using Candida strains in various growth modes, including biofilms. We tested the cytotoxicity of the hit compounds using human gingival fibroblast (hGF) cells to evaluate their clinical safety. Only 35 compounds were identified by screening, which inhibited the metabolic activity of C. albicans by >50%. Of these, 26 compounds had fungistatic effects and nine compounds had fungicidal effects on C. albicans. Five compounds, BAY11-7082, BAY11-7085, sanguinarine chloride hydrate, ellipticine and CV-3988, had strong fungicidal effects and could inhibit the metabolic activity of Candida biofilms. However, BAY11-7082, BAY11-7085, sanguinarine chloride hydrate and ellipticine were cytotoxic to hGF cells at low concentrations. CV-3988 showed no cytotoxicity at a fungicidal concentration. Four of the compounds identified, BAY11-7082, BAY11-7085, sanguinarine chloride hydrate and ellipticine, had toxic effects on Candida strains and hGF cells. In contrast, CV-3988 had fungicidal effects on Candida strains, but low cytotoxic effects on hGF cells. Therefore, this screening reveals agent, CV-3988 that was previously unknown to be antifungal agent, which could be a novel therapies for superficial mucosal candidiasis. PMID

  4. Grazer removal and nutrient enrichment as recovery enhancers for overexploited rocky subtidal habitats.

    PubMed

    Guarnieri, Giuseppe; Bevilacqua, Stanislao; Vignes, Fabio; Fraschetti, Simonetta

    2014-07-01

    Increasing anthropogenic pressures are causing long-lasting regime shifts from high-diversity ecosystems to low-diversity degraded ones. Understanding the effects of multiple threats on ecosystems, and identifying processes allowing for the recovery of biodiversity, are the current major challenges in ecology. In several temperate marine areas, large parts of rocky subtidal habitats characterised by high diversity have been completely degraded to barren grounds by overfishing, including illegal date mussel fishing. Bare areas are characterized by the dominance of sea urchins whose grazing perpetuates the impact of overfishing. We investigated experimentally the separate and combined effects of nutrient enrichment and sea urchin exclusion on the recovery of barren grounds. Our results indicate that the two factors have a synergistic effect leading to the re-establishment of erect macroalgal canopies, enhancing the structural complexity of subtidal assemblages. In particular, in the overfished system considered here, the recovery of disturbed assemblages could occur only if sea urchins are removed. However, the recolonization of barren grounds by erect macroalgae is further enhanced under enriched conditions. This study demonstrates that the recovery of dramatically depleted marine habitats is possible, and provides useful indications for specific management actions, which at present are totally lacking, to achieve the restoration of barren grounds caused by human activity. PMID:24748204

  5. Individual Human Brain Areas Can Be Identified from Their Characteristic Spectral Activation Fingerprints.

    PubMed

    Keitel, Anne; Gross, Joachim

    2016-06-01

    The human brain can be parcellated into diverse anatomical areas. We investigated whether rhythmic brain activity in these areas is characteristic and can be used for automatic classification. To this end, resting-state MEG data of 22 healthy adults was analysed. Power spectra of 1-s long data segments for atlas-defined brain areas were clustered into spectral profiles ("fingerprints"), using k-means and Gaussian mixture (GM) modelling. We demonstrate that individual areas can be identified from these spectral profiles with high accuracy. Our results suggest that each brain area engages in different spectral modes that are characteristic for individual areas. Clustering of brain areas according to similarity of spectral profiles reveals well-known brain networks. Furthermore, we demonstrate task-specific modulations of auditory spectral profiles during auditory processing. These findings have important implications for the classification of regional spectral activity and allow for novel approaches in neuroimaging and neurostimulation in health and disease. PMID:27355236

  6. Default-Mode Network Activity Identified by Group Independent Component Analysis

    NASA Astrophysics Data System (ADS)

    Liu, Conghui; Zhuang, Jie; Peng, Danling; Yu, Guoliang; Yang, Yanhui

    Default-mode network activity refers to some regional increase in blood oxygenation level-dependent (BOLD) signal during baseline than cognitive tasks. Recent functional imaging studies have found co-activation in a distributed network of cortical regions, including ventral anterior cingulate cortex (vACC) and posterior cingulate cortex (PPC) that characterize the default mode of human brain. In this study, general linear model and group independent component analysis (ICA) were utilized to analyze the fMRI data obtained from two language tasks. Both methods yielded similar, but not identical results and detected a resting deactivation network at some midline regions including anterior and posterior cingulate cortex and precuneus. Particularly, the group ICA method segregated functional elements into two separate maps and identified ventral cingulate component and fronto-parietal component. These results suggest that these two components might be linked to different mental function during "resting" baseline.

  7. Urban school leadership for elementary science instruction: Identifying and activating resources in an undervalued school subject

    NASA Astrophysics Data System (ADS)

    Spillane, James P.; Diamond, John B.; Walker, Lisa J.; Halverson, Rich; Jita, Loyiso

    2001-10-01

    This article explores school leadership for elementary school science teaching in an urban setting. We examine how school leaders bring resources together to enhance science instruction when there appear to be relatively few resources available for it. From our study of 13 Chicago elementary (K-8) schools' efforts to lead instructional change in mathematics, language arts, and science education, we show how resources for leading instruction are unequally distributed across subject areas. We also explore how over time leaders in one school successfully identified and activated resources for leading change in science education. The result has been a steady, although not always certain, development of science as an instructional area in the school. We argue that leading change in science education involves the identification and activation of material resources, the development of teachers' and school leaders' human capital, and the development and use of social capital.

  8. Individual Human Brain Areas Can Be Identified from Their Characteristic Spectral Activation Fingerprints

    PubMed Central

    Keitel, Anne; Gross, Joachim

    2016-01-01

    The human brain can be parcellated into diverse anatomical areas. We investigated whether rhythmic brain activity in these areas is characteristic and can be used for automatic classification. To this end, resting-state MEG data of 22 healthy adults was analysed. Power spectra of 1-s long data segments for atlas-defined brain areas were clustered into spectral profiles (“fingerprints”), using k-means and Gaussian mixture (GM) modelling. We demonstrate that individual areas can be identified from these spectral profiles with high accuracy. Our results suggest that each brain area engages in different spectral modes that are characteristic for individual areas. Clustering of brain areas according to similarity of spectral profiles reveals well-known brain networks. Furthermore, we demonstrate task-specific modulations of auditory spectral profiles during auditory processing. These findings have important implications for the classification of regional spectral activity and allow for novel approaches in neuroimaging and neurostimulation in health and disease. PMID:27355236

  9. Using time-driven activity-based costing to identify value improvement opportunities in healthcare.

    PubMed

    Kaplan, Robert S; Witkowski, Mary; Abbott, Megan; Guzman, Alexis Barboza; Higgins, Laurence D; Meara, John G; Padden, Erin; Shah, Apurva S; Waters, Peter; Weidemeier, Marco; Wertheimer, Sam; Feeley, Thomas W

    2014-01-01

    As healthcare providers cope with pricing pressures and increased accountability for performance, they should be rededicating themselves to improving the value they deliver to their patients: better outcomes and lower costs. Time-driven activity-based costing offers the potential for clinicians to redesign their care processes toward that end. This costing approach, however, is new to healthcare and has not yet been systematically implemented and evaluated. This article describes early time-driven activity-based costing work at several leading healthcare organizations in the United States and Europe. It identifies the opportunities they found to improve value for patients and demonstrates how this costing method can serve as the foundation for new bundled payment reimbursement approaches. PMID:25647962

  10. Identifying hazard parameter to develop quantitative and dynamic hazard map of an active volcano in Indonesia

    NASA Astrophysics Data System (ADS)

    Suminar, Wulan; Saepuloh, Asep; Meilano, Irwan

    2016-05-01

    Analysis of hazard assessment to active volcanoes is crucial for risk management. The hazard map of volcano provides information to decision makers and communities before, during, and after volcanic crisis. The rapid and accurate hazard assessment, especially to an active volcano is necessary to be developed for better mitigation on the time of volcanic crises in Indonesia. In this paper, we identified the hazard parameters to develop quantitative and dynamic hazard map of an active volcano. The Guntur volcano in Garut Region, West Java, Indonesia was selected as study area due population are resided adjacent to active volcanoes. The development of infrastructures, especially related to tourism at the eastern flank from the Summit, are growing rapidly. The remote sensing and field investigation approaches were used to obtain hazard parameters spatially. We developed a quantitative and dynamic algorithm to map spatially hazard potential of volcano based on index overlay technique. There were identified five volcano hazard parameters based on Landsat 8 and ASTER imageries: volcanic products including pyroclastic fallout, pyroclastic flows, lava and lahar, slope topography, surface brightness temperature, and vegetation density. Following this proposed technique, the hazard parameters were extracted, indexed, and calculated to produce spatial hazard values at and around Guntur Volcano. Based on this method, the hazard potential of low vegetation density is higher than high vegetation density. Furthermore, the slope topography, surface brightness temperature, and fragmental volcanic product such as pyroclastics influenced to the spatial hazard value significantly. Further study to this proposed approach will be aimed for effective and efficient analyses of volcano risk assessment.

  11. Functional analysis of TPM domain containing Rv2345 of Mycobacterium tuberculosis identifies its phosphatase activity.

    PubMed

    Sinha, Avni; Eniyan, Kandasamy; Sinha, Swati; Lynn, Andrew Michael; Bajpai, Urmi

    2015-07-01

    Mycobacterium tuberculosis (Mtb) is the causal agent of tuberculosis, the second largest infectious disease. With the rise of multi-drug resistant strains of M. tuberculosis, serious challenge lies ahead of us in treating the disease. The availability of complete genome sequence of Mtb has improved the scope for identifying new proteins that would not only further our understanding of biology of the organism but could also serve to discover new drug targets. In this study, Rv2345, a hypothetical membrane protein of M. tuberculosis H37Rv, which is reported to be a putative ortholog of ZipA cell division protein has been assigned function through functional annotation using bioinformatics tools followed by experimental validation. Sequence analysis showed Rv2345 to have a TPM domain at its N-terminal region and predicted it to have phosphatase activity. The TPM domain containing region of Rv2345 was cloned and expressed using pET28a vector in Escherichia coli and purified by Nickel affinity chromatography. The purified TPM domain was tested in vitro and our results confirmed it to have phosphatase activity. The enzyme activity was first checked and optimized with pNPP as substrate, followed by using ATP, which was also found to be used as substrate by the purified protein. Hence sequence analysis followed by in vitro studies characterizes TPM domain of Rv2345 to contain phosphatase activity. PMID:25782739

  12. An experimental method to identify neurogenic and myogenic active mechanical states of intestinal motility

    PubMed Central

    Costa, Marcello; Wiklendt, Lukasz; Arkwright, John W.; Spencer, Nicholas J.; Omari, Taher; Brookes, Simon J. H.; Dinning, Phil G.

    2013-01-01

    Excitatory and inhibitory enteric neural input to intestinal muscle acting on ongoing myogenic activity determines the rich repertoire of motor patterns involved in digestive function. The enteric neural activity cannot yet be established during movement of intact intestine in vivo or in vitro. We propose the hypothesis that is possible to deduce indirectly, but reliably, the state of activation of the enteric neural input to the muscle from measurements of the mechanical state of the intestinal muscle. The fundamental biomechanical model on which our hypothesis is based is the “three-element model” proposed by Hill. Our strategy is based on simultaneous video recording of changes in diameters and intraluminal pressure with a fiber-optic manometry in isolated segments of rabbit colon. We created a composite spatiotemporal map (DPMap) from diameter (DMap) and pressure changes (PMaps). In this composite map rhythmic myogenic motor patterns can readily be distinguished from the distension induced neural peristaltic contractions. Plotting the diameter changes against corresponding pressure changes at each location of the segment, generates “orbits” that represent the state of the muscle according to its ability to contract or relax actively or undergoing passive changes. With a software developed in MatLab, we identified twelve possible discrete mechanical states and plotted them showing where the intestine actively contracted and relaxed isometrically, auxotonically or isotonically, as well as where passive changes occurred or was quiescent. Clustering all discrete active contractions and relaxations states generated for the first time a spatio-temporal map of where enteric excitatory and inhibitory neural input to the muscle occurs during physiological movements. Recording internal diameter by an impedance probe proved equivalent to measuring external diameter, making possible to further develop similar strategy in vivo and humans. PMID:23596400

  13. Identifying the structural requirements for chromosomal aberration by incorporating molecular flexibility and metabolic activation of chemicals.

    PubMed

    Mekenyan, Ovanes; Todorov, Milen; Serafimova, Rossitsa; Stoeva, Stoyanka; Aptula, Aynur; Finking, Robert; Jacob, Elard

    2007-12-01

    Modeling the potential of chemicals to induce chromosomal damage has been hampered by the diversity of mechanisms which condition this biological effect. The direct binding of a chemical to DNA is one of the underlying mechanisms that is also responsible for bacterial mutagenicity. Disturbance of DNA synthesis due to inhibition of topoisomerases and interaction of chemicals with nuclear proteins associated with DNA (e.g., histone proteins) were identified as additional mechanisms leading to chromosomal aberrations (CA). A comparative analysis of in vitro genotoxic data for a large number of chemicals revealed that more than 80% of chemicals that elicit bacterial mutagenicity (as indicated by the Ames test) also induce CA; alternatively, only 60% of chemicals that induce CA have been found to be active in the Ames test. In agreement with this relationship, a battery of models is developed for modeling CA. It combines the Ames model for bacterial mutagenicity, which has already been derived and integrated into the Optimized Approach Based on Structural Indices Set (OASIS) tissue metabolic simulator (TIMES) platform, and a newly derived model accounting for additional mechanisms leading to CA. Both models are based on the classical concept of reactive alerts. Some of the specified alerts interact directly with DNA or nuclear proteins, whereas others are applied in a combination of two- or three-dimensional quantitative structure-activity relationship models assessing the degree of activation of the alerts from the rest of the molecules. The use of each of the alerts has been justified by a mechanistic interpretation of the interaction. In combination with a rat liver S9 metabolism simulator, the model explained the CA induced by metabolically activated chemicals that do not elicit activity in the parent form. The model can be applied in two ways: with and without metabolic activation of chemicals. PMID:18052113

  14. Aldehyde Dehydrogenase Activity Identifies a Population of Human Skeletal Muscle Cells With High Myogenic Capacities

    PubMed Central

    Vauchez, Karine; Marolleau, Jean-Pierre; Schmid, Michel; Khattar, Patricia; Chapel, Alain; Catelain, Cyril; Lecourt, Séverine; Larghéro, Jérôme; Fiszman, Marc; Vilquin, Jean-Thomas

    2009-01-01

    Aldehyde dehydrogenase 1A1 (ALDH) activity is one hallmark of human bone marrow (BM), umbilical cord blood (UCB), and peripheral blood (PB) primitive progenitors presenting high reconstitution capacities in vivo. In this study, we have identified ALDH+ cells within human skeletal muscles, and have analyzed their phenotypical and functional characteristics. Immunohistofluorescence analysis of human muscle tissue sections revealed rare endomysial cells. Flow cytometry analysis using the fluorescent substrate of ALDH, Aldefluor, identified brightly stained (ALDHbr) cells with low side scatter (SSClo), in enzymatically dissociated muscle biopsies, thereafter abbreviated as SMALD+ (for skeletal muscle ALDH+) cells. Phenotypical analysis discriminated two sub-populations according to CD34 expression: SMALD+/CD34− and SMALD+/CD34+ cells. These sub-populations did not initially express endothelial (CD31), hematopoietic (CD45), and myogenic (CD56) markers. Upon sorting, however, whereas SMALD+/CD34+ cells developed in vitro as a heterogeneous population of CD56− cells able to differentiate in adipoblasts, the SMALD+/CD34− fraction developed in vitro as a highly enriched population of CD56+ myoblasts able to form myotubes. Moreover, only the SMALD+/CD34− population maintained a strong myogenic potential in vivo upon intramuscular transplantation. Our results suggest that ALDH activity is a novel marker for a population of new human skeletal muscle progenitors presenting a potential for cell biology and cell therapy. PMID:19738599

  15. Repurposing of the Open Access Malaria Box for Kinetoplastid Diseases Identifies Novel Active Scaffolds against Trypanosomatids.

    PubMed

    Kaiser, Marcel; Maes, Louis; Tadoori, Leela Pavan; Spangenberg, Thomas; Ioset, Jean-Robert

    2015-06-01

    Phenotypic screening had successfully been used for hit generation, especially in the field of neglected diseases, in which feeding the drug pipeline with new chemotypes remains a constant challenge. Here, we catalyze drug discovery research using a publicly available screening tool to boost drug discovery. The Malaria Box, assembled by the Medicines for Malaria Venture, is a structurally diverse set of 200 druglike and 200 probelike compounds distilled from more than 20,000 antimalarial hits from corporate and academic libraries. Repurposing such compounds has already identified new scaffolds against cryptosporidiosis and schistosomiasis. In addition to initiating new hit-to-lead activities, screening the Malaria Box against a plethora of other parasites would enable the community to better understand the similarities and differences between them. We describe the screening of the Malaria Box and triaging of the identified hits against kinetoplastids responsible for human African trypanosomiasis (Trypanosoma brucei), Chagas disease (Trypanosoma cruzi), and visceral leishmaniasis (Leishmania donovani and Leishmania infantum). The in vitro and in vivo profiling of the most promising active compounds with respect to efficacy, toxicity, pharmacokinetics, and complementary druggable properties are presented and a collaborative model used as a way to accelerate the discovery process discussed. PMID:25690568

  16. An Active Type I-E CRISPR-Cas System Identified in Streptomyces avermitilis

    PubMed Central

    Qiu, Yi; Wang, Shiwei; Chen, Zhi; Guo, Yajie; Song, Yuan

    2016-01-01

    CRISPR-Cas systems, the small RNA-dependent immune systems, are widely distributed in prokaryotes. However, only a small proportion of CRISPR-Cas systems have been identified to be active in bacteria. In this work, a naturally active type I-E CRISPR-Cas system was found in Streptomyces avermitilis. The system shares many common genetic features with the type I-E system of Escherichia coli, and meanwhile shows unique characteristics. It not only degrades plasmid DNA with target protospacers, but also acquires new spacers from the target plasmid DNA. The naive features of spacer acquisition in the type I-E system of S. avermitilis were investigated and a completely conserved PAM 5’-AAG-3’ was identified. Spacer acquisition displayed differential strand bias upstream and downstream of the priming spacer, and irregular integrations of new spacers were observed. In addition, introduction of this system into host conferred phage resistance to some extent. This study will give new insights into adaptation mechanism of the type I-E systems in vivo, and meanwhile provide theoretical foundation for applying this system on the genetic modification of S. avermitilis. PMID:26901661

  17. A molecular approach to identify active microbes in environmental eukaryote clone libraries.

    PubMed

    Stoeck, Thorsten; Zuendorf, Alexandra; Breiner, Hans-Werner; Behnke, Anke

    2007-02-01

    A rapid method for the simultaneous extraction of RNA and DNA from eukaryote plankton samples was developed in order to discriminate between indigenous active cells and signals from inactive or even dead organisms. The method was tested using samples from below the chemocline of an anoxic Danish fjord. The simple protocol yielded RNA and DNA of a purity suitable for amplification by reverse transcription-polymerase chain reaction (RT-PCR) and PCR, respectively. We constructed an rRNA-derived and an rDNA-derived clone library to assess the composition of the microeukaryote assemblage under study and to identify physiologically active constituents of the community. We retrieved nearly 600 protistan target clones, which grouped into 84 different phylotypes (98% sequence similarity). Of these phylotypes, 27% occurred in both libraries, 25% exclusively in the rRNA library, and 48% exclusively in the rDNA library. Both libraries revealed good correspondence of the general community composition in terms of higher taxonomic ranks. They were dominated by anaerobic ciliates and heterotrophic stramenopile flagellates thriving below the fjord's chemocline. The high abundance of these bacterivore organisms points out their role as a major trophic link in anoxic marine systems. A comparison of the two libraries identified phototrophic dinoflagellates, "uncultured marine alveolates group I," and different parasites, which were exclusively detected with the rDNA-derived library, as nonindigenous members of the anoxic microeukaryote community under study. PMID:17264997

  18. Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation.

    PubMed

    Li, Minghui; Kales, Stephen C; Ma, Ke; Shoemaker, Benjamin A; Crespo-Barreto, Juan; Cangelosi, Andrew L; Lipkowitz, Stanley; Panchenko, Anna R

    2016-02-01

    Oncogenic mutations in the monomeric Casitas B-lineage lymphoma (Cbl) gene have been found in many tumors, but their significance remains largely unknown. Several human c-Cbl (CBL) structures have recently been solved, depicting the protein at different stages of its activation cycle and thus providing mechanistic insight underlying how stability-activity tradeoffs in cancer-related proteins-may influence disease onset and progression. In this study, we computationally modeled the effects of missense cancer mutations on structures representing four stages of the CBL activation cycle to identify driver mutations that affect CBL stability, binding, and activity. We found that recurrent, homozygous, and leukemia-specific mutations had greater destabilizing effects on CBL states than random noncancer mutations. We further tested the ability of these computational models, assessing the changes in CBL stability and its binding to ubiquitin-conjugating enzyme E2, by performing blind CBL-mediated EGFR ubiquitination assays in cells. Experimental CBL ubiquitin ligase activity was in agreement with the predicted changes in CBL stability and, to a lesser extent, with CBL-E2 binding affinity. Two thirds of all experimentally tested mutations affected the ubiquitin ligase activity by either destabilizing CBL or disrupting CBL-E2 binding, whereas about one-third of tested mutations were found to be neutral. Collectively, our findings demonstrate that computational methods incorporating multiple protein conformations and stability and binding affinity evaluations can successfully predict the functional consequences of cancer mutations on protein activity, and provide a proof of concept for mutations in CBL. PMID:26676746

  19. Triptolide, an active compound identified in a traditional Chinese herb, induces apoptosis of rheumatoid synovial fibroblasts

    PubMed Central

    Kusunoki, Natsuko; Yamazaki, Ryuta; Kitasato, Hidero; Beppu, Moroe; Aoki, Haruhito; Kawai, Shinichi

    2004-01-01

    Background Extracts of Tripterygium wilfordii Hook F (TWHF), a traditional Chinese herb, have been reported to show efficacy in patients with rheumatoid arthritis (RA). Since RA is not only characterized by inflammation but also by synovial proliferation in the joints, we examined whether triptolide (a constituent of TWHF) could influence the proliferation of rheumatoid synovial fibroblasts (RSF) by induction of apoptosis. Results RSF were obtained from RA patients during surgery and were treated with triptolide under various conditions. The viability and proliferation of RSF were measured by the 4-[3-(4-iodophenyl)-2-(4-nitrophenyl)-2H-5-tetrazolio]-1,3-benzene disulfonate (WST-1) assay and by 5-bromo-2'-deoxyuridine incorporation, respectively. Apoptosis was identified by detection of DNA fragmentation using an enzyme-linked immunosorbent assay and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling (TUNEL). The role of caspases in apoptosis of RSF was analyzed by measuring caspase-3 activity. Activation of the peroxisome proliferator-activated receptor (PPAR) γ was assessed by a luciferase reporter gene assay using RSF transfected with a plasmid containing the peroxisome proliferator response element. Triptolide decreased viability, inhibited proliferation, and induced apoptosis of RSF in a concentration-dependent manner at very low (nM) concentrations. Caspase-3 activity was increased by treatment with triptolide and was suppressed by caspase inhibitors. Although PPARγ activation was induced by 15-deoxy-Δ12,14-prostaglandin J2, triptolide did not induce it under the same experimental conditions. An extract of TWHF also induced DNA fragmentation in RSF. Conclusion The mechanism of action remains to be studied; however, triptolide may possibly have a disease-modifying effect in patients with RA. PMID:15040811

