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Sample records for identify active grazers

  1. Cosmopolitan heterotrophic microeukaryotes are active bacterial grazers in experimental oil-polluted systems.

    PubMed

    Dalby, Andrew P; Kormas, Konstantinos Ar; Christaki, Urania; Karayanni, Hera

    2008-01-01

    We investigated the population dynamics and prevailing 18S rDNA phylotypes of microeukaryotes (grazers of bacteria and as such their dynamics should be taken into account in bioremediation practices in situ.

  2. Invertebrate grazers affect metal/metalloid fixation during litter decomposition.

    PubMed

    Schaller, Jörg; Brackhage, Carsten

    2015-01-01

    Plant litter and organic sediments are main sinks for metals and metalloids in aquatic ecosystems. The effect of invertebrates as key species in aquatic litter decomposition on metal/metalloid fixation by organic matter is described only for shredders, but for grazers as another important animal group less is known. Consequently, a laboratory batch experiment was conducted to examine the effect of invertebrate grazers (Lymnaea stagnalis L.) on metal/metalloid fixation/remobilization during aquatic litter decomposition. It could be shown that invertebrate grazers facilitate significantly the formation of smaller sizes of particulate organic matter (POM), as shown previously for invertebrate shredders. The metal/metalloid binding capacity of these smaller particles of POM is higher compared to leaf litter residuals. But element enrichment is not as high as shown previously for the effect by invertebrate shredders. Invertebrate grazers enhance also the mobilization of selected elements to the water, in the range also proven for invertebrate shredders but different for the different elements. Nonetheless invertebrate grazers activity during aquatic litter decomposition leads to a metal/metalloid fixation into leaf litter as part of sediment organic matter. Hence, the effect of invertebrate grazers on metal/metalloid fixation/remobilization contrasts partly with former assessments revealing the possibility of an enhanced metal/metalloid fixation.

  3. 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

  4. 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.

  5. 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

  6. β-cyclocitral, a grazer defence signal unique to the cyanobacterium Microcystis.

    PubMed

    Jüttner, Friedrich; Watson, Susan B; von Elert, Eric; Köster, Oliver

    2010-12-01

    β-Cyclocitral is often present in eutrophic waters and is a well known source of airborne and drinking water malodor, but its production and functional ecology are unresolved. This volatile organic compound (VOC) is derived from the catalytic breakdown of β-carotene, and evidence indicates that it is produced by the activation of a specific carotene oxygenase by all species of the bloom-forming cyanobacterium Microcystis. Previous work has shown that β-cyclocitral affects grazer behavior, but the nature of this interaction and its influence on predator-prey dynamics was unresolved. The present study combined analytical and behavioral studies to evaluate this interaction by using Microcystis NRC-1 and Daphnia magna. Results showed that β-cyclocitral was undetectable in live Microcystis cells, or present only at extremely low concentrations (2.6 amol /cell). In contrast, cell rupture activated a rapid carotene oxygenase reaction, which produced high amounts (77 ± 5.5 amol β-cyclocitral/cell), corresponding to a calculated maximum intracellular concentration of 2.2 mM. The behavioral response of Daphnia magna to β-cyclocitral was evaluated in a bbe© Daphnia toximeter, where β-cyclocitral treatments induced a marked increase in swimming velocity. Acclimation took place within a few minutes, when Daphnia returned to normal swimming velocity while still exposed to β-cyclocitral. The minimum VOC concentration (odor threshold) that elicited a significant grazer response was 750 nM β-cyclocitral, some 2,900 times lower than the per capita yield of a growing Microcystis cell after activation. Under natural conditions, initial grazer-related or other mode of cell rupture would lead to the development of a robust β-cyclocitral microzone around Microcystis colonies, thus acting as both a powerful repellent and signal of poor quality food to grazers.

  7. Professional Development: Identifying Effective Instructional Coaching Activities

    ERIC Educational Resources Information Center

    Mannino, Gina

    2014-01-01

    The purpose of this study was to identify the instructional coaching activities most used by instructional coaches in southeast Texas school districts and to test if there was a relationship between the use of instructional coaching and perceived improvement in the instructional practices of teachers and student achievement. The participants for…

  8. Grazer cues induce stealth behavior in marine dinoflagellates

    PubMed Central

    Selander, Erik; Jakobsen, Hans H.; Lombard, Fabien; Kiørboe, Thomas

    2011-01-01

    Chain formation is common among phytoplankton organisms but the underlying reasons and consequences are poorly understood. Here we show that chain formation is strongly impaired by waterborne cues from copepod grazers in the dinoflagellate Alexandrium tamarense. Chains of Alexandrium cells exposed to copepod cues responded by splitting into single cells or shorter chains. Motion analysis revealed significantly lower swimming velocities for single cells compared with chains, with two- to fivefold higher simulated predator encounter rates for two- and four-cell chains, respectively. In addition, the few remaining two-cell chains in grazed treatments were swimming at approximately half the speed of two-cell chains in treatments without grazers, which reduced encounter rates with grazers to values similar to that of single cells. Chain length plasticity and swimming behavior constitute unique mechanisms to reduce encounters with grazers. We argue that dinoflagellates can regulate the balance between motility and predator avoidance by adjusting chain length. The high predator encounter rate for motile chains may have contributed to the low prevalence of chain formation in motile phytoplankton compared with in nonmotile phytoplankton where chain formation is more common. PMID:21368128

  9. 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.

  10. 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.

  11. 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...

  12. 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…

  13. Stream grazers determine their crawling direction on the basis of chemical and particulate microalgal cues.

    PubMed

    Katano, Izumi; Doi, Hideyuki

    2014-01-01

    This study aimed to determine the association between herbivore behavior and cues from producers. We used stream grazer Glossosoma larvae and determined their crawling direction in relation to chemical and visual cues from microalgae. The experimental treatments included control (no cue), particulate (chemical and particulate cues), and dissolved (chemical cue) cues from microalgae. The experimental water samples were randomly placed into either arm of a Y-shaped channel, and the crawling direction of the grazers was determined. Although the grazers crawled toward the arm containing either particulate or dissolved cues, they preferred the arm with particulate cues. This suggested that grazers responded well to both particulate (i.e., drifting algal cells) and chemical (algal smell) cues, and that particulate cues were more important for foraging. In natural habitats, grazers detect cues from producers and change their behaviors to maintain a balance between top-down and bottom-up cues.

  14. Interspecific competition for shelters in territorial and gregarious intertidal grazers: consequences for individual behaviour.

    PubMed

    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

  15. 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

  16. Experimental removal and recovery of subtidal grazers highlights the importance of functional redundancy and temporal context.

    PubMed

    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.

  17. 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.

  18. 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

  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. 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.

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

    PubMed

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

    2015-11-16

    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.

  2. Toxigenic effects of diatoms on grazers, phytoplankton and other microbes: a review.

    PubMed

    Ianora, Adrianna; Miralto, Antonio

    2010-03-01

    Traditionally, diatoms have been regarded as providing the bulk of the food that sustains the marine food chain and important fisheries. However, this view was challenged almost two decades ago on the basis of laboratory and field studies showing that when copepods, the principal predators of diatoms, feed on certain diatom diets, they produce abnormal eggs that either fail to develop to hatching or hatch into malformed (i.e. teratogenic) nauplii that die soon afterwards. Over the years, many explanations have been advanced to explain the causes for reproductive failure in copepods and other marine and freshwater invertebrates including diatom toxicity, or nutritional deficiency and poor assimilation of essential compounds in the animal gut. Here we review the literature concerning the first possibility, that diatoms produce cytotoxic compounds responsible for growth inhibition and teratogenic activity, potentially sabotaging future generations of grazers by inducing poor recruitment. The cytotoxic compounds responsible for these effects are short chain polyunsaturated aldehydes (PUAs) and other oxygenated fatty acid degradation products such as hydroxides, oxo-acids, and epoxyalcohols (collectively termed oxylipins) that are cleaved from fatty acid precursors by enzymes activated within seconds after crushing of cells. Such toxins are suggested to have multiple simultaneous functions in that they not only deter herbivore feeding but some also act as allelopathic agents against other phytoplankton cells, thereby affecting the growth of competitors, and also signalling population-level cell death and termination of blooms, with possible consequences for food web structure and community composition. Some oxylipins also play a role in driving marine bacterial community diversity, with neutral, positive or negative interactions depending on the species, thereby shaping the structure of bacterial communities during diatom blooms. Several reviews have already been

  3. 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

  4. 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.

  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 Activity Cliff Generators of PPAR Ligands Using SAS Maps.

    PubMed

    Méndez-Lucio, Oscar; Pérez-Villanueva, Jaime; Castillo, Rafael; Medina-Franco, José L

    2012-12-01

    Structure-activity relationships (SAR) of compound databases play a key role in hit identification and lead optimization. In particular, activity cliffs, defined as a pair of structurally similar molecules that present large changes in potency, provide valuable SAR information. Herein, we introduce the concept of activity cliff generator, defined as a molecular structure that has a high probability to form activity cliffs with molecules tested in the same biological assay. To illustrate this concept, we discuss a case study where Structure-Activity Similarity maps were used to systematically identify and analyze activity cliff generators present in a dataset of 168 compounds tested against three peroxisome-proliferator-activated receptor (PPAR) subtypes. Single-target and dual-target activity cliff generators for PPARα and δ were identified. In addition, docking calculations of compounds that were classified as cliff generators helped to suggest a hot spot in the target protein responsible of activity cliffs and to analyze its implication in ligand-enzyme interaction.

  7. Trophic cascades result in large-scale coralline algae loss through differential grazer effects.

    PubMed

    O'Leary, Jennifer K; McClanahan, Timothy R

    2010-12-01

    Removal of predators can have strong indirect effects on primary producers through trophic cascades. Crustose coralline algae (CCA) are major primary producers worldwide that may be influenced by predator removal through changes in grazer composition and biomass. CCA have been most widely studied in Caribbean and temperate reefs, where cover increases with increasing grazer biomass due to removal of competitive fleshy algae. However, each of these systems has one dominant grazer type, herbivorous fishes or sea urchins, which may not be functionally equivalent. Where fishes and sea urchins co-occur, fishing can result in a phase shift in the grazing community with subsequent effects on CCA and other substrata. Kenyan reefs have herbivorous fishes and sea urchins, providing an opportunity to determine the relative impacts of each grazer type and evaluate potential human-induced trophic cascades. We hypothesized that fish benefit CCA, abundant sea urchins erode CCA, and that fishing indirectly reduces CCA cover by removing sea urchin predators. We used closures and fished reefs as a large-scale, long-term natural experiment to assess how fishing and resultant changes in communities affect CCA abundance. We used a short-term caging experiment to directly test the effects of grazing on CCA. CCA cover declined with increasing fish and sea urchin abundance, but the negative impact of sea urchin grazing was much stronger than that of fishes. Abundant sea urchins reduced the CCA growth rate to almost zero and prevented CCA accumulation. A warming event (El Niño Southern Oscillation, ENSO) occurred during the 18-year study and had a strong but short-term positive effect on CCA cover. However, the effect of the ENSO on CCA was lower in magnitude than the effect of sea urchin grazing. We compare our results with worldwide literature on bioerosion by fishes and sea urchins. Grazer influence depends on whether benefits of fleshy algae removal outweigh costs of grazer

  8. Identifying Associations between Student Achievement and Parental Involvement Activities

    ERIC Educational Resources Information Center

    Waddle, Ann R.

    2011-01-01

    The revision and renewal of the Elementary and Secondary Education Act of 1965 will likely expand its parental involvement component to engage educators, parents, and community partners in supporting public education for children. This revisions call for best practices, but current literature fails to identify specific activities associated…

  9. A Focused Screen Identifies Antifolates with Activity on Mycobacterium tuberculosis

    PubMed Central

    Kumar, Anuradha; Colmenarejo, Gonzalo; Pérez, Esther; Gonzalez, Ruben R.; Torres, Pedro; Calvo, David; Gómez, Ruben M.; Ortega, Fátima; Jiménez, Elena; Gabarro, Raquel C.; Rullás, Joaquín; Ballell, Lluis

    2015-01-01

    Antifolates are widely used to treat several diseases but are not currently used in the first-line treatment of tuberculosis, despite evidence that some of these molecules can target Mycobacterium tuberculosis (Mtb) bacilli in vitro. To identify new antifolate candidates for animal-model efficacy studies of tuberculosis, we paired knowledge and tools developed in academia with the infrastructure and chemistry resources of a large pharmaceutical company. Together we curated a focused library of 2508 potential antifolates, which were then tested for activity against live Mtb. We identified 210 primary hits, confirmed the on-target activity of potent compounds, and now report the identification and characterization of 5 hit compounds, representative of 5 different chemical scaffolds. These antifolates have potent activity against Mtb and represent good starting points for improvement that could lead to in vivo efficacy studies. PMID:26771003

  10. The effect of functional response on stability of a grazer population on a landscape

    USGS Publications Warehouse

    Basset, A.D.; DeAngelis, D.L.; Diffendorfer, J.E.

    1997-01-01

    The dynamics of interacting consumer and resource populations is one of the most thoroughly studied problems of theoretical population biology. Among the key results from the study of simple mathematical models of interacting populations is that the Holling Type 2 functional response tends to be unstable for a wide range of realistic parameters. Functional responses such as Holling Type 3, which might be thought of as implicitly incorporating the existence of consumer refuges, are more stable than the Type 2. We studied consumer—resource models with these different functional responses on a landscape level by modeling grazers that can disperse across a space of patchily distributed grass resources. For certain assumptions concerning the movement of grazers on the landscape, the effect of these functional responses on stability is reversed; the Holling Type 2 functional response confers greater stability. The reason for this apparently paradoxical result is that the Holling Type 2 functional response allows grazers to graze individual grass patches to lower levels than Type 3, as the energy balance remains favorable for grazing at lower grass biomasses. However, this local overexploitation leads the grazers to be slower in reaching areas of the landscape where resource densities are higher. It decreases the likelihood that the resource will be overexploited over the whole landscape simultaneously, which results in a stronger tendency towards system stability. It appears, then, that consumer overexploitation of resources locally may contribute to lower stability.

  11. 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...

  12. Phenotypic Approaches to Identify Inhibitors of B Cell Activation

    PubMed Central

    Kim, Suzie; Wiener, Jake; Rao, Navin L.; Milla, Marcos E.; DiSepio, Daniel

    2015-01-01

    An EPIC label-free phenotypic platform was developed to explore B cell receptor (BCR) and CD40R-mediated B cell activation. The phenotypic assay measured the association of RL non-Hodgkin’s lymphoma B cells expressing lymphocyte function-associated antigen 1 (LFA-1) to intercellular adhesion molecule 1 (ICAM-1)-coated EPIC plates. Anti-IgM (immunoglobulin M) mediated BCR activation elicited a response that was blocked by LFA-1/ICAM-1 specific inhibitors and a panel of Bruton’s tyrosine kinase (BTK) inhibitors. LFA-1/ICAM-1 association was further increased on coapplication of anti-IgM and mega CD40L when compared to individual application of either. Anti-IgM, mega CD40L, or the combination of both displayed distinct kinetic profiles that were inhibited by treatment with a BTK inhibitor. We also established a FLIPR-based assay to measure B cell activation in Ramos Burkitt’s lymphoma B cells and an RL cell line. Anti-IgM-mediated BCR activation elicited a robust calcium response that was inhibited by a panel of BTK inhibitors. Conversely, CD40R activation did not elicit a calcium response in the FLIPR assay. Compared to the FLIPR, the EPIC assay has the propensity to identify inhibitors of both BCR and CD40R-mediated B cell activation and may provide more pharmacological depth or novel mechanisms of action for inhibition of B cell activation. PMID:25948491

  13. Interaction strength between different grazers and macroalgae mediated by ocean acidification over warming gradients.

    PubMed

    Sampaio, E; Rodil, I F; Vaz-Pinto, F; Fernández, A; Arenas, F

    2017-04-01

    Since the past century, rising CO2 levels have led to global changes (ocean warming and acidification) with subsequent effects on marine ecosystems and organisms. Macroalgae-herbivore interactions have a main role in the regulation of marine community structure (top-down control). Gradients of warming prompt complex non-linear effects on organism metabolism, cascading into altered trophic interactions and community dynamics. However, not much is known on how will acidification and grazer assemblage composition shape these effects. Within this context, we aimed to assess the combined effects of warming gradients and acidification on macroalgae-herbivore interactions, using three cosmopolitan species, abundant in the Iberian Peninsula and closely associated in nature: the amphipod Melita palmata, the gastropod Gibbula umbilicalis, and the green macroalga Ulva rigida. Under two CO2 treatments (ΔCO2 ≃ 450 μatm) across a temperature gradient (13.5, 16.6, 19.9 and 22.1 °C), two mesocosm experiments were performed to assess grazer consumption rates and macroalgae-herbivore interaction, respectively. Warming (Experiment I and II) and acidification (Experiment II) prompted negative effects in grazer's survival and species-specific differences in consumption rates. M. palmata was shown to be the stronger grazer per biomass (but not per capita), and also the most affected by climate stressors. Macroalgae-herbivore interaction strength was markedly shaped by the temperature gradient, while simultaneous acidification lowered thermal optimal threshold. In the near future, warming and acidification are likely to strengthen top-down control, but further increases in disturbances may lead to bottom-up regulated communities. Finally, our results suggest that grazer assemblage composition may modulate future macroalgae-herbivore interactions.

  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. The OPTX Project. V. Identifying Distant Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Trouille, L.; Barger, A. J.; Tremonti, C.

    2011-11-01

    The Baldwin, Phillips, and Terlevich emission-line ratio diagnostic ([O III]/Hβ versus [N II]/Hα, hereafter BPT diagram) efficiently separates galaxies whose signal is dominated by star formation (BPT-SF) from those dominated by active galactic nucleus (AGN) activity (BPT-AGN). Yet this BPT diagram is limited to z < 0.5, the redshift at which [N II]λ6584 leaves the optical spectral window. Using the Sloan Digital Sky Survey (SDSS), we construct a new diagnostic, or TBT diagram, that is based on rest-frame g - z color, [Ne III]λ3869, and [O II]λλ3726 + 3729 and can be used for galaxies out to z < 1.4. The TBT diagram identifies 98.7% of the SDSS BPT-AGN as TBT-AGN and 97% of the SDSS BPT-SF as TBT-SF. Furthermore, it identifies 97% of the OPTX Chandra X-ray-selected AGNs as TBT-AGN. This is in contrast to the BPT diagram, which misidentifies 20% of X-ray-selected AGNs as BPT-SF. We use the Great Observatories Origins Deep Survey North and Lockman Hole galaxy samples, with their accompanying deep Chandra imaging, to perform X-ray and infrared stacking analyses to further validate our TBT-AGN and TBT-SF selections; that is, we verify the dominance of AGN activity in the former and star formation activity in the latter. Finally, we address the inclusion of the majority of the BPT-comp (sources lying between the BPT-SF and BPT-AGN regimes) in our TBT-AGN regime. We find that the stacked BPT-comp source is X-ray hard (langΓeffrang = 1.0+0.4 -0.4) and has a high X-ray luminosity to total infrared luminosity ratio. This suggests that, on average, the X-ray signal in BPT-comp is dominated by obscured or low accretion rate AGN activity rather than by star formation, supporting their inclusion in the TBT-AGN regime. Some of the data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration

  16. How to Identify Success Among Networks That Promote Active Living

    PubMed Central

    Litt, Jill; Varda, Danielle; Reed, Hannah; Retrum, Jessica; Tabak, Rachel; Gustat, Jeanette; Tompkins, Nancy O’Hara

    2017-01-01

    Objectives We evaluated organization- and network-level factors that influence organizations’ perceived success. This is important for managing interorganizational networks, which can mobilize communities to address complex health issues such as physical activity, and for achieving change. Methods In 2011, we used structured interview and network survey data from 22 states in the United States to estimate multilevel random-intercept models to understand organization- and network-level factors that explain perceived network success. Results A total of 53 of 59 “whole networks” met the criteria for inclusion in the analysis (89.8%). Coordinators identified 559 organizations, with 3 to 12 organizations from each network taking the online survey (response rate: 69.7%; range: 33%–100%). Occupying a leadership position (P < .01), the amount of time with the network (P < .05), and support from community leaders (P < .05) emerged as correlates of perceived success. Conclusions Organizations’ perceptions of success can influence decisions about continuing involvement and investment in networks designed to promote environment and policy change for active living. Understanding these factors can help leaders manage complex networks that involve diverse memberships, varied interests, and competing community-level priorities. PMID:26378863

  17. 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

  18. Grazers and Phytoplankton Growth in the Oceans: an Experimental and Evolutionary Perspective

    PubMed Central

    Ratti, Simona; Knoll, Andrew H.; Giordano, Mario

    2013-01-01

    The taxonomic composition of phytoplankton responsible for primary production on continental shelves has changed episodically through Earth history. Geological correlations suggest that major changes in phytoplankton composition correspond in time to changes in grazing and seawater chemistry. Testing hypotheses that arise from these correlations requires experimentation, and so we carried out a series of experiments in which selected phytoplankton species were grown in treatments that differed with respect to the presence or absence of grazers as well as seawater chemistry. Both protistan (Euplotes sp.) and microarthropod (Acartia tonsa) grazers changed the growth dynamics and biochemical composition of the green alga Tetraselmis suecica, the diatom Thalassiosira weissflogii, and the cyanobacterium Synechococcus sp., increasing the specific growth rate and palatability of the eukaryotic algae, while decreasing or leaving unchanged both parameters in the cyanobacteria. Synechococcus (especially) and Thalassiosira produced toxins effective against the copepod, but ciliate growth was unaffected. Acartia induced a 4-6 fold increase of Si cell quota in the diatom, but Euplotes had no similar effect. The differential growth responses of the eukaryotic algae and cyanobacteria to ciliate grazing may help to explain the apparently coeval radiation of eukaryophagic protists and rise of eukaryotes to ecological prominence as primary producers in Neoproterozoic oceans. The experimental results suggest that phytoplankton responses to the later radiation of microarthropod grazers were clade-specific, and included changes in growth dynamics, toxin synthesis, encystment, and (in diatoms) enhanced Si uptake. PMID:24204815

  19. Grazers and phytoplankton growth in the oceans: an experimental and evolutionary perspective.

    PubMed

    Ratti, Simona; Knoll, Andrew H; Giordano, Mario

    2013-01-01

    The taxonomic composition of phytoplankton responsible for primary production on continental shelves has changed episodically through Earth history. Geological correlations suggest that major changes in phytoplankton composition correspond in time to changes in grazing and seawater chemistry. Testing hypotheses that arise from these correlations requires experimentation, and so we carried out a series of experiments in which selected phytoplankton species were grown in treatments that differed with respect to the presence or absence of grazers as well as seawater chemistry. Both protistan (Euplotes sp.) and microarthropod (Acartia tonsa) grazers changed the growth dynamics and biochemical composition of the green alga Tetraselmis suecica, the diatom Thalassiosira weissflogii, and the cyanobacterium Synechococcus sp., increasing the specific growth rate and palatability of the eukaryotic algae, while decreasing or leaving unchanged both parameters in the cyanobacteria. Synechococcus (especially) and Thalassiosira produced toxins effective against the copepod, but ciliate growth was unaffected. Acartia induced a 4-6 fold increase of Si cell quota in the diatom, but Euplotes had no similar effect. The differential growth responses of the eukaryotic algae and cyanobacteria to ciliate grazing may help to explain the apparently coeval radiation of eukaryophagic protists and rise of eukaryotes to ecological prominence as primary producers in Neoproterozoic oceans. The experimental results suggest that phytoplankton responses to the later radiation of microarthropod grazers were clade-specific, and included changes in growth dynamics, toxin synthesis, encystment, and (in diatoms) enhanced Si uptake.

  20. Grazer diversity interacts with biogenic habitat heterogeneity to accelerate intertidal algal succession.

    PubMed

    Whalen, Matthew A; Aquilino, Kristin M; Stachowicz, John J

    2016-08-01

    Environmental heterogeneity contributes to coexistence by allowing species with different traits to persist when different species perform best at different times or places. This interaction between niche differences and environmental variability may also help explain relationships between biodiversity and ecosystem functioning, but few data are available to rigorously evaluate this hypothesis. We assessed how a biologically relevant aspect of environmental heterogeneity interacts with species diversity to determine ecosystem processes in a natural rocky intertidal community. We used field removals to factorially manipulate biogenic habitat heterogeneity (barnacles, bare rock, and plots that were 50/50 mixes of the two habitat types) and gastropod grazer species richness and then tracked algal community succession and recovery over the course of 1 yr. We found that herbivore diversity, substrate heterogeneity, and their interaction played unique roles in the peak abundance and timing of occurrence of different algal functional groups. Early successional microalgae were most heavily grazed in diverse herbivore assemblages and those with barnacles present, which was likely due to complementary feeding strategies among all three grazers. In contrast, late successional macroalgae were strongly influenced by the presence of a habitat generalist limpet. In this herbivore's absence, heterogeneous habitats (i.e., mixtures of bare rock and barnacles) experienced the greatest algal accumulation, which was partly a result of complementary habitat use by the remaining herbivores. The complex way habitat identity and heterogeneity altered grazer-algal interactions in our study suggests species' differences and environmental heterogeneity both separately and interactively contribute to the relationship between biodiversity and ecosystem functions.