  20. Cluster Analysis of Tumor Suppressor Genes in Canine Leukocytes Identifies Activation State

    PubMed Central

    Daly, Julie-Anne; Mortlock, Sally-Anne; Taylor, Rosanne M.; Williamson, Peter

    2015-01-01

    Cells of the immune system undergo activation and subsequent proliferation in the normal course of an immune response. Infrequently, the molecular and cellular events that underlie the mechanisms of proliferation are dysregulated and may lead to oncogenesis, leading to tumor formation. The most common forms of immunological cancers are lymphomas, which in dogs account for 8%–20% of all cancers, affecting up to 1.2% of the dog population. Key genes involved in negatively regulating proliferation of lymphocytes include a group classified as tumor suppressor genes (TSGs). These genes are also known to be associated with progression of lymphoma in humans, mice, and dogs and are potential candidates for pathological grading and diagnosis. The aim of the present study was to analyze TSG profiles in stimulated leukocytes from dogs to identify genes that discriminate an activated phenotype. A total of 554 TSGs and three gene set collections were analyzed from microarray data. Cluster analysis of three subsets of genes discriminated between stimulated and unstimulated cells. These included 20 most upregulated and downregulated TSGs, TSG in hallmark gene sets significantly enriched in active cells, and a selection of candidate TSGs, p15 (CDKN2B), p18 (CDKN2C), p19 (CDKN1A), p21 (CDKN2A), p27 (CDKN1B), and p53 (TP53) in the third set. Analysis of two subsets suggested that these genes or a subset of these genes may be used as a specialized PCR set for additional analysis. PMID:27478369

  1. In vivo RNAi screen identifies NLK as a negative regulator of mesenchymal activity in glioblastoma

    PubMed Central

    Cho, Hee Jin; Lee, Jin-Ku; Kim, Gi-Soo; Han, Suji; Kim, Woon Jin; Shin, Yong Jae; Joo, Kyeung Min; Paddison, Patrick J.; Ishitani, Tohru; Lee, Jeongwu; Nam, Do-Hyun

    2015-01-01

    Glioblastoma (GBM) is the most lethal brain cancer with profound genomic alterations. While the bona fide tumor suppressor genes such as PTEN, NF1, and TP53 have high frequency of inactivating mutations, there may be the genes with GBM-suppressive roles for which genomic mutation is not a primary cause for inactivation. To identify such genes, we employed in vivo RNAi screening approach using the patient-derived GBM xenograft models. We found that Nemo-Like Kinase (NLK) negatively regulates mesenchymal activities, a characteristic of aggressive GBM, in part via inhibition of WNT/β-catenin signaling. Consistent with this, we found that NLK expression is especially low in a subset of GBMs that harbors high WNT/mesenchymal activities. Restoration of NLK inhibited WNT and mesenchymal activities, decreased clonogenic growth and survival, and impeded tumor growth in vivo. These data unravel a tumor suppressive role of NLK and support the feasibility of combining oncogenomics with in vivo RNAi screen. PMID:26023737

  2. Identifying minimal hepatic encephalopathy in cirrhotic patients by measuring spontaneous brain activity.

    PubMed

    Chen, Hua-Jun; Zhang, Ling; Jiang, Long-Feng; Chen, Qiu-Feng; Li, Jun; Shi, Hai-Bin

    2016-08-01

    It has been demonstrated that minimal hepatic encephalopathy (MHE) is associated with aberrant regional intrinsic brain activity in cirrhotic patients. However, few studies have investigated whether altered intrinsic brain activity can be used as a biomarker of MHE among cirrhotic patients. In this study, 36 cirrhotic patients (with MHE, n = 16; without MHE [NHE], n = 20) underwent resting-state functional magnetic resonance imaging (fMRI). Spontaneous brain activity was measured by examining the amplitude of low-frequency fluctuations (ALFF) in the fMRI signal. MHE was diagnosed based on the Psychometric Hepatic Encephalopathy Score (PHES). A two-sample t-test was used to determine the regions of interest (ROIs) in which ALFF differed significantly between the two groups; then, ALFF values within ROIs were selected as classification features. A linear discriminative analysis was used to differentiate MHE patients from NHE patients. The leave-one-out cross-validation method was used to estimate the performance of the classifier. The classification analysis was 80.6 % accurate (81.3 % sensitivity and 80.0 % specificity) in terms of distinguishing between the two groups. Six ROIs were identified as the most discriminative features, including the bilateral medial frontal cortex/anterior cingulate cortex, posterior cingulate cortex/precuneus, left precentral and postcentral gyrus, right lingual gyrus, middle frontal gyrus, and inferior/superior parietal lobule. The ALFF values within ROIs were correlated with PHES in cirrhotic patients. Our findings suggest that altered regional brain spontaneous activity is a useful biomarker for MHE detection among cirrhotic patients. PMID:26886109

  3. Tetrandrine identified in a small molecule screen to activate mesenchymal stem cells for enhanced immunomodulation

    PubMed Central

    Yang, Zijiang; Concannon, John; Ng, Kelvin S.; Seyb, Kathleen; Mortensen, Luke J.; Ranganath, Sudhir; Gu, Fangqi; Levy, Oren; Tong, Zhixiang; Martyn, Keir; Zhao, Weian; Lin, Charles P.; Glicksman, Marcie A.; Karp, Jeffrey M.

    2016-01-01

    Pre-treatment or priming of mesenchymal stem cells (MSC) prior to transplantation can significantly augment the immunosuppressive effect of MSC-based therapies. In this study, we screened a library of 1402 FDA-approved bioactive compounds to prime MSC. We identified tetrandrine as a potential hit that activates the secretion of prostaglandin E2 (PGE2), a potent immunosuppressive agent, by MSC. Tetrandrine increased MSC PGE2 secretion through the NF-κB/COX-2 signaling pathway. When co-cultured with mouse macrophages (RAW264.7), tetrandrine-primed MSC attenuated the level of TNF-α secreted by RAW264.7. Furthermore, systemic transplantation of primed MSC into a mouse ear skin inflammation model significantly reduced the level of TNF-α in the inflamed ear, compared to unprimed cells. Screening of small molecules to pre-condition cells prior to transplantation represents a promising strategy to boost the therapeutic potential of cell therapy. PMID:27457881

  4. Tetrandrine identified in a small molecule screen to activate mesenchymal stem cells for enhanced immunomodulation.

    PubMed

    Yang, Zijiang; Concannon, John; Ng, Kelvin S; Seyb, Kathleen; Mortensen, Luke J; Ranganath, Sudhir; Gu, Fangqi; Levy, Oren; Tong, Zhixiang; Martyn, Keir; Zhao, Weian; Lin, Charles P; Glicksman, Marcie A; Karp, Jeffrey M

    2016-01-01

    Pre-treatment or priming of mesenchymal stem cells (MSC) prior to transplantation can significantly augment the immunosuppressive effect of MSC-based therapies. In this study, we screened a library of 1402 FDA-approved bioactive compounds to prime MSC. We identified tetrandrine as a potential hit that activates the secretion of prostaglandin E2 (PGE2), a potent immunosuppressive agent, by MSC. Tetrandrine increased MSC PGE2 secretion through the NF-κB/COX-2 signaling pathway. When co-cultured with mouse macrophages (RAW264.7), tetrandrine-primed MSC attenuated the level of TNF-α secreted by RAW264.7. Furthermore, systemic transplantation of primed MSC into a mouse ear skin inflammation model significantly reduced the level of TNF-α in the inflamed ear, compared to unprimed cells. Screening of small molecules to pre-condition cells prior to transplantation represents a promising strategy to boost the therapeutic potential of cell therapy. PMID:27457881

  5. Past Strategies and Future Directions for Identifying AMP-Activated Protein Kinase (AMPK) Modulators

    PubMed Central

    Sinnett, Sarah E.; Brenman, Jay E.

    2014-01-01

    AMP-activated protein kinase (AMPK) is a promising therapeutic target for cancer, type II diabetes, and other illnesses characterized by abnormal energy utilization. During the last decade, numerous labs have published a range of methods for identifying novel AMPK modulators. The current understanding of AMPK structure and regulation, however, has propelled a paradigm shift in which many researchers now consider ADP to be an additional regulatory nucleotide of AMPK. How can the AMPK community apply this new understanding of AMPK signaling to translational research? Recent insights into AMPK structure, regulation, and holoenzyme-sensitive signaling may provide the hindsight needed to clearly evaluate the strengths and weaknesses of past AMPK drug discovery efforts. Improving future strategies for AMPK drug discovery will require pairing the current understanding of AMPK signaling with improved experimental designs. PMID:24583089

  6. Transcriptome correlation analysis identifies two unique craniosynostosis subtypes associated with IRS1 activation

    PubMed Central

    Mecham, B.; Park, S. S.; Wilkerson, H.; Farin, F. M.; Beyer, R. P.; Bammler, T. K.; Mangravite, L. M.; Cunningham, M. L.

    2012-01-01

    The discovery of causal mechanisms associated with nonsyndromic craniosynostosis has proven to be a difficult task due to the complex nature of the disease. In this study, differential transcriptome correlation analysis was used to identify two molecularly distinct subtypes of nonsyndromic craniosynostosis, termed subtype A and subtype B. In addition to unique correlation structure, subtype A was also associated with high IGF pathway expression, whereas subtype B was associated with high integrin expression. To identify a pathologic link between altered gene correlation/expression and the disease state, phosphorylation assays were performed on primary osteoblast cell lines derived from cases within subtype A or subtype B, as well as on primary osteoblast cell lines with novel IGF1R variants previously reported by our lab (Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. Am J Med Genet A 155A: 91–97, 2011). Elevated IRS1 (pan-tyr) and GSK3β (ser-9) phosphorylation were observed in two novel IGF1R variants with receptor L domain mutations. In subtype A, a hypomineralization phenotype coupled with decreased phosphorylation of IRS1 (ser-312), p38 (thr-180/tyr-182), and p70S6K (thr-412) was observed. In subtype B, decreased phosphorylation of IRS1 (ser-312) as well as increased phosphorylation of Akt (ser-473), GSK3β (ser-9), IGF1R (tyr-1135/tyr-1136), JNK (thr-183/tyr-187), p70S6K (thr-412), and pRPS6 (ser-235/ser-236) was observed, thus implicating the activation of IRS1-mediated Akt signaling in potentiating craniosynostosis in this subtype. Taken together, these results suggest that despite the stimulation of different pathways, activating phosphorylation patterns for IRS1 were consistent in cell lines from both subtypes and the IGF1R variants, thus implicating a key role for IRS1 in the pathogenesis of nonsyndromic craniosynostosis. PMID:23073384

  7. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

    PubMed Central

    Chen, Luonan; Wu, Ling-Yun; Wang, Yong; Zhang, Shihua; Zhang, Xiang-Sun

    2006-01-01

    Background Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. Results We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from and . Conclusion A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven. PMID:16948858

  8. Using Light-at-Night (LAN) Satellite Data for Identifying Clusters of Economic Activities in Europe

    NASA Astrophysics Data System (ADS)

    Rybnikova, N. A.; Portnov, B. A.

    2015-04-01

    Enterprises organized in clusters are often efficient in stimulating urban development, productivity and profit outflows. Identifying clusters of economic activities (EAs) thus becomes an important step in devising regional development policies, aimed at facilitating regional economic development. However, a major problem with cluster identification stems from limited reporting of specific EAs by individual countries and administrative entities. Even Eurostat, which maintains most advances regional databases, provides data for less than 50% of all regional subdivisions of the 3rd tier of the Nomenclature of Territorial Units for Statistics (NUTS3). Such poor reporting impedes identification of EA clusters and economic forces behind them. In this study, we test a possibility that missing data on geographic concentrations of EAs can be reconstructed using Light-at-Night (LAN) satellite measurements, and that such reconstructed data can then be used for the identification of EA clusters. As we hypothesize, LAN, captured by satellite sensors, is characterized by different intensity, depending on its source - production facilities, services, etc., - and this information can be used for EA identification. The study was carried out in three stages. First, using nighttime satellite images, we determined what types of EAs can be identified, with a sufficient degree of accuracy, by LAN they emit. Second, we calculated multivariate statistical models, linking EAs concentrations with LAN intensities and several locational and development attributes of NUTS3 regions in Europe. Next, using the obtained statistical models, we restored missing data on EAs across NUTS3 regions in Europe and identified clusters of EAs, using spatial analysis tools.

  9. Identifying Feasible Physical Activity Programs for Long-Term Care Homes in the Ontario Context

    PubMed Central

    Shakeel, Saad; Newhouse, Ian; Malik, Ali; Heckman, George

    2015-01-01

    Background Structured exercise programs for frail institutionalized seniors have shown improvement in physical, functional, and psychological health of this population. However, the ‘feasibility’ of implementation of such programs in real settings is seldom discussed. The purpose of this systematic review was to gauge feasibility of exercise and falls prevention programs from the perspective of long-term care homes in Ontario, given the recent changes in funding for publically funded physiotherapy services. Method Six electronic databases were searched by two independent researchers for randomized controlled trials that targeted long-term care residents and included exercise as an independent component of the intervention. Results A total of 39 studies were included in this review. A majority of these interventions were led by physiotherapist(s), carried out three times per week for 30–45 minutes per session. However, a few group-based interventions that were led by long-term care staff, volunteers, or trained non-exercise specialists were identified that also required minimal equipment. Conclusion This systematic review has identified ‘feasible’ physical activity and falls prevention programs that required minimal investment in staff and equipment, and demonstrated positive outcomes. Implementation of such programs represents cost-effective means of providing long-term care residents with meaningful gains in physical, psychological, and social health. PMID:26180563

  10. Identifying non-point sources of endocrine active compounds and their biological impacts in freshwater lakes.

    PubMed

    Baker, Beth H; Martinovic-Weigelt, Dalma; Ferrey, Mark; Barber, Larry B; Writer, Jeffery H; Rosenberry, Donald O; Kiesling, Richard L; Lundy, James R; Schoenfuss, Heiko L

    2014-10-01

    Contaminants of emerging concern, particularly endocrine active compounds (EACs), have been identified as a threat to aquatic wildlife. However, little is known about the impact of EACs on lakes through groundwater from onsite wastewater treatment systems (OWTS). This study aims to identify specific contributions of OWTS to Sullivan Lake, Minnesota, USA. Lake hydrology, water chemistry, caged bluegill sunfish (Lepomis macrochirus), and larval fathead minnow (Pimephales promelas) exposures were used to assess whether EACs entered the lake through OWTS inflow and the resultant biological impact on fish. Study areas included two OWTS-influenced near-shore sites with native bluegill spawning habitats and two in-lake control sites without nearby EAC sources. Caged bluegill sunfish were analyzed for plasma vitellogenin concentrations, organosomatic indices, and histological pathologies. Surface and porewater was collected from each site and analyzed for EACs. Porewater was also collected for laboratory exposure of larval fathead minnow, before analysis of predator escape performance and gene expression profiles. Chemical analysis showed EACs present at low concentrations at each study site, whereas discrete variations were reported between sites and between summer and fall samplings. Body condition index and liver vacuolization of sunfish were found to differ among study sites as did gene expression in exposed larval fathead minnows. Interestingly, biological exposure data and water chemistry did not match. Therefore, although results highlight the potential impacts of seepage from OWTS, further investigation of mixture effects and life history factor as well as chemical fate is warranted. PMID:24974177

  11. Temporal population dynamics of dinoflagellate Prorocentrum minimum in a semi-enclosed mariculture pond and its relationship to environmental factors and protozoan grazers

    NASA Astrophysics Data System (ADS)

    Xu, Henglong; Min, Gi-Sik; Choi, Joong-Ki; Zhu, Mingzhuang; Jiang, Yong; Al-Rasheid, Khaled A. S.

    2010-01-01

    The ecological processes and interrelationships between protists, either autotrophic or heterotrophic, and environmental factors in mariculture ponds are largely unknown. This study investigated the temporal dynamics of potentially harmful dinoflagellate, Prorocentrum minimum (Pavillard) Schiller, and its relationship to physico-chemical factors and protozoan grazers over a complete cycle in a semi-enclosed shrimp-farming pond near Qingdao, Northern China. P. minimum occurred frequently in low numbers from June to August, followed by a sharp increase from the middle of August, reaching a single maximum peak value of 2.2×105 cells L-1 in October. Temporal variation in abundance was positively correlated with dissolved nitrogen, but showed a significant inverse relationship to abundance of the dominant ciliates, Tintinnopsis lohmanni and Askenasia stellaris. The results provide statistical evidence that the number of P. minimum increased with increasing nitrogen, and the suppression or shortening of algal bloom may be associated with protozoan grazers, such as Tintinnopsis lohmanni, in mariculture ponds.

  12. Identifying candidate causal variants responsible for altered activity of the ABCB1 multidrug resistance gene.

    PubMed

    Soranzo, Nicole; Cavalleri, Gianpiero L; Weale, Michael E; Wood, Nicholas W; Depondt, Chantal; Marguerie, Richard; Sisodiya, Sanjay M; Goldstein, David B

    2004-07-01

    The difficulty of fine localizing the polymorphisms responsible for genotype-phenotype correlations is emerging as an important constraint in the implementation and interpretation of genetic association studies, and calls for the definition of protocols for the follow-up of associated variants. One recent example is the 3435C>T polymorphism in the multidrug transporter gene ABCB1, associated with protein expression and activity, and with several clinical conditions. Available data suggest that 3435C>T may not directly cause altered transport activity, but may be associated with one or more causal variants in the poorly characterized stretch of linkage disequilibrium (LD) surrounding it. Here we describe a strategy for the follow-up of reported associations, including a Bayesian formalization of the associated interval concept previously described by Goldstein. We focus on the region of high LD around 3435C>T to compile an exhaustive list of variants by (1) using a relatively coarse set of marker typings to assess the pattern of LD, and (2) resequencing derived and ancestral chromosomes at 3435C>T through the associated interval. We identified three intronic sites that are strongly associated with the 3435C>T polymorphism. One of them is associated with multidrug resistance in patients with epilepsy (chi2 = 3.78, P = 0.052), and sits within a stretch of significant evolutionary conservation. We argue that these variants represent additional candidates for influencing multidrug resistance due to P-glycoprotein activity, with the IVS 26+80 T>C being the best candidate among the three intronic sites. Finally, we describe a set of six haplotype tagging single-nucleotide polymorphisms that represent common ABCB1 variation surrounding 3435C>T in Europeans. PMID:15197162

  13. Effects of light and nutrients on periphyton and the fatty acid composition and somatic growth of invertebrate grazers in subtropical streams.

    PubMed

    Guo, Fen; Kainz, Martin J; Sheldon, Fran; Bunn, Stuart E

    2016-06-01

    Algal polyunsaturated fatty acids (PUFA), essential for somatic growth and reproduction of aquatic animals, are influenced by ambient environmental conditions, including light and nutrients. Few studies have addressed the extent to which changes in algal PUFA can influence stream herbivore PUFA profiles and the implications for stream food webs. We manipulated subtropical stream periphyton by applying two light levels (open and shaded canopy) and two nutrient regimes (ambient and enriched) to investigate the response of PUFA and somatic growth in stream herbivores. After 6 weeks, the relative content of periphyton PUFA (%) changed distinctly and differed among treatments. Periphyton in the control treatment with open canopy showed a decline in eicosapentaenoic acid (EPA) relative to initial conditions, whereas shading increased EPA and total highly unsaturated FA (HUFA), but decreased α-linolenic acid (ALA), linoleic acid and total C18 PUFA. The interaction of open canopy and added nutrients increased periphyton ALA compared with initial conditions, while the combined effects of shading and added nutrients led to greater total HUFA. FA similarity between stream grazers (the mayfly Austrophlebioides and caddisfly Helicopsyche) and periphyton increased with periphyton HUFA content. In addition, the growth of large instars of both grazers also increased in response to increased periphyton HUFA %. Our findings show that environmental changes, associated with riparian canopy and nutrients, can lead to changes in periphyton PUFA composition that in turn affect growth and PUFA composition in stream grazers. PMID:26883960

  14. Large-scale associations between macroalgal cover and grazer biomass on mid-depth reefs in the Caribbean

    NASA Astrophysics Data System (ADS)

    Williams, I.; Polunin, N.

    2001-05-01

    Since the 1970s, macroalgae have become considerably more abundant on many Caribbean reefs and overfishing of grazing fishes has been implicated as a contributory factor. We explored relationships between algal cover and grazers (biomass of herbivorous fishes and abundance of the sea-urchin Diadema antillarum) on mid-depth reefs (12-15 m) in 19 areas at seven locations in Jamaica, Barbados, Belize, Grand Cayman and Cuba, between April 1997 and April 1998. Diadema antillarum density was never >0.01 m-2, while herbivorous fish biomass (acanthurids and scarids ≥12 cm total length) varied from 2-5 g m-2 in Jamaica to 17.1 g m-2 in Barbados, and was strongly correlated, negatively with macroalgal cover and positively with 'cropped' substratum (sum of 'bare', turf and crustose-coralline substrata) cover. However, overfishing of herbivorous fishes alone cannot explain the widespread abundance of macroalgae, as even on lightly fished reefs, macroalgal cover was mostly >20%. Herbivorous fish populations on those reefs were apparently only able to maintain approximately 40-60% of reef substratum in cropped states, but due to low space-occupation by coral and other invertebrates, 70-90% of substratum was available to algae. The abundance of macroalgae on lightly fished reefs may therefore be a symptom of low coral cover in combination with the continuing absence of Diadema antillarum.

  15. Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines as Cell-Active Histone Demethylase Inhibitors

    PubMed Central

    Kawamura, Akane; Rose, Nathan R.; Ng, Stanley S.; Quinn, Amy M.; Rai, Ganesha; Mott, Bryan T.; Beswick, Paul; Klose, Robert J.; Oppermann, Udo; Jadhav, Ajit; Heightman, Tom D.; Maloney, David J.; Schofield, Christopher J.; Simeonov, Anton

    2010-01-01

    Background Small molecule modulators of epigenetic processes are currently sought as basic probes for biochemical mechanisms, and as starting points for development of therapeutic agents. Nε-Methylation of lysine residues on histone tails is one of a number of post-translational modifications that together enable transcriptional regulation. Histone lysine demethylases antagonize the action of histone methyltransferases in a site- and methylation state-specific manner. Nε-Methyllysine demethylases that use 2-oxoglutarate as co-factor are associated with diverse human diseases, including cancer, inflammation and X-linked mental retardation; they are proposed as targets for the therapeutic modulation of transcription. There are few reports on the identification of templates that are amenable to development as potent inhibitors in vivo and large diverse collections have yet to be exploited for the discovery of demethylase inhibitors. Principal Findings High-throughput screening of a ∼236,000-member collection of diverse molecules arrayed as dilution series was used to identify inhibitors of the JMJD2 (KDM4) family of 2-oxoglutarate-dependent histone demethylases. Initial screening hits were prioritized by a combination of cheminformatics, counterscreening using a coupled assay enzyme, and orthogonal confirmatory detection of inhibition by mass spectrometric assays. Follow-up studies were carried out on one of the series identified, 8-hydroxyquinolines, which were shown by crystallographic analyses to inhibit by binding to the active site Fe(II) and to modulate demethylation at the H3K9 locus in a cell-based assay. Conclusions These studies demonstrate that diverse compound screening can yield novel inhibitors of 2OG dependent histone demethylases and provide starting points for the development of potent and selective agents to interrogate epigenetic regulation. PMID:21124847

  16. Yeast-Based High-Throughput Screens to Identify Novel Compounds Active against Brugia malayi

    PubMed Central

    Bilsland, Elizabeth; Bean, Daniel M.; Devaney, Eileen; Oliver, Stephen G.

    2016-01-01

    Background Lymphatic filariasis is caused by the parasitic worms Wuchereria bancrofti, Brugia malayi or B. timori, which are transmitted via the bites from infected mosquitoes. Once in the human body, the parasites develop into adult worms in the lymphatic vessels, causing severe damage and swelling of the affected tissues. According to the World Health Organization, over 1.2 billion people in 58 countries are at risk of contracting lymphatic filariasis. Very few drugs are available to treat patients infected with these parasites, and these have low efficacy against the adult stages of the worms, which can live for 7–15 years in the human body. The requirement for annual treatment increases the risk of drug-resistant worms emerging, making it imperative to develop new drugs against these devastating diseases. Methodology/Principal Findings We have developed a yeast-based, high-throughput screening system whereby essential yeast genes are replaced with their filarial or human counterparts. These strains are labeled with different fluorescent proteins to allow the simultaneous monitoring of strains with parasite or human genes in competition, and hence the identification of compounds that inhibit the parasite target without affecting its human ortholog. We constructed yeast strains expressing eight different Brugia malayi drug targets (as well as seven of their human counterparts), and performed medium-throughput drug screens for compounds that specifically inhibit the parasite enzymes. Using the Malaria Box collection (400 compounds), we identified nine filarial specific inhibitors and confirmed the antifilarial activity of five of these using in vitro assays against Brugia pahangi. Conclusions/Significance We were able to functionally complement yeast deletions with eight different Brugia malayi enzymes that represent potential drug targets. We demonstrated that our yeast-based screening platform is efficient in identifying compounds that can discriminate between

  17. Gametocytocidal Screen Identifies Novel Chemical Classes with Plasmodium falciparum Transmission Blocking Activity

    PubMed Central

    Sanders, Natalie G.; Sullivan, David J.; Mlambo, Godfree; Dimopoulos, George; Tripathi, Abhai K.

    2014-01-01

    Discovery of transmission blocking compounds is an important intervention strategy necessary to eliminate and eradicate malaria. To date only a small number of drugs that inhibit gametocyte development and thereby transmission from the mosquito to the human host exist. This limitation is largely due to a lack of screening assays easily adaptable to high throughput because of multiple incubation steps or the requirement for high gametocytemia. Here we report the discovery of new compounds with gametocytocidal activity using a simple and robust SYBR Green I- based DNA assay. Our assay utilizes the exflagellation step in male gametocytes and a background suppressor, which masks the staining of dead cells to achieve healthy signal to noise ratio by increasing signal of viable parasites and subtracting signal from dead parasites. By determining the contribution of exflagellation to fluorescent signal and using appropriate cutoff values, we were able to screen for gametocytocidal compounds. After assay validation and optimization, we screened an FDA approved drug library of approximately 1500 compounds, as well as the 400 compound MMV malaria box and identified 44 gametocytocidal compounds with sub to low micromolar IC50s. Major classes of compounds with gametocytocidal activity included quaternary ammonium compounds with structural similarity to choline, acridine-like compounds similar to quinacrine and pyronaridine, as well as antidepressant, antineoplastic, and anthelminthic compounds. Top drug candidates showed near complete transmission blocking in membrane feeding assays. This assay is simple, reproducible and demonstrated robust Z-factor values at low gametocytemia levels, making it amenable to HTS for identification of novel and potent gametocytocidal compounds. PMID:25157792

  18. Loop substitution as a tool to identify active sites of interleukin-1 beta.

    PubMed

    Palla, E; Bensi, G; Solito, E; Buonamassa, D T; Fassina, G; Raugei, G; Spano, F; Galeotti, C; Mora, M; Domenighini, M

    1993-06-25

    By computer analysis of the amino acid sequence of human interleukin-1 beta (IL-1 beta) and of the human type I IL-1 receptor (IL-1RI), we have identified two hydropathically complementary peptides (Fassina, G., Roller, P. P., Olson, A. D., Thorgeirsson, S. S., and Omichinski, J. G. (1989) J. Biol. Chem. 264, 11252-11257) capable of binding to each other. The sequence of the IL-1 beta peptide corresponds to that of residues 88-99 (loop 7 of the crystal structure of mature IL-1 beta) of mature IL-1 beta, one of the exposed and highly charged regions of the molecule. The substitution of this loop with an amino acid sequence of the same length but different hydropathic profile generates a mutant with drastically reduced binding activity to IL-1RI. In contrast, the binding affinity to the type II IL-1R (IL-1RII) is the same as that of wild type IL-1 beta. The results show that 1) loop 7 is part of the binding site of IL-1 beta to IL-1RI, but not to IL-1RII. 2) The structure of the mutant protein is not grossly altered except locally at the position of the substituted loop. 3) The substitution of amino acids by site-directed mutagenesis of the loop 7 region generates mutants with binding affinity constants slightly lower than that of wild type IL-1 beta and not comparable to that of the loop substitution analogue. 4. All mutants analyzed, including the loop substitutions, are biologically active, confirming the structural integrity of the proteins. We propose a binding site in which the cooperation of several low energy bonds extended over a wide area results in a high affinity complex between IL-1 and the type I receptor. PMID:7685764

  19. CD45 Isoform Profile Identifies Natural Killer (NK) Subsets with Differential Activity

    PubMed Central

    Krzywinska, Ewelina; Cornillon, Amelie; Allende-Vega, Nerea; Vo, Dang-Nghiem; Rene, Celine; Lu, Zhao-Yang; Pasero, Christine; Olive, Daniel; Fegueux, Nathalie; Ceballos, Patrick; Hicheri, Yosr; Sobecki, Michal; Rossi, Jean-François; Cartron, Guillaume; Villalba, Martin

    2016-01-01

    The leucocyte-specific phosphatase CD45 is present in two main isoforms: the large CD45RA and the short CD45RO. We have recently shown that distinctive expression of these isoforms distinguishes natural killer (NK) populations. For example, co-expression of both isoforms identifies in vivo the anti tumor NK cells in hematological cancer patients. Here we show that low CD45 expression associates with less mature, CD56bright, NK cells. Most NK cells in healthy human donors are CD45RA+CD45RO-. The CD45RA-RO+ phenotype, CD45RO cells, is extremely uncommon in B or NK cells, in contrast to T cells. However, healthy donors possess CD45RAdimRO- (CD45RAdim cells), which show immature markers and are largely expanded in hematopoietic stem cell transplant patients. Blood borne cancer patients also have more CD45RAdim cells that carry several features of immature NK cells. However, and in opposition to their association to NK cell progenitors, they do not proliferate and show low expression of the transferrin receptor protein 1/CD71, suggesting low metabolic activity. Moreover, CD45RAdim cells properly respond to in vitro encounter with target cells by degranulating or gaining CD69 expression. In summary, they are quiescent NK cells, with low metabolic status that can, however, respond after encounter with target cells. PMID:27100180

  20. Host Protein Biomarkers Identify Active Tuberculosis in HIV Uninfected and Co-infected Individuals

    PubMed Central

    Achkar, Jacqueline M.; Cortes, Laetitia; Croteau, Pascal; Yanofsky, Corey; Mentinova, Marija; Rajotte, Isabelle; Schirm, Michael; Zhou, Yiyong; Junqueira-Kipnis, Ana Paula; Kasprowicz, Victoria O.; Larsen, Michelle; Allard, René; Hunter, Joanna; Paramithiotis, Eustache

    2015-01-01

    Biomarkers for active tuberculosis (TB) are urgently needed to improve rapid TB diagnosis. The objective of this study was to identify serum protein expression changes associated with TB but not latent Mycobacterium tuberculosis infection (LTBI), uninfected states, or respiratory diseases other than TB (ORD). Serum samples from 209 HIV uninfected (HIV−) and co-infected (HIV+) individuals were studied. In the discovery phase samples were analyzed via liquid chromatography and mass spectrometry, and in the verification phase biologically independent samples were analyzed via a multiplex multiple reaction monitoring mass spectrometry (MRM-MS) assay. Compared to LTBI and ORD, host proteins were significantly differentially expressed in TB, and involved in the immune response, tissue repair, and lipid metabolism. Biomarker panels whose composition differed according to HIV status, and consisted of 8 host proteins in HIV− individuals (CD14, SEPP1, SELL, TNXB, LUM, PEPD, QSOX1, COMP, APOC1), or 10 host proteins in HIV+ individuals (CD14, SEPP1, PGLYRP2, PFN1, VASN, CPN2, TAGLN2, IGFBP6), respectively, distinguished TB from ORD with excellent accuracy (AUC = 0.96 for HIV− TB, 0.95 for HIV+ TB). These results warrant validation in larger studies but provide promise that host protein biomarkers could be the basis for a rapid, blood-based test for TB. PMID:26501113

  1. Host Protein Biomarkers Identify Active Tuberculosis in HIV Uninfected and Co-infected Individuals.

    PubMed

    Achkar, Jacqueline M; Cortes, Laetitia; Croteau, Pascal; Yanofsky, Corey; Mentinova, Marija; Rajotte, Isabelle; Schirm, Michael; Zhou, Yiyong; Junqueira-Kipnis, Ana Paula; Kasprowicz, Victoria O; Larsen, Michelle; Allard, René; Hunter, Joanna; Paramithiotis, Eustache

    2015-09-01

    Biomarkers for active tuberculosis (TB) are urgently needed to improve rapid TB diagnosis. The objective of this study was to identify serum protein expression changes associated with TB but not latent Mycobacterium tuberculosis infection (LTBI), uninfected states, or respiratory diseases other than TB (ORD). Serum samples from 209 HIV uninfected (HIV(-)) and co-infected (HIV(+)) individuals were studied. In the discovery phase samples were analyzed via liquid chromatography and mass spectrometry, and in the verification phase biologically independent samples were analyzed via a multiplex multiple reaction monitoring mass spectrometry (MRM-MS) assay. Compared to LTBI and ORD, host proteins were significantly differentially expressed in TB, and involved in the immune response, tissue repair, and lipid metabolism. Biomarker panels whose composition differed according to HIV status, and consisted of 8 host proteins in HIV(-) individuals (CD14, SEPP1, SELL, TNXB, LUM, PEPD, QSOX1, COMP, APOC1), or 10 host proteins in HIV(+) individuals (CD14, SEPP1, PGLYRP2, PFN1, VASN, CPN2, TAGLN2, IGFBP6), respectively, distinguished TB from ORD with excellent accuracy (AUC = 0.96 for HIV(-) TB, 0.95 for HIV(+) TB). These results warrant validation in larger studies but provide promise that host protein biomarkers could be the basis for a rapid, blood-based test for TB. PMID:26501113

  2. Identifying active vascular microcalcification by 18F-sodium fluoride positron emission tomography

    PubMed Central

    Irkle, Agnese; Vesey, Alex T.; Lewis, David Y.; Skepper, Jeremy N.; Bird, Joseph L. E.; Dweck, Marc R.; Joshi, Francis R.; Gallagher, Ferdia A.; Warburton, Elizabeth A.; Bennett, Martin R.; Brindle, Kevin M.; Newby, David E.; Rudd, James H.; Davenport, Anthony P.

    2015-01-01

    Vascular calcification is a complex biological process that is a hallmark of atherosclerosis. While macrocalcification confers plaque stability, microcalcification is a key feature of high-risk atheroma and is associated with increased morbidity and mortality. Positron emission tomography and X-ray computed tomography (PET/CT) imaging of atherosclerosis using 18F-sodium fluoride (18F-NaF) has the potential to identify pathologically high-risk nascent microcalcification. However, the precise molecular mechanism of 18F-NaF vascular uptake is still unknown. Here we use electron microscopy, autoradiography, histology and preclinical and clinical PET/CT to analyse 18F-NaF binding. We show that 18F-NaF adsorbs to calcified deposits within plaque with high affinity and is selective and specific. 18F-NaF PET/CT imaging can distinguish between areas of macro- and microcalcification. This is the only currently available clinical imaging platform that can non-invasively detect microcalcification in active unstable atherosclerosis. The use of 18F-NaF may foster new approaches to developing treatments for vascular calcification. PMID:26151378

  3. Anomaly detection driven active learning for identifying suspicious tracks and events in WAMI video

    NASA Astrophysics Data System (ADS)

    Miller, David J.; Natraj, Aditya; Hockenbury, Ryler; Dunn, Katherine; Sheffler, Michael; Sullivan, Kevin

    2012-06-01

    We describe a comprehensive system for learning to identify suspicious vehicle tracks from wide-area motion (WAMI) video. First, since the road network for the scene of interest is assumed unknown, agglomerative hierarchical clustering is applied to all spatial vehicle measurements, resulting in spatial cells that largely capture individual road segments. Next, for each track, both at the cell (speed, acceleration, azimuth) and track (range, total distance, duration) levels, extreme value feature statistics are both computed and aggregated, to form summary (p-value based) anomaly statistics for each track. Here, to fairly evaluate tracks that travel across different numbers of spatial cells, for each cell-level feature type, a single (most extreme) statistic is chosen, over all cells traveled. Finally, a novel active learning paradigm, applied to a (logistic regression) track classifier, is invoked to learn to distinguish suspicious from merely anomalous tracks, starting from anomaly-ranked track prioritization, with ground-truth labeling by a human operator. This system has been applied to WAMI video data (ARGUS), with the tracks automatically extracted by a system developed in-house at Toyon Research Corporation. Our system gives promising preliminary results in highly ranking as suspicious aerial vehicles, dismounts, and traffic violators, and in learning which features are most indicative of suspicious tracks.

  4. A Modified Reverse One-Hybrid Screen Identifies Transcriptional Activation Domains in PHYTOCHROME-INTERACTING FACTOR 3

    PubMed Central

    Dalton, Jutta C.; Bätz, Ulrike; Liu, Jason; Curie, Gemma L.; Quail, Peter H.

    2016-01-01

    Transcriptional activation domains (TADs) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput manner. A plant transcriptional activator, PIF3 (phytochrome interacting factor 3), was fused to the yeast GAL4-DNA-binding Domain (BD), driving expression of the URA3 (Orotidine 5′-phosphate decarboxylase) reporter, and used for negative selection on 5-fluroorotic acid (5FOA). Randomly mutagenized variants of PIF3 were then selected for a loss or reduction in transcriptional activation activity by survival on FOA. In the process, we developed a strategy to eliminate false positives from negative selection that can be used for both reverse-1- and 2-hybrid screens. With this method we were able to identify two distinct regions in PIF3 with transcriptional activation activity, both of which are functionally conserved in PIF1, PIF4, and PIF5. Both are collectively necessary for full PIF3 transcriptional activity, but neither is sufficient to induce transcription autonomously. We also found that the TAD appear to overlap physically with other PIF3 functions, such as phyB binding activity and consequent phosphorylation. Our protocol should provide a valuable tool for identifying, analyzing and characterizing novel TADs in eukaryotic transcription factors, and thus potentially contribute to the unraveling of the mechanism underlying transcriptional activation. PMID:27379152

  5. Identifying the controls of wildfire activity in Namibia using multivariate statistics

    NASA Astrophysics Data System (ADS)

    Mayr, Manuel; Le Roux, Johan; Samimi, Cyrus

    2015-04-01

    Despite large areas of Namibia being unaffected by fires due to aridity, substantial burning in the northern and north-eastern parts of the country is observed every year. Within the fire-affected regions, a strong spatial and inter-annual variability characterizes the dry-season fire situation. In order to understand these patterns, it appears critical to identify the causative factors behind fire occurrence and to examine their interactions in detail. Furthermore, most studies dealing with causative factor examination focus either on the local or the regional scale. However, these scales seem to be inappropriate from a management perspective, as fire-related strategic action plans are most often set up nationwide. Here, we will present an examination of the fire regimes of Namibia based on a dataset conducted by Le Roux (2011). A decade-spanning fire record (1994-2003) derived from NOAA's Advanced Very High Resolution Radiometer (AVHRR) imagery was used to generate four fire regime metrics (Burned Area, Fire Season Length, Month of Peak Fire Season, and Fire Return Period) and quantitative information on vegetation and phenology derived from Normalized Difference Vegetation Index (NDVI) time series. Further variables contained by this dataset are related to climate, biodiversity, and human activities. Le Roux (2011) analyzed the correlations between the fire metrics mentioned above and the predictor variables. We hypothesize that linear correlations (as estimated by correlation coefficients) simplify the interactions between response and predictor variables. For instance, moderate population densities could induce the highest number of fires, whereas the complete absence of humans lacks one major source of ignition. Around highly populated areas, in contrary, fuels are usually reduced and space is more fragmented - thus, the initiation and spread of a potential fire could as well be inhibited. From a total of over 40 explanatory variables, we will initially use

  6. In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination.

    PubMed

    Bayry, Jagadeesh; Tchilian, Elma Z; Davies, Matthew N; Forbes, Emily K; Draper, Simon J; Kaveri, Srini V; Hill, Adrian V S; Kazatchkine, Michel D; Beverley, Peter C L; Flower, Darren R; Tough, David F

    2008-07-22

    Adjuvants are substances that enhance immune responses and thus improve the efficacy of vaccination. Few adjuvants are available for use in humans, and the one that is most commonly used (alum) often induces suboptimal immunity for protection against many pathogens. There is thus an obvious need to develop new and improved adjuvants. We have therefore taken an approach to adjuvant discovery that uses in silico modeling and structure-based drug-design. As proof-of-principle we chose to target the interaction of the chemokines CCL22 and CCL17 with their receptor CCR4. CCR4 was posited as an adjuvant target based on its expression on CD4(+)CD25(+) regulatory T cells (Tregs), which negatively regulate immune responses induced by dendritic cells (DC), whereas CCL17 and CCL22 are chemotactic agents produced by DC, which are crucial in promoting contact between DC and CCR4(+) T cells. Molecules identified by virtual screening and molecular docking as CCR4 antagonists were able to block CCL22- and CCL17-mediated recruitment of human Tregs and Th2 cells. Furthermore, CCR4 antagonists enhanced DC-mediated human CD4(+) T cell proliferation in an in vitro immune response model and amplified cellular and humoral immune responses in vivo in experimental models when injected in combination with either Modified Vaccinia Ankara expressing Ag85A from Mycobacterium tuberculosis (MVA85A) or recombinant hepatitis B virus surface antigen (rHBsAg) vaccines. The significant adjuvant activity observed provides good evidence supporting our hypothesis that CCR4 is a viable target for rational adjuvant design. PMID:18621704

  7. IDENTIFYING LUMINOUS ACTIVE GALACTIC NUCLEI IN DEEP SURVEYS: REVISED IRAC SELECTION CRITERIA

    SciTech Connect

    Donley, J. L.; Koekemoer, A. M.; Brusa, M.; Salvato, M.; Capak, P.; Cardamone, C. N.; Civano, F.; Ilbert, O.; Impey, C. D.; Kartaltepe, J. S.; Miyaji, T.; Sanders, D. B.; Trump, J. R.

    2012-04-01

    Spitzer/IRAC selection is a powerful tool for identifying luminous active galactic nuclei (AGNs). For deep IRAC data, however, the AGN selection wedges currently in use are heavily contaminated by star-forming galaxies, especially at high redshift. Using the large samples of luminous AGNs and high-redshift star-forming galaxies in COSMOS, we redefine the AGN selection criteria for use in deep IRAC surveys. The new IRAC criteria are designed to be both highly complete and reliable, and incorporate the best aspects of the current AGN selection wedges and of infrared power-law selection while excluding high-redshift star-forming galaxies selected via the BzK, distant red galaxy, Lyman-break galaxy, and submillimeter galaxy criteria. At QSO luminosities of log L{sub 2-10keV}(erg s{sup -1}) {>=}44, the new IRAC criteria recover 75% of the hard X-ray and IRAC-detected XMM-COSMOS sample, yet only 38% of the IRAC AGN candidates have X-ray counterparts, a fraction that rises to 52% in regions with Chandra exposures of 50-160 ks. X-ray stacking of the individually X-ray non-detected AGN candidates leads to a hard X-ray signal indicative of heavily obscured to mildly Compton-thick obscuration (log N{sub H} (cm{sup -2}) = 23.5 {+-} 0.4). While IRAC selection recovers a substantial fraction of luminous unobscured and obscured AGNs, it is incomplete to low-luminosity and host-dominated AGNs.

  8. 30 CFR 285.803 - How must I conduct my approved activities to protect essential fish habitats identified and...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... protect essential fish habitats identified and described under the Magnuson-Stevens Fishery Conservation... activities to protect essential fish habitats identified and described under the Magnuson-Stevens Fishery... essential fish habitat or habitat areas of particular concern may be adversely affected by your...

  9. 30 CFR 285.803 - How must I conduct my approved activities to protect essential fish habitats identified and...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... protect essential fish habitats identified and described under the Magnuson-Stevens Fishery Conservation... fish habitats identified and described under the Magnuson-Stevens Fishery Conservation and Management Act? (a) If, during the conduct of your approved activities, MMS finds that essential fish habitat...

  10. 30 CFR 585.803 - How must I conduct my approved activities to protect essential fish habitats identified and...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... protect essential fish habitats identified and described under the Magnuson-Stevens Fishery Conservation... fish habitats identified and described under the Magnuson-Stevens Fishery Conservation and Management Act? (a) If, during the conduct of your approved activities, BOEM finds that essential fish habitat...

  11. 30 CFR 585.803 - How must I conduct my approved activities to protect essential fish habitats identified and...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... protect essential fish habitats identified and described under the Magnuson-Stevens Fishery Conservation... fish habitats identified and described under the Magnuson-Stevens Fishery Conservation and Management Act? (a) If, during the conduct of your approved activities, BOEM finds that essential fish habitat...

  12. 30 CFR 585.803 - How must I conduct my approved activities to protect essential fish habitats identified and...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... protect essential fish habitats identified and described under the Magnuson-Stevens Fishery Conservation... fish habitats identified and described under the Magnuson-Stevens Fishery Conservation and Management Act? (a) If, during the conduct of your approved activities, BOEM finds that essential fish habitat...

  13. Identifying Key Features of Effective Active Learning: The Effects of Writing and Peer Discussion

    ERIC Educational Resources Information Center

    Linton, Debra L.; Pangle, Wiline M.; Wyatt, Kevin H.; Powell, Karli N.; Sherwood, Rachel E.

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between…

  14. Involvement in Extracurricular Activities: Identifying Differences in Perceptions of School Climate

    ERIC Educational Resources Information Center

    Martinez, Andrew; Coker, Crystal; McMahon, Susan D.; Cohen, Jonathan; Thapa, Amrit

    2016-01-01

    Many youth participate in extracurricular activities, and research has linked activity participation with school engagement and academic success. Social-ecological theory suggests that the social contexts of different types of extracurricular activities may differentially affect student outcomes. Yet, there is scant research examining the relation…

  15. Differences in EEG Alpha Activity between Gifted and Non-Identified Individuals: Insights into Problem Solving.

    ERIC Educational Resources Information Center

    Jausovec, Norbert

    1997-01-01

    This study examined differences in electroencephalography (EEG) alpha activity between gifted and nongifted Slovenian student-teachers (N=17 each). Gifted students showed greater left hemisphere activation than nongifted subjects in relaxed states, but lower activation during problem solving. The same pattern was observed in overall hemispheric…

  16. A Path Analysis to Identify the Psychosocial Factors Influencing Physical Activity and Bone Health in Middle-School Girls

    PubMed Central

    Sharma, Shreela V.; Hoelscher, Deanna M.; Kelder, Steven H.; Diamond, Pamela M.; Day, R. Sue; Hergenroeder, Albert C.

    2011-01-01

    Background The purpose of this study was to identify pathways used by psychosocial factors to influence physical activity and bone health in middle-school girls. Methods Baseline data from the Incorporating More Physical Activity and Calcium in Teens (IMPACT) study collected in 2001 to 2003 were used. IMPACT was a 1 1/2 years nutrition and physical activity intervention study designed to improve bone density in 717 middle-school girls in Texas. Structural Equations Modeling was used to examine the interrelationships and identify the direct and indirect pathways used by various psychosocial and environmental factors to influence physical activity and bone health. Results Results show that physical activity self-efficacy and social support (friend, family engagement, and encouragement in physical activity) had a significant direct and indirect influence on physical activity with participation in sports teams as the mediator. Participation in sports teams had a direct effect on both physical activity (β= 0.20, P < .05) and bone health and (β=0.13, P < .05). Conclusion The current study identified several direct and indirect pathways that psychosocial factors use to influence physical activity and bone health among adolescent girls. These findings are critical for the development of effective interventions for promoting bone health in this population. PMID:19953837

  17. Screening of Transient Receptor Potential Canonical Channel Activators Identifies Novel Neurotrophic Piperazine Compounds.