  1. Grazers, browsers, and fire influence the extent and spatial pattern of tree cover in the Serengeti.

    PubMed

    Holdo, Ricardo M; Holt, Robert D; Fryxell, John M

    2009-01-01

    Vertebrate herbivores and fire are known to be important drivers of vegetation dynamics in African savannas. It is of particular importance to understand how changes in herbivore population density, especially of elephants, and fire frequency will affect the amount of tree cover in savanna ecosystems, given the critical importance of tree cover for biodiversity, ecosystem function, and human welfare. We developed a spatially realistic simulation model of vegetation, fire, and dominant herbivore dynamics, tailored to the Serengeti ecosystem of east Africa. The model includes key processes such as tree-grass competition, fire, and resource-based density dependence and adaptive movement by herbivores. We used the model to project the ecosystem 100 years into the future from its present state under different fire, browsing (determined by elephant population density), and grazing (with and without wildebeest present) regimes. The model produced the following key results: (1) elephants and fire exert synergistic negative effects on woody cover; when grazers are excluded, the impact of fire and the strength of the elephant-fire interaction increase; (2) at present population densities of 0.15 elephants/km2, the total amount of woody cover is predicted to remain stable in the absence of fire, but the mature tree population is predicted to decline regardless of the fire regime; without grazers present to mitigate the effects of fire, the size structure of the tree population will become dominated by seedlings and mature trees; (3) spatial heterogeneity in tree cover varies unimodally with elephant population density; fire increases heterogeneity in the presence of grazers and decreases it in their absence; (4) the marked rainfall gradient in the Serengeti directly affects the pattern of tree cover in the absence of fire; with fire, the woody cover is determined by the grazing patterns of the migratory wildebeest, which are partly rainfall driven. Our results show that, in

  2. Sparse activity of identified dentate granule cells during spatial exploration

    PubMed Central

    Diamantaki, Maria; Frey, Markus; Berens, Philipp; Preston-Ferrer, Patricia; Burgalossi, Andrea

    2016-01-01

    In the dentate gyrus – a key component of spatial memory circuits – granule cells (GCs) are known to be morphologically diverse and to display heterogeneous activity profiles during behavior. To resolve structure–function relationships, we juxtacellularly recorded and labeled single GCs in freely moving rats. We found that the vast majority of neurons were silent during exploration. Most active GCs displayed a characteristic spike waveform, fired at low rates and showed spatial activity. Primary dendritic parameters were sufficient for classifying neurons as active or silent with high accuracy. Our data thus support a sparse coding scheme in the dentate gyrus and provide a possible link between structural and functional heterogeneity among the GC population. DOI: http://dx.doi.org/10.7554/eLife.20252.001 PMID:27692065

  3. Identifying healthcare activities using a real-time location system.

    PubMed

    Cagle, Rick; Darling, Erika; Kim, Bo

    2014-01-01

    This article discusses human resource allocation in a Veterans Health Administration audiology clinic as a model for clinics facing similar challenges in maximizing quality, safety, and effectiveness of care. A framework is proposed combining automatic identification technology with simulation and visualization software, asserting a relationship between location of staff within the facility and clinical activity, focusing healthcare staff on high-value activities to deliver safe, quality care. This enables "what-if" analyses of potential resource allocation scenarios, correlating location information from radiofrequency identification tags worn by clinicians and technicians in the clinic as part of a real-time location system, then inferring probable activity from the data. Once the baseline "as-is" can be established, the model will be refined to supply predictive analyses of resource allocation and management. Simulations of activities in specialized spaces saves time managing resources, which means more time can be spent on patient safety and increased satisfaction.

  4. MEG identifies dorsal medial brain activations during sleep.

    PubMed

    Ioannides, Andreas A; Kostopoulos, George K; Liu, Lichan; Fenwick, Peter B C

    2009-01-15

    All sleep stages contain epochs with high-amplitude electrophysiological phasic events, alternating with quieter "core periods." High-amplitude and core state properties cannot be disentangled with PET and fMRI. Here from high temporal resolution magnetoencephalography data, regional changes in neuronal activity were extracted during core periods in different frequency bands for each sleep stage and waking. We found that gamma-band activity increases in precuneus during light sleep (stages 1/2) and in the left dorso-medial prefrontal cortex (L-DMPFC) during deep sleep (stages 3/4). The L-DMPFC activated area expands laterally during rapid eye movement (REM) sleep, into a volume of about 5 cm(3) bounded by regions attributed to Theory of Mind (ToM) and default systems, both involved in introspection. Gamma band activity in this area was higher during REM sleep than other sleep stages and active wakefulness. There is a tantalizing correspondence between increased wide-band activity (dominated by low frequencies) in early non-REM (NREM) sleep stages and increases in gamma-band activity in late NREM and REM periods that we attribute to a lateral disinhibition mechanism. The results provide a description of regional electrophysiological changes in awake state, light and deep sleep, and REM sleep. These changes are most pronounced in the L-DMPFC and the other areas around the dorsal midline that are close to, but do not overlap with areas of the default and ToM systems, suggesting that the DMPFC, particularly in the left hemisphere, plays an important role in late NREM stages, in REM and possibly in dreaming.

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

    PubMed

    Wurtz, Robert H

    2015-09-19

    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.

  6. Grazers and vitamins shape chain formation in a bloom-forming dinoflagellate, Cochlodinium polykrikoides.

    PubMed

    Jiang, Xiaodong; Lonsdale, Darcy J; Gobler, Christopher J

    2010-10-01

    Predators influence the phenotype of prey through both natural selection and induction. We investigated the effects of grazers and nutrients on chain formation in a dinoflagellate, Cochlodinium polykrikoides, which forms dense blooms and has deleterious effects on marine ecosystems around the world. Field populations of C. polykrikoides formed longer chains than laboratory cultures without grazers. In the field, chain length of C. polykrikoides was positively correlated with the abundance of the copepod Acartia tonsa. Chain length of C. polykrikoides increased when exposed to live females of A. tonsa or its fresh (<24 h post-isolation) exudates for 48 h. These results suggest that dissolved chemical cues released by A. tonsa induce chain formation in C. polykrikoides. Ingestion rate of A. tonsa on four-cell chains of C. polykrikoides was lower than on single cells, suggesting that chain formation may be an effective anti-grazing defense. Finally, nutrient amendment experiments demonstrated that vitamins (B(1), B(7), and B(12)) increased the chain length of C. polykrikoides both singly and collectively, while trace metals and inorganic nutrients did not, showing that vitamins may also influence chain formation in this species.

  7. Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers.

    PubMed

    Pearson, Joseph C; McKay, Daniel J; Lieb, Jason D; Crews, Stephen T

    2016-10-15

    One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.

  8. Basophil Activation Test identifies the patients with Chronic Spontaneous Urticaria suffering the most active disease

    PubMed Central

    Curto‐Barredo, Laia; Yelamos, Jose; Gimeno, Ramon; Mojal, Sergi; Pujol, Ramon M.

    2016-01-01

    Abstract Introduction The basophil activation test showing CD63 up regulation could be a specific and sensitive in vitro complementary text to the in vivo autologous serum skin test for the activity assessment of the patients suffering autoimmune chronic spontaneous urticaria. The aim of this study is to define the basophil activation test as a useful tool in clinical practice in order to identify those patients with more active disease. Methods We screened 139 patients (96 women) diagnosed of chronic spontaneous urticaria using simultaneously autologous serum skin test and basophil activation test and their relationship with disease activity. Results Positive autologous serum skin test was found in 56.8%; from them, 31.6% were basophil activation test positive. Negative autologous serum skin test result was found in the 43.2% of the sample that showed negative CD63 expression results in all cases, except one. Patients with positive autologous serum skin test and positive CD63 by basophil activation test showed significant higher Urticaria Activity Score of 7 days (P = 0.004) and of 3 weeks (P = 0.001) than patients with positive autologous serum skin test and negative CD63 (mean ± standard deviation [SD] 26.57 ± 10.56 versus 18.40 ± 12.05 for the Urticaria Activity Score of 7 days and 56.47 ± 23.78 versus 39.88 ± 25.44 for the Urticaria Activity Score of 3 weeks). Conclusions The CD63 expression on basophils appears as a reliable in vitro marker, useful in clinical practice in combination with autologous serum skin test to define chronic spontaneous urticaria patients with the highest urticaria activity that impairs a normal life. PMID:27980778

  9. 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.

  10. 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

  11. 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

  12. 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…

  13. 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...

  14. 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

  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.

  16. 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…

  17. Identifying and Activating Receptive Vocabulary by an Online Vocabulary Survey and an Online Writing Task

    ERIC Educational Resources Information Center

    Lin, Ivy Chuhui; Kawai, Goh

    2016-01-01

    Seeking to identify and activate the Receptive Vocabulary (RV) of English Language Learners (ELLs), we designed (1) an online five category multiple-choice vocabulary survey that more quickly measures vocabulary knowledge, and (2) an online creative writing task where ELLs chose RV items identified in step (1). While RV items of highly proficient…

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

    PubMed

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

    2009-09-20

    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.

  20. 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

  1. Gastropod grazers and nutrients, but not light, interact in determining periphytic algal diversity.

    PubMed

    Liess, Antonia; Kahlert, Maria

    2007-05-01

    The potential interactions of grazing, nutrients and light in influencing autotroph species diversity have not previously been considered. Earlier studies have shown that grazing and nutrients interact in determining autotroph species diversity, since grazing decreases species diversity when nutrients (i.e. N or P) limit autotroph growth, but increases it when nutrients are replete. We hypothesized that increased light intensities would intensify the interactions between grazing and nutrients on algal species diversity, resulting in even stronger reductions in algal species diversity through grazing under nutrient-poor conditions, and to even stronger increases of algal species diversity through grazing under nutrient-rich conditions. We studied the effects of grazing (absent, present), nutrients (ambient, N + P enriched) and light (low light, high light) on benthic algal diversity and periphyton C:nutrient ratios (which can indicate algal nutrient limitation) in a factorial laboratory experiment, using the gastropod grazer Viviparus viviparus. Grazing decreased algal biomass and algal diversity, but increased C:P and N:P ratios of periphyton. Grazing also affected periphyton species composition, by decreasing the proportion of Spirogyra sp. and increasing the proportion of species in the Chaetophorales. Grazing effects on diversity as well as on periphyton N:P ratios were weakened when nutrients were added (interaction between grazing and nutrients). Chlorophyll a (Chl a) per area increased with nutrient addition and decreased with high light intensities. Light did not increase the strength of the interaction between grazing and nutrients on periphytic algal diversity. This study shows that nutrient addition substantially reduced the negative effects of grazing on periphytic algal diversity, whereas light did not interact with grazing or nutrient enrichment in determining periphytic algal diversity.

  2. Variable viral and grazer control of prokaryotic growth efficiency in temperate freshwater lakes (French Massif Central).

    PubMed

    Ram, A S Pradeep; Palesse, S; Colombet, J; Sabart, M; Perriere, F; Sime-Ngando, T

    2013-11-01

    The effects of viral lysis and heterotrophic nanoflagellate grazing (top down forces) on prokaryotic mortality and their subsequent impact on their metabolism were estimated in the upper euphotic and deeper aphotic depth of 11 freshwater lakes located in the French Massif Central. The standing stocks of viruses (VA) and heterotrophic nanoflagellate (HNF) varied significantly (p < 0.05) with sampled depth. VA was substantially (twofold on an average) and significantly higher (p < 0.03) at the aphotic compared to euphotic depth, whereas the reverse was true (p < 0.02) for HNF. Among the prokaryote subgroup, high nucleic acid content prokaryotes explained for significant variability in the total VA and served as principle host target for viral proliferation. Like standing stocks, flagellate grazing and viral infection rates also followed similar patterns. In the investigated lakes, the mechanism for regulating prokaryotic production varied with sampled depth from grazing control in the euphotic to control due to viral lysis in the aphotic. We also tested the hypothesis of top down control on prokaryotic growth efficiency (PGE, which we used as an index of prokaryotic physiological and energetic status at the community level) at both depths. Overall, among the studied lakes, PGE varied widely (4-51 %) with significantly (p < 0.05) lower values in the aphotic (mean = 18 ± 4 %) than euphotic depth (mean = 32 ± 9 %). Contrasting observations on the top down control of PGE between sampled depths were observed. The presence of grazers was found to stimulate PGE at the euphotic, whereas viruses through their lytic infection had a strong negative impact on PGE at the aphotic depth. Such observed differences in PGE and the mechanism controlling prokaryotic production with depth could eventually have strong implication on carbon and nutrient flux patterns in the studied lakes.

  3. Large grazers modify effects of aboveground-belowground interactions on small-scale plant community composition.

    PubMed

    Veen, G F Ciska; Geuverink, Elzemiek; Olff, Han

    2012-02-01

    Aboveground and belowground organisms influence plant community composition by local interactions, and their scale of impact may vary from millimeters belowground to kilometers aboveground. However, it still poorly understood how large grazers that select their forage on large spatial scales interact with small-scale aboveground-belowground interactions on plant community heterogeneity. Here, we investigate how cattle (Bos taurus) modify the effects of interactions between yellow meadow ants (Lasius flavus) and European brown hares (Lepus europaeus) on the formation of small-scale heterogeneity in vegetation composition. In the absence of cattle, hares selectively foraged on ant mounds, while under combined grazing by hares and cattle, vertebrate grazing pressure was similar on and off mounds. Ant mounds that were grazed by only hares had a different plant community composition compared to their surroundings: the cover of the grazing-intolerant grass Elytrigia atherica was reduced on ant mounds, whereas the relative cover of the more grazing-tolerant and palatable grass Festuca rubra was enhanced. Combined grazing by hares and cattle, resulted in homogenization of plant community composition on and off ant mounds, with high overall cover of F. rubra. We conclude that hares can respond to local ant-soil-vegetation interactions, because they are small, selective herbivores that make their foraging decisions on a local scale. This results in small-scale plant patches on mounds of yellow meadow ants. In the presence of cattle, which are less selective aboveground herbivores, local plant community patterns triggered by small-scale aboveground-belowground interactions can disappear. Therefore, cattle modify the consequences of aboveground-belowground interactions for small-scale plant community composition.

  4. Using wearable cameras to categorise type and context of accelerometer-identified episodes of physical activity

    PubMed Central

    2013-01-01

    Background Accelerometers can identify certain physical activity behaviours, but not the context in which they take place. This study investigates the feasibility of wearable cameras to objectively categorise the behaviour type and context of participants’ accelerometer-identified episodes of activity. Methods Adults were given an Actical hip-mounted accelerometer and a SenseCam wearable camera (worn via lanyard). The onboard clocks on both devices were time-synchronised. Participants engaged in free-living activities for 3 days. Actical data were cleaned and episodes of sedentary, lifestyle-light, lifestyle-moderate, and moderate-to-vigorous physical activity (MVPA) were identified. Actical episodes were categorised according to their social and environmental context and Physical Activity (PA) compendium category as identified from time-matched SenseCam images. Results There were 212 days considered from 49 participants from whom SenseCam images and associated Actical data were captured. Using SenseCam images, behaviour type and context attributes were annotated for 386 (out of 3017) randomly selected episodes (such as walking/transportation, social/not-social, domestic/leisure). Across the episodes, 12 categories that aligned with the PA Compendium were identified, and 114 subcategory types were identified. Nineteen percent of episodes could not have their behaviour type and context categorized; 59% were outdoors versus 39% indoors; 33% of episodes were recorded as leisure time activities, with 33% transport, 18% domestic, and 15% occupational. 33% of the randomly selected episodes contained direct social interaction and 22% were in social situations where the participant wasn’t involved in direct engagement. Conclusion Wearable camera images offer an objective method to capture a spectrum of activity behaviour types and context across 81% of accelerometer-identified episodes of activity. Wearable cameras represent the best objective method currently

  5. 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…

  6. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.

    PubMed

    Nagari, Anusha; Murakami, Shino; Malladi, Venkat S; Kraus, W Lee

    2017-01-01

    Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.

  7. 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.

  8. Natural selection for grazer resistance to toxic cyanobacteria: evolution of phenotypic plasticity?

    PubMed

    Hairston, N G; Holtmeier, C L; Lampert, W; Weider, L J; Post, D M; Fischer, J M; Cáceres, C E; Fox, J A; Gaedke, U

    2001-11-11

    We studied the selection response of the freshwater grazing zooplankter, Daphnia galeata, to increased abundance of cyanobacteria in its environment. Cyanobacteria are a poor-quality and often toxic food. Distinct genotypes of D. galeata were hatched from diapausing eggs extracted from three time horizons in the sediments of Lake Constance, Europe, covering the period 1962 to 1997, a time of change in both the prevalence of planktonic cyanobacteria and levels of phosphorus pollution. We assessed whether the grazers evolved to become more resistant to dietary cyanobacteria by exposing genetically distinct clones to two diets, one composed only of the nutritious green alga, Scenedesmus obliquus (good food), and the other a mixture of S. obliquus and the toxic cyanobacterium Microcvstis aeruginosa (poor food). Genotype performance was measured as the specific rate of weight gain from neonate to maturity (gj). We evaluated evolutionary change in the Daphnia population using an analysis of reaction norms based on relative (log-transformed) changes in gj. Log(gj) is a measure of the proportional effect of dietary cyanobacteria on other fitness components of the Daphnia phenotype. For comparison, we also analyze absolute (i.e., nontransformed) changes in gj and discuss the interpretations of the two approaches. Statistical results using a general linear model demonstrate a significant effect of genotype (showing differences in gj among genotypes), a significant genotype x food-type interaction (showing differences in phenotypic plasticity among genotypes), and, in the case of log-transformed data, a significant sediment-genotype-age x food-type interaction. The latter shows that phenotypic plasticity evolved over the period studied. Two constraints act on response to selection in the D. galeata-Lake Constance system. First, gj on a diet containing poor food is highly correlated with gj on a diet of good food, thus evolving resistance also meant evolving an increase in gj

  9. Custom active RFId solution for children tracking and identifying in a resuscitation ward.

    PubMed

    Iadanza, Ernesto; Dori, Fabrizio

    2009-01-01

    In this work is discussed an active RFId system to track and identify patients in a children's critical care ward. The technical solutions may be very different according to the patients type, age and cognitive conditions and according to the hospital shapes. The proposed system to track and identify patients has been developed taking into account all the constraints induced by the particular environment. The system is composed of five different hardware devices and a tracking software, purposely designed and realized.

  10. A Systematic Approach to Identify Markers of Distinctly Activated Human Macrophages

    PubMed Central

    Sudan, Bayan; Wacker, Mark A.; Wilson, Mary E.; Graff, Joel W.

    2015-01-01

    Polarization has been a useful concept for describing activated macrophage phenotypes and gene expression profiles. However, macrophage activation status within tumors and other settings are often inferred based on only a few markers. Complicating matters for relevance to human biology, many macrophage activation markers have been best characterized in mice and sometimes are not similarly regulated in human macrophages. To identify novel markers of activated human macrophages, gene expression profiles for human macrophages of a single donor subjected to 33 distinct activating conditions were obtained and a set of putative activation markers were subsequently evaluated in macrophages from multiple donors using integrated fluidic circuit (IFC)-based RT-PCR. Using unsupervised hierarchical clustering of the microarray screen, highly altered transcripts (>4-fold change in expression) sorted the macrophage transcription profiles into two major and 13 minor clusters. Among the 1874 highly altered transcripts, over 100 were uniquely altered in one major or two related minor clusters. IFC PCR-derived data confirmed the microarray results and determined the kinetics of expression of potential macrophage activation markers. Transcripts encoding chemokines, cytokines, and cell surface were prominent in our analyses. The activation markers identified by this study could be used to better characterize tumor-associated macrophages from biopsies as well as other macrophage populations collected from human clinical samples. PMID:26074920

  11. Vertical distribution and in situ feeding of marine particle-grazers in relation to their food, the microplankton

    SciTech Connect

    Napp, J.M.

    1986-01-01

    A cruise was completed to measure the vertical distributions of plant biomass, growth, size and species composition, nutritional content and the zooplankton biomass and species composition. There were no consistent differences in the size spectra of particles between the regions of highest plant biomass and highest growth rates. Species known to be noxious or distasteful to the zooplankton were not members of either assemblage. The nutritional content of the particulate matter was greatest at the plant biomass maximum. Thus there was no evidence that the region of higher plant growth rates was a better place for zooplankton to feed. The diurnal distribution of zooplankton biomass was not consistently related to the vertical distributions of plant biomass, primary productivity, or productivity/chlorophyll. At night, the vertical distribution of zooplankton biomass was consistently related to the vertical distribution of plant biomass. There were species whose vertical distributions were consistently related to either the vertical distribution of plant biomass or productivity/chlorophyll a but not primary productivity, contrary to the observations of others. The total grazing pressure, measured in situ with a new design of grazing chamber and an isotopic carrier which labels the particulate matter day and night, indicated that the daily production of plant carbon was much greater than its rate of removal by the grazers. Thus, it is not necessary for the grazer biomass maximum to be located above the chlorophyll a maximum in order for that feature to persist.

  12. Distribution and drift dispersal dynamics of a caddisfly grazer in response to resource abundance and its ontogeny

    PubMed Central

    Mitsuhashi, Hiromune; Doi, Hideyuki; Isobe, Yu; Oishi, Tadashi

    2017-01-01

    Stream grazers have a major impact on food web structure and the productivity of stream ecosystems; however, studies on the longitudinal (upstream versus downstream) and temporal changes in their drift dynamics and resulting distributions remain limited. Here, we investigated the longitudinal and temporal distributions and drift propensity of a trichopteran grazer, the caddisfly, Micrasema quadriloba, during its life cycle in a Japanese stream. The distribution of larvae significantly shifted downstream during the fifth instar larval stage during late winter; with periphyton abundance (i.e. their food source) showing similar shifts downstream. Therefore, our results show that the drift dispersal the caddisfly occurs in response to decline in available food resources (i.e. food-resource scarcity) and an increase in food requirements by growing individuals. Furthermore, our results show that this observed longitudinal shift in larval distribution varies through their life cycle, because the drift dispersal of fifth instar larvae was greater than that of immature larvae. The correlation between periphyton abundance and drift propensity of fourth instar larvae was not statistically significant, whereas that of fifth instar larvae was significantly negative. In conclusion, we detected an ontogenetic shift in drift propensity, which might explain the longitudinal and temporal distributions of this species. PMID:28280576

  13. Model-Eliciting Activities as a Tool to Develop and Identify Creatively Gifted Mathematicians

    ERIC Educational Resources Information Center

    Chamberlin, Scott A.; Moon, Sidney M.

    2005-01-01

    This article addresses the use of Model-Eliciting Activities (MEAs) as a (curricular) tool to develop mathematical creativity and identify students who are creatively gifted in mathematics. The thesis of this article is that by using MEAs, gifted educators can: (a) provide students with opportunities to develop creative and applied mathematical…

  14. Ecological Congruence Assessment for Classroom Activities and Routines: Identifying Goals and Intervention Practices in Childcare.

    ERIC Educational Resources Information Center

    Wolery, Mark; Brashers, Margaret Sigalove; Neitzel, Jennifer C.

    2002-01-01

    This article explains how educators can use the ecological congruence assessment process for identifying functional goals for young children with disabilities. Process steps include: teacher collects information about functioning in usual classroom activities, routines, and transitions; summarizes the collected information; and shares the…

  15. Using Active Learning to Identify Health Information Technology Related Patient Safety Events.

    PubMed

    Fong, Allan; Howe, Jessica L; Adams, Katharine T; Ratwani, Raj M

    2017-01-18

    The widespread adoption of health information technology (HIT) has led to new patient safety hazards that are often difficult to identify. Patient safety event reports, which are self-reported descriptions of safety hazards, provide one view of potential HIT-related safety events. However, identifying HIT-related reports can be challenging as they are often categorized under other more predominate clinical categories. This challenge of identifying HIT-related reports is exacerbated by the increasing number and complexity of reports which pose challenges to human annotators that must manually review reports. In this paper, we apply active learning techniques to support classification of patient safety event reports as HIT-related. We evaluated different strategies and demonstrated a 30% increase in average precision of a confirmatory sampling strategy over a baseline no active learning approach after 10 learning iterations.

  16. 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

  17. 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

  18. Synthesis and Structure activity relationships of EGCG Analogues, A Recently Identified Hsp90 Inhibitor

    PubMed Central

    Khandelwal, Anuj; Hall, Jessica

    2014-01-01

    Epigallocatechin-3-gallate (EGCG), the principal polyphenol isolated from green tea, was recently shown to inhibit Hsp90, however structure-activity relationships for this natural product have not yet been produced. Herein, we report the synthesis and biological evaluation of EGCG analogues to establish structure-activity relationships between EGCG and Hsp90. All four rings as well as the linker connecting the C- and the D-rings were systematically investigated, which led to the discovery of compounds that inhibit Hs90 and display improvement in efficacy over EGCG. Anti-proliferative activity of all the analogues was determined against MCF-7 and SKBr3 cell lines and Hsp90 inhibitory activity of four most potent analogues was further evaluated by western blot analyses and degradation of Hsp90-dependent client proteins. Prenyl substituted aryl ester of 3,5-dihydroxychroman-3-ol ring system was identified as novel scaffold that exhibit Hsp90 inhibitory activity. PMID:23834230

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

    PubMed Central

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

    2016-01-01

    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 G60A mutant that possesses efficient defatty-acylase activity, but has significantly decreased deacetylase activity in vitro and no detectable deacetylase activity in cells. The G60A mutant has 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 SIRT6’s defatty-acylase activity regulates the secretion of numerous proteins. Interestingly, many ribosomal proteins were secreted via exosomes from Sirt6 KO mouse embryonic fibroblasts, and these exosomes increased NIH 3T3 cell proliferation compared with control exosomes. Our data supports that distinct activities of SIRT6 regulate different pathways, and that the G60A mutant is a useful tool to study the contribution of the defatty-acylase activity to SIRT6’s various functions. PMID:27322069

  20. 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.

  1. Removal of novel antiandrogens identified in biological effluents of domestic wastewater by activated carbon.

    PubMed

    Ma, Dehua; Chen, Lujun; Liu, Rui

    2017-04-10

    Environmental antiandrogenic (AA) contaminants in effluents from wastewater treatment plants have the potential for negative impacts on wildlife and human health. The aim of our study was to identify chemical contaminants with likely AA activity in the biological effluents and evaluate the removal of these antiandrogens (AAs) during advanced treatment comprising adsorption onto granular activated carbon (GAC). In this study, profiling of AA contaminants in biological effluents and tertiary effluents was conducted using effect-directed analysis (EDA) including high performance liquid chromatography (HPLC) fractionation, a recombinant yeast screen containing androgen receptor (YAS), in combination with mass spectrometry analyses. Analysis of a wastewater secondary effluent from a membrane bioreactor revealed complex profiles of AA activity comprising 14 HPLC fractions and simpler profiles of GAC effluents with only 2 to 4 moderately polar HPLC fractions depending on GAC treatment conditions. Gas chromatography-mass spectrometry and ultra-high performance liquid chromatography-nanospray mass spectrometry analyses of AA fractions in the secondary effluent resulted in detection of over 10 chemical contaminants, which showed inhibition of YAS activity and were potential AAs. The putative AAs included biocides, food additives, flame retardants, pharmaceuticals and industrial contaminants. To our knowledge, it is the first time that the AA properties of N-ethyl-2-isopropyl-5-methylcyclohexanecarboxamide (WS3), cetirizine, and oxcarbazepine are reported. The EDA used in this study was proven to be a powerful tool to identify novel chemical structures with AA activity in the complex aquatic environment. The adsorption process to GAC of all the identified antiandrogens, except WS3 and triclosan, fit well with the pseudo-second order kinetics models. Adsorption to GAC could further remove most of the AAs identified in the biological effluents with high efficiencies.

  2. 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

  3. Antihypertensive activity of peptides identified in the in vitro gastrointestinal digest of pork meat.

    PubMed

    Escudero, Elizabeth; Toldrá, Fidel; Sentandreu, Miguel Angel; Nishimura, Hitoshi; Arihara, Keizo

    2012-07-01

    This study investigated the in vivo antihypertensive activity of three novel peptides identified in the in vitro digest of pork meat. These peptides were RPR, KAPVA and PTPVP and all of them showed significant antihypertensive activity after oral administration to spontaneously hypertensive rats, RPR being the peptide with the greatest in vivo activity. To our knowledge, this is the first report showing the in vivo antihypertensive action of the three peptides from nebulin (RPR) and titin (KAPVA and PTPVP), thus confirming their reported in vitro angiotensin I-converting enzyme (ACE) inhibitory activity. These findings suggest that pork meat could constitute a source of bioactive constituents that could be utilized in functional foods or nutraceuticals.

  4. Extensive mutagenesis of a transcriptional activation domain identifies single hydrophobic and acidic amino acids important for activation in vivo.

    PubMed Central

    Sainz, M B; Goff, S A; Chandler, V L

    1997-01-01

    C1 is a transcriptional activator of genes encoding biosynthetic enzymes of the maize anthocyanin pigment pathway. C1 has an amino terminus homologous to Myb DNA-binding domains and an acidic carboxyl terminus that is a transcriptional activation domain in maize and yeast cells. To identify amino acids critical for transcriptional activation, an extensive random mutagenesis of the C1 carboxyl terminus was done. The C1 activation domain is remarkably tolerant of amino acid substitutions, as changes at 34 residues had little or no effect on transcriptional activity. These changes include introduction of helix-incompatible amino acids throughout the C1 activation domain and alteration of most single acidic amino acids, suggesting that a previously postulated amphipathic alpha-helix is not required for activation. Substitutions at two positions revealed amino acids important for transcriptional activation. Replacement of leucine 253 with a proline or glutamine resulted in approximately 10% of wild-type transcriptional activation. Leucine 253 is in a region of C1 in which several hydrophobic residues align with residues important for transcriptional activation by the herpes simplex virus VP16 protein. However, changes at all other hydrophobic residues in C1 indicate that none are critical for C1 transcriptional activation. The other important amino acid in C1 is aspartate 262, as a change to valine resulted in only 24% of wild-type transcriptional activation. Comparison of our C1 results with those from VP16 reveal substantial differences in which amino acids are required for transcriptional activation in vivo by these two acidic activation domains. PMID:8972191

  5. 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.

  6. 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

  7. 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.

  8. Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation

    PubMed Central

    Chavarría-Smith, Joseph; Mitchell, Patrick S.

    2016-01-01

    Inflammasomes are cytosolic multi-protein complexes that initiate immune responses to infection by recruiting and activating the Caspase-1 protease. Human NLRP1 was the first protein shown to form an inflammasome, but its physiological mechanism of activation remains unknown. Recently, specific variants of mouse and rat NLRP1 were found to be activated upon N-terminal cleavage by the anthrax lethal factor protease. However, agonists for other NLRP1 variants, including human NLRP1, are not known, and it remains unclear if they are also activated by proteolysis. Here we demonstrate that two mouse NLRP1 paralogs (NLRP1AB6 and NLRP1BB6) are also activated by N-terminal proteolytic cleavage. We also demonstrate that proteolysis within a specific N-terminal linker region is sufficient to activate human NLRP1. Evolutionary analysis of primate NLRP1 shows the linker/cleavage region has evolved under positive selection, indicative of pathogen-induced selective pressure. Collectively, these results identify proteolysis as a general mechanism of NLRP1 inflammasome activation that appears to be contributing to the rapid evolution of NLRP1 in rodents and primates. PMID:27926929

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Accelerometer tags: detecting and identifying activities in fish and the effect of sampling frequency.

    PubMed

    Broell, Franziska; Noda, Takuji; Wright, Serena; Domenici, Paolo; Steffensen, John Fleng; Auclair, Jean-Pierre; Taggart, Christopher T

    2013-04-01

    Monitoring and measuring the behaviour and movement of aquatic animals in the wild is typically challenging, though micro-accelerometer (archival or telemetry) tags now provide the means to remotely identify and quantify behavioural states and rates such as resting, swimming and migrating, and to estimate activity and energy budgets. Most studies use low-frequency (≤32 Hz) accelerometer sampling because of battery and data-archiving constraints. In this study we assessed the effect of sampling frequency (aliasing) on activity detection probability using the great sculpin (Myoxocephalus polyacanthoceaphalus) as a model species. Feeding strikes and escape responses (fast-start activities) and spontaneous movements among seven different great sculpin were triggered, observed and recorded using video records and a tri-axial accelerometer sampling at 100 Hz. We demonstrate that multiple parameters in the time and probability domains can statistically differentiate between activities with high detection (90%) and identification (80%) probabilities. Detection probability for feeding and escape activities decreased by 50% when sampling at <10 Hz. Our analyses illustrate additional problems associated with aliasing and how activity and energy-budget estimates can be compromised and misinterpreted. We recommend that high-frequency (>30 Hz) accelerometer sampling be used in similar laboratory and field studies. If battery and/or data storage is limited, we also recommend archiving the events via an on-board algorithm that determines the highest likelihood and subsequent archiving of the various event classes of interest.

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

    PubMed

    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. 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

  18. 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.

  19. High-content screen using zebrafish (Danio rerio) embryos identifies a novel kinase activator and inhibitor.

    PubMed

    Geldenhuys, Werner J; Bergeron, Sadie A; Mullins, Jackie E; Aljammal, Rowaa; Gaasch, Briah L; Chen, Wei-Chi; Yun, June; Hazlehurst, Lori A

    2017-02-28

    In this report we utilized zebrafish (Danio rerio) embryos in a phenotypical high-content screen (HCS) to identify novel leads in a cancer drug discovery program. We initially validated our HCS model using the flavin adenosine dinucleotide (FAD) containing endoplasmic reticulum (ER) enzyme, endoplasmic reticulum oxidoreductase (ERO1) inhibitor EN460. EN460 showed a dose response effect on the embryos with a dose of 10μM being significantly lethal during early embryonic development. The HCS campaign which employed a small library identified a promising lead compound, a naphthyl-benzoic acid derivative coined compound 1 which had significant dosage and temporally dependent effects on notochord and muscle development in zebrafish embryos. Screening a 369 kinase member panel we show that compound 1 is a PIM3 kinase inhibitor (IC50=4.078μM) and surprisingly a DAPK1 kinase agonist/activator (EC50=39.525μM). To our knowledge this is the first example of a small molecule activating DAPK1 kinase. We provide a putative model for increased phosphate transfer in the ATP binding domain when compound 1 is virtually docked with DAPK1. Our data indicate that observable phenotypical changes can be used in future zebrafish screens to identify compounds acting via similar molecular signaling pathways.

  20. 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

  1. 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

  2. Differential activation of an identified motor neuron and neuromodulation provide Aplysia's retractor muscle an additional function.

    PubMed

    McManus, Jeffrey M; Lu, Hui; Cullins, Miranda J; Chiel, Hillel J

    2014-08-15

    To survive, animals must use the same peripheral structures to perform a variety of tasks. How does a nervous system employ one muscle to perform multiple functions? We addressed this question through work on the I3 jaw muscle of the marine mollusk Aplysia californica's feeding system. This muscle mediates retraction of Aplysia's food grasper in multiple feeding responses and is innervated by a pool of identified neurons that activate different muscle regions. One I3 motor neuron, B38, is active in the protraction phase, rather than the retraction phase, suggesting the muscle has an additional function. We used intracellular, extracellular, and muscle force recordings in several in vitro preparations as well as recordings of nerve and muscle activity from intact, behaving animals to characterize B38's activation of the muscle and its activity in different behavior types. We show that B38 specifically activates the anterior region of I3 and is specifically recruited during one behavior, swallowing. The function of this protraction-phase jaw muscle contraction is to hold food; thus the I3 muscle has an additional function beyond mediating retraction. We additionally show that B38's typical activity during in vivo swallowing is insufficient to generate force in an unmodulated muscle and that intrinsic and extrinsic modulation shift the force-frequency relationship to allow contraction. Using methods that traverse levels from individual neuron to muscle to intact animal, we show how regional muscle activation, differential motor neuron recruitment, and neuromodulation are key components in Aplysia's generation of multifunctionality.

  3. Mutagenesis and behavioral screening for altered circadian activity identifies the mouse mutant, Wheels.

    PubMed

    Pickard, G E; Sollars, P J; Rinchik, E M; Nolan, P M; Bucan, M

    1995-12-24

    The molecular processes underlying the generation of circadian behavior in mammals are virtually unknown. To identify genes that regulate or alter circadian activity rhythms, a mouse mutagenesis program was initiated in conjunction with behavioral screening for alterations in circadian period (tau), a fundamental property of the biological clock. Male mice of the inbred BALB/c strain, treated with the potent mutagen N-ethyl-N-nitrosourea were mated with wild-type hybrids. Wheel-running activity of approximately 300 male progeny was monitored for 6-10 weeks under constant dark (DD) conditions. The tau DD of a single mouse (#187) was longer than the population mean by more than three standard deviations (24.20 vs. 23.32 +/- 0.02 h; mean +/- S.E.M.; n = 277). In addition, mouse #187 exhibited other abnormal phenotypes, including hyperactive bi-directional circling/spinning activity and an abnormal response to light. Heterozygous progeny of the founder mouse, generated from outcrossings with wild-type C57BL/6J mice, displayed lengthened tau DD although approximately 20% of the animals showed no wheel-running activity despite being quite active. Under light:dark conditions, all animals displaying circling behavior that ran in the activity wheels exhibited robust wheel-running activity at lights-ON and these animals also showed enhanced wheel-running activity in constant light conditions. The genetic dissection of the complex behavior associated with this mutation was facilitated by the previously described genetic mapping of the mutant locus causing circling behavior, designated Wheels (Whl), to the subcentromeric portion of mouse chromosome 4. In this report, the same locus is shown to be responsible for the abnormal responses to light and presumably for the altered circadian behavior. Characterization of the gene altered in the novel Whl mutation will contribute to understanding the molecular elements involved in mammalian circadian regulation.

  4. Air-cathode microbial fuel cell array: a device for identifying and characterizing electrochemically active microbes.

    PubMed

    Hou, Huijie; Li, Lei; de Figueiredo, Paul; Han, Arum

    2011-01-15

    Microbial fuel cells (MFCs) have generated excitement in environmental and bioenergy communities due to their potential for coupling wastewater treatment with energy generation and powering diverse devices. The pursuit of strategies such as improving microbial cultivation practices and optimizing MFC devices has increased power generating capacities of MFCs. However, surprisingly few microbial species with electrochemical activity in MFCs have been identified because current devices do not support parallel analyses or high throughput screening. We have recently demonstrated the feasibility of using advanced microfabrication methods to fabricate an MFC microarray. Here, we extend these studies by demonstrating a microfabricated air-cathode MFC array system. The system contains 24 individual air-cathode MFCs integrated onto a single chip. The device enables the direct and parallel comparison of different microbes loaded onto the array. Environmental samples were used to validate the utility of the air-cathode MFC array system and two previously identified isolates, 7Ca (Shewanella sp.) and 3C (Arthrobacter sp.), were shown to display enhanced electrochemical activities of 2.69 mW/m(2) and 1.86 mW/m(2), respectively. Experiments using a large scale conventional air-cathode MFC validated these findings. The parallel air-cathode MFC array system demonstrated here is expected to promote and accelerate the discovery and characterization of electrochemically active microbes.

  5. 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

  6. A Novel Heptapeptide with Tyrosinase Inhibitory Activity Identified from a Phage Display Library.

    PubMed

    Nie, Huali; Liu, Lin; Yang, Huiqin; Guo, Hongzhen; Liu, Xiang; Tan, Yuanhao; Wang, Wen; Quan, Jing; Zhu, Limin

    2017-01-01

    Peptidic inhibition of the enzyme tyrosinase, responsible for skin pigmentation and food browning, would be extremely useful for the food, cosmetics, and pharmaceutical industries. In order to identify novel inhibitory peptides, a library of short sequence oligopeptides was screened to reveal direct interaction with the tyrosinase. A phage displaying heptapeptide (IQSPHFF) was found to bind most strongly to tyrosinase. The inhibitory activity of the heptapeptide was evaluated using mushroom tyrosinase. The results showed that the peptide inhibited both the monophenolase and diphenolase activities of mushroom tyrosinase with IC50 values of 1.7 and 4.0 mM, respectively. The heptapeptide is thought to be a reversible competitive inhibitor of diphenolase with the inhibition constants (Ki) of 0.765 mM. To further investigate how the heptapeptide exerts its inhibitory effect, a docking study between tyrosinase and heptapeptide was performed. The simulation showed that the heptapeptide binds in the active site of the enzyme near the catalytically active Cu ions and forms hydrogen bonds with five histidine residues on the active site. Phage display technology is thus a useful approach for the screening of potential tyrosinase inhibitors and could be widely applicable to a much wider range of enzymes.

  7. Newly identified active faults in the Pollino seismic gap, southern Italy, and their seismotectonic significance

    NASA Astrophysics Data System (ADS)

    Brozzetti, Francesco; Cirillo, Daniele; de Nardis, Rita; Cardinali, Mauro; Lavecchia, Giusy; Orecchio, Barbara; Presti, Debora; Totaro, Cristina

    2017-01-01

    The following is a geological study of a Quaternary and active normal fault-system, which crops out in the Pollino area, a seismogenic sector of the Southern Apennines, Italy. From 2010 to 2014, this area was affected by long lasting seismic activity characterized by three major events which occurred in May 2012 (Mw 4.3), in October 2012 (Mw 5.2) and in June 2014 (Mw 4.0). The integration of structural-geological data with morpho-structural and remote sensing analyses, led to define the geometry, the kinematics, the cross-cutting relationships and the slip rates of the inferred active fault segments within and near the epicentral area. We reconstructed an asymmetric extensional pattern characterized by low-angle, E and NNE-dipping faults, and by antithetic, high-angle, SW- to WSW-dipping faults. The geometry of the faults at depth was constrained using high-resolution hypocenter distributions. The overall system fits well with the deformation field obtained from focal mechanisms and geodetic data. Comparing the fault pattern with the time-space evolution of the Pollino seismic activity, we identified the seismogenic sources in two, near-parallel, WSW-dipping faults, whose seismogenic potential were assessed. The peculiar perpendicular-to-fault-strike evolution of the seismic activity, is discussed in the frame of the reconstructed seismotectonic model.

  8. A Fluorescence-Based Thermal Shift Assay Identifies Inhibitors of Mitogen Activated Protein Kinase Kinase 4

    PubMed Central

    Krishna, Sankar N.; Luan, Chi-Hao; Mishra, Rama K.; Xu, Li; Scheidt, Karl A.; Anderson, Wayne F.; Bergan, Raymond C.

    2013-01-01

    Prostate cancer (PCa) is the second highest cause of cancer death in United States males. If the metastatic movement of PCa cells could be inhibited, then mortality from PCa could be greatly reduced. Mitogen-activated protein kinase kinase 4 (MAP2K4) has previously been shown to activate pro-invasion signaling pathways in human PCa. Recognizing that MAP2K4 represents a novel and validated therapeutic target, we sought to develop and characterize an efficient process for the identification of small molecules that target MAP2K4. Using a fluorescence-based thermal shift assay (FTS) assay, we first evaluated an 80 compound library of known kinase inhibitors, thereby identifying 8 hits that thermally stabilized MAP2K4 in a concentration dependent manner. We then developed an in vitro MAP2K4 kinase assay employing the biologically relevant downstream substrates, JNK1 and p38 MAPK, to evaluate kinase inhibitory function. In this manner, we validated the performance of our initial FTS screen. We next applied this approach to a 2000 compound chemically diverse library, identified 7 hits, and confirmed them in the in vitro kinase assay. Finally, by coupling our structure-activity relationship data to MAP2K4's crystal structure, we constructed a model for ligand binding. It predicts binding of our identified inhibitory compounds to the ATP binding pocket. Herein we report the creation of a robust inhibitor-screening platform with the ability to inform the discovery and design of new and potent MAP2K4 inhibitors. PMID:24339940

  9. 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

  10. 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.

  11. Spontaneous activity of morphologically identified ganglion cells in the developing ferret retina.

    PubMed

    Liets, Lauren C; Olshausen, Bruno A; Wang, Guo-Yong; Chalupa, Leo M

    2003-08-13

    Whole-cell patch-clamp recordings were made from morphologically identified ganglion cells in the intact retina of developing ferrets. As early as 3 d after birth, all ganglion cells exhibited bursts of spontaneous activity, with the interval between bursts gradually decreasing with maturity. By 2 weeks after birth, ganglion cells could be morphologically differentiated into three major classes (alpha, beta, and gamma), and at this time each cell class was characterized by a distinct pattern of spontaneous activity. Dual patch-clamp recordings from pairs of neighboring cells revealed that cells of all morphological classes burst in a coordinated manner, regardless of cell type. These observations suggest that a common mechanism underlies the bursting patterns exhibited by all ganglion cell classes, and that class-specific firing patterns emerge coincident with retinal ganglion cell morphological differentiation.

  12. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    NASA Astrophysics Data System (ADS)

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-09-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

  13. Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

    PubMed Central

    Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

    2016-01-01

    Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations. PMID:27666090

  14. 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.

  15. 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.

  16. 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.

  17. Chemical Constituents Identified from Fruit Body of Cordyceps bassiana and Their Anti-Inflammatory Activity.

    PubMed

    Suh, Wonse; Nam, Gyeongsug; Yang, Woo Seok; Sung, Gi-Ho; Shim, Sang Hee; Cho, Jae Youl

    2017-03-01

    Cordyceps bassiana is one of Cordyceps species with anti-oxidative, anti-cancer, anti-inflammatory, anti-diabetic, anti-obesity, anti-angiogenic, and anti-nociceptive activities. This mushroom has recently demonstrated to have an ability to reduce 2,4-dinitrofluorobenzene-induced atopic dermatitis symptoms in NC/Nga mice. In this study, we further examined phytochemical properties of this mushroom by column chromatography and HPLC analysis. By chromatographic separation and spectroscopic analysis, 8 compounds, such as 1,9-dimethylguanine (1), adenosine (2), uridine (3), nicotinamide (4), 3-methyluracil (5), 1,7-dimethylxanthine (6), nudifloric acid (7), and mannitol (8) were identified from 6 different fractions and 4 more subfractions. Through evaluation of their anti-inflammatory activities using reporter gene assay and mRNA analysis, compound 1 was found to block luciferase activity induced by NF-κB and AP-1, suppress the mRNA levels of cyclooxygenase (COX)-2 and tumor necrosis factor (TNF)-α. Therefore, our data strongly suggests that compound 1 acts as one of major principles in Cordyceps bassiana with anti-inflammatory and anti-atopic dermatitis activities.

  18. Chemical Constituents Identified from Fruit Body of Cordyceps bassiana and Their Anti-Inflammatory Activity

    PubMed Central

    Suh, Wonse; Nam, Gyeongsug; Yang, Woo Seok; Sung, Gi-Ho; Shim, Sang Hee; Cho, Jae Youl

    2017-01-01

    Cordyceps bassiana is one of Cordyceps species with anti-oxidative, anti-cancer, anti-inflammatory, anti-diabetic, anti-obesity, anti-angiogenic, and anti-nociceptive activities. This mushroom has recently demonstrated to have an ability to reduce 2,4-dinitrofluorobenzene-induced atopic dermatitis symptoms in NC/Nga mice. In this study, we further examined phytochemical properties of this mushroom by column chromatography and HPLC analysis. By chromatographic separation and spectroscopic analysis, 8 compounds, such as 1,9-dimethylguanine (1), adenosine (2), uridine (3), nicotinamide (4), 3-methyluracil (5), 1,7-dimethylxanthine (6), nudifloric acid (7), and mannitol (8) were identified from 6 different fractions and 4 more subfractions. Through evaluation of their anti-inflammatory activities using reporter gene assay and mRNA analysis, compound 1 was found to block luciferase activity induced by NF-κB and AP-1, suppress the mRNA levels of cyclooxygenase (COX)-2 and tumor necrosis factor (TNF)-α. Therefore, our data strongly suggests that compound 1 acts as one of major principles in Cordyceps bassiana with anti-inflammatory and anti-atopic dermatitis activities. PMID:27530115

  19. Spiperone, identified through compound screening, activates calcium-dependent chloride secretion in the airway

    PubMed Central

    Liang, Lihua; MacDonald, Kelvin; Schwiebert, Erik M.; Zeitlin, Pamela L.; Guggino, William B.

    2009-01-01

    Cystic fibrosis (CF) is caused by mutations in the gene producing the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR functions as a Cl− channel. Its dysfunction limits Cl− secretion and enhances Na+ absorption, leading to viscous mucus in the airway. Ca2+-activated Cl− channels (CaCCs) are coexpressed with CFTR in the airway surface epithelia. Increases in cytosolic Ca2+ activate the epithelial CaCCs, which provides an alternative Cl− secretory pathway in CF. We developed a screening assay and screened a library for compounds that could enhance cytoplasmic Ca2+, activate the CaCC, and increase Cl− secretion. We found that spiperone, a known antipsychotic drug, is a potent intracellular Ca2+ enhancer and demonstrated that it stimulates intracellular Ca2+, not by acting in its well-known role as an antagonist of serotonin 5-HT2 or dopamine D2 receptors, but through a protein tyrosine kinase-coupled phospholipase C-dependent pathway. Spiperone activates CaCCs, which stimulates Cl− secretion in polarized human non-CF and CF airway epithelial cell monolayers in vitro and in CFTR-knockout mice in vivo. In conclusion, we have identified spiperone as a new therapeutic platform for correction of defective Cl− secretion in CF via a pathway independent of CFTR. PMID:18987251

  20. Development of a QPatch automated electrophysiology assay for identifying KCa3.1 inhibitors and activators.

    PubMed

    Jenkins, David Paul; Yu, Weifeng; Brown, Brandon M; Løjkner, Lars Damgaard; Wulff, Heike

    2013-01-01

    The intermediate-conductance Ca(2+)-activated K(+) channel KCa3.1 (also known as KCNN4, IK1, or the Gárdos channel) plays an important role in the activation of T and B cells, mast cells, macrophages, and microglia by regulating membrane potential, cellular volume, and calcium signaling. KCa3.1 is further involved in the proliferation of dedifferentiated vascular smooth muscle cells and fibroblast and endothelium-derived hyperpolarization responses in the vascular endothelium. Accordingly, KCa3.1 inhibitors are therapeutically interesting as immunosuppressants and for the treatment of a wide range of fibroproliferative disorders, whereas KCa3.1 activators constitute a potential new class of endothelial function preserving antihypertensives. Here, we report the development of QPatch assays for both KCa3.1 inhibitors and activators. During assay optimization, the Ca(2+) sensitivity of KCa3.1 was studied using varying intracellular Ca(2+) concentrations. A free Ca(2+) concentration of 1 μM was chosen to optimally test inhibitors. To identify activators, which generally act as positive gating modulators, a lower Ca(2+) concentration (∼200 nM) was used. The QPatch results were benchmarked against manual patch-clamp electrophysiology by determining the potency of several commonly used KCa3.1 inhibitors (TRAM-34, NS6180, ChTX) and activators (EBIO, riluzole, SKA-31). Collectively, our results demonstrate that the QPatch provides a comparable but much faster approach to study compound interactions with KCa3.1 channels in a robust and reliable assay.

  1. Identifying transcription start sites and active enhancer elements using BruUV-seq.

    PubMed

    Magnuson, Brian; Veloso, Artur; Kirkconnell, Killeen S; de Andrade Lima, Leonardo Carmo; Paulsen, Michelle T; Ljungman, Emily A; Bedi, Karan; Prasad, Jayendra; Wilson, Thomas E; Ljungman, Mats

    2015-12-11

    BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5'-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3'-5' degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells.

  2. Identifying transcription start sites and active enhancer elements using BruUV-seq

    PubMed Central

    Magnuson, Brian; Veloso, Artur; Kirkconnell, Killeen S.; Lima, Leonardo Carmo de Andrade; Paulsen, Michelle T.; Ljungman, Emily A.; Bedi, Karan; Prasad, Jayendra; Wilson, Thomas E.; Ljungman, Mats

    2015-01-01

    BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5′-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3′–5′ degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells. PMID:26656874

  3. Systematic Repurposing Screening in Xenograft Models Identifies Approved Drugs with Novel Anti-Cancer Activity

    PubMed Central

    Roix, Jeffrey J.; Harrison, S. D.; Rainbolt, Elizabeth A.; Meshaw, Kathryn R.; McMurry, Avery S.; Cheung, Peter; Saha, Saurabh

    2014-01-01

    Approved drugs target approximately 400 different mechanisms of action, of which as few as 60 are currently used as anti-cancer therapies. Given that on average it takes 10–15 years for a new cancer therapeutic to be approved, and the recent success of drug repurposing for agents such as thalidomide, we hypothesized that effective, safe cancer treatments may be found by testing approved drugs in new therapeutic settings. Here, we report in-vivo testing of a broad compound collection in cancer xenograft models. Using 182 compounds that target 125 unique target mechanisms, we identified 3 drugs that displayed reproducible activity in combination with the chemotherapeutic temozolomide. Candidate drugs appear effective at dose equivalents that exceed current prescription levels, suggesting that additional pre-clinical efforts will be needed before these drugs can be tested for efficacy in clinical trials. In total, we suggest drug repurposing is a relatively resource-intensive method that can identify approved medicines with a narrow margin of anti-cancer activity. PMID:25093583

  4. Research resource: modulators of glucocorticoid receptor activity identified by a new high-throughput screening assay.

    PubMed

    Blackford, John A; Brimacombe, Kyle R; Dougherty, Edward J; Pradhan, Madhumita; Shen, Min; Li, Zhuyin; Auld, Douglas S; Chow, Carson C; Austin, Christopher P; Simons, S Stoney

    2014-07-01

    Glucocorticoid steroids affect almost every type of tissue and thus are widely used to treat a variety of human pathological conditions. However, the severity of numerous side effects limits the frequency and duration of glucocorticoid treatments. Of the numerous approaches to control off-target responses to glucocorticoids, small molecules and pharmaceuticals offer several advantages. Here we describe a new, extended high-throughput screen in intact cells to identify small molecule modulators of dexamethasone-induced glucocorticoid receptor (GR) transcriptional activity. The novelty of this assay is that it monitors changes in both GR maximal activity (A(max)) and EC(50) (the position of the dexamethasone dose-response curve). Upon screening 1280 chemicals, 10 with the greatest changes in the absolute value of A(max) or EC(50) were selected for further examination. Qualitatively identical behaviors for 60% to 90% of the chemicals were observed in a completely different system, suggesting that other systems will be similarly affected by these chemicals. Additional analysis of the 10 chemicals in a recently described competition assay determined their kinetically defined mechanism and site of action. Some chemicals had similar mechanisms of action despite divergent effects on the level of the GR-induced product. These combined assays offer a straightforward method of identifying numerous new pharmaceuticals that can alter GR transactivation in ways that could be clinically useful.