    PubMed

    Sawamura, Seishiro; Hatano, Masahiko; Takada, Yoshinori; Hino, Kyosuke; Kawamura, Tetsuya; Tanikawa, Jun; Nakagawa, Hiroshi; Hase, Hideharu; Nakao, Akito; Hirano, Mitsuru; Rotrattanadumrong, Rachapun; Kiyonaka, Shigeki; Mori, Masayuki X; Nishida, Motohiro; Hu, Yaopeng; Inoue, Ryuji; Nagata, Ryu; Mori, Yasuo

    2016-03-01

    Transient receptor potential canonical (TRPC) proteins form Ca(2+)-permeable cation channels activated upon stimulation of metabotropic receptors coupled to phospholipase C. Among the TRPC subfamily, TRPC3 and TRPC6 channels activated directly by diacylglycerol (DAG) play important roles in brain-derived neurotrophic factor (BDNF) signaling, promoting neuronal development and survival. In various disease models, BDNF restores neurologic deficits, but its therapeutic potential is limited by its poor pharmacokinetic profile. Elucidation of a framework for designing small molecules, which elicit BDNF-like activity via TRPC3 and TRPC6, establishes a solid basis to overcome this limitation. We discovered, through library screening, a group of piperazine-derived compounds that activate DAG-activated TRPC3/TRPC6/TRPC7 channels. The compounds [4-(5-chloro-2-methylphenyl)piperazin-1-yl](3-fluorophenyl)methanone (PPZ1) and 2-[4-(2,3-dimethylphenyl)piperazin-1-yl]-N-(2-ethoxyphenyl)acetamide (PPZ2) activated, in a dose-dependent manner, recombinant TRPC3/TRPC6/TRPC7 channels, but not other TRPCs, in human embryonic kidney cells. PPZ2 activated native TRPC6-like channels in smooth muscle cells isolated from rabbit portal vein. Also, PPZ2 evoked cation currents and Ca(2+) influx in rat cultured central neurons. Strikingly, both compounds induced BDNF-like neurite growth and neuroprotection, which were abolished by a knockdown or inhibition of TRPC3/TRPC6/TRPC7 in cultured neurons. Inhibitors of Ca(2+) signaling pathways, except calcineurin, impaired neurite outgrowth promotion induced by PPZ compounds. PPZ2 increased activation of the Ca(2+)-dependent transcription factor, cAMP response element-binding protein. These findings suggest that Ca(2+) signaling mediated by activation of DAG-activated TRPC channels underlies neurotrophic effects of PPZ compounds. Thus, piperazine-derived activators of DAG-activated TRPC channels provide important insights for future development of a

  18. Identifying High School Physical Education Physical Activity Patterns after High School

    ERIC Educational Resources Information Center

    Barney, David; Pleban, Francis T.; Wilkinson, Carol; Prusak, Keven A.

    2015-01-01

    National standards for physical education (PE) encompass five principles for the purpose of defining what high school students should recognize and be able to perform as a result of a quality PE program. The expectation is that youth will develop an active, healthy lifestyle into adulthood from activities and skills taught in PE. Researchers from…

  19. Identifying the Barriers and Facilitators to Participation in Physical Activity for Children with Down Syndrome

    ERIC Educational Resources Information Center

    Barr, M.; Shields, N.

    2011-01-01

    Background: Many children with Down syndrome do not undertake the recommended amount of daily physical activity. The aim of this study was to explore the barriers and facilitators to physical activity for this group. Methods: Eighteen in-depth interviews were conducted with 20 parents (16 mothers, 4 fathers) of children with Down syndrome aged…

  20. Identifying Key Features of Effective Active Learning: The Effects of Writing and Peer Discussion

    PubMed Central

    Pangle, Wiline M.; Wyatt, Kevin H.; Powell, Karli N.; Sherwood, Rachel E.

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between three sections taught by three different instructors in a full factorial design. The data set was analyzed by generalized linear mixed-effect models with three independent variables: student aptitude, treatment, and instructor, and three dependent (assessment) variables: change in score on pre- and postactivity clicker questions, and coding scores on in-class writing and exam essays. All independent variables had significant effects on student performance for at least one of the dependent variables. Students with higher aptitude scored higher on all assessments. Student scores were higher on exam essay questions when the activity was implemented with a writing component compared with peer discussion only. There was a significant effect of instructor, with instructors showing different degrees of effectiveness with active-learning techniques. We suggest that individual writing should be implemented as part of active learning whenever possible and that instructors may need training and practice to become effective with active learning. PMID:25185230

  1. Critical narrative review to identify educational strategies promoting physical activity in preschool.

    PubMed

    Kreichauf, S; Wildgruber, A; Krombholz, H; Gibson, E L; Vögele, C; Nixon, C A; Douthwaite, W; Moore, H J; Manios, Y; Summerbell, C D

    2012-03-01

    The aim of this narrative review is critically to evaluate educational strategies promoting physical activity that are used in the preschool setting in the context of obesity prevention programmes. Literature search was conducted between April and August 2010 in English and German databases (PubMED, PsychINFO, PSYNDEX, ERIC, FIS Bildung). Outcomes considered were time and intensity of physical activity, motor skills or measures of body composition. A total of 19 studies were included. Ten studies added physical activity lessons into their curriculum, one study provided more time for free play, eight studies focused on the social and play environment. Studies reporting positive outcomes implemented physical activity sessions that lasted at least 30 min d(-1). Several studies showed that children are most active in the first 10-15 min. The existence or installation of playground markings or fixed play equipment had no effect, whereas the presence or addition of portable play equipment was positively correlated with moderate-to-vigorous physical activity. Teacher training may be a key element for successful interventions. To overcome time constraints, a suggested solution is to integrate physical activity into daily routines and other areas of the preschool curriculum. PMID:22309068

  2. Organized Activities During High School and Adjustment One Year Post High School: Identifying Social Mediators.

    PubMed

    Viau, Annie; Denault, Anne-Sophie; Poulin, François

    2015-08-01

    This longitudinal study investigated social capital as a way through which youths' organized activities promote their future adjustment. Specifically, we examined social mediators of the associations between intensity, duration, and breadth of participation from age 14 to 17 and adjustment at age 18. Two social mediators were tested: support from the activity leader and social integration into the activity peer group. In addition, we examined how these mediation effects vary across gender. The sample consisted of 228 French Canadian adolescents (65 % girls). Youths were surveyed yearly from age 12 to 18. Controlling for prior adjustment at age 12, greater duration of participation from age 14 to 17 was associated with lower problematic alcohol use and higher civic engagement at age 18 through support from the activity leader. In addition, for boys only, greater duration of participation was associated with fewer subsequent depressive symptoms through social integration into the activity peer group. Overall, our results suggest that sustained participation allows youths to develop positive social experiences within organized activities, which, in turn, promote their future adjustment. Moreover, boys might benefit more from social experiences in organized activities than girls, at least with respect to depressive symptoms. PMID:25404238

  3. Identifying key features of effective active learning: the effects of writing and peer discussion.

    PubMed

    Linton, Debra L; Pangle, Wiline M; Wyatt, Kevin H; Powell, Karli N; Sherwood, Rachel E

    2014-01-01

    We investigated some of the key features of effective active learning by comparing the outcomes of three different methods of implementing active-learning exercises in a majors introductory biology course. Students completed activities in one of three treatments: discussion, writing, and discussion + writing. Treatments were rotated weekly between three sections taught by three different instructors in a full factorial design. The data set was analyzed by generalized linear mixed-effect models with three independent variables: student aptitude, treatment, and instructor, and three dependent (assessment) variables: change in score on pre- and postactivity clicker questions, and coding scores on in-class writing and exam essays. All independent variables had significant effects on student performance for at least one of the dependent variables. Students with higher aptitude scored higher on all assessments. Student scores were higher on exam essay questions when the activity was implemented with a writing component compared with peer discussion only. There was a significant effect of instructor, with instructors showing different degrees of effectiveness with active-learning techniques. We suggest that individual writing should be implemented as part of active learning whenever possible and that instructors may need training and practice to become effective with active learning. PMID:25185230

  4. An activation tagging screen to identify novel genes for Fusarium head blight (FHB) resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this project is to identify plant genes that confer resistance against FHB and reduced DON accumulation. The identification of such genes offers the possibility to more fully understand the mechanisms of Fusarium susceptibility and to design transgenic strategies to increase FHB resistan...

  5. 15 CFR 930.33 - Identifying Federal agency activities affecting any coastal use or resource.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... which has minimal or no environmental effects may still have effects on a coastal use (e.g., effects on public access and recreational opportunities, protection of historic property) or a coastal resource, if... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Identifying Federal agency...

  6. 15 CFR 930.33 - Identifying Federal agency activities affecting any coastal use or resource.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... which has minimal or no environmental effects may still have effects on a coastal use (e.g., effects on public access and recreational opportunities, protection of historic property) or a coastal resource, if... 15 Commerce and Foreign Trade 3 2013-01-01 2013-01-01 false Identifying Federal agency...

  7. 15 CFR 930.33 - Identifying Federal agency activities affecting any coastal use or resource.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... which has minimal or no environmental effects may still have effects on a coastal use (e.g., effects on public access and recreational opportunities, protection of historic property) or a coastal resource, if... 15 Commerce and Foreign Trade 3 2014-01-01 2014-01-01 false Identifying Federal agency...

  8. 15 CFR 930.33 - Identifying Federal agency activities affecting any coastal use or resource.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... which has minimal or no environmental effects may still have effects on a coastal use (e.g., effects on public access and recreational opportunities, protection of historic property) or a coastal resource, if... 15 Commerce and Foreign Trade 3 2011-01-01 2011-01-01 false Identifying Federal agency...

  9. 15 CFR 930.33 - Identifying Federal agency activities affecting any coastal use or resource.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... which has minimal or no environmental effects may still have effects on a coastal use (e.g., effects on public access and recreational opportunities, protection of historic property) or a coastal resource, if... 15 Commerce and Foreign Trade 3 2012-01-01 2012-01-01 false Identifying Federal agency...

  10. Mapping present and future potential distribution patterns for a meso-grazer guild in the Baltic Sea

    PubMed Central

    Leidenberger, Sonja; De Giovanni, Renato; Kulawik, Robert; Williams, Alan R; Bourlat, Sarah J; Maggs, Christine

    2015-01-01

    Aim The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterized by many special features, including endemic species that may be particularly threatened by climate change. We mapped potential distribution patterns under present and future conditions for a community with three trophic levels. We analysed climate-induced changes in the species' distribution patterns and examined possible consequences for the chosen food web. Location Baltic Sea and northern Europe. Methods We developed two open-source workflow-based analytical tools: one for ecological niche modelling and another for raster layer comparison to compute the extent and intensity of change in species' potential distributions. Individual ecological niche models were generated under present conditions and then projected into a future climate change scenario (2050) for a food web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesiculosus and Fucus radicans) and their fish predator (Gasterosteus aculeatus). We used occurrence data from the Global Biodiversity Information Facility (GBIF), literature and museum collections, together with five environmental layers at a resolution of 5 and 30 arc-minutes. Results Habitat suitability for Idotea balthica and Idotea chelipes in the Baltic Sea seems to be mostly determined by temperature and ice cover rather than by salinity. 2050 predictions for all modelled species show a northern/north-eastern shift in the Baltic Sea. The distribution ranges for Idotea granulosa and G. aculeatus are predicted to become patchier in the Baltic than in the rest of northern Europe, where the species will gain more suitable habitats. Main conclusions For the Baltic Sea, climate-induced changes resulted in a gain of suitable habitats for F. vesiculosus,I. chelipes and I. balthica, whereas lower habitat suitability was predicted for I. granulosa,F. radicans and G. aculeatus. The predicted north-eastern shift of I. balthica

  11. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

    PubMed Central

    Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle; Malmstrom, Rex R.; Woyke, Tanja; Orphan, Victoria J.

    2016-01-01

    To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought. PMID:27357680

  12. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia.

    PubMed

    Hatzenpichler, Roland; Connon, Stephanie A; Goudeau, Danielle; Malmstrom, Rex R; Woyke, Tanja; Orphan, Victoria J

    2016-07-12

    To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought. PMID:27357680

  13. Combined Rational Design and a High Throughput Screening Platform for Identifying Chemical Inhibitors of a Ras-activating Enzyme*

    PubMed Central

    Evelyn, Chris R.; Biesiada, Jacek; Duan, Xin; Tang, Hong; Shang, Xun; Papoian, Ruben; Seibel, William L.; Nelson, Sandra; Meller, Jaroslaw; Zheng, Yi

    2015-01-01

    The Ras family small GTPases regulate multiple cellular processes, including cell growth, survival, movement, and gene expression, and are intimately involved in cancer pathogenesis. Activation of these small GTPases is catalyzed by a special class of enzymes, termed guanine nucleotide exchange factors (GEFs). Herein, we developed a small molecule screening platform for identifying lead hits targeting a Ras GEF enzyme, SOS1. We employed an ensemble structure-based virtual screening approach in combination with a multiple tier high throughput experimental screen utilizing two complementary fluorescent guanine nucleotide exchange assays to identify small molecule inhibitors of GEF catalytic activity toward Ras. From a library of 350,000 compounds, we selected a set of 418 candidate compounds predicted to disrupt the GEF-Ras interaction, of which dual wavelength GDP dissociation and GTP-loading experimental screening identified two chemically distinct small molecule inhibitors. Subsequent biochemical validations indicate that they are capable of dose-dependently inhibiting GEF catalytic activity, binding to SOS1 with micromolar affinity, and disrupting GEF-Ras interaction. Mutagenesis studies in conjunction with structure-activity relationship studies mapped both compounds to different sites in the catalytic pocket, and both inhibited Ras signaling in cells. The unique screening platform established here for targeting Ras GEF enzymes could be broadly useful for identifying lead inhibitors for a variety of small GTPase-activating GEF reactions. PMID:25825487

  14. Identifying signatures of plasma waves and reconnection associated with Kelvin-Helmholtz activity

    NASA Astrophysics Data System (ADS)

    Moore, Thomas Wesley

    The magnetopause marks the boundary between the shocked solar wind and magnetospheric plasma. Understanding the dynamics of the plasma processes at the magnetopause boundary is crucial to the study of plasma transport into the magnetosphere. Previous studies have shown that there exists a temperature asymmetry in the plasma sheet. During northward IMF, the cold component ions are 30-40% hotter in the dawn flank plasma sheet compared to the dusk flank. However, the mechanisms responsible are still not entirely clear. Recent work has shown that reconnection in Kelvin-Helmholtz vortices can transport plasma into the magnetosphere. Previous studies have also shown that mode conversion at the magnetopause can generate kinetic Alfven wave (KAW) activity. Both magnetic reconnection and plasma wave activity can heat plasma. In this thesis we look for new cases of Kelvin-Helmholtz Instability (KHI) from Cluster spacecraft data and search for signatures of associated magnetic reconnection and plasma wave activity.

  15. Repellent activity of constituents identified in Foeniculum vulgare fruit against Aedes aegypti (Diptera: Culicidae).

    PubMed

    Kim, Do-Hyoung; Kim, Soon-Il; Chang, Kyu-Sik; Ahn, Young-Joon

    2002-11-20

    The repellent activity of materials derived from the methanol extract of fruits from Foeniculum vulgareagainst hungry Aedes aegypti females was examined using skin and patch tests and compared with that of the commercial N,N-diethyl-m-toluamide (deet) and (Z)-9-octadecenoic acid. The biologically active constituents of the Foeniculum fruits were characterized as (+)-fenchone and (E)-9-octadecenoic acid by spectroscopic analyses. Responses varied according to compound, dose, and exposure time. In a skin test with female mosquitoes, at a dose of 0.4 mg/cm(2), (+)-fenchone and (Z)-9-octadecenoic acid exhibited moderate repellent activity at 30 min after treatment, whereas deet provided >1 h of protection against adult mosquitoes at 0.2 mg/cm(2). (Z)-9-Octadecenoic acid was a more potent repellent agent than (E)-9-octadecenoic acid. (+)-Fenchone and (E)-9-octadecenoic acid merit further study as potential mosquito repellent agents or as lead compounds. PMID:12428949

  16. Triterpenoid resinous metabolites from the genus Boswellia: pharmacological activities and potential species-identifying properties

    PubMed Central

    2013-01-01

    The resinous metabolites commonly known as frankincense or olibanum are produced by trees of the genus Boswellia and have attracted increasing popularity in Western countries in the last decade for their various pharmacological activities. This review described the pharmacological specific details mainly on anti-inflammatory, anti-carcinogenic, anti-bacterial and apoptosis-regulating activities of individual triterpenoid together with the relevant mechanism. In addition, species-characterizing triterpenic markers with the methods for their detection, bioavailability, safety and other significant properties were reviewed for further research. PMID:24028654

  17. Identifying correlates and determinants of physical activity in youth: How can we advance the field?

    PubMed

    Atkin, Andrew J; van Sluijs, Esther M F; Dollman, James; Taylor, Wendell C; Stanley, Rebecca M

    2016-06-01

    This commentary provides a critical discussion of current research investigating the correlates and determinants of physical activity in young people, with specific focus on conceptual, theoretical and methodological issues. We draw on current child and adolescent literature and our own collective expertise to illustrate our discussion. We conclude with recommendations that will strengthen future research and help to advance the field. PMID:26940254

  18. IDENTIFYING RECENT SURFACE MINING ACTIVITIES USING A NORMALIZED DIFFERENCE VEGETATION INDEX (NDVI) CHANGE DETECTION METHOD

    EPA Science Inventory



    Coal mining is a major resource extraction activity on the Appalachian Mountains. The increased size and frequency of a specific type of surface mining, known as mountain top removal-valley fill, has in recent years raised various environmental concerns. During mountainto...

  19. Using Concept Mapping to Identify Action Steps for Physical Activity Promotion in Cancer Treatment

    ERIC Educational Resources Information Center

    Fitzpatrick, Sean Joseph; Zizzi, Sam J.

    2014-01-01

    Background: The benefits of exercise during and after cancer treatment represent research areas that have received increased attention throughout the past 2 decades. Numerous benefits have been observed for cancer survivors who are physically active, yet oncologists have been slow to incorporate exercise counseling into practice. Purpose: The…

  20. 3D Printing in Instructional Settings: Identifying a Curricular Hierarchy of Activities

    ERIC Educational Resources Information Center

    Brown, Abbie

    2015-01-01

    A report of a year-long study in which the author engaged in 3D printing activity in order to determine how to facilitate and support skill building, concept attainment, and increased confidence with its use among teachers. Use of 3D printing tools and their applications in instructional settings are discussed. A hierarchy of 3D printing…

  1. Identifying and Measuring the Activities That Impact Musical Growth from High School through Graduate School.

    ERIC Educational Resources Information Center

    Bobbett, Gordon C.; And Others

    The impact that high school and college experiences and activities have on students' musical independence (MI) was investigated. MI is related to the actual production and performance of music, as opposed to musical achievement or the mastery of any academic skill related to music. Colwell's Musical Achievement Test 3, Musical Achievement Test 4,…

  2. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To fully understand how bacteria respond to their environment, it is essential to assess genome-wide transcriptional activity. New high throughput sequencing technologies make it possible to query the transcriptome of an organism in an efficient unbiased manner. We applied a strand-specific method t...

  3. Zoosporicidal activity of polyflavonoid tannin identified in Lannea coromandelica stem bark against phytopathogenic oomycete Aphanomyces cochlioides.

    PubMed

    Islam, Md Tofazzal; Ito, Toshiaki; Sakasai, Mitsuyoshi; Tahara, Satoshi

    2002-11-01

    In a survey of nonhost plant secondary metabolites regulating motility and viability of zoospores of the Aphanomyces cochlioides, we found that stem bark extracts of Lannea coromandelica remarkably inhibited motility of zoospores followed by lysis. Bioassay-guided fractionation and chemical characterization of Lannea extracts by MALDI-TOF-MS revealed that the active constituents were angular type polyflavonoid tannins. Commercial polyflavonoid tannins, Quebracho and Mimosa, also showed identical zoosporicidal activity. Against zoospores, the motility-inhibiting and lytic activities were more pronounced in Lannea extracts (MIC 0.1 microg/mL) than in Quebracho (MIC 0.5 microg/mL) and Mimosa (MIC 0.5 microg/mL). Scanning electron microscopic observation visualized that both Lannea and commercial tannins caused lysis of cell membrane followed by fragmentation of cellular materials. Naturally occurring polyflavonoid tannin merits further study as potential zoospore regulating agent or as lead compound. To the best of our knowledge, this is the first report of zoosporicidal activity of natural polyflavonoid tannins against an oomycete phytopathogen. PMID:12405764

  4. Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach

    NASA Astrophysics Data System (ADS)

    Lejzerowicz, Franck; Voltsky, Ivan; Pawlowski, Jan

    2013-02-01

    Metagenetics represents an efficient and rapid tool to describe environmental diversity patterns of microbial eukaryotes based on ribosomal DNA sequences. However, the results of metagenetic studies are often biased by the presence of extracellular DNA molecules that are persistent in the environment, especially in deep-sea sediment. As an alternative, short-lived RNA molecules constitute a good proxy for the detection of active species. Here, we used a metatranscriptomic approach based on RNA-derived (cDNA) sequences to study the diversity of the deep-sea benthic foraminifera and compared it to the metagenetic approach. We analyzed 257 ribosomal DNA and cDNA sequences obtained from seven sediments samples collected in the Sea of Japan at depths ranging from 486 to 3665 m. The DNA and RNA-based approaches gave a similar view of the taxonomic composition of foraminiferal assemblage, but differed in some important points. First, the cDNA dataset was dominated by sequences of rotaliids and robertiniids, suggesting that these calcareous species, some of which have been observed in Rose Bengal stained samples, are the most active component of foraminiferal community. Second, the richness of monothalamous (single-chambered) foraminifera was particularly high in DNA extracts from the deepest samples, confirming that this group of foraminifera is abundant but not necessarily very active in the deep-sea sediments. Finally, the high divergence of undetermined sequences in cDNA dataset indicate the limits of our database and lack of knowledge about some active but possibly rare species. Our study demonstrates the capability of the metatranscriptomic approach to detect active foraminiferal species and prompt its use in future high-throughput sequencing-based environmental surveys.

  5. Can the vector space model be used to identify biological entity activities?

    PubMed Central

    2011-01-01

    Background Biological systems are commonly described as networks of entity interactions. Some interactions are already known and integrate the current knowledge in life sciences. Others remain unknown for long periods of time and are frequently discovered by chance. In this work we present a model to predict these unknown interactions from a textual collection using the vector space model (VSM), a well known and established information retrieval model. We have extended the VSM ability to retrieve information using a transitive closure approach. Our objective is to use the VSM to identify the known interactions from the literature and construct a network. Based on interactions established in the network our model applies the transitive closure in order to predict and rank new interactions. Results We have tested and validated our model using a collection of patent claims issued from 1976 to 2005. From 266,528 possible interactions in our network, the model identified 1,027 known interactions and predicted 3,195 new interactions. Iterating the model according to patent issue dates, interactions found in a given past year were often confirmed by patent claims not in the collection and issued in more recent years. Most confirmation patent claims were found at the top 100 new interactions obtained from each subnetwork. We have also found papers on the Web which confirm new inferred interactions. For instance, the best new interaction inferred by our model relates the interaction between the adrenaline neurotransmitter and the androgen receptor gene. We have found a paper that reports the partial dependence of the antiapoptotic effect of adrenaline on androgen receptor. Conclusions The VSM extended with a transitive closure approach provides a good way to identify biological interactions from textual collections. Specifically for the context of literature-based discovery, the extended VSM contributes to identify and rank relevant new interactions even if these

  6. Identifying a Highly Active Copper Catalyst for KA(2) Reaction of Aromatic Ketones.

    PubMed

    Cai, Yujuan; Tang, Xinjun; Ma, Shengming

    2016-02-12

    The well-established A(3) coupling reaction of terminal alkynes, aldehydes, and amines provides the most straightforward approach to propargylic amines. However, the related reaction of ketones, especially aromatic ketones, is still a significant challenge. A highly efficient catalytic protocol has been developed for the coupling of aromatic ketones with amines and terminal alkynes, in which Cu(I) , generated in situ from the reduction of CuBr2 with sodium ascorbate, has been identified as the highly efficient catalyst. Since propargylic amines are versatile synthetic intermediates and important units in pharmaceutical products, such an advance will greatly stimulate research interest involving the previously unavailable propargylic amines. PMID:26660459

  7. Morphological and physiological responses of seagrasses (Alismatales) to grazers (Testudines: Cheloniidae) and the role of these responses as grazing patch abandonment cues.