  5. Ubiquitin-Activated Interaction Traps (UBAITs) identify E3 ligase binding partners.

    PubMed

    O'Connor, Hazel F; Lyon, Nancy; Leung, Justin W; Agarwal, Poonam; Swaim, Caleb D; Miller, Kyle M; Huibregtse, Jon M

    2015-12-01

    We describe a new class of reagents for identifying substrates, adaptors, and regulators of HECT and RING E3s. UBAITs (Ubiquitin-Activated Interaction Traps) are E3-ubiquitin fusion proteins and, in an E1- and E2-dependent manner, the C-terminal ubiquitin moiety forms an amide linkage to proteins that interact with the E3, enabling covalent co-purification of the E3 with partner proteins. We designed UBAITs for both HECT (Rsp5, Itch) and RING (Psh1, RNF126, RNF168) E3s. For HECT E3s, trapping of interacting proteins occurred in vitro either through an E3 thioester-linked lariat intermediate or through an E2 thioester intermediate, and both WT and active-site mutant UBAITs trapped known interacting proteins in yeast and human cells. Yeast Psh1 and human RNF126 and RNF168 UBAITs also trapped known interacting proteins when expressed in cells. Human RNF168 is a key mediator of ubiquitin signaling that promotes DNA double-strand break repair. Using the RNF168 UBAIT, we identify H2AZ--a histone protein involved in DNA repair--as a new target of this E3 ligase. These results demonstrate that UBAITs represent powerful tools for profiling a wide range of ubiquitin ligases.

  6. Balancing protein stability and activity in cancer: a new approach for identifying driver mutations affecting CBL ubiquitin ligase activation

    PubMed Central

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

    2015-01-01

    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 provide 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 did random non-cancer 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

  7. 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

  8. Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities

    PubMed Central

    Itakura, Haruka; Achrol, Achal S.; Mitchell, Lex A.; Loya, Joshua J.; Liu, Tiffany; Westbroek, Erick M.; Feroze, Abdullah H.; Rodriguez, Scott; Echegaray, Sebastian; Azad, Tej D.; Yeom, Kristen W.; Napel, Sandy; Rubin, Daniel L.; Chang, Steven D.; Harsh, Griffith R.; Gevaert, Olivier

    2015-01-01

    Glioblastoma (GBM) is the most common and highly lethal primary malignant brain tumor in adults. There is a dire need for easily accessible, noninvasive biomarkers that can delineate underlying molecular activities and predict response to therapy. To this end, we sought to identify subtypes of GBM, differentiated solely by quantitative MR imaging features, that could be used for better management of GBM patients. Quantitative image features capturing the shape, texture, and edge sharpness of each lesion were extracted from MR images of 121 patients with de novo, solitary, unilateral GBM. Three distinct phenotypic “clusters” emerged in the development cohort using consensus clustering with 10,000 iterations on these image features. These three clusters—pre-multifocal, spherical, and rim-enhancing, names reflecting their image features—were validated in an independent cohort consisting of 144 multi-institution patients with similar tumor characteristics from The Cancer Genome Atlas (TCGA). Each cluster mapped to a unique set of molecular signaling pathways using pathway activity estimates derived from analysis of TCGA tumor copy number and gene expression data with the PARADIGM algorithm. Distinct pathways, such as c-Kit and FOXA, were enriched in each cluster, indicating differential molecular activities as determined by image features. Each cluster also demonstrated differential probabilities of survival, indicating prognostic importance. Our imaging method offers a noninvasive approach to stratify GBM patients and also provides unique sets of molecular signatures to inform targeted therapy and personalized treatment of GBM. PMID:26333934

  9. Topographical Subcomponents of Electrical Brain Activity Allow to Identify Semantic Learning.

    PubMed

    Skrandies, Wolfgang; Shinoda, Haruo

    2017-03-03

    We investigated the change of event-related brain activity elicited by reading meaningful or meaningless Japanese symbols in 20 healthy German adults. In a learning phase of about 20 min, subjects acquired the meaning of 20 Kanji characters. As control stimuli 20 different Kanji characters were presented. Electrical brain activity was obtained before and after learning, The mean learning performance of all subjects was 92.5% correct responses. EEG was measured simultaneously from 30 channels, artifacts were removed offline, and the data before and after learning were compared. We found five spatial principal components that accounted for 83.8% of the variance. A significant interaction between training time (before/after learning) and stimulus (learning/control) illustrates a significant relation between successful learning and topographical changes of brain activity elicited by Kanji characters. Effects that were induced by learning were seen at short latencies in the order of 100 ms. In addition, we present evidence that differences in the weighted combination of spatial components allow to identify experimental conditions successfully by linear discriminant analysis using topographical ERP data of a single time point. In conclusion, semantic meaning can be aquired rapidly and it is associated with specific changes of ERP components.

  10. Genome-Wide Expression Profiling Identifies Type 1 Interferon Response Pathways in Active Tuberculosis

    PubMed Central

    Ottenhoff, Tom H. M.; Zhang, Mingzi M.; Wong, Hazel E. E.; Sahiratmadja, Edhyana; Khor, Chiea Chuen; Alisjahbana, Bachti; van Crevel, Reinout; Marzuki, Sangkot; Seielstad, Mark; van de Vosse, Esther; Hibberd, Martin L.

    2012-01-01

    Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains the leading cause of mortality from a single infectious agent. Each year around 9 million individuals newly develop active TB disease, and over 2 billion individuals are latently infected with M.tb worldwide, thus being at risk of developing TB reactivation disease later in life. The underlying mechanisms and pathways of protection against TB in humans, as well as the dynamics of the host response to M.tb infection, are incompletely understood. We carried out whole-genome expression profiling on a cohort of TB patients longitudinally sampled along 3 time-points: during active infection, during treatment, and after completion of curative treatment. We identified molecular signatures involving the upregulation of type-1 interferon (α/β) mediated signaling and chronic inflammation during active TB disease in an Indonesian population, in line with results from two recent studies in ethnically and epidemiologically different populations in Europe and South Africa. Expression profiles were captured in neutrophil-depleted blood samples, indicating a major contribution of lymphocytes and myeloid cells. Expression of type-1 interferon (α/β) genes mediated was also upregulated in the lungs of M.tb infected mice and in infected human macrophages. In patients, the regulated gene expression-signature normalized during treatment, including the type-1 interferon mediated signaling and a concurrent opposite regulation of interferon-gamma. Further analysis revealed IL15RA, UBE2L6 and GBP4 as molecules involved in the type-I interferon response in all three experimental models. Our data is highly suggestive that the innate immune type-I interferon signaling cascade could be used as a quantitative tool for monitoring active TB disease, and provide evidence that components of the patient’s blood gene expression signature bear similarities to the pulmonary and macrophage response to mycobacterial infection

  11. 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.

  12. Circuits constructed from identified Aplysia neurons exhibit multiple patterns of persistent activity.

    PubMed Central

    Kleinfeld, D; Raccuia-Behling, F; Chiel, H J

    1990-01-01

    We have used identified neurons from the abdominal ganglion of the mollusc Aplysia to construct and analyze two circuits in vitro. Each of these circuits was capable of producing two patterns of persistent activity; that is, they had bistable output states. The output could be switched between the stable states by a brief, external input. One circuit consisted of cocultured L10 and left upper quadrant (LUQ) neurons that formed reciprocal, inhibitory connections. In one stable state L10 was active and the LUQ was quiescent, whereas in the other stable state L10 was quiescent and the LUQ was active. A second circuit consisted of co-cultured L7 and L12 neurons that formed reciprocal, excitatory connections. In this circuit, both cells were quiescent in one stable state and both cells fired continuously in the other state. Bistable output in both circuits resulted from the nonlinear firing characteristics of each neuron and the feedback between the two neurons. We explored how the stability of the neuronal output could be controlled by the background currents injected into each neuron. We observed a relatively well-defined range of currents for which bistability occurred, consistent with the values expected from the measured strengths of the connections and a simple model. Outside of the range, the output was stable in only a single state. These results suggest how stable patterns of output are produced by some in vivo circuits and how command neurons from higher neural centers may control the activity of these circuits. The criteria that guided us in forming our circuits in culture were derived from theoretical studies on the properties of certain neuronal network models (e.g., Hopfield, J. J. 1984. Proc. Natl. Acad. Sci. USA. 81:3088-3092). Our results show that circuits consisting of only two co-cultured neurons can exhibit bistable output states of the form hypothesized to occur in populations of neurons. Images FIGURE 3 PMID:2344460

  13. 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

  14. 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

    2016-07-26

    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.

  15. Antimicrobial activity of the scolopendrasin V peptide identified from the centipede, Scolopendra subspinipes mutilans.

    PubMed

    Lee, Joon Ha; Kim, In-Woo; Kim, Mi-Ae; Ahn, Mi-Young; Yun, Eun-Young; Hwang, Jae Sam

    2016-10-25

    In a previous study, we analyzed the transcriptome of Scolopendra subspinipes mutilans using next generation sequencing technology and identified several antimicrobial peptide candidates. One of peptides, scolopendrasin V, was selected based on the physicochemical properties of antimicrobial peptides using a bioinformatics strategy. In this study, we assessed the antimicrobial activities of scolopendrasin V by using radial diffusion assay and colony count assay. We also investigated the mode of action of scolopendrasin V using flow cytometry. We found that scolopendrasin V's mechanism of action involved binding to the surface of microorganisms via a specific interaction with lipopolysaccharides, lipoteichoic acid, and peptidoglycans, which are components of the bacterial membrane. These results provide a basis for developing peptide antibiotics.

  16. 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.

  17. Functional measures developed for clinical populations identified impairment among active workers with upper extremity disorders

    PubMed Central

    Gardner, Bethany T.; Dale, Ann Marie; Buckner-Petty, Skye; Rachford, Robert; Strickland, Jaime; Kaskutas, Vicki; Evanoff, Bradley

    2017-01-01

    Purpose Few studies have explored measures of function across a range of health outcomes in a general working population. Using four upper extremity (UE) case definitions from the scientific literature, we described the performance of functional measures of work, activities of daily living, and overall health. Methods A sample of 573 workers completed several functional measures: modified recall versions of the QuickDASH, Levine Functional Status Scale (FSS), DASH Work module (DASH-W), and standard SF-8 physical component score. We determined case status based on four UE case definitions: 1) UE symptoms, 2) UE musculoskeletal disorders (MSD), 3) carpal tunnel syndrome (CTS), and 4) work limitations due to UE symptoms. We calculated effect sizes for each case definition to show the magnitude of the differences that were detected between cases and non-cases for each case definition on each functional measure. Sensitivity and specificity analyses showed how well each measure identified functional impairments across the UE case definitions. Results All measures discriminated between cases and non-cases for each case definition with the largest effect sizes for CTS and work limitations, particularly for the modified FSS and DASH-W measures. Specificity was high and sensitivity was low for outcomes of UE symptoms and UE MSD in all measures. Sensitivity was high for CTS and work limitations. Conclusions Functional measures developed specifically for use in clinical, treatment-seeking populations may identify mild levels of impairment in relatively healthy, active working populations, but measures performed better among workers with CTS or those reporting limitations at work. PMID:26091980

  18. Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo

    PubMed Central

    Jiang, Yue; Gong, Naihua Natalie; Hu, Xiaoyang Serene; Ni, Mengjue Jessica; Pasi, Radhika

    2015-01-01

    The mammalian olfactory system uses a large family of odorant receptors to detect and discriminate amongst a myriad of volatile odor molecules. Understanding odor coding requires comprehensive mapping between odorant receptors and corresponding odors. Here we present high–throughput in vivo identification of odorant receptor repertoires responding to odorants, using phosphorylated ribosome immunoprecipitation of mRNA from olfactory epithelium of odor–stimulated mice followed by RNA–Seq. This approach screens the endogenously expressed odorant receptors against an odor in one set of experiments, using awake and freely behaving mice. In combination with validations in a heterologous system, we identify sets of odorant receptors for two odorants, acetophenone and 2,5–dihydro–2,4,5–trimethylthiazoline (TMT), encompassing 69 odorant receptor–odorant pairs. We also identified shared amino acid residues specific to the acetophenone or TMT receptors, and developed models to predict receptor activation by acetophenone. This study provides a means to understand the combinatorial coding of odors in vivo. PMID:26322927

  19. A High-Throughput Screen Identifies a New Natural Product with Broad-Spectrum Antibacterial Activity

    PubMed Central

    Ymele-Leki, Patrick; Cao, Shugeng; Sharp, Jared; Lambert, Kathleen G.; McAdam, Alexander J.; Husson, Robert N.; Tamayo, Giselle; Clardy, Jon; Watnick, Paula I.

    2012-01-01

    Due to the inexorable invasion of our hospitals and communities by drug-resistant bacteria, there is a pressing need for novel antibacterial agents. Here we report the development of a sensitive and robust but low-tech and inexpensive high-throughput metabolic screen for novel antibiotics. This screen is based on a colorimetric assay of pH that identifies inhibitors of bacterial sugar fermentation. After validation of the method, we screened over 39,000 crude extracts derived from organisms that grow in the diverse ecosystems of Costa Rica and identified 49 with reproducible antibacterial effects. An extract from an endophytic fungus was further characterized, and this led to the discovery of three novel natural products. One of these, which we named mirandamycin, has broad-spectrum antibacterial activity against Escherichia coli, Pseudomonas aeruginosa, Vibrio cholerae, methicillin-resistant Staphylococcus aureus, and Mycobacterium tuberculosis. This demonstrates the power of simple high throughput screens for rapid identification of new antibacterial agents from environmental samples. PMID:22359585

  20. 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

  1. Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity.

    PubMed

    D'Angelo, Rosemarie C; Ouzounova, Maria; Davis, April; Choi, Daejin; Tchuenkam, Stevie M; Kim, Gwangil; Luther, Tahra; Quraishi, Ahmed A; Senbabaoglu, Yasin; Conley, Sarah J; Clouthier, Shawn G; Hassan, Khaled A; Wicha, Max S; Korkaya, Hasan

    2015-03-01

    Developmental pathways such as Notch play a pivotal role in tissue-specific stem cell self-renewal as well as in tumor development. However, the role of Notch signaling in breast cancer stem cells (CSC) remains to be determined. We utilized a lentiviral Notch reporter system to identify a subset of cells with a higher Notch activity (Notch(+)) or reduced activity (Notch(-)) in multiple breast cancer cell lines. Using in vitro and mouse xenotransplantation assays, we investigated the role of the Notch pathway in breast CSC regulation. Breast cancer cells with increased Notch activity displayed increased sphere formation as well as expression of breast CSC markers. Interestingly Notch(+) cells displayed higher Notch4 expression in both basal and luminal breast cancer cell lines. Moreover, Notch(+) cells demonstrated tumor initiation capacity at serial dilutions in mouse xenografts, whereas Notch(-) cells failed to generate tumors. γ-Secretase inhibitor (GSI), a Notch blocker but not a chemotherapeutic agent, effectively targets these Notch(+) cells in vitro and in mouse xenografts. Furthermore, elevated Notch4 and Hey1 expression in primary patient samples correlated with poor patient survival. Our study revealed a molecular mechanism for the role of Notch-mediated regulation of breast CSCs and provided a compelling rationale for CSC-targeted therapeutics.

  2. Notch reporter activity in breast cancer cell lines identifies a subset of cells with stem cell activity

    PubMed Central

    Davis, April; Choi, Daejin; Tchuenkam, Stevie M.; Kim, Gwangil; Luther, Tahra; Quraishi, Ahmed A.; Senbabaoglu, Yasin; Conley, Sarah J.; Clouthier, Shawn G.; Hassan, Khaled A.; Wicha, Max S.; Korkaya, Hasan

    2015-01-01

    Developmental pathways such as Notch play a pivotal role in tissue specific stem cell self-renewal as well as in tumor development. However, the role of Notch signaling in breast cancer stem cells (CSC) remains to be determined. We utilized a lentiviral Notch reporter system to identify a subset of cells with a higher Notch activity (Notch+) or reduced activity (Notch-) in multiple breast cancer cell lines. Using in vitro and mouse xenotransplantation assays we investigated the role of Notch pathway in breast CSC regulation. Breast cancer cells with increased Notch activity displayed increased sphere formation as well as expression of breast CSC markers. Interestingly Notch+ cells displayed higher Notch4 expression in both basal and luminal breast cancer cell lines. Moreover, Notch+ cells demonstrated tumor initiation capacity at serial dilutions in mouse xenografts while Notch- cells failed to generate tumors. Gamma-secretase inhibitor (GSI), a Notch blocker but not a chemotherapeutic agent effectively targets these Notch+ cells in vitro and in mouse xenografts. Furthermore, elevated Notch4 and Hey1 expression in primary patient samples correlated with poor patient survival. Our studies reveal molecular mechanism for the role of Notch mediated regulation of breast CSCs and provide a compelling rationale for CSC targeted therapeutics. PMID:25673823

  3. Ubiquitination and regulation of AURKA identifies a hypoxia-independent E3 ligase activity of VHL.

    PubMed

    Hasanov, E; Chen, G; Chowdhury, P; Weldon, J; Ding, Z; Jonasch, E; Sen, S; Walker, C L; Dere, R

    2017-01-23

    The hypoxia-regulated tumor-suppressor von Hippel-Lindau (VHL) is an E3 ligase that recognizes its substrates as part of an oxygen-dependent prolyl hydroxylase (PHD) reaction, with hypoxia-inducible factor α (HIFα) being its most notable substrate. Here we report that VHL has an equally important function distinct from its hypoxia-regulated activity. We find that Aurora kinase A (AURKA) is a novel, hypoxia-independent target for VHL ubiquitination. In contrast to its hypoxia-regulated activity, VHL mono-, rather than poly-ubiquitinates AURKA, in a PHD-independent reaction targeting AURKA for degradation in quiescent cells, where degradation of AURKA is required to maintain the primary cilium. Tumor-associated variants of VHL differentiate between these two functions, as a pathogenic VHL mutant that retains intrinsic ability to ubiquitinate HIFα is unable to ubiquitinate AURKA. Together, these data identify VHL as an E3 ligase with important cellular functions under both normoxic and hypoxic conditions.Oncogene advance online publication, 23 January 2017; doi:10.1038/onc.2016.495.

  4. Exome and genome sequencing of nasopharynx cancer identifies NF-κB pathway activating mutations

    PubMed Central

    Li, Yvonne Y; Chung, Grace T. Y.; Lui, Vivian W. Y.; To, Ka-Fai; Ma, Brigette B. Y.; Chow, Chit; Woo, John K, S.; Yip, Kevin Y.; Seo, Jeongsun; Hui, Edwin P.; Mak, Michael K. F.; Rusan, Maria; Chau, Nicole G.; Or, Yvonne Y. Y.; Law, Marcus H. N.; Law, Peggy P. Y.; Liu, Zoey W. Y.; Ngan, Hoi-Lam; Hau, Pok-Man; Verhoeft, Krista R.; Poon, Peony H. Y.; Yoo, Seong-Keun; Shin, Jong-Yeon; Lee, Sau-Dan; Lun, Samantha W. M.; Jia, Lin; Chan, Anthony W. H.; Chan, Jason Y. K.; Lai, Paul B. S.; Fung, Choi-Yi; Hung, Suet-Ting; Wang, Lin; Chang, Ann Margaret V.; Chiosea, Simion I.; Hedberg, Matthew L.; Tsao, Sai-Wah; van Hasselt, Andrew C.; Chan, Anthony T. C.; Grandis, Jennifer R.; Hammerman, Peter S.; Lo, Kwok-Wai

    2017-01-01

    Nasopharyngeal carcinoma (NPC) is an aggressive head and neck cancer characterized by Epstein-Barr virus (EBV) infection and dense lymphocyte infiltration. The scarcity of NPC genomic data hinders the understanding of NPC biology, disease progression and rational therapy design. Here we performed whole-exome sequencing (WES) on 111 micro-dissected EBV-positive NPCs, with 15 cases subjected to further whole-genome sequencing (WGS), to determine its mutational landscape. We identified enrichment for genomic aberrations of multiple negative regulators of the NF-κB pathway, including CYLD, TRAF3, NFKBIA and NLRC5, in a total of 41% of cases. Functional analysis confirmed inactivating CYLD mutations as drivers for NPC cell growth. The EBV oncoprotein latent membrane protein 1 (LMP1) functions to constitutively activate NF-κB signalling, and we observed mutual exclusivity among tumours with somatic NF-κB pathway aberrations and LMP1-overexpression, suggesting that NF-κB activation is selected for by both somatic and viral events during NPC pathogenesis. PMID:28098136

  5. Disease Combinations Associated with Physical Activity Identified: The SMILE Cohort Study

    PubMed Central

    Dörenkamp, Sarah; Mesters, Ilse; Schepers, Jan; Vos, Rein; van den Akker, Marjan; Teijink, Joep; de Bie, Rob

    2016-01-01

    In the search of predictors of inadequate physical activity, an investigation was conducted into the association between multimorbidity and physical activity (PA). So far the sum of diseases used as a measure of multimorbidity reveals an inverse association. How specific combinations of chronic diseases are associated with PA remains unclear. The objective of this study is to identify clusters of multimorbidity that are associated with PA. Cross-sectional data of 3,386 patients from the 2003 wave of the Dutch cohort study SMILE were used. Ward's agglomerative hierarchical clustering was executed to establish multimorbidity clusters. Chi-square statistics were used to assess the association between clusters of chronic diseases and PA, measured in compliance with the Dutch PA guideline. The highest rate of PA guideline compliance was found in patients the majority of whom suffer from liver disease, back problems, rheumatoid arthritis, osteoarthritis, and inflammatory joint disease (62.4%). The lowest rate of PA guideline compliance was reported in patients with heart disease, respiratory disease, and diabetes mellitus (55.8%). Within the group of people with multimorbidity, those suffering from heart disease, respiratory disease, and/or diabetes mellitus may constitute a priority population as PA has proven to be effective in the prevention and cure of all three disorders. PMID:26881231

  6. Identifying active faults in Switzerland using relocated earthquake catalogs and optimal anisotropic dynamic clustering

    NASA Astrophysics Data System (ADS)

    Wagner, M.; Wang, Y.; Husen, S.; Woessner, J.; Kissling, E. H.; Ouillon, G.; Giardini, D.; Sornette, D.

    2010-12-01

    Active fault zones are the causal locations of most earthquakes, which release tectonic stresses. Yet, identification and association of faults and earthquakes is not straightforward. On the one hand, many earthquakes occur on faults that are unknown. On the other hand, systematic biases and uncertainties in earthquake locations hamper the association of earthquakes and known faults. We tackle the problem of linking earthquakes to faults by relocating them in a non-linear probabilistic manner and by applying a three-dimensional optimal anisotropic dynamic clustering approach to the relocated events to map fault networks. Non-linear probabilistic earthquake location allows to compute probability density functions that provide the complete probabilistic solution to the earthquake hypocenter location problem, including improved information on location uncertainties. To improve absolute earthquake locations we use a newly developed combined controlled-source seismology and local earthquake tomography model, which allows the use of secondary phases, such as PmP. Dynamic clustering is a very general image processing technique that allows partitioning a set of data points. Our improved optimal anisotropic dynamic clustering technique accounts for uncertainties in earthquake locations by the use of probability density functions, as provided by non-linear probabilistic earthquake location. Hence, number and size of the reconstructed faults is controlled by earthquake location uncertainty. We apply our approach to seismicity in Switzerland to identify active faults in the region. Relocated earthquake catalogs and associated fault networks will be compared to already existing information on faults, such as geological and seismotectonic maps, to derive a more complete picture of active faulting in Switzerland.

  7. 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.

  8. Feeding by the heterotrophic dinoflagellate Oxyrrhis marina on the red-tide raphidophyte Heterosigma akashiwo: a potential biological method to control red tides using mass-cultured grazers.

    PubMed

    Jeong, Hae Jin; Kim, Jae Seong; Yoo, Yeong Du; Kim, Seong Taek; Kim, Tae Hoon; Park, Myung Gil; Lee, Chang Hoon; Seong, Kyeong Ah; Kang, Nam Seon; Shim, Jae Hyung

    2003-01-01

    As part of the development of a method to control the outbreak and persistence of red tides using mass-cultured heterotrophic protist grazers, we measured the growth and ingestion rates of cultured Oxyrrhis marina (a heterotrophic dinoflagellate) on cultured Heterosigma akashiwo (a raphidophyte) in bottles in the laboratory and in mesocosms (ca. 60 liter) in nature, and those of the cultured grazer on natural populations of the red-tide organism in mesocosms set up in nature. In the bottle incubation, specific growth rates of O. marina increased rapidly with increasing concentration of cultured prey up to ca. 950 ng C ml(-1) (equivalent to 9,500 cells ml(-1)), but were saturated at higher concentrations. Maximum specific growth rate (mumax), KGR (prey concentration sustaining 0.5 mumax) and threshold prey concentration of O. marina on H. akashiwo were 1.43 d(-1), 104 ng C ml(-1), and 8.0 ng C ml(-1), respectively. Maximum ingestion and clearance rates of O. marina were 1.27 ng C grazer(-1) d(-1) and 0.3 microl grazer(-1) h(-1), respectively. Cultured O. marina grew well effectively reducing cultured and natural populations of H. akashiwo down to a very low concentration within 3 d in the mesocosms. The growth and ingestion rates of cultured O. marina on natural populations of H. akashiwo in the mesocosms were 39% and 40%, respectively, of those calculated based on the results from the bottle incubation in the laboratory, while growth and ingestion rates of cultured O. marina on cultured H. akashiwo in the mesocosms were 55% and 36%, respectively. Calculated grazing impact by O. marina on natural populations of H. akashiwo suggests that O. marina cultured on a large scale could be used for controlling red tides by H. akashiwo near aquaculture farms that are located in small ponds, lagoons, semi-enclosed bays, and large land-aqua tanks to which fresh seawater should be frequently supplied.

  9. 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

  10. 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

  11. Identifying a Selective Substrate and Inhibitor Pair for the Evaluation of CYP2J2 Activity

    PubMed Central

    Lee, Caroline A.; Jones, J. P.; Katayama, Jonathan; Kaspera, Rüdiger; Jiang, Ying; Freiwald, Sascha; Smith, Evan; Walker, Gregory S.