    PubMed

    Lacey, Elizabeth A; Collado-Vides, Ligia; Fourqurean, James W

    2014-12-01

    Green sea turtles, Chelonia mydas, are grazers influencing the distribution of seagrass within shallow coastal ecosystems, yet the drivers behind C. mydas patch use within seagrass beds are largely unknown. Current theories center on food quality (nutrient content) as the plant responds to grazing disturbances; however, no study has monitored these parameters in a natural setting without grazer manipulation. To determine the morphological and physiological responses potentially influencing seagrass recovery from grazing disturbances, seagrasses were monitored for one year under three different grazing scenarios (turtle grazed, fish grazed and ungrazed) in a tropical ecosystem in Akumal Bay, Quintana Roo, Mexico. Significantly less soluble carbohydrates and increased nitrogen and phosphorus content in Thalassia testudinum were indicative of the stresses placed on seagrasses during herbivory. To determine if these physiological responses were the drivers of the heterogeneous grazing behavior by C. mydas recorded in Akumal Bay, patches were mapped and monitored over a six-month interval. The abandoned patches had the lowest standing crop rather than leaf nutrient or rhi- zome soluble carbohydrate content. This suggests a modified Giving Up Density (GUD) behavior: the critical threshold where cost of continued grazing does not provide minimum nutrients, therefore, new patches must be utilized, explains resource abandonment and mechanism behind C. mydas grazing. This study is the first to apply GUD theory, often applied in terrestrial literature, to explain marine herbivore grazing behavior. PMID:25720186

  8. High-content screening identifies kinase inhibitors that overcome venetoclax resistance in activated CLL cells.

    PubMed

    Oppermann, Sina; Ylanko, Jarkko; Shi, Yonghong; Hariharan, Santosh; Oakes, Christopher C; Brauer, Patrick M; Zúñiga-Pflücker, Juan C; Leber, Brian; Spaner, David E; Andrews, David W

    2016-08-18

    Novel agents such as the Bcl-2 inhibitor venetoclax (ABT-199) are changing treatment paradigms for chronic lymphocytic leukemia (CLL) but important problems remain. Although some patients exhibit deep and durable responses to venetoclax as a single agent, other patients harbor subpopulations of resistant leukemia cells that mediate disease recurrence. One hypothesis for the origin of resistance to venetoclax is by kinase-mediated survival signals encountered in proliferation centers that may be unique for individual patients. An in vitro microenvironment model was developed with primary CLL cells that could be incorporated into an automated high-content microscopy-based screen of kinase inhibitors (KIs) to identify agents that may improve venetoclax therapy in a personalized manner. Marked interpatient variability was noted for which KIs were effective; nevertheless, sunitinib was identified as the most common clinically available KI effective in overcoming venetoclax resistance. Examination of the underlying mechanisms indicated that venetoclax resistance may be induced by microenvironmental signals that upregulate antiapoptotic Bcl-xl, Mcl-1, and A1, which can be counteracted more efficiently by sunitinib than by ibrutinib or idelalisib. Although patient-specific drug responses are common, for many patients, combination therapy with sunitinib may significantly improve the therapeutic efficacy of venetoclax. PMID:27297795

  9. High-content screening identifies kinase inhibitors that overcome venetoclax resistance in activated CLL cells

    PubMed Central

    Oppermann, Sina; Ylanko, Jarkko; Shi, Yonghong; Hariharan, Santosh; Oakes, Christopher C.; Brauer, Patrick M.; Zúñiga-Pflücker, Juan C.; Leber, Brian; Spaner, David E.

    2016-01-01

    Novel agents such as the Bcl-2 inhibitor venetoclax (ABT-199) are changing treatment paradigms for chronic lymphocytic leukemia (CLL) but important problems remain. Although some patients exhibit deep and durable responses to venetoclax as a single agent, other patients harbor subpopulations of resistant leukemia cells that mediate disease recurrence. One hypothesis for the origin of resistance to venetoclax is by kinase-mediated survival signals encountered in proliferation centers that may be unique for individual patients. An in vitro microenvironment model was developed with primary CLL cells that could be incorporated into an automated high-content microscopy-based screen of kinase inhibitors (KIs) to identify agents that may improve venetoclax therapy in a personalized manner. Marked interpatient variability was noted for which KIs were effective; nevertheless, sunitinib was identified as the most common clinically available KI effective in overcoming venetoclax resistance. Examination of the underlying mechanisms indicated that venetoclax resistance may be induced by microenvironmental signals that upregulate antiapoptotic Bcl-xl, Mcl-1, and A1, which can be counteracted more efficiently by sunitinib than by ibrutinib or idelalisib. Although patient-specific drug responses are common, for many patients, combination therapy with sunitinib may significantly improve the therapeutic efficacy of venetoclax. PMID:27297795

  10. Identifying and Enhancing the Strengths of Gifted Learners, K-8: Easy-to-Use Activities and Lessons

    ERIC Educational Resources Information Center

    Maccagnano, Ann Marie

    2007-01-01

    Educators can identify children's strengths early on and gain insight into each student's unique abilities by using the numerous ideas and informal assessments in this exciting guide. Gifted and talented specialist Ann Maccagnano offers K-8 teachers challenging activities and engaging lessons to develop and nurture gifted learners' talents.…

  11. Newly identified essential amino acid residues affecting ^8-sphingolipid desaturase activity revealed by site-directed mutagenesis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to identify amino acid residues crucial for the enzymatic activity of ^8-sphingolipid desaturases, a sequence comparison was performed among ^8-sphingolipid desaturases and ^6-fatty acid desaturase from various plants. In addition to the known conserved cytb5 (cytochrome b5) HPGG motif and...

  12. Using Tandem Mass Spectrometry in Targeted Mode to Identify Activators of Class IA PI3K in Cancer

    PubMed Central

    Yang, Xuemei; Turke, Alexa B.; Qi, Jie; Song, Youngchul; Rexer, Brent N.; Miller, Todd W.; Jänne, Pasi A.; Arteaga, Carlos L.; Cantley, Lewis C.; Engelman, Jeffrey A.; Asara, John M.

    2011-01-01

    PI3K is activated in some cancers by direct mutation, but it is activated more commonly in cancer by mutation of upstream acting receptor tyrosine kinases (TKs). At present, there is no systematic method to determine which TK signaling cascades activate PI3K in certain cancers, despite the likely utility of such information to help guide selection of tyrosine kinase inhibitor (TKI) drug strategies for personalized therapy. Here we present a quantitative tandem mass spectrometry (LC/MS/MS) approach that identifies upstream activators of PI3K both in vitro and in vivo. Using non-small cell lung carcinoma (NSCLC) to illustrate this approach, we demonstrate a correct identification of the mechanism of PI3K activation in several models, thereby identifying the most appropriate TKI to down-regulate PI3K signaling. This approach also determined the molecular mechanisms and adaptors required for PI3K activation following inhibition of the mTOR kinase TORC1. We further validated the approach in breast cancer cells with mutational activation of PIK3CA, where tandem mass spectrometry detected and quantitatively measured the abundance of a helical domain mutant (E545K) of PIK3CA connected to PI3K activation. Overall, our findings establish a mass spectrometric approach to identify functional interactions that govern PI3K regulation in cancer cells. Using this technique to define the pathways which activate PI3K signaling in a given tumor could help inform clinical decision making by helping guide personalized therapeutic strategies for different patients. PMID:21775521

  13. Active-passive correlation spectroscopy - A new technique for identifying ocean color algorithm spectral regions

    NASA Technical Reports Server (NTRS)

    Hoge, F. E.; Swift, R. N.

    1986-01-01

    A new active-passive airborne data correlation technique has been developed which allows the validation of existing in-water oceoan color algorithms and the rapid search, identification, and evaluation of new sensor band locations and algorithm wavelength intervals. Thus far, applied only in conjunction with the spectral curvature algorithm (SCA), the active-passive correlation spectroscopy (APCS) technique shows that (1) the usual 490-nm (center-band) chlorophyll SCA could satisfactorily be placed anywhere within the nominal 460-510-nm interval, and (2) two other spectral regions, 645-660 and 680-695 nm, show considerable promise for chlorophyll pigment measurement. Additionally, the APCS method reveals potentially useful wavelength regions (at 600 and about 670 nm) of very low chlorophyll-in-water spectral curvature into which accessory pigment algorithms for phycoerythrin might be carefully positioned. In combination, the APCS and SCA methods strongly suggest that significant information content resides within the seemingly featureless ocean color spectrum.

  14. Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone.

    PubMed

    Tsang, Kit Man; Starost, Matthew F; Nesterova, Maria; Boikos, Sosipatros A; Watkins, Tonya; Almeida, Madson Q; Harran, Michelle; Li, Andrew; Collins, Michael T; Cheadle, Christopher; Mertz, Edward L; Leikin, Sergey; Kirschner, Lawrence S; Robey, Pamela; Stratakis, Constantine A

    2010-05-11

    A population of stromal cells that retains osteogenic capacity in adult bone (adult bone stromal cells or aBSCs) exists and is under intense investigation. Mice heterozygous for a null allele of prkar1a (Prkar1a(+/-)), the primary receptor for cyclic adenosine monophosphate (cAMP) and regulator of protein kinase A (PKA) activity, developed bone lesions that were derived from cAMP-responsive osteogenic cells and resembled fibrous dysplasia (FD). Prkar1a(+/-) mice were crossed with mice that were heterozygous for catalytic subunit Calpha (Prkaca(+/-)), the main PKA activity-mediating molecule, to generate a mouse model with double heterozygosity for prkar1a and prkaca (Prkar1a(+/-)Prkaca(+/-)). Unexpectedly, Prkar1a(+/-)Prkaca(+/-) mice developed a greater number of osseous lesions starting at 3 months of age that varied from the rare chondromas in the long bones and the ubiquitous osteochondrodysplasia of vertebral bodies to the occasional sarcoma in older animals. Cells from these lesions originated from an area proximal to the growth plate, expressed osteogenic cell markers, and showed higher PKA activity that was mostly type II (PKA-II) mediated by an alternate pattern of catalytic subunit expression. Gene expression profiling confirmed a preosteoblastic nature for these cells but also showed a signature that was indicative of mesenchymal-to-epithelial transition and increased Wnt signaling. These studies show that a specific subpopulation of aBSCs can be stimulated in adult bone by alternate PKA and catalytic subunit activity; abnormal proliferation of these cells leads to skeletal lesions that have similarities to human FD and bone tumors. PMID:20421483

  15. Selective activity of deguelin identifies therapeutic targets for androgen receptor-positive breast cancer.

    PubMed

    Robles, Andrew J; Cai, Shengxin; Cichewicz, Robert H; Mooberry, Susan L

    2016-06-01

    Triple-negative breast cancers (TNBC) are aggressive malignancies with no effective targeted therapies. Recent gene expression profiling of these heterogeneous cancers and the classification of cell line models now allows for the identification of compounds with selective activities against molecular subtypes of TNBC. The natural product deguelin was found to have selective activity against MDA-MB-453 and SUM-185PE cell lines, which both model the luminal androgen receptor (LAR) subtype of TNBC. Deguelin potently inhibited proliferation of these cells with GI50 values of 30 and 61 nM, in MDA-MB-453 and SUM-185PE cells, respectively. Deguelin had exceptionally high selectivity, 197 to 566-fold, for these cell lines compared to cell lines representing other TNBC subtypes. Deguelin's mechanisms of action were investigated to determine how it produced these potent and selective effects. Our results show that deguelin has dual activities, inhibiting PI3K/Akt/mTOR signaling, and decreasing androgen receptor levels and nuclear localization. Based on these data, we hypothesized that the combination of the mTOR inhibitor rapamycin and the antiandrogen enzalutamide would have efficacy in LAR models. Rapamycin and enzalutamide showed additive effects in MDA-MB-453 cells, and both drugs had potent antitumor efficacy in a LAR xenograft model. These results suggest that the combination of antiandrogens and mTOR inhibitors might be an effective strategy for the treatment of androgen receptor-expressing TNBC. PMID:27255535

  16. hTERT promoter activity identifies osteosarcoma cells with increased EMT characteristics

    PubMed Central

    YU, LING; LIU, SHIQING; GUO, WEICHUN; ZHANG, CHUN; ZHANG, BO; YAN, HUICHAO; WU, ZHENG

    2014-01-01

    Epithelial-mesenchymal transition (EMT) is a critical step in order for epithelial-derived malignancies to metastasize, however, its role in mesenchymal-derived tumors, i.e., osteosarcoma, remains unclear. Cancer stem cells (CSCs) are enriched with cells that undergo EMT. The activity of telomerase is maintained in normal stem cells and a number of malignant tumors. The current study observed the heterogeneity of telomerase activity among individual osteosarcoma cells. We hypothesized that telomerase-positive (TELpos) cells are enriched for stem cell-like and EMT properties. A human telomerase reverse transcriptase (hTERT) promoter-reporter was applied to assess the telomerase activity of individual MG63 osteosarcoma cells and sort them into TELpos and telomerase-negative (TELneg) subpopulations. It was found that the TELpos cells exhibited an enhanced ability to form sarcospheres in vitro. In addition, TELpos cells exhibited a higher expression of vimentin, accompanied by an increased long/short axis ratio. A panel of EMT-related genes was evaluated by quantitative PCR and western blot analysis, and were found to be significantly upregulated in TELpos cells. Next, the in vitro migration capacity was examined by Transwell assay, which confirmed that TELpos cells are more prone to migration (2.6 fold). The results of the present study support the concept that EMT also applies to mesenchymal-derived osteosarcoma and draws a connection between telomerase and EMT characteristics. PMID:24348856

  17. An activation antigen on a subpopulation of B lymphocytes identified by the monoclonal antibody CMRF-17.

    PubMed

    Peach, S F; Davidson, S E; McKenzie, J L; Nimmo, J C; Hart, D N

    1989-07-01

    The identification of membrane molecules expressed on subpopulations of B lymphocytes is of potential significance because these molecules may be candidates for regulating the activation, proliferation and differentiation of B cells. A new monoclonal antibody, CMRF-17, which reacts with a subpopulation of tonsil B lymphocytes has been produced. The antibody did not react with T lymphocytes in tonsil or peripheral blood nor most peripheral blood B lymphocytes but did label erythrocytes and some platelets. In tonsil, the germinal centre cells, cells in the interfollicular region and endothelial cells were positive, but mantle zone B cells were negative. Double labelling experiments showed that CMRF-17 reacted with activated tonsillar lymphocytes. The antigen recognized by CMRF-17 was heat stable, resistant to treatment with proteolytic enzymes and neuraminidase and was shown to be a carbohydrate determinant on one or more glycolipids. These characteristics of the antigen recognized by CMRF-17 and its pattern of reactivity distinguish this antibody from other monoclonal antibodies recognizing B-cell activation markers. It was notable that of the B-lymphoid malignancies tested to date, including those of probable follicular origin, few stained with CMRF-17. PMID:2474491

  18. Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma

    PubMed Central

    Byrum, Stephanie D.; Larson, Signe K.; Avaritt, Nathan L.; Moreland, Linley E.; Mackintosh, Samuel G.; Cheung, Wang L.; Tackett, Alan J.

    2013-01-01

    Molecular pathways regulating melanoma initiation and progression are potential targets of therapeutic development for this aggressive cancer. Identification and molecular analysis of these pathways in patients has been primarily restricted to targeted studies on individual proteins. Here, we report the most comprehensive analysis of formalin-fixed paraffin-embedded human melanoma tissues using quantitative proteomics. From 61 patient samples, we identified 171 proteins varying in abundance among benign nevi, primary melanoma, and metastatic melanoma. Seventy-three percent of these proteins were validated by immunohistochemistry staining of malignant melanoma tissues from the Human Protein Atlas database. Our results reveal that molecular pathways involved with tumor cell proliferation, motility, and apoptosis are mis-regulated in melanoma. These data provide the most comprehensive proteome resource on patient melanoma and reveal insight into the molecular mechanisms driving melanoma progression. PMID:23976835

  19. Identifying water on our Moon and organics in the outer Solar System with active reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    Hibbitts, C. A.; Spiers, G. D.; Hansen, G. B.

    2005-08-01

    Infrared reflectance spectroscopy has successfully characterized H2O and identified organic molecules on many Solar System objects. However, passive reflectance spectroscopy cannot detect water in the permanently shadowed regions of the Moon. Similarly, the mid-IR fingerprints of organics on the surfaces of outer solar system objects cannot be detected passively because the sunlight is too dim and the surfaces are too cold. The strongest absorption band for condensed water and ice is near 3 microns. Organic molecules have strong absorptions near 3.4 microns, with spectral fingerprints necessary for unique identification present from approximately 5 to 10 microns. Given a sufficiently strong source of illumination, water hidden in shadows on the Moon and organic molecules in the outer solar system would be detectable and identifiable. Quantum Cascade (QC) laser technology is now becoming sufficiently capable to support reflectance spectroscopy at some of these wavelengths from orbit. Conceived under the HCIPE program in support of Prometheus missions, this technique is intrinsically very scalable. For instance, water can be detected using only two wavelengths and its physical state can be characterized with only five. Requiring an optical power of 2W per wavelength for sufficient signal-to-noise, the total power consumption by the lasing system would be approximately 80 and 200W, respectively. Currently, a continuous power output at 3 μm of 200 mWatts has been demonstrated. With beam combining, an optical power of 2 Watts is currently achievable. On the Moon, this would enable the detection of as little as 100ppm water. Radar and neutron spectroscopy measurements suggest there may be > 1000 ppm of water-ice present in permanent crater shadows on the Moon [Feldman et al., 1998; 2000; Nozette et al., 1996] which, if present the surface regolith would stabily exist adsorbed on the grains [Hodges, 2002; Cocks et al., 2002].

  20. Quantitative high-throughput screening: A titration-based approach that efficiently identifies biological activities in large chemical libraries

    PubMed Central

    Inglese, James; Auld, Douglas S.; Jadhav, Ajit; Johnson, Ronald L.; Simeonov, Anton; Yasgar, Adam; Zheng, Wei; Austin, Christopher P.

    2006-01-01

    High-throughput screening (HTS) of chemical compounds to identify modulators of molecular targets is a mainstay of pharmaceutical development. Increasingly, HTS is being used to identify chemical probes of gene, pathway, and cell functions, with the ultimate goal of comprehensively delineating relationships between chemical structures and biological activities. Achieving this goal will require methodologies that efficiently generate pharmacological data from the primary screen and reliably profile the range of biological activities associated with large chemical libraries. Traditional HTS, which tests compounds at a single concentration, is not suited to this task, because HTS is burdened by frequent false positives and false negatives and requires extensive follow-up testing. We have developed a paradigm, quantitative HTS (qHTS), tested with the enzyme pyruvate kinase, to generate concentration–response curves for >60,000 compounds in a single experiment. We show that this method is precise, refractory to variations in sample preparation, and identifies compounds with a wide range of activities. Concentration–response curves were classified to rapidly identify pyruvate kinase activators and inhibitors with a variety of potencies and efficacies and elucidate structure–activity relationships directly from the primary screen. Comparison of qHTS with traditional single-concentration HTS revealed a high prevalence of false negatives in the single-point screen. This study demonstrates the feasibility of qHTS for accurately profiling every compound in large chemical libraries (>105 compounds). qHTS produces rich data sets that can be immediately mined for reliable biological activities, thereby providing a platform for chemical genomics and accelerating the identification of leads for drug discovery. PMID:16864780

  1. Multi-scale surface electromyography modeling to identify changes in neuromuscular activation with myofascial pain.

    PubMed

    Jiang, Ching-Fen; Lin, Yu-Ching; Yu, Nan-Ying

    2013-01-01

    To solve the limitations in using the conventional parametric measures to define myofascial pain, a 3-D multi-scale wavelet energy variation graph is proposed as a way to inspect the pattern of surface electromyography (SEMG) variation between the dominant and nondominant sides at different frequency scales during a muscle contraction cycle and the associated changes with the upper-back myofascial pain. The model was developed based on the property of the wavelet energy of the SEMG signal revealing the degree of correspondence between the shape of the motor unit action potential and the wavelet waveform at a certain scale in terms of the frequency band. The characteristic pattern of the graph for each group (30 normal and 26 patient subjects) was first derived and revealed the dominant-hand effect and the changes with myofascial pain. Through comparison of individual graphs across subjects, we found that the graph pattern reveals a sensitivity of 53.85% at a specificity of 83.33% in the identification of myofascial pain. The changes in these patterns provide insight into the transformation between different fiber recruitment, which cannot be explored using conventional SEMG features. Therefore, this multi-scale analysis model could provide a reliable SEMG features to identify myofascial pain. PMID:23070369

  2. Assessment of the in vitro antimicrobial activity of Lactobacillus species for identifying new potential antibiotics.

    PubMed

    Dubourg, Grégory; Elsawi, Ziena; Raoult, Didier

    2015-11-01

    The bacteriocin-mediated antimicrobial properties of Lactobacillus spp. have been widely studied, leading to the use of these micro-organisms in the food industry as preservative agents against foodborne pathogens. In an era in which antibiotic resistance is becoming a public health issue, the antimicrobial activity of Lactobacillus spp. could be used for the discovery of new potential antibiotics. Thus, it is essential to have an accurate method of screening the production of antimicrobial agents by prokaryotes. Many in vitro assays have been published to date, largely concerning but not limited to Lactobacillus spp. However, these methods mainly use the spot-on-the-lawn method, which is prone to contamination during the overlay stage, with protocols using methanol vapours or the reverse side agar technique being applied to avoid such contamination. In this study, a method combining the spot-on-the-lawn and well diffusion methods was tested, permitting clear identification of inhibition zones from eight Lactobacillus spp. towards clinical isolates of 12 species (11 bacteria and 1 yeast) commonly found in human pathology. Lactobacillus plantarum CIP 106786 and Lactobacillus rhamnosus CSUR P567 exhibited the widest antimicrobial activity, whereas Lactobacillus acidophilus strain DSM 20079 was relatively inactive. In addition, the putative MIC(50) of L. rhamnosus against Proteus mirabilis was estimated at 1.1×10(9)CFU/mL using culture broth dilution. In conclusion, considering the increasing cultivable bacterial human repertoire, these findings open the way of an effective method to screen in vitro for the production of potential antimicrobial compounds. PMID:26163158

  3. A highly selective, reversible inhibitor identified by comparative chemoproteomics modulates diacylglycerol lipase activity in neurons

    PubMed Central

    Baggelaar, Marc P.; Chameau, Pascal J. P.; Kantae, Vasudev; Hummel, Jessica; Hsu, Ku-Lung; Janssen, Freek; van der Wel, Tom; Soethoudt, Marjolein; Deng, Hui; den Dulk, Hans; Allarà, Marco; Florea, Bogdan I.; Di Marzo, Vincenzo; Wadman, Wytse J.; Kruse, Chris G.; Overkleeft, Herman S.; Hankemeier, Thomas; Werkman, Taco R.; Cravatt, Benjamin F.; van der Stelt, Mario

    2016-01-01

    Diacylglycerol lipase (DAGL)-α and -β are enzymes responsible for the biosynthesis of the endocannabinoid 2-arachidonoylglycerol (2-AG). Selective and reversible inhibitors are required to study the function of DAGLs in neuronal cells in an acute and temporal fashion, but they are currently lacking. Here, we describe the identification of a highly selective DAGL inhibitor using structure-guided and a chemoproteomics strategy to characterize the selectivity of the inhibitor in complex proteomes. Key to the success of this approach is the use of comparative and competitive activity-based proteome profiling (ABPP), in which broad-spectrum and tailor-made activity-based probes are combined to report on the inhibition of a protein family in its native environment. Competitive ABPP with broad-spectrum fluorophosphonate-based probes and specific β-lactone-based probes led to the discovery of α-ketoheterocycle LEI105 as a potent, highly selective and reversible dual DAGL-α/DAGL-β inhibitor. LEI105 did not affect other enzymes involved in endocannabinoid metabolism including abhydrolase domain-containing protein 6, abhydrolase domain-containing protein 12, monoacylglycerol lipase and fatty acid amide hydrolase and did not display affinity for the cannabinoid CB1 receptor. Targeted lipidomics revealed that LEI105 concentration-dependently reduced 2-AG levels, but not anandamide levels, in Neuro2A cells. We show that cannabinoid CB1-receptor-mediated short-term synaptic plasticity in a mouse hippocampal slice model can be reduced by LEI105. Thus, we have developed a highly selective DAGL inhibitor and provide new pharmacological evidence to support the hypothesis that ‘on demand biosynthesis’ of 2-AG is responsible for retrograde signaling. PMID:26083464

  4. Mitochondrial impairment by PPAR agonists and statins identified via immunocaptured OXPHOS complex activities and respiration

    SciTech Connect

    Nadanaciva, Sashi; Dykens, James A.; Bernal, Autumn; Capaldi, Roderick A.; Will, Yvonne

    2007-09-15

    Mitochondrial impairment is increasingly implicated in the etiology of toxicity caused by some thiazolidinediones, fibrates, and statins. We examined the effects of members of these drug classes on respiration of isolated rat liver mitochondria using a phosphorescent oxygen sensitive probe and on the activity of individual oxidative phosphorylation (OXPHOS) complexes using a recently developed immunocapture technique. Of the six thiazolidinediones examined, ciglitazone, troglitazone, and darglitazone potently disrupted mitochondrial respiration. In accord with these data, ciglitazone and troglitazone were also potent inhibitors of Complexes II + III, IV, and V, while darglitazone predominantly inhibited Complex IV. Of the six statins evaluated, lovastatin, simvastatin, and cerivastatin impaired mitochondrial respiration the most, with simvastatin and lovastatin impairing multiple OXPHOS Complexes. Within the class of fibrates, gemfibrozil more potently impaired respiration than fenofibrate, clofibrate, or ciprofibrate. Gemfibrozil only modestly inhibited Complex I, fenofibrate inhibited Complexes I, II + III, and V, and clofibrate inhibited Complex V. Our findings with the two complementary methods indicate that (1) some members of each class impair mitochondrial respiration, whereas others have little or no effect, and (2) the rank order of mitochondrial impairment accords with clinical adverse events observed with these drugs. Since the statins are frequently co-prescribed with the fibrates or thiazolidinediones, various combinations of these three drug classes were also analyzed for their mitochondrial effects. In several cases, the combination additively uncoupled or inhibited respiration, suggesting that some combinations are more likely to yield clinically relevant drug-induced mitochondrial side effects than others.