    2012-01-01

    CYP2J2, an arachidonic acid epoxygenase, is recognized for its role in the first-pass metabolism of astemizole and ebastine. To fully assess the role of CYP2J2 in drug metabolism, a selective substrate and potent specific chemical inhibitor are essential. In this study, we report amiodarone 4-hydoxylation as a specific CYP2J2-catalyzed reaction with no CYP3A4, or other drug-metabolizing enzyme, involvement. Amiodarone 4-hydroxylation enabled the determination of liver relative activity factor and intersystem extrapolation factor for CYP2J2. Amiodarone 4-hydroxylation correlated with astemizole O-demethylation but not with CYP2J2 protein content in a sample of human liver microsomes. To identify a specific CYP2J2 inhibitor, 138 drugs were screened using terfenadine and astemizole as probe substrates with recombinant CYP2J2. Forty-two drugs inhibited CYP2J2 activity by ≥50% at 30 μM, but inhibition was substrate-dependent. Of these, danazol was a potent inhibitor of both hydroxylation of terfenadine (IC50 = 77 nM) and O-demethylation of astemizole (Ki = 20 nM), and inhibition was mostly competitive. Danazol inhibited CYP2C9, CYP2C8, and CYP2D6 with IC50 values of 1.44, 1.95, and 2.74 μM, respectively. Amiodarone or astemizole were included in a seven-probe cocktail for cytochrome P450 (P450) drug-interaction screening potential, and astemizole demonstrated a better profile because it did not appreciably interact with other P450 probes. Thus, danazol, amiodarone, and astemizole will facilitate the ability to determine the metabolic role of CYP2J2 in hepatic and extrahepatic tissues. PMID:22328583

  12. Identifying a selective substrate and inhibitor pair for the evaluation of CYP2J2 activity.

    PubMed

    Lee, Caroline A; Jones, J P; Katayama, Jonathan; Kaspera, Rüdiger; Jiang, Ying; Freiwald, Sascha; Smith, Evan; Walker, Gregory S; Totah, Rheem A

    2012-05-01

    CYP2J2, an arachidonic acid epoxygenase, is recognized for its role in the first-pass metabolism of astemizole and ebastine. To fully assess the role of CYP2J2 in drug metabolism, a selective substrate and potent specific chemical inhibitor are essential. In this study, we report amiodarone 4-hydoxylation as a specific CYP2J2-catalyzed reaction with no CYP3A4, or other drug-metabolizing enzyme, involvement. Amiodarone 4-hydroxylation enabled the determination of liver relative activity factor and intersystem extrapolation factor for CYP2J2. Amiodarone 4-hydroxylation correlated with astemizole O-demethylation but not with CYP2J2 protein content in a sample of human liver microsomes. To identify a specific CYP2J2 inhibitor, 138 drugs were screened using terfenadine and astemizole as probe substrates with recombinant CYP2J2. Forty-two drugs inhibited CYP2J2 activity by ≥50% at 30 μM, but inhibition was substrate-dependent. Of these, danazol was a potent inhibitor of both hydroxylation of terfenadine (IC(50) = 77 nM) and O-demethylation of astemizole (K(i) = 20 nM), and inhibition was mostly competitive. Danazol inhibited CYP2C9, CYP2C8, and CYP2D6 with IC(50) values of 1.44, 1.95, and 2.74 μM, respectively. Amiodarone or astemizole were included in a seven-probe cocktail for cytochrome P450 (P450) drug-interaction screening potential, and astemizole demonstrated a better profile because it did not appreciably interact with other P450 probes. Thus, danazol, amiodarone, and astemizole will facilitate the ability to determine the metabolic role of CYP2J2 in hepatic and extrahepatic tissues.

  13. 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

  14. 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

  15. 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

  16. Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes.

    PubMed

    Liu, Xianpeng; Zhao, Bo; Sun, Limin; Bhuripanyo, Karan; Wang, Yiyang; Bi, Yingtao; Davuluri, Ramana V; Duong, Duc M; Nanavati, Dhaval; Yin, Jun; Kiyokawa, Hiroaki

    2017-01-30

    Protein ubiquitination is mediated sequentially by ubiquitin activating enzyme E1, ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. Uba1 was thought to be the only E1 until the recent identification of Uba6. To differentiate the biological functions of Uba1 and Uba6, we applied an orthogonal ubiquitin transfer (OUT) technology to profile their ubiquitination targets in mammalian cells. By expressing pairs of an engineered ubiquitin and engineered Uba1 or Uba6 that were generated for exclusive interactions, we identified 697 potential Uba6 targets and 527 potential Uba1 targets with 258 overlaps. Bioinformatics analysis reveals substantial differences in pathways involving Uba1- and Uba6-specific targets. We demonstrate that polyubiquitination and proteasomal degradation of ezrin and CUGBP1 require Uba6, but not Uba1, and that Uba6 is involved in the control of ezrin localization and epithelial morphogenesis. These data suggest that distinctive substrate pools exist for Uba1 and Uba6 that reflect non-redundant biological roles for Uba6.

  17. 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.

  18. Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes

    PubMed Central

    Liu, Xianpeng; Zhao, Bo; Sun, Limin; Bhuripanyo, Karan; Wang, Yiyang; Bi, Yingtao; Davuluri, Ramana V.; Duong, Duc M.; Nanavati, Dhaval; Yin, Jun; Kiyokawa, Hiroaki

    2017-01-01

    Protein ubiquitination is mediated sequentially by ubiquitin activating enzyme E1, ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. Uba1 was thought to be the only E1 until the recent identification of Uba6. To differentiate the biological functions of Uba1 and Uba6, we applied an orthogonal ubiquitin transfer (OUT) technology to profile their ubiquitination targets in mammalian cells. By expressing pairs of an engineered ubiquitin and engineered Uba1 or Uba6 that were generated for exclusive interactions, we identified 697 potential Uba6 targets and 527 potential Uba1 targets with 258 overlaps. Bioinformatics analysis reveals substantial differences in pathways involving Uba1- and Uba6-specific targets. We demonstrate that polyubiquitination and proteasomal degradation of ezrin and CUGBP1 require Uba6, but not Uba1, and that Uba6 is involved in the control of ezrin localization and epithelial morphogenesis. These data suggest that distinctive substrate pools exist for Uba1 and Uba6 that reflect non-redundant biological roles for Uba6. PMID:28134249

  19. 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

  20. 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

  1. Structure-activity relationship study around guanabenz identifies two derivatives retaining antiprion activity but having lost α2-adrenergic receptor agonistic activity.

    PubMed

    Nguyen, Phu Hai; Hammoud, Hassan; Halliez, Sophie; Pang, Yanhong; Evrard, Justine; Schmitt, Martine; Oumata, Nassima; Bourguignon, Jean-Jacques; Sanyal, Suparna; Beringue, Vincent; Blondel, Marc; Bihel, Frédéric; Voisset, Cécile

    2014-10-15

    Guanabenz (GA) is an orally active α2-adrenergic agonist that has been used for many years for the treatment of hypertension. We recently described that GA is also active against both yeast and mammalian prions in an α2-adrenergic receptor-independent manner. These data suggest that this side-activity of GA could be explored for the treatment of prion-based diseases and other amyloid-based disorders. In this perspective, the potent antihypertensive activity of GA happens to be an annoying side-effect that could limit its use. In order to get rid of GA agonist activity at α2-adrenergic receptors, we performed a structure-activity relationship study around GA based on changes of the chlorine positions on the benzene moiety and then on the modifications of the guanidine group. Hence, we identified the two derivatives 6 and 7 that still possess a potent antiprion activity but were totally devoid of any agonist activity at α2-adrenergic receptors. Similarly to GA, 6 and 7 were also able to inhibit the protein folding activity of the ribosome (PFAR) which has been suggested to be involved in prion appearance/maintenance. Therefore, these two GA derivatives are worth being considered as drug candidates.

  2. Identifying Luminous Active Galactic Nuclei in Deep Surveys: Revised IRAC Selection Criteria

    NASA Astrophysics Data System (ADS)

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

    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 2-10 keV(erg s-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 H (cm-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.

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. Using Model-Eliciting Activities as a Tool to Identify and Develop Mathematically Creative Students

    ERIC Educational Resources Information Center

    Coxbill, Emmy; Chamberlin, Scott A.; Weatherford, Jennifer

    2013-01-01

    Traditional classroom methods for identifying mathematically creative students have been inadequate. Identifying students who could potentially be mathematically creative is instrumental in the development of students and in meeting their affective and educational needs. One prospective identification tool is the use of model-eliciting activities…

  10. 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…

  11. 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…

  12. 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…

  13. 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

  14. 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…

  15. 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…

  16. [Creation and validation of an instrument to identify nursing activities in pediatric wards: information for determining workload].

    PubMed

    Santos, Nanci Cristiano; Fugulin, Fernanda Maria Togeiro

    2013-10-01

    The aim of this study was to develop and validate an instrument for identifying nursing activities performed in a pediatric ward and to provide a basis for defining the workload of these units. The instrument was developed by selecting the activities relevant to pediatric nursing from the Nursing Intervention Classification and then submitting them to a panel of judges for validation. The panel considered the selected activities relevant and representative of pediatric nursing practice. Now that representative activities for the nursing workload have been identified, we envision new studies to verify their usefulness in practice. Determining the amount of time each activity takes to perform will help to develop a system for measuring the workloads of nursing teams in pediatric wards.

  17. PM2: a partitioning-mining-measuring method for identifying progressive changes in older adults' sleeping activity.

    PubMed

    Lin, Qiang; Zhang, Daqing; Connelly, Kay; Zhou, Xingshe; Ni, Hongbo

    2014-01-01

    As people age, their health typically declines, resulting in difficulty in performing daily activities. Sleep-related problems are common issues with older adults, including shifts in circadian rhythms. A detection method is proposed to identify progressive changes in sleeping activity using a three-step process: partitioning, mining, and measuring. Specifically, the original spatiotemporal representation of each sleeping activity instance was first transformed into a sequence of equal-sized segments, or symbols, via a partitioning process. A data-mining-based algorithm was proposed to find symbols that are not present in all instances of a sleeping activity. Finally, a measuring process was responsible for evaluating the changes in these symbols. Experimental evaluation conducted on a group of datasets of older adults showed that the proposed method is able to identify progressive changes in sleeping activity.

  18. 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.

  19. 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.

  20. Identifying Active Travel Behaviors in Challenging Environments Using GPS, Accelerometers, and Machine Learning Algorithms

    PubMed Central

    Ellis, Katherine; Godbole, Suneeta; Marshall, Simon; Lanckriet, Gert; Staudenmayer, John; Kerr, Jacqueline

    2014-01-01

    Background: Active travel is an important area in physical activity research, but objective measurement of active travel is still difficult. Automated methods to measure travel behaviors will improve research in this area. In this paper, we present a supervised machine learning method for transportation mode prediction from global positioning system (GPS) and accelerometer data. Methods: We collected a dataset of about 150 h of GPS and accelerometer data from two research assistants following a protocol of prescribed trips consisting of five activities: bicycling, riding in a vehicle, walking, sitting, and standing. We extracted 49 features from 1-min windows of this data. We compared the performance of several machine learning algorithms and chose a random forest algorithm to classify the transportation mode. We used a moving average output filter to smooth the output predictions over time. Results: The random forest algorithm achieved 89.8% cross-validated accuracy on this dataset. Adding the moving average filter to smooth output predictions increased the cross-validated accuracy to 91.9%. Conclusion: Machine learning methods are a viable approach for automating measurement of active travel, particularly for measuring travel activities that traditional accelerometer data processing methods misclassify, such as bicycling and vehicle travel. PMID:24795875

  1. 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

  2. Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity

    PubMed Central

    Mathew, Mark D.; Mathew, Neal D.; Miller, Angela; Simpson, Mike; Au, Vinci; Garland, Stephanie; Gestin, Marie; Edgley, Mark L.; Flibotte, Stephane; Balgi, Aruna; Chiang, Jennifer; Giaever, Guri; Dean, Pamela; Tung, Audrey; Roberge, Michel; Roskelley, Calvin; Forge, Tom; Nislow, Corey; Moerman, Donald

    2016-01-01

    Background The lack of new anthelmintic agents is of growing concern because it affects human health and our food supply, as both livestock and plants are affected. Two principal factors contribute to this problem. First, nematode resistance to anthelmintic drugs is increasing worldwide and second, many effective nematicides pose environmental hazards. In this paper we address this problem by deploying a high throughput screening platform for anthelmintic drug discovery using the nematode Caenorhabditis elegans as a surrogate for infectious nematodes. This method offers the possibility of identifying new anthelmintics in a cost-effective and timely manner. Methods/Principal findings Using our high throughput screening platform we have identified 14 new potential anthelmintics by screening more than 26,000 compounds from the Chembridge and Maybridge chemical libraries. Using phylogenetic profiling we identified a subset of the 14 compounds as potential anthelmintics based on the relative sensitivity of C. elegans when compared to yeast and mammalian cells in culture. We showed that a subset of these compounds might employ mechanisms distinct from currently used anthelmintics by testing diverse drug resistant strains of C. elegans. One of these newly identified compounds targets mitochondrial complex II, and we used structural analysis of the target to suggest how differential binding of this compound may account for its different effects in nematodes versus mammalian cells. Conclusions/Significance The challenge of anthelmintic drug discovery is exacerbated by several factors; including, 1) the biochemical similarity between host and parasite genomes, 2) the geographic location of parasitic nematodes and 3) the rapid development of resistance. Accordingly, an approach that can screen large compound collections rapidly is required. C. elegans as a surrogate parasite offers the ability to screen compounds rapidly and, equally importantly, with specificity, thus

  3. Use of cells expressing gamma subunit variants to identify diverse mechanisms of AMPK activation.

    PubMed

    Hawley, Simon A; Ross, Fiona A; Chevtzoff, Cyrille; Green, Kevin A; Evans, Ashleigh; Fogarty, Sarah; Towler, Mhairi C; Brown, Laura J; Ogunbayo, Oluseye A; Evans, A Mark; Hardie, D Grahame

    2010-06-09

    A wide variety of agents activate AMPK, but in many cases the mechanisms remain unclear. We generated isogenic cell lines stably expressing AMPK complexes containing AMP-sensitive (wild-type, WT) or AMP-insensitive (R531G) gamma2 variants. Mitochondrial poisons such as oligomycin and dinitrophenol only activated AMPK in WT cells, as did AICAR, 2-deoxyglucose, hydrogen peroxide, metformin, phenformin, galegine, troglitazone, phenobarbital, resveratrol, and berberine. Excluding AICAR, all of these also inhibited cellular energy metabolism, shown by increases in ADP:ATP ratio and/or by decreases in cellular oxygen uptake measured using an extracellular flux analyzer. By contrast, A769662, the Ca(2+) ionophore, A23187, osmotic stress, and quercetin activated both variants to varying extents. A23187 and osmotic stress also increased cytoplasmic Ca(2+), and their effects were inhibited by STO609, a CaMKK inhibitor. Our approaches distinguish at least six different mechanisms for AMPK activation and confirm that the widely used antidiabetic drug metformin activates AMPK by inhibiting mitochondrial respiration.

  4. 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

  5. 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

  6. Combined rational design and a high throughput screening platform for identifying chemical inhibitors of a Ras-activating enzyme.

    PubMed

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

    2015-05-15

    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.

  7. 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…

  8. 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...

  9. 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...

  10. 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…

  11. Proteomics-Identified Bvg-Activated Autotransporters Protect against Bordetella pertussis in a Mouse Model

    PubMed Central

    de Gouw, Daan; Jonge, Marien I. de.; Hermans, Peter W. M.; Wessels, Hans J. C. T.; Zomer, Aldert; Berends, Alinda; Pratt, Catherine; Berbers, Guy A.; Mooi, Frits R.; Diavatopoulos, Dimitri A.

    2014-01-01

    Pertussis is a highly infectious respiratory disease of humans caused by the bacterium Bordetella pertussis. Despite high vaccination coverage, pertussis has re-emerged globally. Causes for the re-emergence of pertussis include limited duration of protection conferred by acellular pertussis vaccines (aP) and pathogen adaptation. Pathogen adaptations involve antigenic divergence with vaccine strains, the emergence of strains which show enhanced in vitro expression of a number of virulence-associated genes and of strains that do not express pertactin, an important aP component. Clearly, the identification of more effective B. pertussis vaccine antigens is of utmost importance. To identify novel antigens, we used proteomics to identify B. pertussis proteins regulated by the master virulence regulatory system BvgAS in vitro. Five candidates proteins were selected and it was confirmed that they were also expressed in the lungs of naïve mice seven days after infection. The five proteins were expressed in recombinant form, adjuvanted with alum and used to immunize mice as stand-alone antigens. Subsequent respiratory challenge showed that immunization with the autotransporters Vag8 and SphB1 significantly reduced bacterial load in the lungs. Whilst these antigens induced strong opsonizing antibody responses, we found that none of the tested alum-adjuvanted vaccines - including a three-component aP - reduced bacterial load in the nasopharynx, suggesting that alternative immunological responses may be required for efficient bacterial clearance from the nasopharynx. PMID:25133400

  12. Proteomics-identified Bvg-activated autotransporters protect against bordetella pertussis in a mouse model.

    PubMed

    de Gouw, Daan; Gouw, Daan de; de Jonge, Marien I; Jonge, Marien I de; Hermans, Peter W M; Wessels, Hans J C T; Zomer, Aldert; Berends, Alinda; Pratt, Catherine; Berbers, Guy A; Mooi, Frits R; Diavatopoulos, Dimitri A

    2014-01-01

    Pertussis is a highly infectious respiratory disease of humans caused by the bacterium Bordetella pertussis. Despite high vaccination coverage, pertussis has re-emerged globally. Causes for the re-emergence of pertussis include limited duration of protection conferred by acellular pertussis vaccines (aP) and pathogen adaptation. Pathogen adaptations involve antigenic divergence with vaccine strains, the emergence of strains which show enhanced in vitro expression of a number of virulence-associated genes and of strains that do not express pertactin, an important aP component. Clearly, the identification of more effective B. pertussis vaccine antigens is of utmost importance. To identify novel antigens, we used proteomics to identify B. pertussis proteins regulated by the master virulence regulatory system BvgAS in vitro. Five candidates proteins were selected and it was confirmed that they were also expressed in the lungs of naïve mice seven days after infection. The five proteins were expressed in recombinant form, adjuvanted with alum and used to immunize mice as stand-alone antigens. Subsequent respiratory challenge showed that immunization with the autotransporters Vag8 and SphB1 significantly reduced bacterial load in the lungs. Whilst these antigens induced strong opsonizing antibody responses, we found that none of the tested alum-adjuvanted vaccines - including a three-component aP - reduced bacterial load in the nasopharynx, suggesting that alternative immunological responses may be required for efficient bacterial clearance from the nasopharynx.

  13. Identifying key areas for active interprofessional learning partnerships: A facilitated dialogue.

    PubMed

    Steven, Kathryn; Angus, Allyson; Breckenridge, Jenna; Davey, Peter; Tully, Vicki; Muir, Fiona

    2016-11-01

    Student and service user involvement is recognised as an important factor in creating interprofessional education (IPE) opportunities. We used a team-based learning approach to bring together undergraduate health professional students, early career professionals (ECPs), public partners, volunteers, and carers to explore learning partnerships. Influenced by evaluative inquiry, this qualitative study used a free text response to allow participants to give their own opinion. A total of 153 participants (50 public partners and 103 students and professionals representing 11 healthcare professions) took part. Participants were divided into mixed groups of six (n = 25) and asked to identify areas where students, professionals, and public could work together to improve health professional education. Each group documented their discussions by summarising agreed areas and next steps. Responses were collected and transcribed for inductive content analysis. Seven key themes (areas for joint working) were identified: communication, public as partners, standards of conduct, IPE, quality improvement, education, and learning environments. The team-based learning format enabled undergraduate and postgraduate health professionals to achieve consensus with public partners on areas for IPE and collaboration. Some of our results may be context-specific but the approach is generalisable to other areas.

  14. 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

  15. 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.

  16. Impaired antigen presentation and potent phagocytic activity identifying tumor-tolerant human monocytes.

    PubMed

    Soares-Schanoski, Alessandra; Jurado, Teresa; Córdoba, Raúl; Siliceo, María; Fresno, Carlos Del; Gómez-Piña, Vanesa; Toledano, Victor; Vallejo-Cremades, Maria T; Alfonso-Iñiguez, Sergio; Carballo-Palos, Arkaitz; Fernández-Ruiz, Irene; Cubillas-Zapata, Carolina; Biswas, Subhra K; Arnalich, Francisco; García-Río, Francisco; López-Collazo, Eduardo

    2012-06-29

    Monocyte exposure to tumor cells induces a transient state in which these cells are refractory to further exposure to cancer. This phenomenon, termed "tumor tolerance", is characterized by a decreased production of proinflammatory cytokines in response to tumors. In the past, we found that this effect comprises IRAK-M up regulation and TLR4 and CD44 activation. Herein we have established a human model of tumor tolerance and have observed a marked down-regulation of MHCII molecules as well as the MHCII master regulator, CIITA, in monocytes/macrophages. These cells combine an impaired capability for antigen presentation with potent phagocytic activity and exhibit an M2-like phenotype. In addition circulating monocytes isolated from Chronic Lymphocytic Leukemia patients exhibited the same profile as tumor tolerant cells after tumor ex vivo exposition.

  17. 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.

  18. Temporal selectivity in midbrain electrosensory neurons identified by modal variation in active sensing.

    PubMed

    Pluta, Scott R; Kawasaki, Masashi

    2010-07-01

    Mormyrid weakly electric fish actively sense their surroundings by continuously emitting discrete pulses of electricity separated by varying intervals of silence. The temporal pattern of this pulsing behavior is related to context. While resting in the absence of an overt stimulus, baseline interpulse intervals (IPIs) mostly range 200-450 ms, and sequential variation is relatively high. Spontaneously, or following the presentation of a novel stimulus, IPIs transiently shorten during the performance of an electromotor "burst" display. We made intracellular whole cell recordings in vivo from neurons in the lateral nucleus of the torus semicircularis while the fish's dynamic pulsing behavior modified the temporal pattern of stimulation. Stimulation was designed to simulate the spatial patterns of AM that occur during the electrolocation of a resistive object. We discovered that toral neurons selectively respond to stimulation during a particular mode of electromotor activity. Two types of temporally selective neurons were discovered: baseline-selective neurons that displayed significantly higher postsynaptic potential (PSP) amplitude and spike count per electric organ discharge (EOD) during baseline electromotor activity and burst-selective neurons that displayed significantly higher PSP amplitude and spike count per EOD during electromotor burst displays. Interval-dependent changes in the strength of excitation and inhibition contributed to their selectivity.

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

    PubMed Central

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

    1989-01-01

    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. Images Figure 1 Figure 3 PMID:2474491

  20. Active root-inhabiting microbes identified by rapid incorporation of plant-derived carbon into RNA

    PubMed Central

    Vandenkoornhuyse, Philippe; Mahé, Stéphane; Ineson, Philip; Staddon, Phil; Ostle, Nick; Cliquet, Jean-Bernard; Francez, André-Jean; Fitter, Alastair H.; Young, J. Peter W.

    2007-01-01

    Plant roots harbor a large diversity of microorganisms that have an essential role in ecosystem functioning. To better understand the level of intimacy of root-inhabiting microbes such as arbuscular mycorrhizal fungi and bacteria, we provided 13CO2 to plants at atmospheric concentration during a 5-h pulse. We expected microbes dependent on a carbon flux from their host plant to become rapidly labeled. We showed that a wide variety of microbes occurred in roots, mostly previously unknown. Strikingly, the greatest part of this unsuspected diversity corresponded to active primary consumers. We found 17 bacterial phylotypes co-occurring within roots of a single plant, including five potentially new phylotypes. Fourteen phylotypes were heavily labeled with the 13C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and 13C-enriched RNAs, we demonstrated differential activity in C consumption among these root-inhabiting microbes. Arbuscular mycorrhizal fungal RNAs were heavily labeled, confirming the high carbon flux from the plant to the fungal compartment, but some of the fungi present appeared to be much more active than others. The results presented here reveal the possibility of uncharacterized root symbioses. PMID:17939995

  1. 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.…

  2. 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...

  3. SAFE-Tools: a Web-based application for identifying active faults

    NASA Astrophysics Data System (ADS)

    Atakan, K.; Sebrier, M.; Camelbeeck, T.; Siame, L.; Valensise, G.; Winter, T.

    2003-04-01

    Recognition of active faults, particularly in low seismicity regions such as Western Europe, has been a subject puzzling seismologists for many years. These regions are generally characterized by low-hazard but high-risk, due to the concentration of human and material properties with high-vulnerability. Detecting tectonic deformations that may lead to destructive earthquakes in such areas requires innovative research strategies that suit climate, slowly deforming fault, and heavily human-modified areas. The variety and amount of information involved in the characterization of slowly deforming faults are in general disseminated in several institutions with no easy access to. This information should be gathered, parameterized and stored in a way that make them feasible to be used in seismic hazard studies. In this sense, within the framework of the European project SAFE (Slow Active Faults in Europe; EVG1-2000-22005) a Web-based application (SAFE-Tools) for diagnosing slow active faults is developed. The basic design of the SAFE-Tools (SAFE-T) is based on server-client architecture, with data communication and visualization occurring through the Internet. The system is developed using the Java programming language and operates through an Internet browser. SAFE-T handles both parametric and graphical (image) data with a display and manipulation capability of pre-prepared data sets from a relational database with an interactive processing capacity all conducted through applets. A distributed database structure is developed opening a possibility for a network of interconnected servers. Layers of graphical data (e.g. geological maps, DEM images etc.) and sets of parametric data (e.g. historical or instrumental earthquake catalogues) are entered to the system either through an interactive process using HTML-forms, or as a bulk entry. Data are stored as geographical co-ordinate points with different attributes in the relational database. For identification of active faults

  4. Repurposing Approach Identifies Auranofin with Broad Spectrum Antifungal Activity That Targets Mia40-Erv1 Pathway

    PubMed Central

    Thangamani, Shankar; Maland, Matthew; Mohammad, Haroon; Pascuzzi, Pete E.; Avramova, Larisa; Koehler, Carla M.; Hazbun, Tony R.; Seleem, Mohamed N.

    2017-01-01

    Current antifungal therapies have limited effectiveness in treating invasive fungal infections. Furthermore, the development of new antifungal is currently unable to keep pace with the urgent demand for safe and effective new drugs. Auranofin, an FDA-approved drug for the treatment of rheumatoid arthritis, inhibits growth of a diverse array of clinical isolates of fungi and represents a new antifungal agent with a previously unexploited mechanism of action. In addition to auranofin's potent antifungal activity against planktonic fungi, this drug significantly reduces the metabolic activity of Candida cells encased in a biofilm. Unbiased chemogenomic profiling, using heterozygous S. cerevisiae deletion strains, combined with growth assays revealed three probable targets for auranofin's antifungal activity—mia40, acn9, and coa4. Mia40 is of particular interest given its essential role in oxidation of cysteine rich proteins imported into the mitochondria. Biochemical analysis confirmed auranofin targets the Mia40-Erv1 pathway as the drug inhibited Mia40 from interacting with its substrate, Cmc1, in a dose-dependent manner similar to the control, MB-7. Furthermore, yeast mitochondria overexpressing Erv1 were shown to exhibit resistance to auranofin as an increase in Cmc1 import was observed compared to wild-type yeast. Further in vivo antifungal activity of auranofin was examined in a Caenorhabditis elegans animal model of Cryptococcus neoformans infection. Auranofin significantly reduced the fungal load in infected C. elegans. Collectively, the present study provides valuable evidence that auranofin has significant promise to be repurposed as a novel antifungal agent and may offer a safe, effective, and quick supplement to current approaches for treating fungal infections. PMID:28149831

  5. Fumigant activity of (E)-anethole identified in Illicium verum fruit against Blattella germanica.

    PubMed

    Chang, Kyu-Sik; Ahn, Young-Joon

    2002-02-01

    The insecticidal activities of materials derived from the fruit of star anise, Illicium verum, against adults of Blattella germanica were examined by direct contact application and fumigation methods, and compared with those of DDVP, deltamethrin and hydramethylnon. The biologically active constituent of the Illicium fruit was characterized as the phenylpropene, (E)-anethole, by spectroscopic analysis. In a filter paper diffusion test with females, (E)-anethole caused 80.3% mortality at 0.159 mg cm-2 at 1 and 3 days after treatment (DAT), whereas 16.7% mortality at 3 DAT was achieved at 0.079 mg cm-2. DDVP and deltamethrin gave > 90% mortality at 0.019 mg cm-2 at 1 DAT. At 0.009 mg cm-2, DDVP and deltamethrin showed 73.3 and 60% mortality at 1 DAT, respectively, but 93.3 and 76.7% mortality at 3 DAT. Hydramethylnon exhibited 0 and 93.3% mortality at 0.159 mg cm-2 at 1 and 3 DAT, respectively, whereas 6.7% mortality at 3 DAT was observed at 0.079 mg cm-2. In a fumigation test with females, (E)-anethole was much more effective in closed cups than in open ones, indicating that the insecticidal activity of the compound was largely attributable to fumigant action. (E)-Anethole and DDVP caused 100% mortality at 0.398 and 0.051 mg cm-2 4 and 1 h after treatment, respectively. (E)-Anethole showed 46.7% mortality at 0.199 mg cm-2 at 3 DAT, whereas deltamethrin and hydramethylnon at 0.796 mg cm-2 was ineffective for 3-day period. As naturally occurring insect-control agents, the I verum fruit-derived materials described could be useful for managing populations of B germanica.

  6. Investigating the antiplasmodial activity of primary sulfonamide compounds identified in open source malaria data.

    PubMed

    Fisher, Gillian M; Bua, Silvia; Del Prete, Sonia; Arnold, Megan S J; Capasso, Clemente; Supuran, Claudiu T; Andrews, Katherine T; Poulsen, Sally-Ann

    2017-04-01

    In the past decade there has been a significant reduction in deaths due to malaria, in part due to the success of the gold standard antimalarial treatment - artemisinin combination therapies (ACTs). However the potential threat of ACT failure and the lack of a broadly effective malaria vaccine are driving efforts to discover new chemical entities (NCEs) to target this disease. The primary sulfonamide (PS) moiety is a component of several clinical drugs, including those for treatment of kidney disease, glaucoma and epilepsy, however this chemotype has not yet been exploited for malaria. In this study 31 PS compounds sourced from the GlaxoSmithKline (GSK) Tres Cantos antimalarial set (TCAMS) were investigated for their ability to selectively inhibit the in vitro growth of Plasmodium falciparum asexual stage malaria parasites. Of these, 14 compounds were found to have submicromolar activity (IC50 0.16-0.89 μM) and a modest selectivity index (SI) for the parasite versus human cells (SI > 12 to >43). As the PS moiety is known to inhibit carbonic anhydrase (CA) enzymes from many organisms, the PS compounds were assessed for recombinant P. falciparum CA (PfCA) mediated inhibition of CO2 hydration. The PfCA inhibition activity did not correlate with antiplasmodial potency. Furthermore, no significant difference in IC50 was observed for P. falciparum versus P. knowlesi (P > 0.05), a Plasmodium species that is not known to contain an annotated PfCA gene. Together these data suggest that the asexual intraerythrocytic stage antiplasmodial activity of the PS compounds examined in this study is likely unrelated to PfCA inhibition.

  7. High Aldehyde Dehydrogenase Activity Identifies a Subset of Human Mesenchymal Stromal Cells with Vascular Regenerative Potential.

    PubMed

    Sherman, Stephen E; Kuljanin, Miljan; Cooper, Tyler T; Putman, David M; Lajoie, Gilles A; Hess, David A

    2017-03-15

    During culture expansion, multipotent mesenchymal stromal cells (MSCs) differentially express aldehyde dehydrogenase (ALDH), an intracellular detoxification enzyme that protects long-lived cells against oxidative stress. Thus, MSC selection based on ALDH-activity may be used to reduce heterogeneity and distinguish MSC subsets with improved regenerative potency. After expansion of human bone marrow-derived MSCs, cell progeny was purified based on low versus high ALDH-activity (ALDH(hi) ) by fluorescence-activated cell sorting, and each subset was compared for multipotent stromal and provascular regenerative functions. Both ALDH(l) ° and ALDH(hi) MSC subsets demonstrated similar expression of stromal cell (>95% CD73(+) , CD90(+) , CD105(+) ) and pericyte (>95% CD146(+) ) surface markers and showed multipotent differentiation into bone, cartilage, and adipose cells in vitro. Conditioned media (CDM) generated by ALDH(hi) MSCs demonstrated a potent proliferative and prosurvival effect on human microvascular endothelial cells (HMVECs) under serum-free conditions and augmented HMVEC tube-forming capacity in growth factor-reduced matrices. After subcutaneous transplantation within directed in vivo angiogenesis assay implants into immunodeficient mice, ALDH(hi) MSC or CDM produced by ALDH(hi) MSC significantly augmented murine vascular cell recruitment and perfused vessel infiltration compared with ALDH(l) ° MSC. Although both subsets demonstrated strikingly similar mRNA expression patterns, quantitative proteomic analyses performed on subset-specific CDM revealed the ALDH(hi) MSC subset uniquely secreted multiple proangiogenic cytokines (vascular endothelial growth factor beta, platelet derived growth factor alpha, and angiogenin) and actively produced multiple factors with chemoattractant (transforming growth factor-β, C-X-C motif chemokine ligand 1, 2, and 3 (GRO), C-C motif chemokine ligand 5 (RANTES), monocyte chemotactic protein 1 (MCP-1), interleukin [IL]-6, IL-8

  8. Functional dissection of the mouse tyrosinase locus control region identifies a new putative boundary activity.

    PubMed

    Giraldo, Patricia; Martínez, Antonio; Regales, Lucía; Lavado, Alfonso; García-Díaz, Angel; Alonso, Angel; Busturia, Ana; Montoliu, Lluís

    2003-11-01

    Locus control regions (LCRs) are complex high-order chromatin structures harbouring several regulatory elements, including enhancers and boundaries. We have analysed the mouse tyrosinase LCR functions, in vitro, in cell lines and, in vivo, in transgenic mice and flies. The LCR-core (2.1 kb), located at -15 kb and carrying a previously described tissue-specific DNase I hypersensitive site, operates as a transcriptional enhancer that efficiently transactivates heterologous promoters in a cell-specific orientation-independent manner. Furthermore, we have investigated the boundary activity of these sequences in transgenic animals and cells. In mice, the LCR fragment (3.7 kb) rescued a weakly expressed reference construct that displays position effects. In Drosophila, the LCR fragment and its core insulated the expression of a white minigene reporter construct from chromosomal position effects. In cells, sequences located 5' from the LCR-core displayed putative boundary activities. We have obtained genomic sequences surrounding the LCR fragment and found a LINE1 repeated element at 5'. In B16 melanoma and L929 fibroblast mouse cells, this element was found heavily methylated, supporting the existence of putative boundary elements that could prevent the spreading of condensed chromatin from the LINE1 sequences into the LCR fragment, experimentally shown to be in an open chromatin structure.

  9. 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

  10. A screen of approved drugs and molecular probes identifies therapeutics with anti-Ebola virus activity.

    PubMed

    Johansen, Lisa M; DeWald, Lisa Evans; Shoemaker, Charles J; Hoffstrom, Benjamin G; Lear-Rooney, Calli M; Stossel, Andrea; Nelson, Elizabeth; Delos, Sue E; Simmons, James A; Grenier, Jill M; Pierce, Laura T; Pajouhesh, Hassan; Lehár, Joseph; Hensley, Lisa E; Glass, Pamela J; White, Judith M; Olinger, Gene G

    2015-06-03

    Currently, no approved therapeutics exist to treat or prevent infections induced by Ebola viruses, and recent events have demonstrated an urgent need for rapid discovery of new treatments. Repurposing approved drugs for emerging infections remains a critical resource for potential antiviral therapies. We tested ~2600 approved drugs and molecular probes in an in vitro infection assay using the type species, Zaire ebolavirus. Selective antiviral activity was found for 80 U.S. Food and Drug Administration-approved drugs spanning multiple mechanistic classes, including selective estrogen receptor modulators, antihistamines, calcium channel blockers, and antidepressants. Results using an in vivo murine Ebola virus infection model confirmed the protective ability of several drugs, such as bepridil and sertraline. Viral entry assays indicated that most of these antiviral drugs block a late stage of viral entry. By nature of their approved status, these drugs have the potential to be rapidly advanced to clinical settings and used as therapeutic countermeasures for Ebola virus infections.

  11. A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity

    PubMed Central

    Takao, Haruna; Hirabayashi, Kei; Nishigaya, Yuki; Kouriki, Haruna; Nakaniwa, Tetsuko; Hagiwara, Yoshinori; Harada, Jiro; Sato, Hideaki; Yamazaki, Toshimasa; Sakakibara, Yoichi; Suiko, Masahito; Asada, Yujiro; Takahashi, Yasuhiro; Yamamoto, Ken; Fukuyama, Keiichi; Sugishima, Masakazu; Wada, Kei

    2017-01-01

    Biliverdin reductase catalyses the last step in haem degradation and produces the major lipophilic antioxidant bilirubin via reduction of biliverdin, using NAD(P)H as a cofactor. Despite the importance of biliverdin reductase in maintaining the redox balance, the molecular details of the reaction it catalyses remain unknown. Here we present the crystal structure of biliverdin reductase in complex with biliverdin and NADP+. Unexpectedly, two biliverdin molecules, which we designated the proximal and distal biliverdins, bind with stacked geometry in the active site. The nicotinamide ring of the NADP+ is located close to the reaction site on the proximal biliverdin, supporting that the hydride directly attacks this position of the proximal biliverdin. The results of mutagenesis studies suggest that a conserved Arg185 is essential for the catalysis. The distal biliverdin probably acts as a conduit to deliver the proton from Arg185 to the proximal biliverdin, thus yielding bilirubin. PMID:28169272

  12. 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.

  13. Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity.

    PubMed

    Davis, Elizabeth; Sloan, Tyler; Aurelius, Krista; Barbour, Angela; Bodey, Elijah; Clark, Brigette; Dennis, Celeste; Drown, Rachel; Fleming, Megan; Humbert, Allison; Glasgo, Elizabeth; Kerns, Trent; Lingro, Kelly; McMillin, MacKenzie; Meyer, Aaron; Pope, Breanna; Stalevicz, April; Steffen, Brittney; Steindl, Austin; Williams, Carolyn; Wimberley, Carmen; Zenas, Robert; Butela, Kristen; Wildschutte, Hans

    2017-01-22

    The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil-derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole-genome sequencing and linker-mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin-resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization.

  14. Mind the Noise When Identifying Computational Models of Cognition from Brain Activity

    PubMed Central

    Kolossa, Antonio; Kopp, Bruno

    2016-01-01

    The aim of this study was to analyze how measurement error affects the validity of modeling studies in computational neuroscience. A synthetic validity test was created using simulated P300 event-related potentials as an example. The model space comprised four computational models of single-trial P300 amplitude fluctuations which differed in terms of complexity and dependency. The single-trial fluctuation of simulated P300 amplitudes was computed on the basis of one of the models, at various levels of measurement error and at various numbers of data points. Bayesian model selection was performed based on exceedance probabilities. At very low numbers of data points, the least complex model generally outperformed the data-generating model. Invalid model identification also occurred at low levels of data quality and under low numbers of data points if the winning model's predictors were closely correlated with the predictors from the data-generating model. Given sufficient data quality and numbers of data points, the data-generating model could be correctly identified, even against models which were very similar to the data-generating model. Thus, a number of variables affects the validity of computational modeling studies, and data quality and numbers of data points are among the main factors relevant to the issue. Further, the nature of the model space (i.e., model complexity, model dependency) should not be neglected. This study provided quantitative results which show the importance of ensuring the validity of computational modeling via adequately prepared studies. The accomplishment of synthetic validity tests is recommended for future applications. Beyond that, we propose to render the demonstration of sufficient validity via adequate simulations mandatory to computational modeling studies. PMID:28082857

  15. Mind the Noise When Identifying Computational Models of Cognition from Brain Activity.

    PubMed

    Kolossa, Antonio; Kopp, Bruno

    2016-01-01

    The aim of this study was to analyze how measurement error affects the validity of modeling studies in computational neuroscience. A synthetic validity test was created using simulated P300 event-related potentials as an example. The model space comprised four computational models of single-trial P300 amplitude fluctuations which differed in terms of complexity and dependency. The single-trial fluctuation of simulated P300 amplitudes was computed on the basis of one of the models, at various levels of measurement error and at various numbers of data points. Bayesian model selection was performed based on exceedance probabilities. At very low numbers of data points, the least complex model generally outperformed the data-generating model. Invalid model identification also occurred at low levels of data quality and under low numbers of data points if the winning model's predictors were closely correlated with the predictors from the data-generating model. Given sufficient data quality and numbers of data points, the data-generating model could be correctly identified, even against models which were very similar to the data-generating model. Thus, a number of variables affects the validity of computational modeling studies, and data quality and numbers of data points are among the main factors relevant to the issue. Further, the nature of the model space (i.e., model complexity, model dependency) should not be neglected. This study provided quantitative results which show the importance of ensuring the validity of computational modeling via adequately prepared studies. The accomplishment of synthetic validity tests is recommended for future applications. Beyond that, we propose to render the demonstration of sufficient validity via adequate simulations mandatory to computational modeling studies.

  16. Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant.

    PubMed

    Hamasy, A; Wang, Q; Blomberg, K E M; Mohammad, D K; Yu, L; Vihinen, M; Berglöf, A; Smith, C I E

    2017-01-01

    Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce, because two nucleotide changes are needed. (3) As BTK variants replaced with other residues are catalytically inactive, they presumably need compensatory mutations, therefore being very scarce. Glycine and tryptophan variants were not yet reported but likely also provide resistance.

  17. Substitution scanning identifies a novel, catalytically active ibrutinib-resistant BTK cysteine 481 to threonine (C481T) variant

    PubMed Central

    Hamasy, A; Wang, Q; Blomberg, K E M; Mohammad, D K; Yu, L; Vihinen, M; Berglöf, A; Smith, C I E

    2017-01-01

    Irreversible Bruton tyrosine kinase (BTK) inhibitors, ibrutinib and acalabrutinib have demonstrated remarkable clinical responses in multiple B-cell malignancies. Acquired resistance has been identified in a sub-population of patients in which mutations affecting BTK predominantly substitute cysteine 481 in the kinase domain for catalytically active serine, thereby ablating covalent binding of inhibitors. Activating substitutions in the BTK substrate phospholipase Cγ2 (PLCγ2) instead confers resistance independent of BTK. Herein, we generated all six possible amino acid substitutions due to single nucleotide alterations for the cysteine 481 codon, in addition to threonine, requiring two nucleotide substitutions, and performed functional analysis. Replacement by arginine, phenylalanine, tryptophan or tyrosine completely inactivated the catalytic activity, whereas substitution with glycine caused severe impairment. BTK with threonine replacement was catalytically active, similar to substitution with serine. We identify three potential ibrutinib resistance scenarios for cysteine 481 replacement: (1) Serine, being catalytically active and therefore predominating among patients. (2) Threonine, also being catalytically active, but predicted to be scarce, because two nucleotide changes are needed. (3) As BTK variants replaced with other residues are catalytically inactive, they presumably need compensatory mutations, therefore being very scarce. Glycine and tryptophan variants were not yet reported but likely also provide resistance. PMID:27282255

  18. Thermal Field Indicator for Identifying Active Faults and its Instability From Laboratory Experiments

    NASA Astrophysics Data System (ADS)

    Ma, J.; Liu, L.; Liu, P.; Ma, S.

    2007-12-01

    The relationship between the thermal filed and strain field during deformation of faults is the physical basis to clarify whether satellite infrared information and the ground temperature field can be used to study fault activity. This study attempts to discuss these problems by experiments in the laboratory. The two-direction servo-control system was used to load on the samples with compressional and extensional en echelon faults. An infrared thermal image system and a contact-type thermometer recorded synchronously variations of the bright temperature field of infrared radiation and temperature field during deformation of the rock specimens. A digital CCD camera and a soft ware based on the digital speckle correlation method (DSCM) was utilized to capture images and to analyze them, yielding processes of displacement and strain fields. The experimental result shows as follows: 1 The temperature is highest at the jog area of the compressional en echelon faults, whereas that is lowest at the extensional en echelon faults prior to failure of the jog area. The record by DSCM displays that the mean strain of the jog area is largest for the compressional en echelon faults, while that is smallest for the extensional en echelon faults. These mean that the temperature field has clear responses to the opposite stress states at the jog areas of two kinds of en echelon faults, providing an indicator for determining whether the fault segment has slid. 2 The en echelon faults experience two deformation stages from stress building up and fault propagating at the jog area to unstable sliding along the fault. Correspondingly the mechanism of heating-up is turned from strain heating into frictional heating. Three kinds of phenomena have been observed at the jog area and its vicinity during the stage of transformation. They are temperature drop, fast fluctuation of temperature, and pulses of temperature rising, respectively. Mechanism of these phenomena is discussed. 3 These

  19. Signature motifs identify an Acinetobacter Cif virulence factor with epoxide hydrolase activity.

    PubMed

    Bahl, Christopher D; Hvorecny, Kelli L; Bridges, Andrew A; Ballok, Alicia E; Bomberger, Jennifer M; Cady, Kyle C; O'Toole, George A; Madden, Dean R

    2014-03-14

    Endocytic recycling of the cystic fibrosis transmembrane conductance regulator (CFTR) is blocked by the CFTR inhibitory factor (Cif). Originally discovered in Pseudomonas aeruginosa, Cif is a secreted epoxide hydrolase that is transcriptionally regulated by CifR, an epoxide-sensitive repressor. In this report, we investigate a homologous protein found in strains of the emerging nosocomial pathogens Acinetobacter nosocomialis and Acinetobacter baumannii ("aCif"). Like Cif, aCif is an epoxide hydrolase that carries an N-terminal secretion signal and can be purified from culture supernatants. When applied directly to polarized airway epithelial cells, mature aCif triggers a reduction in CFTR abundance at the apical membrane. Biochemical and crystallographic studies reveal a dimeric assembly with a stereochemically conserved active site, confirming our motif-based identification of candidate Cif-like pathogenic EH sequences. Furthermore, cif expression is transcriptionally repressed by a CifR homolog ("aCifR") and is induced in the presence of epoxides. Overall, this Acinetobacter protein recapitulates the essential attributes of the Pseudomonas Cif system and thus may facilitate airway colonization in nosocomial lung infections.

  20. Dual activators of Protein Kinase R (PKR) and Protein Kinase R Like Kinase (PERK) Identify Common and Divergent Catalytic Targets

    PubMed Central

    Ming, Jie; Sun, Hong; Cao, Peng; Fusco, Dahlene N.; Chung, Raymond T.; Chorev, Michael; Jin, Qi; Aktas, Bertal H.

    2013-01-01

    Chemical genetics has evolved into a powerful tool for studying gene function in normal- and patho-biology. PKR and PERK, two eukaryotic translation initiation factor 2 alpha (eIF2α) kinases, play critical roles in maintenance of cellular hemostasis, metabolic stability, and anti-viral defenses. Both kinases interact with and phosphorylate additional substrates including tumor suppressor p53 and nuclear protein 90. Loss of function of both kinases has been studied by reverse genetics and recently identified inhibitors. In contrast, activating probes for studying the role of catalytic activity of these kinases are not available. We identified a 3-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-5,7-dihydroxy-4H-chromen-4-one (DHBDC) as specific dual activator of PKR and PERK by screening a chemical library of 20,000 small molecules in a dual luciferase surrogate eIF2α phosphorylation assay. We present here extensive biological characterization and preliminary structure-activity relationship of DHBDC, which phosphorylate eIF2α by activating PKR and PERK but no other eIF2α kinases. These agents also activate downstream effectors of eIF2α phosphorylation; inducing CHOP and suppressing cyclin D1 expression and inhibiting cancer cell proliferation, all in a manner dependent on PKR and PERK. Consistent with the role of eIF2α phosphorylation in viral infection, DHBDC inhibits proliferation of human hepatitis C virus. Finally, DHBDC induces phosphorylation of Ikβα, and activates NF-κB pathway. Surprisingly, activation of NF-κB pathway is dependent on PERK but independent of PKR activity. These data indicate that DHBDC is an invaluable probe for elucidating the role of PKR and PERK in normal- and patho-biology. PMID:23784735

  1. Active gelatinase B is identified by histozymography in the cartilage resorption sites of developing long bones.

    PubMed

    Lee, E R; Murphy, G; El-Alfy, M; Davoli, M A; Lamplugh, L; Docherty, A J; Leblond, C P

    1999-07-01

    In order to determine which proteinases mediate the resorption of endochondral cartilage in the course of long bone development, a novel assay called "histozymography" has been developed. In this assay, frozen sections of tibial head from 21-day-old rats are placed for 4 hr at room temperature on light-exposed photographic emulsion (composed of silver grains embedded in gelatin). We report a localized but complete digestion of emulsion gelatin facing two tissue sites which are, therefore, presumed to contain an active proteinase. One of the sites is localized at the growth plate surface forming the epiphysis/metaphysis interface. The other consists of small patches located within the epiphysis at the edge of the marrow space. Both sites are engaged in the resorption of endochondral cartilage. In both sites, inhibitor tests have established that the involved proteinase is a gelatinase. Furthermore, the use of neutralizing antibodies against gelatinase A or B have demonstrated that only those that are specific for the latter block the reaction. That gelatinase B is present in the two sites has been confirmed by light microscopic immunohistochemistry. Finally, when immunoelectron microscopy is used for fine localization of the cartilage structures that form the epiphysis/metaphysis interface, the enzyme is detected within the 0.5-microm thick edge of the cartilage, and outside the cartilage, it is present in debris composed of type II collagen-rich fibrils in various states of digestion. It is concluded that gelatinase B attacks the edge of an endochondral cartilage and helps to solubilize the type II-collagen-rich fibrillar framework, which is then released as debris for further digestion. This final step opens the way to invasion by capillaries, thereby making possible the replacement of cartilage by bone. Dev Dyn 1999;215:190-205.

  2. 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.

  3. 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

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

    PubMed

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

    2016-03-18

    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.

  5. A liquid phase based C. elegans behavioral analysis system identifies motor activity loss in a nematode Parkinson's disease model.

    PubMed

    Zheng, Maohua; Gorelenkova, Olga; Yang, Jiong; Feng, Zhaoyang

    2012-03-15

    Motor activity of Caenorhabditis elegans is widely used to study the mechanisms ranging from basic neuronal functions to human neurodegenerative diseases. It may also serve as a paradigm to screen for potential therapeutic reagents treating these diseases. Here, we developed an automated, 96-well plate and liquid phase based system that quantifies nematode motor activity in real time. Using this system, we identified an adult-onset, ageing-associated motor activity loss in a transgenic nematode line expressing human pathogenic G2019S mutant LRRK2 (leucine-rich repeat kinase 2), the leading genetic cause of Parkinson's disease characterized by dopaminergic neurodegeneration associated motor deficient mainly in elder citizens. Thus, our system may be used as a platform to screen for potential therapeutic drugs treating Parkinson's disease. It can also be used to monitor motor activity of nematodes in liquid phase at similar scenario.

  6. 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

  7. 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

  8. 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

    2016-05-03

    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.

  9. 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.

  10. 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

  11. 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

  12. Comparative evaluation of features and techniques for identifying activity type and estimating energy cost from accelerometer data.

    PubMed

    Kate, Rohit J; Swartz, Ann M; Welch, Whitney A; Strath, Scott J

    2016-03-01

    Wearable accelerometers can be used to objectively assess physical activity. However, the accuracy of this assessment depends on the underlying method used to process the time series data obtained from accelerometers. Several methods have been proposed that use this data to identify the type of physical activity and estimate its energy cost. Most of the newer methods employ some machine learning technique along with suitable features to represent the time series data. This paper experimentally compares several of these techniques and features on a large dataset of 146 subjects doing eight different physical activities wearing an accelerometer on the hip. Besides features based on statistics, distance based features and simple discrete features straight from the time series were also evaluated. On the physical activity type identification task, the results show that using more features significantly improve results. Choice of machine learning technique was also found to be important. However, on the energy cost estimation task, choice of features and machine learning technique were found to be less influential. On that task, separate energy cost estimation models trained specifically for each type of physical activity were found to be more accurate than a single model trained for all types of physical activities.

  13. 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

  14. Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma

    PubMed Central

    Kreher, Stephan; Bouhlel, M. Amine; Cauchy, Pierre; Lamprecht, Björn; Li, Shuang; Grau, Michael; Hummel, Franziska; Köchert, Karl; Anagnostopoulos, Ioannis; Jöhrens, Korinna; Hummel, Michael; Hiscott, John; Wenzel, Sören-Sebastian; Lenz, Peter; Schneider, Markus; Küppers, Ralf; Scheidereit, Claus; Giefing, Maciej; Siebert, Reiner; Rajewsky, Klaus; Lenz, Georg; Cockerill, Peter N.; Janz, Martin; Dörken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2014-01-01

    Deregulated transcription factor (TF) activities are commonly observed in hematopoietic malignancies. Understanding tumorigenesis therefore requires determining the function and hierarchical role of individual TFs. To identify TFs central to lymphomagenesis, we identified lymphoma type-specific accessible chromatin by global mapping of DNaseI hypersensitive sites and analyzed enriched TF-binding motifs in these regions. Applying this unbiased approach to classical Hodgkin lymphoma (HL), a common B-cell–derived lymphoma with a complex pattern of deregulated TFs, we discovered interferon regulatory factor (IRF) sites among the top enriched motifs. High-level expression of the proinflammatory TF IRF5 was specific to HL cells and crucial for their survival. Furthermore, IRF5 initiated a regulatory cascade in human non-Hodgkin B-cell lines and primary murine B cells by inducing the TF AP-1 and cooperating with NF-κB to activate essential characteristic features of HL. Our strategy efficiently identified a lymphoma type-specific key regulator and uncovered a tumor promoting role of IRF5. PMID:25288773

  15. Identifying profiles of actual and perceived motor competence among adolescents: associations with motivation, physical activity, and sports participation.