  5. Mitochondrial impairment by PPAR agonists and statins identified via immunocaptured OXPHOS complex activities and respiration.

    PubMed

    Nadanaciva, Sashi; Dykens, James A; Bernal, Autumn; Capaldi, Roderick A; Will, Yvonne

    2007-09-15

    Mitochondrial impairment is increasingly implicated in the etiology of toxicity caused by some thiazolidinediones, fibrates, and statins. We examined the effects of members of these drug classes on respiration of isolated rat liver mitochondria using a phosphorescent oxygen sensitive probe and on the activity of individual oxidative phosphorylation (OXPHOS) complexes using a recently developed immunocapture technique. Of the six thiazolidinediones examined, ciglitazone, troglitazone, and darglitazone potently disrupted mitochondrial respiration. In accord with these data, ciglitazone and troglitazone were also potent inhibitors of Complexes II+III, IV, and V, while darglitazone predominantly inhibited Complex IV. Of the six statins evaluated, lovastatin, simvastatin, and cerivastatin impaired mitochondrial respiration the most, with simvastatin and lovastatin impairing multiple OXPHOS Complexes. Within the class of fibrates, gemfibrozil more potently impaired respiration than fenofibrate, clofibrate, or ciprofibrate. Gemfibrozil only modestly inhibited Complex I, fenofibrate inhibited Complexes I, II+III, and V, and clofibrate inhibited Complex V. Our findings with the two complementary methods indicate that (1) some members of each class impair mitochondrial respiration, whereas others have little or no effect, and (2) the rank order of mitochondrial impairment accords with clinical adverse events observed with these drugs. Since the statins are frequently co-prescribed with the fibrates or thiazolidinediones, various combinations of these three drug classes were also analyzed for their mitochondrial effects. In several cases, the combination additively uncoupled or inhibited respiration, suggesting that some combinations are more likely to yield clinically relevant drug-induced mitochondrial side effects than others. PMID:17658574

  6. Using Hydrothermal Plumes and Their Chemical Composition to Identify and Understand Hydrothermal Activity at Explorer Ridge

    NASA Astrophysics Data System (ADS)

    Resing, J.; Lebon, G.; Baker, E.; Walker, S.; Nakamura, K.; Silvers, B.

    2002-12-01

    During June and July, 2002, an extensive survey of the hydrothermal systems of the Explorer Ridge was made aboard the R/V Thomas Thompson. This survey employed hydrocasts and the Autonomous Benthic Explorer (ABE) to locate and map hydrothermal vent fields. A total of 28 hydrocasts (17 verticals and 11 tow-yos) were used to search for hydrothermal activity from 49.5°N to 50.3°N on the Explorer Ridge. During the hydrocasts continuous measurements were made of conductivity, temperature, pressure, light backscatter, eH, Fe, Mn, and pH. Discrete samples were collected for total dissolved Fe and Mn, methane, pH, total CO2, and particulate matter. Most of the strong hydrothermal venting was near the Magic Mountain area of the Explorer Ridge at ~49.76° N, 130.26° W, where strong particulate backscatter signals (~0.130 NTUs) and moderate temperature anomalies (~ 0.05 °C) were detected. The particulate matter causing the backscatter was made up primarily of volatile particulate sulfur (PS) with little to no hydrothermal PFe. PS:PFe ratios exceeded 25 in the areas of most intense venting, . These PFe and PS data suggest that the hydrothermal Fe, if any, is deposited as sulfide minerals beneath the sea floor and that S is far in excess of Fe in the hydrothermal fluids. In the most intense plumes,total dissolvable Fe and Mn were between 20 and 30 nM, pH anomalies exceeded 0.025 pH units (indicating an increase of ~10uM CO2), and methane reached 16nM. These results suggest that the fluids exiting the sea floor are metal-poor and moderately gas-rich.

  7. The nematode Caenorhabditis elegans as a tool to predict chemical activity on mammalian development and identify mechanisms influencing toxicological outcome

    PubMed Central

    Harlow, Philippa H.; Perry, Simon J.; Widdison, Stephanie; Daniels, Shannon; Bondo, Eddie; Lamberth, Clemens; Currie, Richard A.; Flemming, Anthony J.

    2016-01-01

    To determine whether a C. elegans bioassay could predict mammalian developmental activity, we selected diverse compounds known and known not to elicit such activity and measured their effect on C. elegans egg viability. 89% of compounds that reduced C. elegans egg viability also had mammalian developmental activity. Conversely only 25% of compounds found not to reduce egg viability in C. elegans were also inactive in mammals. We conclude that the C. elegans egg viability assay is an accurate positive predictor, but an inaccurate negative predictor, of mammalian developmental activity. We then evaluated C. elegans as a tool to identify mechanisms affecting toxicological outcomes among related compounds. The difference in developmental activity of structurally related fungicides in C. elegans correlated with their rate of metabolism. Knockdown of the cytochrome P450s cyp-35A3 and cyp-35A4 increased the toxicity to C. elegans of the least developmentally active compounds to the level of the most developmentally active. This indicated that these P450s were involved in the greater rate of metabolism of the less toxic of these compounds. We conclude that C. elegans based approaches can predict mammalian developmental activity and can yield plausible hypotheses for factors affecting the biological potency of compounds in mammals. PMID:26987796

  8. A Newly Identified Extrinsic Input Triggers a Distinct Gastric Mill Rhythm via Activation of Modulatory Projection Neurons

    PubMed Central

    Blitz, Dawn M.; White, Rachel S.; Saideman, Shari R.; Cook, Aaron; Christie, Andrew E.; Nadim, Farzan; Nusbaum, Michael P.

    2008-01-01

    Neuronal network flexibility enables animals to respond appropriately to changes in their internal and external states. We are using the isolated crab stomatogastric nervous system to determine how extrinsic inputs contribute to network flexibility. The stomatogastric system includes the well-characterized gastric mill (chewing) and pyloric (filtering of chewed food) motor circuits in the stomatogastric ganglion. Projection neurons with somata in the commissural ganglia (CoGs) regulate these rhythms. Previous work characterized a unique gastric mill rhythm that occurred spontaneously in some preparations, but whose origin remained undetermined. This rhythm includes a distinct protractor phase activity pattern, during which all active gastric mill circuit and projection neurons fire in a pyloric rhythm-timed activity pattern instead of the tonic firing pattern exhibited by these neurons during previously studied gastric mill rhythms. Here we identify a new extrinsic input, the post-oesophageal commissure (POC) neurons, relatively brief stimulation (30 sec) of which triggers a long-lasting (tens of minutes) activation of this novel gastric mill rhythm at least in part via its lasting activation of CoG projection neurons, including the previously identified MCN1 and CPN2. Immunocytochemical and electrophysiological data suggest that the POC neurons excite MCN1 and CPN2 by release of the neuropeptide Cancer borealis tachykinin-related peptide Ia (CabTRP Ia). These data further suggest that the CoG arborization of the POC neurons comprises the previously identified anterior commissural organ (ACO), a CabTRP Ia-containing neurohemal organ. This endocrine pathway thus appears to also have paracrine actions that include activation of a novel and lasting gastric mill rhythm. PMID:18310125

  9. Teachers' instructional goals for science practice: Identifying knowledge gaps using cultural-historical activity theory (CHAT)

    NASA Astrophysics Data System (ADS)

    Farrar, Cynthia Hamen

    In AP Biology, the course goal, with respect to scientific acts and reasoning, has recently shifted toward a reform goal of science practice, where the goal is for students to have a scientific perspective that views science as a practice of a community rather than a body of knowledge. Given this recent shift, this study is interested in the gaps that may exist between an individual teacher's instructional goal and the goals of the AP Biology course. A Cultural-Historical Activity Theory (CHAT) methodology and perspective is used to analyze four teachers' knowledge, practice, and learning. Teachers have content knowledge for teaching, a form of knowledge that is unique for teaching called specialized content knowledge. This specialized content knowledge (SCK) defines their instructional goals, the student outcomes they ultimately aim to achieve with their students. The study employs a cultural-historical continuum of scientific acts and reasoning, which represents the development of the AP Biology goal over time, to study gaps in their instructional goal. The study also analyzes the contradictions within their teaching practice and how teachers address those contradictions to shift their instructional practice and learn. The findings suggest that teachers have different interpretations of the AP Biology goals of science practice, placing their instructional goal at different points along the continuum. Based on the location of their instructional goal, different micro-communities of teachers exist along the continuum, comprised of teachers with a shared goal, language, and culture of their AP Biology teaching. The in-depth study of one teacher's AP Biology teaching, using a CHAT perspective, provides a means for studying the mechanisms that connect SCK to classroom actions and ultimately to instructional practice. CHAT also reveals the nature and importance of contradictions or cognitive dissonance in teacher learning and the types of support teachers need to

  10. Battle between influenza A virus and a newly identified antiviral activity of the PARP-containing ZAPL protein.

    PubMed

    Liu, Chien-Hung; Zhou, Ligang; Chen, Guifang; Krug, Robert M

    2015-11-10

    Previous studies showed that ZAPL (PARP-13.1) exerts its antiviral activity via its N-terminal zinc fingers that bind the mRNAs of some viruses, leading to mRNA degradation. Here we identify a different antiviral activity of ZAPL that is directed against influenza A virus. This ZAPL antiviral activity involves its C-terminal PARP domain, which binds the viral PB2 and PA polymerase proteins, leading to their proteasomal degradation. After the PB2 and PA proteins are poly(ADP-ribosylated), they are associated with the region of ZAPL that includes both the PARP domain and the adjacent WWE domain that is known to bind poly(ADP-ribose) chains. These ZAPL-associated PB2 and PA proteins are then ubiquitinated, followed by proteasomal degradation. This antiviral activity is counteracted by the viral PB1 polymerase protein, which binds close to the PARP domain and causes PB2 and PA to dissociate from ZAPL and escape degradation, explaining why ZAPL only moderately inhibits influenza A virus replication. Hence influenza A virus has partially won the battle against this newly identified ZAPL antiviral activity. Eliminating PB1 binding to ZAPL would be expected to substantially increase the inhibition of influenza A virus replication, so that the PB1 interface with ZAPL is a potential target for antiviral development. PMID:26504237

  11. A high-content EMT screen identifies multiple receptor tyrosine kinase inhibitors with activity on TGFβ receptor.

    PubMed

    Lotz-Jenne, Carina; Lüthi, Urs; Ackerknecht, Sabine; Lehembre, François; Fink, Tobias; Stritt, Manuel; Wirth, Matthias; Pavan, Simona; Bill, Ruben; Regenass, Urs; Christofori, Gerhard; Meyer-Schaller, Nathalie

    2016-05-01

    An epithelial to mesenchymal transition (EMT) enables epithelial tumor cells to break out of the primary tumor mass and to metastasize. Understanding the molecular mechanisms driving EMT in more detail will provide important tools to interfere with the metastatic process. To identify pharmacological modulators and druggable targets of EMT, we have established a novel multi-parameter, high-content, microscopy-based assay and screened chemical compounds with activities against known targets. Out of 3423 compounds, we have identified 19 drugs that block transforming growth factor beta (TGFβ)-induced EMT in normal murine mammary gland epithelial cells (NMuMG). The active compounds include inhibitors against TGFβ receptors (TGFBR), Rho-associated protein kinases (ROCK), myosin II, SRC kinase and uridine analogues. Among the EMT-repressing compounds, we identified a group of inhibitors targeting multiple receptor tyrosine kinases, and biochemical profiling of these multi-kinase inhibitors reveals TGFBR as a thus far unknown target of their inhibitory spectrum. These findings demonstrate the feasibility of a multi-parameter, high-content microscopy screen to identify modulators and druggable targets of EMT. Moreover, the newly discovered "off-target" effects of several receptor tyrosine kinase inhibitors have important consequences for in vitro and in vivo studies and might beneficially contribute to the therapeutic effects observed in vivo. PMID:27036020

  12. Larvicidal activity of medicinal plant extracts and lignan identified in Phryma leptostachya var. asiatica roots against housefly (Musca domestica L.).

    PubMed

    Seo, Seon-Mi; Park, Il-Kwon

    2012-05-01

    Medicinal plant extracts from 27 plant species in 20 families were tested for their larvicidal activity against housefly, Musca domestica (L.). Responses varied with plant material and concentration. Among plant species tested, Phryma leptostachya var. asiatica showed 100% larvicidal activity against M. domestica at 10 mg/g concentration. Larvicidal activities of Atractylodes japonica, Saussurea lappa, Asiasarum sieboldi, and Gleditsia japonica var. koraiensis were 89.3%, 85.3%, 93.3%, and 96.6% at 10 mg/g concentration, respectively. Extracts of Prunus persica, Curcuma longa, and Paeonia moutan produced moderate activity. Larvicidal activity of other plant extracts was less than 50%. Among test plant species, P. leptostachya var. asiatica showed the most potent larvicidal activity. The active constituent of P. leptostachya var. asiatica roots was identified as the leptostachyol acetate by spectroscopic analysis. The LC(50) values of leptostachyol acetate against M. domestica larvae were 0.039 mg/g. Naturally occurring medicinal plant extracts and P. leptostachya var. asiatica root-derived compounds merit further study as potential housefly larval control agents or lead compounds. PMID:22065063

  13. Structural Dissection of the Active Site of Thermotoga maritima β-Galactosidase Identifies Key Residues for Transglycosylating Activity.

    PubMed

    Talens-Perales, David; Polaina, Julio; Marín-Navarro, Julia

    2016-04-13

    Glycoside hydrolases, specifically β-galactosidases, can be used to synthesize galacto-oligosaccharides (GOS) due to the transglycosylating (secondary) activity of these enzymes. Site-directed mutagenesis of a thermoresistant β-galactosidase from Thermotoga maritima has been carried out to study the structural basis of transgalactosylation and to obtain enzymatic variants with better performance for GOS biosynthesis. Rational design of mutations was based on homologous sequence analysis and structural modeling. Analysis of mutant enzymes indicated that residue W959, or an alternative aromatic residue at this position, is critical for the synthesis of β-3'-galactosyl-lactose, the major GOS obtained with the wild-type enzyme. Mutants W959A and W959C, but not W959F, showed an 80% reduced synthesis of this GOS. Other substitutions, N574S, N574A, and F571L, increased the synthesis of β-3'-galactosyl-lactose about 40%. Double mutants F571L/N574S and F571L/N574A showed an increase of about 2-fold. PMID:26998654

  14. Synthetic Lethality Screen Identifies RPS6KA2 as Modifier of Epidermal Growth Factor Receptor Activity in Pancreatic Cancer12

    PubMed Central

    Milosevic, Nada; Kühnemuth, Benjamin; Mühlberg, Leonie; Ripka, Stefanie; Griesmann, Heidi; Lölkes, Carolin; Buchholz, Malte; Aust, Daniela; Pilarsky, Christian; Krug, Sebastian; Gress, Thomas; Michl, Patrick

    2013-01-01

    Pancreatic cancer is characterized by a high degree of resistance to chemotherapy. Epidermal growth factor receptor (EGFR) inhibition using the small-molecule inhibitor erlotinib was shown to provide a small survival benefit in a subgroup of patients. To identify kinases whose inhibition acts synergistically with erlotinib, we employed a kinome-wide small-interfering RNA (siRNA)-based loss-of-function screen in the presence of erlotinib. Of 779 tested kinases, we identified several targets whose inhibition acted synergistically lethal with EGFR inhibition by erlotinib, among them the S6 kinase ribosomal protein S6 kinase 2 (RPS6KA2)/ribosomal S6 kinase 3. Activated RPS6KA2 was expressed in approximately 40% of 123 human pancreatic cancer tissues. RPS6KA2 was shown to act downstream of EGFR/RAS/mitogen-activated protein kinase kinase (MEK)/extracellular-signal regulated kinase (ERK) signaling and was activated by EGF independently of the presence of KRAS mutations. Knockdown of RPS6KA2 by siRNA led to increased apoptosis only in the presence of erlotinib, whereas RPS6KA2 activation or overexpression rescued from erlotinib- and gemcitabine-induced apoptosis. This effect was at least in part mediated by downstream activation of ribosomal protein S6. Genetic as well as pharmacological inhibition of RPS6KA2 by the inhibitor BI-D1870 acted synergistically with erlotinib. By applying this synergistic lethality screen using a kinome-wide RNA interference-library approach, we identified RPS6KA2 as potential drug target whose inhibition synergistically enhanced the effect of erlotinib on tumor cell survival. This kinase therefore represents a promising drug candidate suitable for the development of novel inhibitors for pancreatic cancer therapy. PMID:24403857

  15. Sleeping Beauty transposon screen identifies signaling modules that cooperate with STAT5 activation to induce B cell acute lymphoblastic leukemia

    PubMed Central

    Heltemes-Harris, Lynn M.; Larson, Jon D.; Starr, Timothy K.; Hubbard, Gregory K.; Sarver, Aaron L.; Largaespada, David A.; Farrar, Michael A.

    2015-01-01

    STAT5 activation occurs frequently in human progenitor B cell acute lymphoblastic leukemia (B-ALL). To identify gene alterations that cooperate with STAT5 activation to initiate leukemia we crossed mice expressing a constitutively active form of STAT5 (Stat5b-CA) to mice in which a mutagenic Sleeping Beauty transposon (T2/Onc) was mobilized only in B cells. Stat5b-CA mice typically do not develop B-ALL (<2% penetrance); in contrast, 89% of Stat5b–CA mice in which the T2/Onc transposon had been mobilized died of B-ALL by 3 months of age. High-throughput sequencing approaches were used to identify genes frequently targeted by the T2/Onc transposon; these included Sos1 (74%), Kdm2a (35%), Jak1 (26%), Bmi1 (19%), Prdm14 or Ncoa2 (13%), Cdkn2a (10%), Ikzf1 (8%), Caap1 (6%) and Klf3 (6%). Collectively, these mutations target three major cellular processes: (i) the JAK/STAT5 pathway (ii) progenitor B cell differentiation and (iii) the CDKN2A tumor suppressor pathway. Transposon insertions typically resulted in altered expression of these genes, as well as downstream pathways including STAT5, ERK and p38. Importantly, expression of Sos1 and Kdm2a, and activation of p38, correlated with survival, further underscoring the role these genes and associated pathways play in B-ALL. PMID:26500062

  16. Complexes between tissue-type plasminogen activator and proteinase inhibitors in human plasma, identified with an immunoradiometric assay

    SciTech Connect

    Rijken, D.C.; Juhan-Vague, I.; Collen, D.

    1983-02-01

    Extrinsic (tissue-type) plasminogen activator antigen in human plasma, as measured by a two-site immunoradiometric assay, is composed of a fibrin-adsorbable and a nonadsorbable fraction. Gel filtration on Ultrogel AcA 44 in 1.6M KSCN of the fibrin-adsorbable fraction showed a peak with M/sub r/ approx. =70,000, which contained plasminogen activator activity and was assumed to represent free extrinsic plasminogen activator. The nonadsorbable fraction showed a broad peak with M/sub r/ approx. =140,000 without plasminogen activator activity. Overnight incubation at 37/sup 0/C of postexercise plasma revealed a shift of the M/sub r/ approx. =70,000 peak to the M/sub r/ approx. =140,000 position, suggesting that the M/sub r/ approx. =140,000 peak consists of extrinsic plasminogen activator-protease inhibitor complex(es). ..cap alpha../sub 2/-Antiplasmin is the main inhibitor of extrinsic plasminogen activator in plasma and is probably responsible for the generation of the M/sub r/ approx. =140,000 component. A possible involvement of other plasma proteinase inhibitors was explored by incubation of /sup 125/I-labeled extrinsic plasminogen activator in ..cap alpha../sub 2/-antiplasmin-depleted plasma. A complex was formed with a t1/2 of about 1 hr, which was identified by immunoprecipitation as extrinsic plasminogen activator-..cap alpha../sub 2/-antiplasmin complex. Additional evidence for the presence of extrinsic plasminogen activator complexes with ..cap alpha../sub 2/-antiplasmin and ..cap alpha../sub 1/-antitrypsin in plasma was obtained from two-site immunoradiometric assays. It was concluded that plasma contains both free extrinsic plasminogen activator and plasminogen activator complexes with ..cap alpha../sub 2/-antiplasmin and ..cap alpha../sub 1/-antitrypsin. These complexes are also present in plasma collected on the active site inhibitor, D-Phe-Pro-Arg-CH/sub 2/Cl, at rest and after exercise and are therefore assumed to circulate in vivo. (JMT)

  17. Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current.

    PubMed

    Assmy, Philipp; Smetacek, Victor; Montresor, Marina; Klaas, Christine; Henjes, Joachim; Strass, Volker H; Arrieta, Jesús M; Bathmann, Ulrich; Berg, Gry M; Breitbarth, Eike; Cisewski, Boris; Friedrichs, Lars; Fuchs, Nike; Herndl, Gerhard J; Jansen, Sandra; Krägefsky, Sören; Latasa, Mikel; Peeken, Ilka; Röttgers, Rüdiger; Scharek, Renate; Schüller, Susanne E; Steigenberger, Sebastian; Webb, Adrian; Wolf-Gladrow, Dieter

    2013-12-17

    Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 wk. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux. PMID:24248337

  18. Multi-scale responses of soil stability and invasive plants to removal of non-native grazers from an arid conservation reserve

    USGS Publications Warehouse

    Beever, E.A.; Huso, M.; Pyke, D.A.

    2006-01-01

    Disturbances and ecosystem recovery from disturbance both involve numerous processes that operate on multiple spatial and temporal scales. Few studies have investigated how gradients of disturbance intensity and ecosystem responses are distributed across multiple spatial resolutions and also how this relationship changes through time during recovery. We investigated how cover of non-native species and soil-aggregate stability (a measure of vulnerability to erosion by water) in surface and subsurface soils varied spatially during grazing by burros and cattle and whether patterns in these variables changed after grazer removal from Mojave National Preserve, California, USA. We compared distance from water and number of ungulate defecations — metrics of longer-term and recent grazing intensity, respectively, — as predictors of our response variables. We used information-theoretic analyses to compare hierarchical linear models that accounted for important covariates and allowed for interannual variation in the disturbance–response relationship at local and landscape scales. Soil stability was greater under perennial vegetation than in bare interspaces, and surface soil stability decreased with increasing numbers of ungulate defecations. Stability of surface samples was more affected by time since removal of grazers than was stability of subsurface samples, and subsurface soil stability in bare spaces was not related to grazing intensity, time since removal, or any of our other predictors. In the high rainfall year (2003) after cattle had been removed for 1–2 years, cover of all non-native plants averaged nine times higher than in the low-rainfall year (2002). Given the heterogeneity in distribution of large-herbivore impacts that we observed at several resolutions, hierarchical analyses provided a more complete understanding of the spatial and temporal complexities of disturbance and recovery processes in arid ecosystems.

  19. Thick-shelled, grazer-protected diatoms decouple ocean carbon and silicon cycles in the iron-limited Antarctic Circumpolar Current

    PubMed Central

    Assmy, Philipp; Smetacek, Victor; Montresor, Marina; Klaas, Christine; Henjes, Joachim; Strass, Volker H.; Arrieta, Jesús M.; Bathmann, Ulrich; Berg, Gry M.; Breitbarth, Eike; Cisewski, Boris; Friedrichs, Lars; Fuchs, Nike; Herndl, Gerhard J.; Jansen, Sandra; Krägefsky, Sören; Latasa, Mikel; Peeken, Ilka; Röttgers, Rüdiger; Scharek, Renate; Schüller, Susanne E.; Steigenberger, Sebastian; Webb, Adrian; Wolf-Gladrow, Dieter

    2013-01-01

    Diatoms of the iron-replete continental margins and North Atlantic are key exporters of organic carbon. In contrast, diatoms of the iron-limited Antarctic Circumpolar Current sequester silicon, but comparatively little carbon, in the underlying deep ocean and sediments. Because the Southern Ocean is the major hub of oceanic nutrient distribution, selective silicon sequestration there limits diatom blooms elsewhere and consequently the biotic carbon sequestration potential of the entire ocean. We investigated this paradox in an in situ iron fertilization experiment by comparing accumulation and sinking of diatom populations inside and outside the iron-fertilized patch over 5 wk. A bloom comprising various thin- and thick-shelled diatom species developed inside the patch despite the presence of large grazer populations. After the third week, most of the thinner-shelled diatom species underwent mass mortality, formed large, mucous aggregates, and sank out en masse (carbon sinkers). In contrast, thicker-shelled species, in particular Fragilariopsis kerguelensis, persisted in the surface layers, sank mainly empty shells continuously, and reduced silicate concentrations to similar levels both inside and outside the patch (silica sinkers). These patterns imply that thick-shelled, hence grazer-protected, diatom species evolved in response to heavy copepod grazing pressure in the presence of an abundant silicate supply. The ecology of these silica-sinking species decouples silicon and carbon cycles in the iron-limited Southern Ocean, whereas carbon-sinking species, when stimulated by iron fertilization, export more carbon per silicon. Our results suggest that large-scale iron fertilization of the silicate-rich Southern Ocean will not change silicon sequestration but will add carbon to the sinking silica flux. PMID:24248337

  20. Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen.

    PubMed

    Kozlov, Sergei V; Waardenberg, Ashley J; Engholm-Keller, Kasper; Arthur, Jonathan W; Graham, Mark E; Lavin, Martin

    2016-03-01

    Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

  1. High-resolution water column survey to identify active sublacustrine hydrothermal discharge zones within Lake Rotomahana, North Island, New Zealand

    NASA Astrophysics Data System (ADS)

    Walker, Sharon L.; de Ronde, Cornel E. J.; Fornari, Daniel; Tivey, Maurice A.; Stucker, Valerie K.

    2016-03-01

    Autonomous underwater vehicles were used to conduct a high-resolution water column survey of Lake Rotomahana using temperature, pH, turbidity, and oxidation-reduction potential (ORP) to identify active hydrothermal discharge zones within the lake. Five areas with active sublacustrine venting were identified: (1) the area of the historic Pink Terraces; (2) adjacent to the western shoreline subaerial "Steaming Cliffs," boiling springs and geyser; (3) along the northern shoreline to the east of the Pink Terrace site; (4) the newly discovered Patiti hydrothermal system along the south margin of the 1886 Tarawera eruption rift zone; and (5) a location in the east basin (northeast of Patiti Island). The Pink Terrace hydrothermal system was active prior to the 1886 eruption of Mount Tarawera, but venting along the western shoreline, in the east basin, and the Patiti hydrothermal system appear to have been initiated in the aftermath of the eruption, similar to Waimangu Valley to the southwest. Different combinations of turbidity, pH anomalies (both positive and negative), and ORP responses suggest vent fluid compositions vary over short distances within the lake. The seasonal period of stratification limits vertical transport of heat to the surface layer and the hypolimnion temperature of Lake Rotomahana consequently increases with an average warming rate of ~ 0.010 °C/day due to both convective hydrothermal discharge and conductive geothermal heating. A sudden temperature increase occurred during our 2011 survey and was likely the response to an earthquake swarm just 11 days prior.

  2. Identifying New Drug Targets for Potent Phospholipase D Inhibitors: Combining Sequence Alignment, Molecular Docking, and Enzyme Activity/Binding Assays.

    PubMed

    Djakpa, Helene; Kulkarni, Aditya; Barrows-Murphy, Scheneque; Miller, Greg; Zhou, Weihong; Cho, Hyejin; Török, Béla; Stieglitz, Kimberly

    2016-05-01

    Phospholipase D enzymes cleave phospholipid substrates generating choline and phosphatidic acid. Phospholipase D from Streptomyces chromofuscus is a non-HKD (histidine, lysine, and aspartic acid) phospholipase D as the enzyme is more similar to members of the diverse family of metallo-phosphodiesterase/phosphatase enzymes than phospholipase D enzymes with active site HKD repeats. A highly efficient library of phospholipase D inhibitors based on 1,3-disubstituted-4-amino-pyrazolopyrimidine core structure was utilized to evaluate the inhibition of purified S. chromofuscus phospholipase D. The molecules exhibited inhibition of phospholipase D activity (IC50 ) in the nanomolar range with monomeric substrate diC4 PC and micromolar range with phospholipid micelles and vesicles. Binding studies with vesicle substrate and phospholipase D strongly indicate that these inhibitors directly block enzyme vesicle binding. Following these compelling results as a starting point, sequence searches and alignments with S. chromofuscus phospholipase D have identified potential new drug targets. Using AutoDock, inhibitors were docked into the enzymes selected from sequence searches and alignments (when 3D co-ordinates were available) and results analyzed to develop next-generation inhibitors for new targets. In vitro enzyme activity assays with several human phosphatases demonstrated that the predictive protocol was accurate. The strategy of combining sequence comparison, docking, and high-throughput screening assays has helped to identify new drug targets and provided some insight into how to make potential inhibitors more specific to desired targets. PMID:26691755

  3. An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression.

    PubMed

    Reniere, Michelle L; Whiteley, Aaron T; Portnoy, Daniel A

    2016-07-01

    Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. In this study, we took advantage of the robust up-regulation of ActA that occurs intracellularly and expressed Cre recombinase from the actA promoter and 5' untranslated region in a strain in which loxP sites flanked essential genes, so that activation of actA led to bacterial death. Upon screening for transposon mutants that survived intracellularly, six genes were identified as necessary for ActA expression. Strikingly, most of the genes, including gshF, spxA1, yjbH, and ohrA, are predicted to play important roles in bacterial redox regulation. The mutants identified in the genetic selection fell into three broad categories: (1) those that failed to reach the cytosolic compartment; (2) mutants that entered the cytosol, but failed to activate the master virulence regulator PrfA; and (3) mutants that entered the cytosol and activated transcription of actA, but failed to synthesize it. The identification of mutants defective in vacuolar escape suggests that up-regulation of ActA occurs in the host cytosol and not the vacuole. Moreover, these results provide evidence for two non-redundant cytosolic cues; the first results in allosteric activation of PrfA via increased glutathione levels and transcriptional activation of actA while the second results in translational activation of actA and requires yjbH. Although the precise host cues have not yet been identified, we suggest that intracellular redox stress occurs as a consequence of both host and pathogen remodeling their metabolism upon infection. PMID:27414028

  4. An In Vivo Selection Identifies Listeria monocytogenes Genes Required to Sense the Intracellular Environment and Activate Virulence Factor Expression

    PubMed Central

    Portnoy, Daniel A.

    2016-01-01

    Listeria monocytogenes is an environmental saprophyte and facultative intracellular bacterial pathogen with a well-defined life-cycle that involves escape from a phagosome, rapid cytosolic growth, and ActA-dependent cell-to-cell spread, all of which are dependent on the master transcriptional regulator PrfA. The environmental cues that lead to temporal and spatial control of L. monocytogenes virulence gene expression are poorly understood. In this study, we took advantage of the robust up-regulation of ActA that occurs intracellularly and expressed Cre recombinase from the actA promoter and 5’ untranslated region in a strain in which loxP sites flanked essential genes, so that activation of actA led to bacterial death. Upon screening for transposon mutants that survived intracellularly, six genes were identified as necessary for ActA expression. Strikingly, most of the genes, including gshF, spxA1, yjbH, and ohrA, are predicted to play important roles in bacterial redox regulation. The mutants identified in the genetic selection fell into three broad categories: (1) those that failed to reach the cytosolic compartment; (2) mutants that entered the cytosol, but failed to activate the master virulence regulator PrfA; and (3) mutants that entered the cytosol and activated transcription of actA, but failed to synthesize it. The identification of mutants defective in vacuolar escape suggests that up-regulation of ActA occurs in the host cytosol and not the vacuole. Moreover, these results provide evidence for two non-redundant cytosolic cues; the first results in allosteric activation of PrfA via increased glutathione levels and transcriptional activation of actA while the second results in translational activation of actA and requires yjbH. Although the precise host cues have not yet been identified, we suggest that intracellular redox stress occurs as a consequence of both host and pathogen remodeling their metabolism upon infection. PMID:27414028

  5. High Throughput Kinomic Profiling of Human Clear Cell Renal Cell Carcinoma Identifies Kinase Activity Dependent Molecular Subtypes

    PubMed Central

    Mehta, Amitkumar; Welaya, Karim; Chen, Dongquan; Duarte, Christine W.; Ghatalia, Pooja; Arafat, Waleed; Madan, Ankit; Sudarshan, Sunil; Naik, Gurudatta; Grizzle, William E.; Choueiri, Toni K.; Sonpavde, Guru

    2015-01-01

    Despite the widespread use of kinase-targeted agents in clear cell renal cell carcinoma (CC-RCC), comprehensive kinase activity evaluation (kinomic profiling) of these tumors is lacking. Thus, kinomic profiling of CC-RCC may assist in devising a classification system associated with clinical outcomes, and help identify potential therapeutic targets. Fresh frozen CC-RCC tumor lysates from 41 clinically annotated patients who had localized disease at diagnosis were kinomically profiled using the PamStation®12 high-content phospho-peptide substrate microarray system (PamGene International). Twelve of these patients also had matched normal kidneys available that were also profiled. Unsupervised hierarchical clustering and supervised comparisons based on tumor vs. normal kidney and clinical outcome (tumor recurrence) were performed and coupled with advanced network modeling and upstream kinase prediction methods. Unsupervised clustering analysis of localized CC-RCC tumors identified 3 major kinomic groups associated with inflammation (A), translation initiation (B), and immune response and cell adhesions (C) processes. Potential driver kinases implicated include PFTAIRE (PFTK1), PKG1, and SRC, which were identified in groups A, B, and C, respectively. Of the 9 patients who had tumor recurrence, only one was found in Group B. Supervised analysis showed decreased kinase activity of CDK1 and RSK1-4 substrates in those which progressed compared to others. Twelve tumors with matching normal renal tissue implicated increased PIM’s and MAPKAPK’s in tumors compared to adjacent normal renal tissue. As such, comprehensive kinase profiling of CC-RCC tumors could provide a functional classification strategy for patients with localized disease and identify potential therapeutic targets. PMID:26406598

  6. An Action Research Inquiry into the Relationship Among Aerobic Activities, Memory, and Stress with Students Identified as Gifted

    NASA Astrophysics Data System (ADS)

    Ford, Denise Marie

    Students identified as gifted come from varying socio-economic strata and nationalities with a range of talents and temperaments comprising a diverse community. They may experience stress for a variety of reasons. Although a certain amount of stress can enhance the learning process, too much stress can impede learning, especially memory. Strategies have been offered for relieving stress, yet the benefits of physical activities as stress reducers for the gifted have frequently been overlooked. The purpose of this study was to investigate the relationship among aerobic activity, stress, and memory ability in students in an elementary school gifted program. An exceptional aspect of this research was that the students were an integral part of their own study. As co-researchers they had a vested interest in what they were doing, enhancing the significance of the experience and heightening learning. This action research project conducted in a mid-western school district with fourth and fifth grade students examined the impact of aerobic movement on physical indicators of stress and memory. The study lasted twelve weeks with data collected on physical indicators of stress, memory test scores, parent observations, interviews with students, a parent focus group session, observational data, student comments, and investigator/teacher journal. By infusing regular exercise into curricula, stress levels in students identified as gifted were examined. Students' scores on declarative memory tasks conducted with and without an accompanying aerobic activity were documented. Students learned of the delicate relationship between stress and memory as they studied the physiology of the brain. Twenty-four hour retention rates of declarative memory items were higher when a 20-minute aerobic activity intervention preceded the memory activity. Perceived stress levels were lowered for 14 of the 16 co-researchers. Students indicated a positive attitude toward physical activity and its

  7. Phosphoproteomic analysis of anaplastic lymphoma kinase (ALK) downstream signaling pathways identifies signal transducer and activator of transcription 3 as a functional target of activated ALK in neuroblastoma cells

    PubMed Central

    Sattu, Kamaraj; Hochgräfe, Falko; Wu, Jianmin; Umapathy, Ganesh; Schönherr, Christina; Ruuth, Kristina; Chand, Damini; Witek, Barbara; Fuchs, James; Li, Pui-Kai; Hugosson, Fredrik; Daly, Roger J; Palmer, Ruth H; Hallberg, Bengt

    2013-01-01

    Activation of the anaplastic lymphoma kinase (ALK) receptor tyrosine kinase is a key oncogenic mechanism in a growing number of tumor types. In the majority of cases, ALK is activated by fusion with a dimerizing partner protein as a result of chromosomal translocation events, most studied in the case of the nucleophosmin–ALK and echinoderm microtubule-associated protein-like 4–ALK oncoproteins. It is now also appreciated that the full-length ALK receptor can be activated by point mutations and by deletions within the extracellular domain, such as those observed in neuroblastoma. Several studies have employed phosphoproteomics approaches to find substrates of ALK fusion proteins. In this study, we used MS-based phosphotyrosine profiling to characterize phosphotyrosine signaling events associated with the full-length ALK receptor. A number of previously identified and novel targets were identified. One of these, signal transducer and activator of transcription 3 (STAT3), has previously been observed to be activated in response to oncogenic ALK signaling, but the significance of this in signaling from the full-length ALK receptor has not been explored further. We show here that activated ALK robustly activates STAT3 on Tyr705 in a number of independent neuroblastoma cell lines. Furthermore, knockdown of STAT3 by RNA interference resulted in a reduction in myelocytomatosis neuroblastom (MYCN) protein levels downstream of ALK signaling. These observations, together with a decreased level of MYCN and inhibition of neuroblastoma cell growth in the presence of STAT3 inhibitors, suggest that activation of STAT3 is important for ALK signaling activity in neuroblastoma. PMID:23889739

  8. Identifying activating mutations in the EGFR gene: prognostic and therapeutic implications in non-small cell lung cancer.

    PubMed

    Lopes, Gabriel Lima; Vattimo, Edoardo Filippo de Queiroz; Castro Junior, Gilberto de

    2015-01-01

    Lung cancer is the leading cause of cancer-related deaths worldwide. Promising new therapies have recently emerged from the development of molecular targeted drugs; particularly promising are those blocking the signal transduction machinery of cancer cells. One of the most widely studied cell signaling pathways is that of EGFR, which leads to uncontrolled cell proliferation, increased cell angiogenesis, and greater cell invasiveness. Activating mutations in the EGFR gene (deletions in exon 19 and mutation L858R in exon 21), first described in 2004, have been detected in approximately 10% of all non-squamous non-small cell lung cancer (NSCLC) patients in Western countries and are the most important predictors of a response to EGFR tyrosine-kinase inhibitors (EGFR-TKIs). Studies of the EGFR-TKIs gefitinib, erlotinib, and afatinib, in comparison with platinum-based regimens, as first-line treatments in chemotherapy-naïve patients have shown that the EGFR-TKIs produce gains in progression-free survival and overall response rates, although only in patients whose tumors harbor activating mutations in the EGFR gene. Clinical trials have also shown EGFR-TKIs to be effective as second- and third-line therapies in advanced NSCLC. Here, we review the main aspects of EGFR pathway activation in NSCLC, underscore the importance of correctly identifying activating mutations in the EGFR gene, and discuss the main outcomes of EGFR-TKI treatment in NSCLC. PMID:26398757

  9. Identifying activating mutations in the EGFR gene: prognostic and therapeutic implications in non-small cell lung cancer *

    PubMed Central

    Lopes, Gabriel Lima; Vattimo, Edoardo Filippo de Queiroz; de Castro, Gilberto

    2015-01-01

    Abstract Lung cancer is the leading cause of cancer-related deaths worldwide. Promising new therapies have recently emerged from the development of molecular targeted drugs; particularly promising are those blocking the signal transduction machinery of cancer cells. One of the most widely studied cell signaling pathways is that of EGFR, which leads to uncontrolled cell proliferation, increased cell angiogenesis, and greater cell invasiveness. Activating mutations in the EGFR gene (deletions in exon 19 and mutation L858R in exon 21), first described in 2004, have been detected in approximately 10% of all non-squamous non-small cell lung cancer (NSCLC) patients in Western countries and are the most important predictors of a response to EGFR tyrosine-kinase inhibitors (EGFR-TKIs). Studies of the EGFR-TKIs gefitinib, erlotinib, and afatinib, in comparison with platinum-based regimens, as first-line treatments in chemotherapy-naïve patients have shown that the EGFR-TKIs produce gains in progression-free survival and overall response rates, although only in patients whose tumors harbor activating mutations in the EGFR gene. Clinical trials have also shown EGFR-TKIs to be effective as second- and third-line therapies in advanced NSCLC. Here, we review the main aspects of EGFR pathway activation in NSCLC, underscore the importance of correctly identifying activating mutations in the EGFR gene, and discuss the main outcomes of EGFR-TKI treatment in NSCLC. PMID:26398757

  10. A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation

    PubMed Central

    Duren, Zhana; Wang, Yong

    2016-01-01

    Chromatin regulators (CRs) are crucial for connecting the chromatin level and transcriptome level by modulating chromatin structures, establishing, and maintaining epigenetic modifications. We present a systematic method to identify MOdulation of transcriptional regulation via CHromatin Activity (MOCHA) from gene expression data and demonstrate its advantage in associating CRs to their chromatin localization and understand CRs’ function. We first re-construct the CRs modulation network by integrating the correlation and conditional correlation concepts. Then we quantify the chromatin activity as hidden variable in network by integrating the upstream and downstream information. We applied MOCHA to systematically explore the interplay of CRs, TFs, and target genes in mouse embryonic stem cells (ESC). As a result, MOCHA identified 420 chromatin regulators with modulation preference, including Pou5f1 and Eed. We found that BAF complex, NuRD complex, and polycomb-group proteins, regulate the delicate balance between pluripotency and differentiation by modulating key TFs including Klf4, Tcf3, and Max; NuRD complex members Mbd3 and Hdac1 may modulate Klf4 to achieve its dual functional roles in pluripotent and differentiation stages;Imprinted gene H19 and Igf2 are modulated by DNA methylation, histone acetylation, and insulator CTCF. Finally, we analyzed CR’s combinational modulation pattern by constructing a CR-CR interaction network. PMID:26949222

  11. In silico repositioning-chemogenomics strategy identifies new drugs with potential activity against multiple life stages of Schistosoma mansoni.

    PubMed

    Neves, Bruno J; Braga, Rodolpho C; Bezerra, José C B; Cravo, Pedro V L; Andrade, Carolina H

    2015-01-01

    Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries. Because praziquantel is the only drug in therapeutic use, the risk of drug resistance is a concern. In the search for new schistosomicidal drugs, we performed a target-based chemogenomics screen of a dataset of 2,114 proteins to identify drugs that are approved for clinical use in humans that may be active against multiple life stages of Schistosoma mansoni. Each of these proteins was treated as a potential drug target, and its amino acid sequence was used to interrogate three databases: Therapeutic Target Database (TTD), DrugBank and STITCH. Predicted drug-target interactions were refined using a combination of approaches, including pairwise alignment, conservation state of functional regions and chemical space analysis. To validate our strategy, several drugs previously shown to be active against Schistosoma species were correctly predicted, such as clonazepam, auranofin, nifedipine, and artesunate. We were also able to identify 115 drugs that have not yet been experimentally tested against schistosomes and that require further assessment. Some examples are aprindine, gentamicin, clotrimazole, tetrabenazine, griseofulvin, and cinnarizine. In conclusion, we have developed a systematic and focused computer-aided approach to propose approved drugs that may warrant testing and/or serve as lead compounds for the design of new drugs against schistosomes. PMID:25569258

  12. In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni

    PubMed Central

    Neves, Bruno J.; Braga, Rodolpho C.; Bezerra, José C. B.; Cravo, Pedro V. L.; Andrade, Carolina H.

    2015-01-01

    Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries. Because praziquantel is the only drug in therapeutic use, the risk of drug resistance is a concern. In the search for new schistosomicidal drugs, we performed a target-based chemogenomics screen of a dataset of 2,114 proteins to identify drugs that are approved for clinical use in humans that may be active against multiple life stages of Schistosoma mansoni. Each of these proteins was treated as a potential drug target, and its amino acid sequence was used to interrogate three databases: Therapeutic Target Database (TTD), DrugBank and STITCH. Predicted drug-target interactions were refined using a combination of approaches, including pairwise alignment, conservation state of functional regions and chemical space analysis. To validate our strategy, several drugs previously shown to be active against Schistosoma species were correctly predicted, such as clonazepam, auranofin, nifedipine, and artesunate. We were also able to identify 115 drugs that have not yet been experimentally tested against schistosomes and that require further assessment. Some examples are aprindine, gentamicin, clotrimazole, tetrabenazine, griseofulvin, and cinnarizine. In conclusion, we have developed a systematic and focused computer-aided approach to propose approved drugs that may warrant testing and/or serve as lead compounds for the design of new drugs against schistosomes. PMID:25569258

  13. A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation.

    PubMed

    Duren, Zhana; Wang, Yong

    2016-01-01

    Chromatin regulators (CRs) are crucial for connecting the chromatin level and transcriptome level by modulating chromatin structures, establishing, and maintaining epigenetic modifications. We present a systematic method to identify MOdulation of transcriptional regulation via CHromatin Activity (MOCHA) from gene expression data and demonstrate its advantage in associating CRs to their chromatin localization and understand CRs' function. We first re-construct the CRs modulation network by integrating the correlation and conditional correlation concepts. Then we quantify the chromatin activity as hidden variable in network by integrating the upstream and downstream information. We applied MOCHA to systematically explore the interplay of CRs, TFs, and target genes in mouse embryonic stem cells (ESC). As a result, MOCHA identified 420 chromatin regulators with modulation preference, including Pou5f1 and Eed. We found that BAF complex, NuRD complex, and polycomb-group proteins, regulate the delicate balance between pluripotency and differentiation by modulating key TFs including Klf4, Tcf3, and Max; NuRD complex members Mbd3 and Hdac1 may modulate Klf4 to achieve its dual functional roles in pluripotent and differentiation stages;Imprinted gene H19 and Igf2 are modulated by DNA methylation, histone acetylation, and insulator CTCF. Finally, we analyzed CR's combinational modulation pattern by constructing a CR-CR interaction network. PMID:26949222

  14. Drug-repositioning screening identified piperlongumine as a direct STAT3 inhibitor with potent activity against breast cancer.

    PubMed

    Bharadwaj, U; Eckols, T K; Kolosov, M; Kasembeli, M M; Adam, A; Torres, D; Zhang, X; Dobrolecki, L E; Wei, W; Lewis, M T; Dave, B; Chang, J C; Landis, M D; Creighton, C J; Mancini, M A; Tweardy, D J

    2015-03-12

    Signal transducer and activator of transcription (STAT) 3 regulates many cardinal features of cancer including cancer cell growth, apoptosis resistance, DNA damage response, metastasis, immune escape, tumor angiogenesis, the Warburg effect and oncogene addiction and has been validated as a drug target for cancer therapy. Several strategies have been used to identify agents that target Stat3 in breast cancer but none has yet entered into clinical use. We used a high-throughput fluorescence microscopy search strategy to identify compounds in a drug-repositioning library (Prestwick library) that block ligand-induced nuclear translocation of Stat3 and identified piperlongumine (PL), a natural product isolated from the fruit of the pepper Piper longum. PL inhibited Stat3 nuclear translocation, inhibited ligand-induced and constitutive Stat3 phosphorylation, and modulated expression of multiple Stat3-regulated genes. Surface plasmon resonance assay revealed that PL directly inhibited binding of Stat3 to its phosphotyrosyl peptide ligand. Phosphoprotein antibody array analysis revealed that PL does not modulate kinases known to activate Stat3 such as Janus kinases, Src kinase family members or receptor tyrosine kinases. PL inhibited anchorage-independent and anchorage-dependent growth of multiple breast cancer cell lines having increased pStat3 or total Stat3, and induced apoptosis. PL also inhibited mammosphere formation by tumor cells from patient-derived xenografts. PL's antitumorigenic function was causally linked to its Stat3-inhibitory effect. PL was non-toxic in mice up to a dose of 30 mg/kg/day for 14 days and caused regression of breast cancer cell line xenografts in nude mice. Thus, PL represents a promising new agent for rapid entry into the clinic for use in treating breast cancer, as well as other cancers in which Stat3 has a role. PMID:24681959

  15. A high-content, multiplexed screen in human breast cancer cells identifies profilin-1 inducers with anti-migratory activities.