    PubMed

    De Meester, An; Maes, Jolien; Stodden, David; Cardon, Greet; Goodway, Jacqueline; Lenoir, Matthieu; Haerens, Leen

    2016-11-01

    The present study identified adolescents' motor competence (MC)-based profiles (e.g., high actual and low perceived MC), and accordingly investigated differences in motivation for physical education (PE), physical activity (PA) levels, and sports participation between profiles by using regression analyses. Actual MC was measured with the Körperkoordinationstest für Kinder. Adolescents (n = 215; 66.0% boys; mean age = 13.64 ± .58 years) completed validated questionnaires to assess perceived MC, motivation for PE, PA-levels, and sports participation. Actual and perceived MC were only moderately correlated and cluster analyses identified four groups. Two groups of overestimators (low - overestimation, average - overestimation) were identified (51%), who particularly displayed better motivation for PE when compared to their peers who accurately estimated themselves (low - accurate, average - accurate). Moreover, adolescents with low actual MC, but high perceived MC were significantly more active than adolescents with low actual MC who accurately estimated themselves. Results pointed in the same direction for organised sports participation. Underestimators were not found in the current sample, which is positive as underestimation might negatively influence adolescents' motivation to achieve and persist in PA and sports. In conclusion, results emphasise that developing perceived MC, especially among adolescents with low levels of actual MC, seems crucial to stimulate motivation for PE, and engagement in PA and sports.

  16. Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma.

    PubMed

    Kreher, Stephan; Bouhlel, M Amine; Cauchy, Pierre; Lamprecht, Björn; Li, Shuang; Grau, Michael; Hummel, Franziska; Köchert, Karl; Anagnostopoulos, Ioannis; Jöhrens, Korinna; Hummel, Michael; Hiscott, John; Wenzel, Sören-Sebastian; Lenz, Peter; Schneider, Markus; Küppers, Ralf; Scheidereit, Claus; Giefing, Maciej; Siebert, Reiner; Rajewsky, Klaus; Lenz, Georg; Cockerill, Peter N; Janz, Martin; Dörken, Bernd; Bonifer, Constanze; Mathas, Stephan

    2014-10-21

    Deregulated transcription factor (TF) activities are commonly observed in hematopoietic malignancies. Understanding tumorigenesis therefore requires determining the function and hierarchical role of individual TFs. To identify TFs central to lymphomagenesis, we identified lymphoma type-specific accessible chromatin by global mapping of DNaseI hypersensitive sites and analyzed enriched TF-binding motifs in these regions. Applying this unbiased approach to classical Hodgkin lymphoma (HL), a common B-cell-derived lymphoma with a complex pattern of deregulated TFs, we discovered interferon regulatory factor (IRF) sites among the top enriched motifs. High-level expression of the proinflammatory TF IRF5 was specific to HL cells and crucial for their survival. Furthermore, IRF5 initiated a regulatory cascade in human non-Hodgkin B-cell lines and primary murine B cells by inducing the TF AP-1 and cooperating with NF-κB to activate essential characteristic features of HL. Our strategy efficiently identified a lymphoma type-specific key regulator and uncovered a tumor promoting role of IRF5.

  17. Genetic Complementation Screen Identifies a Mitogen-activated Protein Kinase Phosphatase, MKP3, as a Regulator of Dopamine Transporter Trafficking

    PubMed Central

    Larsen, Mads Breum; Prasad, Balakrishna M.; Amara, Susan G.

    2008-01-01

    The antidepressant and cocaine sensitive plasma membrane monoamine transporters are the primary mechanism for clearance of their respective neurotransmitters and serve a pivotal role in limiting monoamine neurotransmission. To identify molecules in pathways that regulate dopamine transporter (DAT) internalization, we used a genetic complementation screen in Xenopus oocytes to identify a mitogen-activated protein (MAP) kinase phosphatase, MKP3/Pyst1/DUSP6, as a molecule that inhibits protein kinase C–induced (PKC) internalization of transporters, resulting in enhanced DAT activity. The involvement of MKP3 in DAT internalization was verified using both overexpression and shRNA knockdown strategies in mammalian cell models including a dopaminergic cell line. Although the isolation of MKP3 implies a role for MAP kinases in DAT internalization, MAP kinase inhibitors have no effect on internalization. Moreover, PKC-dependent down-regulation of DAT does not correlate with the phosphorylation state of several well-studied MAP kinases (ERK1/2, p38, and SAPK/JNK). We also show that MKP3 does not regulate PKC-induced ubiquitylation of DAT but acts at a more downstream step to stabilize DAT at the cell surface by blocking dynamin-dependent internalization and delaying the targeting of DAT for degradation. These results indicate that MKP3 can act to enhance DAT function and identifies MKP3 as a phosphatase involved in regulating dynamin-dependent endocytosis. PMID:18434601

  18. A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse.

    PubMed

    Carlin, Leo M; Evans, Rachel; Milewicz, Hanna; Fernandes, Luis; Matthews, Daniel R; Perani, Michela; Levitt, James; Keppler, Melanie D; Monypenny, James; Coolen, Ton; Barber, Paul R; Vojnovic, Borivoj; Suhling, Klaus; Fraternali, Franca; Ameer-Beg, Simon; Parker, Peter J; Thomas, N Shaun B; Ng, Tony

    2011-11-29

    Natural killer (NK) cells kill tumor cells and virally infected cells, and an effective NK cell response requires processes, such as motility, recognition, and directional secretion, that rely on cytoskeletal rearrangement. The Rho guanosine triphosphatase (GTPase) Cdc42 coordinates cytoskeletal reorganization downstream of many receptors. The Rho-related GTPase from plants 1 (ROP1) exhibits oscillatory activation behavior at the apical plasma membrane of growing pollen tubes; however, a similar oscillation in Rho GTPase activity has so far not been demonstrated in mammalian cells. We hypothesized that oscillations in Cdc42 activity might occur within NK cells as they interact with target cells. Through fluorescence lifetime imaging of a Cdc42 biosensor, we observed that in live NK cells forming immunological synapses with target cells, Cdc42 activity oscillated after exhibiting an initial increase. We used protein-protein interaction networks and structural databases to identify candidate proteins that controlled Cdc42 activity, leading to the design of a targeted short interfering RNA screen. The guanine nucleotide exchange factors RhoGEF6 and RhoGEF7 were necessary for Cdc42 activation within the NK cell immunological synapse. In addition, the kinase Akt and the p85α subunit of phosphoinositide 3-kinase (PI3K) were required for Cdc42 activation, the periodicity of the oscillation in Cdc42 activity, and the subsequent polarization of cytotoxic vesicles toward target cells. Given that PI3Ks are targets of tumor therapies, our findings suggest the need to monitor innate immune function during the course of targeted therapy against these enzymes.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Constitutive activation of the shh-ptc1 pathway by a patched1 mutation identified in BCC.

    PubMed

    Barnes, Elizabeth A; Heidtman, Keely J; Donoghue, Daniel J

    2005-01-27

    Mutations in the transmembrane receptor patched1 (ptc1) are responsible for the majority of basal cell carcinoma (BCC) cases. Many of these mutations, including ptc1-Q688X, result in premature truncation of the ptc1 protein. ptc1-Q688X has been identified in patients with both BCC and nevoid basal cell carcinoma syndrome, an inheritable disorder causing a predisposition to cancer susceptibility. Here we describe a mechanism by which ptc1-Q688X causes constitutive cellular signaling. Cells expressing ptc1-Q688X demonstrate an increase in cell cycle progression and induce cell transformation. The ptc1-Q688X mutant enhances Gli1 activity, a downstream reporter of sonic hedgehog (shh)-ptc1 signaling, independent of shh stimulation. In contrast to wild-type ptc1, ptc1-Q688X fails to associate with endogenous cyclin B1. Expression of nuclear-targeted cyclin B1 derivatives promotes Gli1-dependent transcription, which correlates temporally with cyclin B1-cdk1 kinase activity. Coexpression of wild-type ptc1 with a nuclear-targeted cyclin B1 derivative, mutated to mimic constitutive phosphorylation, dramatically decreases Gli1 activity. In addition, the coexpression of this constitutively nuclear cyclin B1 derivative with ptc1-Q688X substantially enhances foci formation. These studies therefore describe a molecular mechanism for the aberrant activity of ptc1-Q688X that includes the premature activation of the transcription factor Gli1.

  4. Optimization of ligand and lipophilic efficiency to identify an in vivo active furano-pyrimidine Aurora kinase inhibitor.

    PubMed

    Shiao, Hui-Yi; Coumar, Mohane Selvaraj; Chang, Chun-Wei; Ke, Yi-Yu; Chi, Ya-Hui; Chu, Chang-Ying; Sun, Hsu-Yi; Chen, Chun-Hwa; Lin, Wen-Hsing; Fung, Ka-Shu; Kuo, Po-Chu; Huang, Chin-Ting; Chang, Kai-Yen; Lu, Cheng-Tai; Hsu, John T A; Chen, Chiung-Tong; Jiaang, Weir-Torn; Chao, Yu-Sheng; Hsieh, Hsing-Pang

    2013-07-11

    Ligand efficiency (LE) and lipophilic efficiency (LipE) are two important indicators of "drug-likeness", which are dependent on the molecule's activity and physicochemical properties. We recently reported a furano-pyrimidine Aurora kinase inhibitor 4 (LE = 0.25; LipE = 1.75), with potent activity in vitro; however, 4 was inactive in vivo. On the basis of insights obtained from the X-ray co-crystal structure of the lead 4, various solubilizing functional groups were introduced to optimize both the activity and physicochemical properties. Emphasis was placed on identifying potential leads with improved activity as well as better LE and LipE by exercising tight control over the molecular weight and lipophilicity of the molecules. Rational optimization has led to the identification of Aurora kinase inhibitor 27 (IBPR001; LE = 0.26; LipE = 4.78), with improved in vitro potency and physicochemical properties, resulting in an in vivo active (HCT-116 colon cancer xenograft mouse model) anticancer agent.

  5. Tartrazine and sunset yellow are xenoestrogens in a new screening assay to identify modulators of human oestrogen receptor transcriptional activity.

    PubMed

    Axon, Andrew; May, Felicity E B; Gaughan, Luke E; Williams, Faith M; Blain, Peter G; Wright, Matthew C

    2012-08-16

    Primary biliary cirrhosis (PBC) is a cholestatic liver disease of unknown cause that occurs most frequently in post-menopausal women. Since the female sex hormone oestrogen can be cholestatic, we hypothesised that PBC may be triggered in part by chronic exposure to xenoestrogens (which may be more active on a background of low endogenous oestrogen levels seen in post-menopausal women). A reporter gene construct employing a synthetic oestrogen response element predicted to specifically interact with oestrogen receptors (ER) was constructed. Co-transfection of this reporter into an ER null cell line with a variety of nuclear receptor expression constructs indicated that the reporter gene was trans-activated by ERα and ERβ, but not by the androgen, thyroid, progesterone, glucocorticoid or vitamin D receptors. Chemicals linked to PBC were then screened for xenoestrogen activity in the human ERα-positive MCF-7 breast cancer cell line. Using this assay, the coal-derived food and cosmetic colourings--sunset yellow and tartrazine--were identified as novel human ERα activators, activating the human ER with an EC(50%) concentration of 220 and 160 nM, respectively.

  6. Combined single channel and single molecule detection identifies subunit composition of STIM1-activated transient receptor potential canonical (TRPC) channels.

    PubMed

    Asanov, Alexander; Sampieri, Alicia; Moreno, Claudia; Pacheco, Jonathan; Salgado, Alfonso; Sherry, Ryan; Vaca, Luis

    2015-01-01

    Depletion of intracellular calcium ion stores initiates a rapid cascade of events culminating with the activation of the so-called Store-Operated Channels (SOC) at the plasma membrane. Calcium influx via SOC is essential in the initiation of calcium-dependent intracellular signaling and for the refilling of internal calcium stores, ensuring the regeneration of the signaling cascade. In spite of the significance of this evolutionary conserved mechanism, the molecular identity of SOC has been the center of a heated controversy spanning over the last 20 years. Initial studies positioned some members of the transient receptor potential canonical (TRPC) channel superfamily of channels (with the more robust evidence pointing to TRPC1) as a putative SOC. Recent evidence indicates that Stromal Interacting Molecule 1 (STIM1) activates some members from the TRPC family of channels. However, the exact subunit composition of TRPC channels remains undetermined to this date. To identify the subunit composition of STIM1-activated TRPC channels, we developed novel method, which combines single channel electrophysiological measurements based on the patch clamp technique with single molecule fluorescence imaging. We termed this method Single ion Channel Single Molecule Detection technique (SC-SMD). Using SC-SMD method, we have obtained direct evidence of the subunit composition of TRPC channels activated by STIM1. Furthermore, our electrophysiological-imaging SC-SMD method provides evidence at the molecular level of the mechanism by which STIM1 and calmodulin antagonize to modulate TRPC channel activity.

  7. 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

  8. 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

  9. Highly Active Nickel Catalysts for C-H Functionalization Identified through Analysis of Off-Cycle Intermediates.

    PubMed

    Nett, Alex J; Zhao, Wanxiang; Zimmerman, Paul M; Montgomery, John

    2015-06-24

    An inhibitory role of 1,5-cyclooctadiene (COD) in nickel-catalyzed C-H functionalization processes was identified and studied. The bound COD participates in C-H activation by capturing the hydride, leading to a stable off-cycle π-allyl complex that greatly diminished overall catalytic efficiency. Computational studies elucidated the origin of the effect and enabled identification of a 1,5-hexadiene-derived pre-catalyst that avoids the off-cycle intermediate and provides catalytic efficiencies that are superior to those of catalysts derived from Ni(COD)2.

  10. 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

  11. The ATP hydrolyzing transcription activator phage shock protein F of Escherichia coli: identifying a surface that binds sigma 54.

    PubMed

    Bordes, Patricia; Wigneshweraraj, Siva R; Schumacher, Jörg; Zhang, Xiaodong; Chaney, Matthew; Buck, Martin

    2003-03-04

    Members of the protein family called ATPases associated with various cellular activities (AAA(+)) play a crucial role in transforming chemical energy into biological events. AAA(+) proteins are complex molecular machines and typically form ring-shaped oligomeric complexes that are crucial for ATPase activity and mechanism of action. The Escherichia coli transcription activator phage shock protein F (PspF) is an AAA(+) mechanochemical enzyme that functions to sense and relay the energy derived from nucleoside triphosphate hydrolysis to catalyze transcription by the sigma(54)-RNA polymerase. Closed promoter complexes formed by the sigma(54)-RNA polymerase are substrates for the action of PspF. By using a protein fragmentation approach, we identify here at least one sigma(54)-binding surface in the PspF AAA(+) domain. Results suggest that ATP hydrolysis by PspF is coupled to the exposure of at least one sigma(54)-binding surface. This nucleotide hydrolysis-dependent presentation of a substrate binding surface can explain why complexes that form between sigma(54) and PspF are transient and could be part of a mechanism used generally by other AAA(+) proteins to regulate activity.

  12. Identifying Grade/Stage-Related Active Modules in Human Co-regulatory Networks: A Case Study for Breast Cancer

    PubMed Central

    Feng, Chenchen; Li, Wan; Wang, Hong; Zhang, Liangcai; Jia, Xu; Miao, Zhengqiang; Qu, Xiaoli; Li, Weiguo; He, Weiming

    2012-01-01

    Abstract The histological grade/stage of tumor is widely acknowledged as an important clinical prognostic factor for cancer progression. Recent experimental studies have explored the following two topics at the molecular level: (1) whether or not gene expression levels vary by different degrees among different tumor grades/stages, and (2) whether some well-defined modules could distinguish one grade/stage from another. In this article, using breast cancer as an example, we investigated this topic and identified grade/stage-related active modules under the framework of a weighted network integrated from a human protein interaction network and a transcriptional regulatory network. Our results enabled us to draw the conclusion that the gene expression profile could provide more clues about tumor grade, but reveals less evidence about tumor stage. In addition, we found that our modular biomarker method had additional advantages in identifying some tumor grade/stage-related genes with slightly altered expression. According to our case study, the framework we introduced could be used for other cancers to identify their modules during grading or staging. PMID:23215806

  13. A high throughput Cre-lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry.

    PubMed

    Esposito, Anthony M; Cheung, Pamela; Swartz, Talia H; Li, Hongru; Tsibane, Tshidi; Durham, Natasha D; Basler, Christopher F; Felsenfeld, Dan P; Chen, Benjamin K

    2016-03-01

    Enveloped virus entry occurs when viral and cellular membranes fuse releasing particle contents into the target cell. Human immunodeficiency virus (HIV) entry occurs by cell-free virus or virus transferred between infected and uninfected cells through structures called virological synapses. We developed a high-throughput cell-based assay to identify small molecule inhibitors of cell-free or virological synapse-mediated entry. An HIV clone carrying Cre recombinase as a Gag-internal gene fusion releases active Cre into cells upon viral entry activating a recombinatorial gene switch changing dsRed to GFP-expression. A screen of a 1998 known-biological profile small molecule library identified pharmacological HIV entry inhibitors that block both cell-free and cell-to-cell infection. Many top hits were noted as HIV inhibitors in prior studies, but not previously recognized as entry antagonists. Modest therapeutic indices for simvastatin and nigericin were observed in confirmatory HIV infection assays. This robust assay is adaptable to study HIV and heterologous viral pseudotypes.

  14. A high throughput Cre–lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry

    PubMed Central

    Esposito, Anthony M.; Cheung, Pamela; Swartz, Talia H.; Li, Hongru; Tsibane, Tshidi; Durham, Natasha D.; Basler, Christopher F.; Felsenfeld, Dan P.; Chen, Benjamin K.

    2016-01-01

    Enveloped virus entry occurs when viral and cellular membranes fuse releasing particle contents into the target cell. Human immunodeficiency virus (HIV) entry occurs by cell-free virus or virus transferred between infected and uninfected cells through structures called virological synapses. We developed a high-throughput cell-based assay to identify small molecule inhibitors of cell-free or virological synapse-mediated entry. An HIV clone carrying Cre recombinase as a Gag-internal gene fusion releases active Cre into cells upon viral entry activating a recombinatorial gene switch changing dsRed to GFP-expression. A screen of a 1998 known-biological profile small molecule library identified pharmacological HIV entry inhibitors that block both cell-free and cell-to-cell infection. Many top hits were noted as HIV inhibitors in prior studies, but not previously recognized as entry antagonists. Modest therapeutic indices for simvastatin and nigericin were observed in confirmatory HIV infection assays. This robust assay is adaptable to study HIV and heterologous viral pseudotypes. PMID:26803470

  15. 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

  16. 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.

  17. A combined methodology of multiplet and composite focal mechanism techniques for identifying seismologically active zones in Syria

    NASA Astrophysics Data System (ADS)

    Abdul-Wahed, Mohamad; Asfahani, Jamal; Al-Tahhan, Ibrahim

    2011-10-01

    This contribution is an attempt to enlarge the current knowledge about the focal mechanisms as well as the seismotectonic settings in Syria. The seismologically active zones have been identified by applying an appropriate methodology to the events recorded during the period 1995-2003 by the Syrian National Seismological Network (SNSN). The recorded events in Syria were classified as weak during the research period. It was extremely important to propose and apply an appropriate methodology to identify the focal mechanisms generating this seismic activity. The proposed methodology consists of applying a combination of two techniques: the multiplet and the composite focal mechanisms. The combination of many events in one composite focal mechanism was realized by a multiplet technique using the spectral coherence of the events as a measure of similarity. The application of the proposed methodology allows a data set of composite fault plane solutions to be obtained. Most of the composite fault plane solutions had strike-slip mechanisms which are in agreement with the configuration of seismogenic belts in Syria.

  18. Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase.

    PubMed

    Pierdominici-Sottile, Gustavo; Palma, Juliana; Roitberg, Adrian E

    2014-03-01

    Trypanosoma rangeli's sialidase (TrSA) and Trypanosoma cruzi's trans-sialidase (TcTS) are members of the glycoside hydrolase family 33 (GH-33). They share 70% of sequence identity and their crystallographic Cα RMSD is 0.59 Å. Despite these similarities they catalyze different reactions. TcTS transfers sialic acid between glycoconjugates while TrSA can only cleave sialic acid from sialyl-glyconjugates. Significant effort has been invested into unraveling the differences between TrSA and TcTS, and into conferring TrSA with trans-sialidase activity through appropriate point mutations. Recently, we calculated the free-energy change for the formation of the covalent intermediate (CI) in TcTS and performed an energy decomposition analysis of that process. In this article we present a similar study for the formation of the CI in TrSA, as well as in a quintuple mutant (TrSA5mut), which has faint trans-sialidase activity. The comparison of these new results with those previously obtained for TcTS allowed identifying five extra mutations to be introduced in TrSA5mut that should create a mutant (TrSA10mut ) with high trans-sialidase activity.

  19. 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.

  20. Phenanthrene Metabolism in Smokers: Use of a Two-Step Diagnostic Plot Approach to Identify Subjects with Extensive Metabolic Activation

    PubMed Central

    Wang, Jing; Zhong, Yan; Carmella, Steven G.; Hochalter, J. Bradley; Rauch, Diane; Oliver, Andrew; Jensen, Joni; Hatsukami, Dorothy K.; Upadhyaya, Pramod; Hecht, Stephen S.

    2012-01-01

    Polycyclic aromatic hydrocarbons (PAHs) in cigarette smoke are among the most likely causes of lung cancer. PAHs require metabolic activation to initiate the carcinogenic process. Phenanthrene (Phe), a noncarcinogenic PAH, was used as a surrogate of benzo[α]pyrene and related PAHs to study the metabolic activation of PAHs in smokers. A dose of 10 μg of deuterated Phe ([D10]Phe) was administered to 25 healthy smokers in a crossover design, either as an oral solution or by smoking cigarettes containing [D10]Phe. Phe was deuterated to avoid interference from environmental Phe. Intensive blood and urine sampling was performed to quantitate the formation of deuterated r-1,t-2,3,c-4-tetrahydroxy-1,2,3,4-tetrahydrophenanthrene ([D10]PheT), a biomarker of the diol epoxide metabolic activation pathway. In both the oral and smoking arms approximately 6% of the dose was metabolically converted to diol epoxides, with a large intersubject variability in the formation of [D10]PheT observed. Two diagnostic plots were developed to identify subjects with large systemic exposure and significant lung contribution to metabolic activation. The combination of the two plots led to the identification of subjects with substantial local exposure. These subjects produced, in one single pass of [D10]Phe through the lung, a [D10]PheT exposure equivalent to the systemic exposure of a typical subject and may be an indicator of lung cancer susceptibility. Polymorphisms in PAH-metabolizing genes of the 25 subjects were also investigated. The integration of phenotyping and genotyping results indicated that GSTM1-null subjects produced approximately 2-fold more [D10]PheT than did GSTM1-positive subjects. PMID:22674470

  1. An Antifungal Combination Matrix Identifies a Rich Pool of Adjuvant Molecules that Enhance Drug Activity Against Diverse Fungal Pathogens

    PubMed Central

    Robbins, Nicole; Spitzer, Michaela; Yu, Tennison; Cerone, Robert P.; Averette, Anna K.; Bahn, Yong-Sun; Heitman, Joseph; Sheppard, Donald C.; Tyers, Mike; Wright, Gerard D.

    2015-01-01

    SUMMARY There is an urgent need to identify new treatments for fungal infections. By combining sub-lethal concentrations of the known antifungals fluconazole, caspofungin, amphotericin B, terbinafine, benomyl and cyprodinil with ~3600 compounds in diverse fungal species, we generated a deep reservoir of chemical-chemical interactions termed the Antifungal Combinations Matrix (ACM). Follow-up susceptibility testing against a fluconazole resistant isolate of C. albicans unveiled ACM combinations capable of potentiating fluconazole in this clinical strain. We used chemical genetics to elucidate the mode-of-action of the antimycobacterial drug clofazimine, a compound with unreported antifungal activity that synergized with several antifungals. Clofazimine induces a cell membrane stress for which the Pkc1 signaling pathway is required for tolerance. Further tests against additional fungal pathogens, including Aspergillus fumigatus, highlighted that clofazimine exhibits efficacy as a combination agent against multiple fungi. Thus, the ACM is a rich reservoir of chemical combinations with therapeutic potential against diverse fungal pathogens. PMID:26549450

  2. Identifying and characterising PPE7 (Rv0354c) high activity binding peptides and their role in inhibiting cell invasion.

    PubMed

    Díaz, Diana P; Ocampo, Marisol; Varela, Yahson; Curtidor, Hernando; Patarroyo, Manuel A; Patarroyo, Manuel E

    2017-02-15

    This study was aimed at characterising the PPE7 protein from the PE/PPE protein family. The presence and transcription of the rv0354c gene in the Mycobacterium tuberculosis complex was determined and the subcellular localisation of the PPE7 protein on mycobacterial membrane was confirmed by immunoelectron microscope. Two peptides were identified as having high binding activity (HABPs) and were tested in vitro regarding the invasion of Mycobacterium tuberculosis H37Rv. HABP 39224 inhibited invasion in A549 epithelial cells and U937 macrophages by more than 50%, whilst HABP 39225 inhibited invasion by 40% in U937 cells. HABP 39224, located in the protein's C-terminal region, has a completely conserved amino acid sequence in M. tuberculosis complex species and could be selected as a base peptide when designing a subunit-based, anti-tuberculosis vaccine.

  3. 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.