    PubMed

    Joy, Marion E; Vollmer, Laura L; Hulkower, Keren; Stern, Andrew M; Peterson, Cameron K; Boltz, R C Dutch; Roy, Partha; Vogt, Andreas

    2014-01-01

    Profilin-1 (Pfn-1) is a ubiquitously expressed actin-binding protein that is essential for normal cell proliferation and migration. In breast cancer and several other adenocarcinomas, Pfn-1 expression is downregulated when compared to normal tissues. Previous studies from our laboratory have shown that genetically modulating Pfn-1 expression significantly impacts proliferation, migration, and invasion of breast cancer cells in vitro, and mammary tumor growth, dissemination, and metastatic colonization in vivo. Therefore, small molecules that can modulate Pfn-1 expression could have therapeutic potential in the treatment of metastatic breast cancer. The overall goal of this study was to perform a multiplexed phenotypic screen to identify compounds that inhibit cell motility through upregulation of Pfn-1. Screening of a test cassette of 1280 compounds with known biological activities on an Oris™ Pro 384 cell migration platform identified several agents that increased Pfn-1 expression greater than two-fold over vehicle controls and exerted anti-migratory effects in the absence of overt cytotoxicity in MDA-MB-231 human breast cancer cells. Concentration-response confirmation and orthogonal follow-up assays identified two bona fide inducers of Pfn-1, purvalanol and tyrphostin A9, that confirmed in single-cell motility assays and Western blot analyses. SiRNA-mediated knockdown of Pfn-1 abrogated the inhibitory effect of tyrphostin A9 on cell migration, suggesting Pfn-1 is mechanistically linked to tyrphostin A9's anti-migratory activity. The data illustrate the utility of the high-content cell motility assay to discover novel targeted anti-migratory agents by integrating functional phenotypic analyses with target-specific readouts in a single assay platform. PMID:24520372

  16. Altered Secretory Activity of APE1/Ref-1 D148E Variants Identified in Human Patients With Bladder Cancer

    PubMed Central

    2016-01-01

    Purpose: Apurinic/apyrimidinic endonuclease 1/redox factor-1 (APE1/Ref-1) is a multifunctional protein involved in DNA repair and redox modulation. Recently, serum and urinary APE1/Ref-1 levels were reported to be increased in patients with bladder cancer. Genetic variations of APE/Ref-1 are associated with the risk of cancer. However, the effect of APE1/Ref-1 variants on its secretory activity is yet unknown. Methods: APE1/Ref-1 variants were evaluated by DNA sequencing analysis of reverse transcription polymerase chain reaction products in coding DNA sequences (CDS) of APE1/Ref-1 in bladder tissue samples from patients with bladder cancer (n=10). Secretory activity of APE1/Ref-1 variants was evaluated with immunoblot and enzyme-linked immunosorbent assay of the culture medium supernatants. Results: Four different substitution mutants (D148E, I64V/D148E, W67R/D148E, and E86G/D148E) of APE1/Ref-1 were identified in bladder cancer specimens. However, deletion mutants of APE1/Ref-1 CDS were not found. The secretory activity of the APE1/Ref-1 variants (D148E, I64V/D148E, and E86G/D148E) was increased compared to that of wild type APE1/Ref-1. Furthermore, the secretory activity in basal or hyperacetylated conditions was much higher than that in APE1/Ref-1 D148E-transfected HEK293 cells. Conclusions: Taken together, our data suggest that the increased secretory activity of D148E might contribute to increased serum levels of APE1/Ref-1 in patients with bladder cancer. PMID:27230458

  17. A Clinical Algorithm to Identify HIV Patients at High Risk for Incident Active Tuberculosis: A Prospective 5-Year Cohort Study

    PubMed Central

    Lee, Susan Shin-Jung; Lin, Hsi-Hsun; Tsai, Hung-Chin; Su, Ih-Jen; Yang, Chin-Hui; Sun, Hsin-Yun; Hung, Chien-Chin; Sy, Cheng-Len; Wu, Kuan-Sheng; Chen, Jui-Kuang; Chen, Yao-Shen; Fang, Chi-Tai

    2015-01-01

    Background Predicting the risk of tuberculosis (TB) in people living with HIV (PLHIV) using a single test is currently not possible. We aimed to develop and validate a clinical algorithm, using baseline CD4 cell counts, HIV viral load (pVL), and interferon-gamma release assay (IGRA), to identify PLHIV who are at high risk for incident active TB in low-to-moderate TB burden settings where highly active antiretroviral therapy (HAART) is routinely provided. Materials and Methods A prospective, 5-year, cohort study of adult PLHIV was conducted from 2006 to 2012 in two hospitals in Taiwan. HAART was initiated based on contemporary guidelines (CD4 count < = 350/μL). Cox regression was used to identify the predictors of active TB and to construct the algorithm. The validation cohorts included 1455 HIV-infected individuals from previous published studies. Area under the receiver operating characteristic (ROC) curve was calculated. Results Seventeen of 772 participants developed active TB during a median follow-up period of 5.21 years. Baseline CD4 < 350/μL or pVL ≥ 100,000/mL was a predictor of active TB (adjusted HR 4.87, 95% CI 1.49–15.90, P = 0.009). A positive baseline IGRA predicted TB in patients with baseline CD4 ≥ 350/μL and pVL < 100,000/mL (adjusted HR 6.09, 95% CI 1.52–24.40, P = 0.01). Compared with an IGRA-alone strategy, the algorithm improved the sensitivity from 37.5% to 76.5%, the negative predictive value from 98.5% to 99.2%. Compared with an untargeted strategy, the algorithm spared 468 (60.6%) from unnecessary TB preventive treatment. Area under the ROC curve was 0.692 (95% CI: 0.587–0.798) for the study cohort and 0.792 (95% CI: 0.776–0.808) and 0.766 in the 2 validation cohorts. Conclusions A validated algorithm incorporating the baseline CD4 cell count, HIV viral load, and IGRA status can be used to guide targeted TB preventive treatment in PLHIV in low-to-moderate TB burden settings where HAART is routinely provided to all PLHIV. The

  18. A three-dimensional human model of the fibroblast activation that accompanies bronchopulmonary dysplasia identifies Notch-mediated pathophysiology.

    PubMed

    Sucre, Jennifer M S; Wilkinson, Dan; Vijayaraj, Preethi; Paul, Manash; Dunn, Bruce; Alva-Ornelas, Jackelyn A; Gomperts, Brigitte N

    2016-05-15

    Bronchopulmonary dysplasia (BPD) is a leading complication of premature birth and occurs primarily in infants delivered during the saccular stage of lung development. Histopathology shows decreased alveolarization and a pattern of fibroblast proliferation and differentiation to the myofibroblast phenotype. Little is known about the molecular pathways and cellular mechanisms that define BPD pathophysiology and progression. We have developed a novel three-dimensional human model of the fibroblast activation associated with BPD, and using this model we have identified the Notch pathway as a key driver of fibroblast activation and proliferation in response to changes in oxygen. Fetal lung fibroblasts were cultured on sodium alginate beads to generate lung organoids. After exposure to alternating hypoxia and hyperoxia, the organoids developed a phenotypic response characterized by increased α-smooth muscle actin (α-SMA) expression and other genes known to be upregulated in BPD and also demonstrated increased expression of downstream effectors of the Notch pathway. Inhibition of Notch with a γ-secretase inhibitor prevented the development of the pattern of cellular proliferation and α-SMA expression in our model. Analysis of human autopsy tissue from the lungs of infants who expired with BPD demonstrated evidence of Notch activation within fibrotic areas of the alveolar septae, suggesting that Notch may be a key driver of BPD pathophysiology. PMID:26968771

  19. Summing Up Hours of Any Type of Practice Versus Identifying Optimal Practice Activities: Commentary on Macnamara, Moreau, & Hambrick (2016).

    PubMed

    Ericsson, K Anders

    2016-05-01

    In their original article, Ericsson, Krampe, and Tesch-Römer (1993) reviewed the evidence concerning the conditions of optimal learning and found that individualized practice with training tasks (selected by a supervising teacher) with a clear performance goal and immediate informative feedback was associated with marked improvement. We found that this type of deliberate practice was prevalent when advanced musicians practice alone and found its accumulated duration related to attained music performance. In contrast, Macnamara, Moreau, and Hambrick's (2016, this issue) main meta-analysis examines the use of the term deliberate practice to refer to a much broader and less defined concept including virtually any type of sport-specific activity, such as group activities, watching games on television, and even play and competitions. Summing up every hour of any type of practice during an individual's career implies that the impact of all types of practice activity on performance is equal-an assumption that I show is inconsistent with the evidence. Future research should collect objective measures of representative performance with a longitudinal description of all the changes in different aspects of the performance so that any proximal conditions of deliberate practice related to effective improvements can be identified and analyzed experimentally. PMID:27217247

  20. Molecular and Functional Analyses of a Maize Autoactive NB-LRR Protein Identify Precise Structural Requirements for Activity

    PubMed Central

    Wang, Guan-Feng; Ji, Jiabing; EI-Kasmi, Farid; Dangl, Jeffery L.; Johal, Guri; Balint-Kurti, Peter J.

    2015-01-01

    Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance. PMID:25719542

  1. Molecular and functional analyses of a maize autoactive NB-LRR protein identify precise structural requirements for activity.

    PubMed

    Wang, Guan-Feng; Ji, Jiabing; El-Kasmi, Farid; Dangl, Jeffery L; Johal, Guri; Balint-Kurti, Peter J

    2015-02-01

    Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance. PMID:25719542

  2. Gap-junctional channel and hemichannel activity of two recently identified connexin 26 mutants associated with deafness.

    PubMed

    Dalamon, Viviana; Fiori, Mariana C; Figueroa, Vania A; Oliva, Carolina A; Del Rio, Rodrigo; Gonzalez, Wendy; Canan, Jonathan; Elgoyhen, Ana B; Altenberg, Guillermo A; Retamal, Mauricio A

    2016-05-01

    Gap-junction channels (GJCs) are formed by head-to-head association of two hemichannels (HCs, connexin hexamers). HCs and GJCs are permeable to ions and hydrophilic molecules of up to Mr ~1 kDa. Hearing impairment of genetic origin is common, and mutations of connexin 26 (Cx26) are its major cause. We recently identified two novel Cx26 mutations in hearing-impaired subjects, L10P and G109V. L10P forms functional GJCs with slightly altered voltage dependence and HCs with decrease ATP/cationic dye selectivity. G109V does not form functional GJCs, but forms functional HCs with enhanced extracellular Ca(2+) sensitivity and subtle alterations in voltage dependence and ATP/cationic dye selectivity. Deafness associated with G109V could result from decreased GJCs activity, whereas deafness associated to L10P may have a more complex mechanism that involves changes in HC permeability. PMID:26769242

  3. Identifying state-level policy and provision domains for physical education and physical activity in high school

    PubMed Central

    2013-01-01

    Background It is important to quickly and efficiently identify policies that are effective at changing behavior; therefore, we must be able to quantify and evaluate the effect of those policies and of changes to those policies. The purpose of this study was to develop state-level physical education (PE) and physical activity (PA) policy domain scores at the high-school level. Policy domain scores were developed with a focus on measuring policy change. Methods Exploratory factor analysis was used to group items from the state-level School Health Policies and Programs Study (SHPPS) into policy domains. Items that related to PA or PE at the High School level were identified from the 7 SHPPS health program surveys. Data from 2000 and 2006 were used in the factor analysis. RESULTS: From the 98 items identified, 17 policy domains were extracted. Average policy domain change scores were positive for 12 policy domains, with the largest increases for “Discouraging PA as Punishment”, “Collaboration”, and “Staff Development Opportunities”. On average, states increased scores in 4.94 ± 2.76 policy domains, decreased in 3.53 ± 2.03, and had no change in 7.69 ± 2.09 policy domains. Significant correlations were found between several policy domain scores. Conclusions Quantifying policy change and its impact is integral to the policy making and revision process. Our results build on previous research offering a way to examine changes in state-level policies related to PE and PA of high-school students and the faculty and staff who serve them. This work provides methods for combining state-level policies relevant to PE or PA in youth for studies of their impact. PMID:23815860

  4. Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway.

    PubMed

    Shain, A Hunter; Garrido, Maria; Botton, Thomas; Talevich, Eric; Yeh, Iwei; Sanborn, J Zachary; Chung, Jongsuk; Wang, Nicholas J; Kakavand, Hojabr; Mann, Graham J; Thompson, John F; Wiesner, Thomas; Roy, Ritu; Olshen, Adam B; Gagnon, Alexander; Gray, Joe W; Huh, Nam; Hur, Joe S; Busam, Klaus J; Scolyer, Richard A; Cho, Raymond J; Murali, Rajmohan; Bastian, Boris C

    2015-10-01

    Desmoplastic melanoma is an uncommon variant of melanoma with sarcomatous histology, distinct clinical behavior and unknown pathogenesis. We performed low-coverage genome and high-coverage exome sequencing of 20 desmoplastic melanomas, followed by targeted sequencing of 293 genes in a validation cohort of 42 cases. A high mutation burden (median of 62 mutations/Mb) ranked desmoplastic melanoma among the most highly mutated cancers. Mutation patterns strongly implicate ultraviolet radiation as the dominant mutagen, indicating a superficially located cell of origin. Newly identified alterations included recurrent promoter mutations of NFKBIE, encoding NF-κB inhibitor ɛ (IκBɛ), in 14.5% of samples. Common oncogenic mutations in melanomas, in particular in BRAF (encoding p.Val600Glu) and NRAS (encoding p.Gln61Lys or p.Gln61Arg), were absent. Instead, other genetic alterations known to activate the MAPK and PI3K signaling cascades were identified in 73% of samples, affecting NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS and PIK3CA, some of which are candidates for targeted therapies. PMID:26343386

  5. MYD88 L265P and CXCR4 mutations in lymphoplasmacytic lymphoma identify cases with high disease activity.

    PubMed

    Schmidt, Janine; Federmann, Birgit; Schindler, Natalie; Steinhilber, Julia; Bonzheim, Irina; Fend, Falko; Quintanilla-Martinez, Leticia

    2015-06-01

    Recurrent mutations in MYD88 have been identified in >90% of lymphoplasmacytic lymphoma (LPL). Recently, WHIM (warts, hypogammaglobulinaemia, infections, myelokathexis) syndrome-like mutations in CXCR4 have been described in 28% of LPL cases, and seem to impact clinical presentation and response to therapy. We investigated the presence of the MYD88 L265P mutation in 90 decalcified, formalin-fixed, paraffin-embedded (FFPE) bone marrow (BM) biopsies, including 51 cases of LPL, 14 cases of B-cell chronic lymphocytic leukaemia (CLL), 13 cases of marginal zone lymphoma (MZL) and 12 normal controls. In addition, the C-terminal domain of CXCR4 was sequenced in LPL cases. MYD88 L265P was found in 49/51 (96%) LPL cases and in 1/13 (7·6%) MZL (splenic type), whereas all CLL samples remained negative. The two MYD88 wild type LPL cases were associated with cold agglutinin disease. Mutations in CXCR4 were detected in 17/47 (36·2%) LPL cases, which showed a higher extent of BM infiltration and lower leucocyte counts (P = 0·02), haemoglobin (P = 0·05) and platelet counts (P = 0·01). In conclusion the detection of MYD88 L265P mutation in FFPE samples is reliable and useful for subtyping small B-cell lymphomas in BM biopsies. In addition, the presence of CXCR4 mutations identifies a subgroup of LPL patients with higher disease activity. PMID:25819228

  6. Sub-arctic Wetland Greenhouse Gases (CO2, CH4 & N2O) Emissions are Driven by Interactions of Environmental Controls and Herbivore Grazers

    NASA Astrophysics Data System (ADS)

    Kelsey, K.; Leffler, A. J.; Beard, K. H.; Choi, R. T.; Welker, J. M.

    2015-12-01

    Climate change is increasing temperatures, altering precipitation regimes and causing earlier growing seasons, particularly at northern latitudes. Such changes in local environmental conditions have the potential to affect biogeochemical cycling including the exchange of greenhouses gases between the atmosphere and the terrestrial biosphere. In addition to the effects of these environmental controls, animals such as migratory geese also influence biogeochemical cycles through grazing, trampling and delivering nutrient-rich fecal matter. In this work we aimed to quantify how local environmental conditions and the presence of grazing interact as drivers of emissions of three key greenhouse gases, CO2, CH4 and N2O, in coastal wetlands of the Yukon Kuskokwim Delta. We explored the magnitude of emissions across gradients of soil temperature and water table depth, and across vegetation types related to the presence of grazing, ranging from no vegetation through grazed and ungrazed vegetation. We also investigated emissions from grazed areas using experimental manipulations of the timing of grazing and advancement of the growing season. We found that local environmental conditions and use by grazers exert interacting controls on emissions of CO2, CH4 and N2O. Emissions of CO2 and CH4 were positively related to soil temperature and CH4 emissions were inversely related to water table depth, but the relationship varied by vegetation type. Net emissions of CO2 were greatest in ungrazed vegetation types (6.62 umols CO2 m-2 sec-1; p=0.0007) whereas CH4 emissions were greatest in the grazed vegetation (122.56 nmols CH4 m-2 sec-1; p=0.037). Flux of N2O was less than 1 nmol N2O m-2 sec-1 across all landscape positions under typical grazing and temperature conditions, but emissions were stimulated to over 10 nmols m-2 sec-1 when grazing occurred early relative to a typical season. Our results indicate that environmental conditions and the presence of migratory herbivores are both

  7. Combining proteomics and transcriptome sequencing to identify active plant-cell-wall-degrading enzymes in a leaf beetle

    PubMed Central

    2012-01-01

    Background The primary plant cell wall is a complex mixture of polysaccharides and proteins encasing living plant cells. Among these polysaccharides, cellulose is the most abundant and useful biopolymer present on earth. These polysaccharides also represent a rich source of energy for organisms which have evolved the ability to degrade them. A growing body of evidence suggests that phytophagous beetles, mainly species from the superfamilies Chrysomeloidea and Curculionoidea, possess endogenous genes encoding complex and diverse families of so-called plant cell wall degrading enzymes (PCWDEs). The presence of these genes in phytophagous beetles may have been a key element in their success as herbivores. Here, we combined a proteomics approach and transcriptome sequencing to identify PCWDEs present in larval gut contents of the mustard leaf beetle, Phaedon cochleariae. Results Using a two-dimensional proteomics approach, we recovered 11 protein bands, isolated using activity assays targeting cellulose-, pectin- and xylan-degrading enzymes. After mass spectrometry analyses, a total of 13 proteins putatively responsible for degrading plant cell wall polysaccharides were identified; these proteins belong to three glycoside hydrolase (GH) families: GH11 (xylanases), GH28 (polygalacturonases or pectinases), and GH45 (β-1,4-glucanases or cellulases). Additionally, highly stable and proteolysis-resistant host plant-derived proteins from various pathogenesis-related protein (PRs) families as well as polygalacturonase-inhibiting proteins (PGIPs) were also identified from the gut contents proteome. In parallel, transcriptome sequencing revealed the presence of at least 19 putative PCWDE transcripts encoded by the P. cochleariae genome. All of these were specifically expressed in the insect gut rather than the rest of the body, and in adults as well as larvae. The discrepancy observed in the number of putative PCWDEs between transcriptome and proteome analyses could be

  8. Two types of antiprogestins identified by their differential action in transcriptionally active extracts from T47D cells.

    PubMed Central

    Klein-Hitpass, L; Cato, A C; Henderson, D; Ryffel, G U

    1991-01-01

    Transcriptionally active nuclear extracts from human breast carcinoma cells (T47D) were used to compare the action of progestins and several antiprogestins of the 11 beta-aryl substituted steroid series on the DNA-binding properties and the trans-activating potential of progesterone receptor (PR) in vitro. Using the gel-shift assay we identified a novel type of antiprogestin (ZK98299, type I), which in contrast to type II antiprogestins, including RU486, does not induce binding of PR to progesterone response elements (PREs). In competition experiments excess of type I antiprogestin inhibits induction of DNA binding of PR by progestins and type II antiprogestins suggesting that its binding to PR interferes with the formation of stable receptor dimers. Moreover, we demonstrate that the antagonistic action of ZK98299 can be fully mimicked in vitro by using cell-free nuclear extracts from T47D cells and a 'simple' test promoter. In contrast, type II antiprogestins known to induce certain promoters in vivo exert strong agonistic effects on in vitro transcription of the test template used. Images PMID:2030942

  9. Fine Time Course Expression Analysis Identifies Cascades of Activation and Repression and Maps a Putative Regulator of Mammalian Sex Determination

    PubMed Central

    Looger, Loren L.; Ohler, Uwe; Capel, Blanche

    2013-01-01

    In vertebrates, primary sex determination refers to the decision within a bipotential organ precursor to differentiate as a testis or ovary. Bifurcation of organ fate begins between embryonic day (E) 11.0–E12.0 in mice and likely involves a dynamic transcription network that is poorly understood. To elucidate the first steps of sexual fate specification, we profiled the XX and XY gonad transcriptomes at fine granularity during this period and resolved cascades of gene activation and repression. C57BL/6J (B6) XY gonads showed a consistent ∼5-hour delay in the activation of most male pathway genes and repression of female pathway genes relative to 129S1/SvImJ, which likely explains the sensitivity of the B6 strain to male-to-female sex reversal. Using this fine time course data, we predicted novel regulatory genes underlying expression QTLs (eQTLs) mapped in a previous study. To test predictions, we developed an in vitro gonad primary cell assay and optimized a lentivirus-based shRNA delivery method to silence candidate genes and quantify effects on putative targets. We provide strong evidence that Lmo4 (Lim-domain only 4) is a novel regulator of sex determination upstream of SF1 (Nr5a1), Sox9, Fgf9, and Col9a3. This approach can be readily applied to identify regulatory interactions in other systems. PMID:23874228

  10. Activity-guided purification identifies lupeol, a pentacyclic triterpene, as a therapeutic agent multiple pathogenic factors of acne.

    PubMed

    Kwon, Hyuck Hoon; Yoon, Ji Young; Park, Seon Yong; Min, Seonguk; Kim, Yong-il; Park, Ji Yong; Lee, Yun-Sang; Thiboutot, Diane M; Suh, Dae Hun

    2015-06-01

    Acne vulgaris is a nearly universal cutaneous disease characterized by multifactorial pathogenic processes. Because current acne medications have various side effects, investigating new pharmacologically active molecules is important for treating acne. As natural products generally provide various classes of relatively safe compounds with medicinal potentials, we performed activity-guided purification after a series of screenings from the extracts of five medicinal plants to explore alternative acne medications. Lupeol, a pentacyclic triterpene, from the hexane extract of Solanum melongena L. (SM) was identified after instrumental analysis. Lupeol targeted most of the major pathogenic features of acne with desired physicochemical traits. It strongly suppressed lipogenesis by modulating the IGF-1R/phosphatidylinositide 3 kinase (PI3K)/Akt/sterol response element-binding protein-1 (SREBP-1) signaling pathway in SEB-1 sebocytes, and reduced inflammation by suppressing the NF-κB pathway in SEB-1 sebocytes and HaCaT keratinocytes. Lupeol exhibited a marginal effect on cell viability and may have modulated dyskeratosis of the epidermis. Subsequently, histopathological analysis of human patients' acne tissues after applying lupeol for 4 weeks demonstrated that lupeol markedly attenuated the levels of both the number of infiltrated cells and major pathogenic proteins examined in vitro around comedones or sebaceous glands, providing solid evidence for suggested therapeutic mechanisms. These results demonstrate the clinical feasibility of applying lupeol for the treatment of acne. PMID:25647437