  4. TCR repertoire sequencing identifies synovial Treg cell clonotypes in the bloodstream during active inflammation in human arthritis

    PubMed Central

    Spreafico, Roberto; Consolaro, Alessandro; Leong, Jing Yao; Chua, Camillus; Massa, Margherita; Saidin, Suzan; Magni-Manzoni, Silvia; Arkachaisri, Thaschawee; Wallace, Carol A; Gattorno, Marco; Martini, Alberto; Lovell, Daniel J; Albani, Salvatore

    2017-01-01

    Objectives The imbalance between effector and regulatory T (Treg) cells is crucial in the pathogenesis of autoimmune arthritis. Immune responses are often investigated in the blood because of its accessibility, but circulating lymphocytes are not representative of those found in inflamed tissues. This disconnect hinders our understanding of the mechanisms underlying disease. Our goal was to identify Treg cells implicated in autoimmunity at the inflamed joints, and also readily detectable in the blood upon recirculation. Methods We compared Treg cells of patients with juvenile idiopathic arthritis responding or not to therapy by using: (i) T cell receptor (TCR) sequencing, to identify clonotypes shared between blood and synovial fluid; (ii) FOXP3 Treg cell-specific demethylated region DNA methylation assays, to investigate their stability and (iii) flow cytometry and suppression assays to probe their tolerogenic functions. Results We found a subset of synovial Treg cells that recirculated into the bloodstream of patients with juvenile idiopathic and adult rheumatoid arthritis. These inflammation-associated (ia)Treg cells, but not other blood Treg cells, expanded during active disease and proliferated in response to their cognate antigens. Despite the typical inflammatory-skewed balance of immune mechanisms in arthritis, iaTreg cells were stably committed to the regulatory lineage and fully suppressive. A fraction of iaTreg clonotypes were in common with pathogenic effector T cells. Conclusions Using an innovative antigen-agnostic approach, we uncovered a population of bona fide synovial Treg cells readily accessible from the blood and selectively expanding during active disease, paving the way to non-invasive diagnostics and better understanding of the pathogenesis of autoimmunity. PMID:27311837

  5. Conserved valproic-acid-induced lipid droplet formation in Dictyostelium and human hepatocytes identifies structurally active compounds.

    PubMed

    Elphick, Lucy M; Pawolleck, Nadine; Guschina, Irina A; Chaieb, Leila; Eikel, Daniel; Nau, Heinz; Harwood, John L; Plant, Nick J; Williams, Robin S B

    2012-03-01

    Lipid droplet formation and subsequent steatosis (the abnormal retention of lipids within a cell) has been reported to contribute to hepatotoxicity and is an adverse effect of many pharmacological agents including the antiepileptic drug valproic acid (VPA). In this study, we have developed a simple model system (Dictyostelium discoideum) to investigate the effects of VPA and related compounds in lipid droplet formation. In mammalian hepatocytes, VPA increases lipid droplet accumulation over a 24-hour period, giving rise to liver cell damage, and we show a similar effect in Dictyostelium following 30 minutes of VPA treatment. Using (3)H-labelled polyunsaturated (arachidonic) or saturated (palmitic) fatty acids, we shown that VPA treatment of Dictyostelium gives rise to an increased accumulation of both types of fatty acids in phosphatidylcholine, phosphatidylethanolamine and non-polar lipids in this time period, with a similar trend observed in human hepatocytes (Huh7 cells) labelled with [(3)H]arachidonic acid. In addition, pharmacological inhibition of β-oxidation in Dictyostelium phenocopies fatty acid accumulation, in agreement with data reported in mammalian systems. Using Dictyostelium, we then screened a range of VPA-related compounds to identify those with high and low lipid-accumulation potential, and validated these activities for effects on lipid droplet formation by using human hepatocytes. Structure-activity relationships for these VPA-related compounds suggest that lipid accumulation is independent of VPA-catalysed teratogenicity and inositol depletion. These results suggest that Dictyostelium could provide both a novel model system for the analysis of lipid droplet formation in human hepatocytes and a rapid method for identifying VPA-related compounds that show liver toxicology.

  6. Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

    PubMed Central

    Patil, Ashwini; Kumagai, Yutaro; Liang, Kuo-ching; Suzuki, Yutaka; Nakai, Kenta

    2013-01-01

    The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub

  7. Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response.

    PubMed

    Patil, Ashwini; Kumagai, Yutaro; Liang, Kuo-Ching; Suzuki, Yutaka; Nakai, Kenta

    2013-01-01

    The innate immune response is primarily mediated by the Toll-like receptors functioning through the MyD88-dependent and TRIF-dependent pathways. Despite being widely studied, it is not yet completely understood and systems-level analyses have been lacking. In this study, we identified a high-probability network of genes activated during the innate immune response using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network. We classified the immune response into three consecutive time-dependent stages and identified the most probable paths between genes showing a significant change in expression at each stage. The resultant network contained several novel and known regulators of the innate immune response, many of which did not show any observable change in expression at the sampled time points. The response network shows the dominance of genes from specific functional classes during different stages of the immune response. It also suggests a role for the protein phosphatase 2a catalytic subunit α in the regulation of the immunoproteasome during the late phase of the response. In order to clarify the differences between the MyD88-dependent and TRIF-dependent pathways in the innate immune response, time-course gene expression profiles from MyD88-knockout and TRIF-knockout dendritic cells were analyzed. Their response networks suggest the dominance of the MyD88-dependent pathway in the innate immune response, and an association of the circadian regulators and immunoproteasomal degradation with the TRIF-dependent pathway. The response network presented here provides the most probable associations between genes expressed in the early and the late phases of the innate immune response, while taking into account the intermediate regulators. We propose that the method described here can also be used in the identification of time-dependent gene sub

  8. A high throughput Cre–lox activated viral membrane fusion assay identifies pharmacological inhibitors of HIV entry

    SciTech Connect

    Esposito, Anthony M.; Cheung, Pamela; Swartz, Talia H.; Li, Hongru; Tsibane, Tshidi; Durham, Natasha D.; Basler, Christopher F.; Felsenfeld, Dan P.; Chen, Benjamin K.

    2016-03-15

    Enveloped virus entry occurs when viral and cellular membranes fuse releasing particle contents into the target cell. Human immunodeficiency virus (HIV) entry occurs by cell-free virus or virus transferred between infected and uninfected cells through structures called virological synapses. We developed a high-throughput cell-based assay to identify small molecule inhibitors of cell-free or virological synapse-mediated entry. An HIV clone carrying Cre recombinase as a Gag-internal gene fusion releases active Cre into cells upon viral entry activating a recombinatorial gene switch changing dsRed to GFP-expression. A screen of a 1998 known-biological profile small molecule library identified pharmacological HIV entry inhibitors that block both cell-free and cell-to-cell infection. Many top hits were noted as HIV inhibitors in prior studies, but not previously recognized as entry antagonists. Modest therapeutic indices for simvastatin and nigericin were observed in confirmatory HIV infection assays. This robust assay is adaptable to study HIV and heterologous viral pseudotypes. - Highlights: • Cre recombinase viral fusion assay screens cell-free or cell–cell entry inhibitors. • This Gag-iCre based assay is specific for the entry step of HIV replication. • Screened a library of known pharmacologic compounds for HIV fusion antagonists. • Many top hits were previously noted as HIV inhibitors, but here are classified as entry antagonists. Many top hits were previously noted as HIV inhibitors, but not as entry antagonists. • The assay is compatible with pseudotyping with HIV and heterologous viruses.

  9. 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

  10. Multiplex image-based autophagy RNAi screening identifies SMCR8 as ULK1 kinase activity and gene expression regulator

    PubMed Central

    Jung, Jennifer; Nayak, Arnab; Schaeffer, Véronique; Starzetz, Tatjana; Kirsch, Achim K; Müller, Stefan; Dikic, Ivan; Mittelbronn, Michel; Behrends, Christian

    2017-01-01

    Autophagy is an intracellular recycling and degradation pathway that depends on membrane trafficking. Rab GTPases are central for autophagy but their regulation especially through the activity of Rab GEFs remains largely elusive. We employed a RNAi screen simultaneously monitoring different populations of autophagosomes and identified 34 out of 186 Rab GTPase, GAP and GEF family members as potential autophagy regulators, amongst them SMCR8. SMCR8 uses overlapping binding regions to associate with C9ORF72 or with a C9ORF72-ULK1 kinase complex holo-assembly, which function in maturation and formation of autophagosomes, respectively. While focusing on the role of SMCR8 during autophagy initiation, we found that kinase activity and gene expression of ULK1 are increased upon SMCR8 depletion. The latter phenotype involved association of SMCR8 with the ULK1 gene locus. Global mRNA expression analysis revealed that SMCR8 regulates transcription of several other autophagy genes including WIPI2. Collectively, we established SMCR8 as multifaceted negative autophagy regulator. DOI: http://dx.doi.org/10.7554/eLife.23063.001 PMID:28195531

  11. Managing Challenging Behaviors of Dementia in Veterans: Identifying and Changing Activators and Consequences Using STAR-VA.

    PubMed

    Curyto, Kim J; McCurry, Sue M; Luci, Katherine; Karlin, Bradley E; Teri, Linda; Karel, Michele J

    2017-02-01

    One of the most challenging clinical issues for long-term care staff is the management of dementia-related behavioral symptoms. STAR-VA is an interdisciplinary intervention for managing challenging behaviors of Veterans with dementia in Community Living Centers (CLCs) within the U.S. Department of Veterans Affairs. The goals of the current article are to delineate categories of challenging behaviors found in CLCs, the context in which behaviors occurred, and the interventions used by CLC clinical teams when implementing STAR-VA. In 2013, 17 CLC teams completed STAR-VA training, enrolling 71 Veteran participants. Four independent raters identified common assessment and intervention themes for six behavior categories, coding activators, consequences, goal behaviors, and care plans for each category. Successful care plans included staff changes in communication approaches, incorporation of pleasant events into care, and individualized environmental modifications. Findings illustrate the range of interventions that CLC teams may apply as a result of systematic behavioral assessment informing an understanding of activators and consequences of dementia-related behaviors. [Journal of Gerontological Nursing, 43(2), 33-43.].

  12. 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.

  13. Bactericidal activity identified in 2S Albumin from sesame seeds and in silico studies of structure-function relations.

    PubMed

    Maria-Neto, Simone; Honorato, Rodrigo V; Costa, Fábio T; Almeida, Renato G; Amaro, Daniel S; Oliveira, José T A; Vasconcelos, Ilka M; Franco, Octávio L

    2011-06-01

    Pathogenic bacteria constitute an important cause of hospital-acquired infections. However, the misuse of available bactericidal agents has led to the appearance of antibiotic-resistant strains. Thus, efforts to seek new antimicrobials with different action mechanisms would have an enormous impact. Here, a novel antimicrobial protein (SiAMP2) belonging to the 2S albumin family was isolated from Sesamum indicum kernels and evaluated against several bacteria and fungi. Furthermore, in silico analysis was conducted in order to identify conserved residues through other 2S albumin antimicrobial proteins (2S-AMPs). SiAMP2 specifically inhibited Klebsiella sp. Specific regions in the molecule surface where cationic (RR/RRRK) and hydrophobic (MEYWPR) residues are exposed and conserved were proposed as being involved in antimicrobial activity. This study reinforces the hypothesis that plant storage proteins might also play as pathogen protection providing an insight into the mechanism of action for this novel 2S-AMP and evolutionary relations between antimicrobial activity and 2S albumins.

  14. 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

  15. Variomics screen identifies the re-entrant loop of the calcium-activated chloride channel ANO1 that facilitates channel activation.

    PubMed

    Bill, Anke; Popa, M Oana; van Diepen, Michiel T; Gutierrez, Abraham; Lilley, Sarah; Velkova, Maria; Acheson, Kathryn; Choudhury, Hedaythul; Renaud, Nicole A; Auld, Douglas S; Gosling, Martin; Groot-Kormelink, Paul J; Gaither, L Alex

    2015-01-09

    The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases.

  16. Variomics Screen Identifies the Re-entrant Loop of the Calcium-activated Chloride Channel ANO1 That Facilitates Channel Activation*

    PubMed Central

    Bill, Anke; Popa, M. Oana; van Diepen, Michiel T.; Gutierrez, Abraham; Lilley, Sarah; Velkova, Maria; Acheson, Kathryn; Choudhury, Hedaythul; Renaud, Nicole A.; Auld, Douglas S.; Gosling, Martin; Groot-Kormelink, Paul J.; Gaither, L. Alex

    2015-01-01

    The calcium-activated chloride channel ANO1 regulates multiple physiological processes. However, little is known about the mechanism of channel gating and regulation of ANO1 activity. Using a high-throughput, random mutagenesis-based variomics screen, we generated and functionally characterized ∼6000 ANO1 mutants and identified novel mutations that affected channel activity, intracellular trafficking, or localization of ANO1. Mutations such as S741T increased ANO1 calcium sensitivity and rendered ANO1 calcium gating voltage-independent, demonstrating a critical role of the re-entrant loop in coupling calcium and voltage sensitivity of ANO1 and hence in regulating ANO1 activation. Our data present the first unbiased and comprehensive study of the structure-function relationship of ANO1. The novel ANO1 mutants reported have diverse functional characteristics, providing new tools to study ANO1 function in biological systems, paving the path for a better understanding of the function of ANO1 and its role in health and diseases. PMID:25425649

  17. Identifying solutions to increase participation in physical activity interventions within a socio-economically disadvantaged community: a qualitative study

    PubMed Central

    2014-01-01

    Background There is an urgent need to increase population levels of physical activity, particularly amongst those who are socio-economically disadvantaged. Multiple factors influence physical activity behaviour but the generalisability of current evidence to such ‘hard-to-reach’ population subgroups is limited by difficulties in recruiting them into studies. Also, rigorous qualitative studies of lay perceptions and perceptions of community leaders about public health efforts to increase physical activity are sparse. We sought to explore, within a socio-economically disadvantaged community, residents’ and community leaders’ perceptions of physical activity (PA) interventions and issues regarding their implementation, in order to improve understanding of needs, expectations, and social/environmental factors relevant to future interventions. Methods Within an ongoing regeneration project (Connswater Community Greenway), in a socio-economically disadvantaged community in Belfast, we collaborated with a Community Development Agency to purposively sample leaders from public- and voluntary-sector community groups and residents. Individual semi-structured interviews were conducted with 12 leaders. Residents (n = 113), of both genders and a range of ages (14 to 86 years) participated in focus groups (n = 14) in local facilities. Interviews and focus groups were recorded, transcribed verbatim and analysed using a thematic framework. Results Three main themes were identified: awareness of PA interventions; factors contributing to intervention effectiveness; and barriers to participation in PA interventions. Participants reported awareness only of interventions in which they were involved directly, highlighting a need for better communications, both inter- and intra-sectoral, and with residents. Meaningful engagement of residents in planning/organisation, tailoring to local context, supporting volunteers, providing relevant resources and an ‘exit strategy

  18. Screening of the 'Pathogen Box' identifies an approved pesticide with major anthelmintic activity against the barber's pole worm.

    PubMed

    Preston, Sarah; Jiao, Yaqing; Jabbar, Abdul; McGee, Sean L; Laleu, Benoît; Willis, Paul; Wells, Timothy N C; Gasser, Robin B

    2016-12-01

    There is a substantial need to develop new medicines against parasitic diseases via public-private partnerships. Based on high throughput phenotypic screens of largely protozoal pathogens and bacteria, the Medicines for Malaria Venture (MMV) has recently assembled an open-access 'Pathogen Box' containing 400 well-curated chemical compounds. In the present study, we tested these compounds for activity against parasitic stages of the nematode Haemonchus contortus (barber's pole worm). In an optimised, whole-organism screening assay, using exsheathed third-stage (xL3) and fourth-stage (L4) larvae, we measured the inhibition of larval motility, growth and development of H. contortus. We also studied the effect of the 'hit' compound on mitochondrial function by measuring oxygen consumption. Among the 400 Pathogen Box compounds, we identified one chemical, called tolfenpyrad (compound identification code: MMV688934) that reproducibly inhibits xL3 motility as well as L4 motility, growth and development, with IC50 values ranging between 0.02 and 3 μM. An assessment of mitochondrial function showed that xL3s treated with tolfenpyrad consumed significantly less oxygen than untreated xL3s, which was consistent with specific inhibition of complex I of the respiratory electron transport chain in arthropods. Given that tolfenpyrad was developed as a pesticide and has already been tested for absorption, distribution, excretion, biotransformation, toxicity and metabolism, it shows considerable promise for hit-to-lead optimisation and/or repurposing for use against H. contortus and other parasitic nematodes. Future work should assess its activity against hookworms and other pathogens that cause neglected tropical diseases.

  19. Characterization of regulatory T cells identified as CD4+CD25highCD39+ in patients with active tuberculosis

    PubMed Central

    Chiacchio, T; Casetti, R; Butera, O; Vanini, V; Carrara, S; Girardi, E; Di Mitri, D; Battistini, L; Martini, F; Borsellino, G; Goletti, D

    2009-01-01

    Forkhead box P3 (FoxP3) is a transcription factor whose expression characterizes regulatory T cells (Treg), but it is also present on activated T cells, thus hindering correct Treg identification. Using classical markers for Treg recognition, discordant results were found in terms of Treg expansion during active tuberculosis (TB) disease. Recently CD39 has been shown to be an accurate marker for Treg detection. The objectives of this study were: (i) to identify Treg expressing CD39 in patients with TB and to compare the results with those obtained by the standard phenotypic markers; (ii) to evaluate if Treg are expanded in vitro by exogenous interleukin (IL)-2 or by antigen-specific stimulation; and (iii) to characterize Treg function on the modulation of antigen-specific responses. We enrolled 13 patients with pulmonary TB and 12 healthy controls. Treg were evaluated by flow cytometry ex vivo and after antigen-specific in vitro stimulation using CD25, FoxP3, CD127 and CD39 markers. Results indicate that CD39+ cells within the CD4+CD25high cells have Treg properties (absence of interferon-γ production and transforming growth factor-β1 release upon stimulation). Ex vivo analysis did not show significant differences between TB patients and controls of Treg by classical or novel markers. In contrast, a significantly higher percentage of Treg was found in TB patients after antigen-specific stimulation both in the presence or absence of IL-2. Depletion of CD39+ Treg increased RD1-specific responses significantly. In conclusion, CD39 is an appropriate marker for Treg identification in TB. These results can be useful for future studies to monitor Mycobacterium tuberculosis-specific response during TB. PMID:19438599

  20. Identifying Active Faults in Northeast North America Using Hypocenters and Multiscale Edge Wavelet Analyses of Potential Fields

    NASA Astrophysics Data System (ADS)

    Carpenter, K.; Horowitz, F.; Ebinger, C. J.; Navarrete, L. C.; Diaz-Etchevehere, D.

    2015-12-01

    Multiscale edge Poisson wavelet analyses of potential field data ("worms") have a physical interpretation as the locations of lateral boundaries in a source distribution that exactly generates the observed field. The worm technique is therefore well-suited to analyses of crustal-scale stuctures that could be reactivated by tectonic stress or by fluid injection processes, providing new tools to analyze existing continental-scale data sets. Northeastern North America (US, Canada) hosts potentially damaging intraplate earthquakes, yet many of the Proterozoic structures are covered by thick sedimentary sequences or dense vegetation, and crustal structure is relatively poorly known.For the purpose of extending basement structure beneath the Appalachian basin and establishing a consistent regional basis for comparison, we use worms to identify steeply dipping structures in compiled gravity and magnetic anomaly data sets. We compare results to intraplate earthquake locations to assess seismic hazards. Clearly, not all locations of lateral boundaries are faults, and we do not expect all faults to have shown activity in the ~50 years of seismic records available. However, proximity statistics between hypocenters and worms are of interest since they assist in the identification and location of a subset of potentially active faults. We compare structures of lateral mass-density or magnetization contrast with locations of earthquake hypocenters cataloged from the ISC, the NEIC, and the ANF from the EarthScope Transportable Array. We develop a GIS based method for calculating hypocenter/worm proximity, and we will show statistics and maps from this method for the region at the meeting.

  1. Dietary uptake of Cu sorbed to hydrous iron oxide is linked to cellular toxicity and feeding inhibition in a benthic grazer

    USGS Publications Warehouse

    Cain, Daniel J.; Croteau, Marie-Noele; Fuller, Christopher C.; Ringwood, Amy H.

    2016-01-01

    Whereas feeding inhibition caused by exposure to contaminants has been extensively documented, the underlying mechanism(s) are less well understood. For this study, the behavior of several key feeding processes, including ingestion rate and assimilation efficiency, that affect the dietary uptake of Cu were evaluated in the benthic grazer Lymnaea stagnalis following 4–5 h exposures to Cu adsorbed to synthetic hydrous ferric oxide (Cu–HFO). The particles were mixed with a cultured alga to create algal mats with Cu exposures spanning nearly 3 orders of magnitude at variable or constant Fe concentrations, thereby allowing first order and interactive effects of Cu and Fe to be evaluated. Results showed that Cu influx rates and ingestion rates decreased as Cu exposures of the algal mat mixture exceeded 104 nmol/g. Ingestion rate appeared to exert primary control on the Cu influx rate. Lysosomal destabilization rates increased directly with Cu influx rates. At the highest Cu exposure where the incidence of lysosomal membrane damage was greatest (51%), the ingestion rate was suppressed 80%. The findings suggested that feeding inhibition was a stress response emanating from excessive uptake of dietary Cu and cellular toxicity.

  2. Tooth wear in captive giraffes (Giraffa camelopardalis): mesowear analysis classifies free-ranging specimens as browsers but captive ones as grazers.

    PubMed

    Clauss, Marcus; Franz-Odendaal, Tamara A; Brasch, Juliane; Castell, Johanna C; Kaiser, Thomas

    2007-09-01

    Captive giraffe (Giraffa camelopardalis) mostly do not attain the longevity possible for this species and frequently have problems associated with low energy intake and fat storage mobilization. Abnormal tooth wear has been among the causes suggested as an underlying problem. This study utilizes a tooth wear scoring method ("mesowear") primarily used in paleobiology. This scoring method was applied to museum specimens of free-ranging (n=20) and captive (n=41) giraffes. The scoring system allows for the differentiation between attrition--(typical for browsers, as browse contains little abrasive silica) and abrasion--(typical for grazers, as grass contains abrasive silica) dominated tooth wear. The dental wear pattern of the free-ranging population is dominated by attrition, resembles that previously published for free-ranging giraffe, and clusters within browsing herbivores in comparative analysis. In contrast, the wear pattern of the captive population is dominated by abrasion and clusters among grazing herbivores in comparative analyses. A potential explanation for this difference in tooth wear is likely related to the content of abrasive elements in zoo diets. Silica content (measured as acid insoluble ash) is low in browse and alfalfa. However, grass hay and the majority of pelleted compound feeds contain higher amounts of silica. It can be speculated that the abnormal wear pattern in captivity compromises tooth function in captive giraffe, with deleterious long-term consequences.

  3. Activated iron-containing microglia in the human hippocampus identified by magnetic resonance imaging in Alzheimer disease

    PubMed Central

    Zeineh, Michael M.; Chen, Yuanxin; Kitzler, Hagen H.; Hammond, Robert; Vogel, Hannes; Rutt, Brian K.

    2016-01-01

    Although amyloid plaques and neurofibrillary pathology play important roles in Alzheimer disease (AD), our understanding of AD is incomplete, and the contribution of microglia and iron to neurodegeneration is unknown. High-field magnetic resonance imaging (MRI) is exquisitely sensitive to microscopic iron. To explore iron-associated neuroinflammatory AD pathology, we studied AD and control human brain specimens by (1) performing ultra-high resolution ex vivo 7 Tesla MRI, (2) coregistering the MRI with successive histologic staining for iron, microglia, amyloid beta, and tau, and (3) quantifying the relationship between magnetic resonance signal intensity and histological staining. In AD, we identified numerous small MR hypointensities primarily within the subiculum that were best explained by the combination of microscopic iron and activated microglia (p = 0.025), in contradistinction to the relatively lesser contribution of tau or amyloid. Neuropathologically, this suggests that microglial-mediated neurodegeneration may occur in the hippocampal formation in AD and is detectable by ultra-high resolution MRI. PMID:26190634

  4. Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma.

    PubMed

    DeNardo, Bradley D; Holloway, Michael P; Ji, Qinqin; Nguyen, Kevin T; Cheng, Yan; Valentine, Marcus B; Salomon, Arthur; Altura, Rachel A

    2013-01-01

    Neuroblastoma is an embryonal tumor of childhood with a heterogenous clinical presentation that reflects differences in activation of complex biological signaling pathways. Protein phosphorylation is a key component of cellular signal transduction and plays a critical role in processes that control cancer cell growth and survival. We used shotgun LC/MS to compare phosphorylation between a human MYCN amplified neuroblastoma cell line (NB10), modeling a resistant tumor, and a human neural precursor cell line (NPC), modeling a normal baseline neural crest cell. 2181 unique phosphorylation sites representing 1171 proteins and 2598 phosphopeptides were found. Protein kinases accounted for 6% of the proteome, with a predominance of tyrosine kinases, supporting their prominent role in oncogenic signaling pathways. Highly abundant receptor tyrosine kinase (RTK) phosphopeptides in the NB10 cell line relative to the NPC cell line included RET, insulin-like growth factor 1 receptor/insulin receptor (IGF-1R/IR), and fibroblast growth factor receptor 1 (FGFR1). Multiple phosphorylated peptides from downstream mediators of the PI3K/AKT/mTOR and RAS pathways were also highly abundant in NB10 relative to NPC. Our analysis highlights the importance of RET, IGF-1R/IR and FGFR1 as RTKs in neuroblastoma and suggests a methodology that can be used to identify potential novel biological therapeutic targets. Furthermore, application of this previously unexploited technology in the clinic opens the possibility of providing a new wide-scale molecular signature to assess disease progression and prognosis.

  5. Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis

    PubMed Central

    Fertig, Elana J.; Markovic, Ana; Danilova, Ludmila V.; Gaykalova, Daria A.; Cope, Leslie; Chung, Christine H.; Ochs, Michael F.; Califano, Joseph A.

    2013-01-01

    Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and –negative. Global DNA methylation changes are known to drive oncogene and tumor suppressor expression in primary HNSCC of both types. However, significant heterogeneity in DNA methylation within the groups results in different transcriptional profiles and clinical outcomes. We applied a meta-pathway analysis to link gene expression changes to DNA methylation in distinguishing HNSCC subtypes. This approach isolated specific epigenetic changes controlling expression in HPV− HNSCC that distinguish it from HPV+ HNSCC. Analysis of genes identified Hedgehog pathway activation specific to HPV− HNSCC. We confirmed that GLI1, the primary Hedgehog target, showed higher expression in tumors compared to normal samples with HPV− tumors having the highest GLI1 expression, suggesting that increased expression of GLI1 is a potential driver in HPV− HNSCC. Our algorithm for integration of DNA methylation and gene expression can infer biologically significant molecular pathways that may be exploited as therapeutics targets. Our results suggest that therapeutics targeting the Hedgehog pathway may be of benefit in HPV− HNSCC. Similar integrative analysis of high-throughput coupled DNA methylation and expression datasets may yield novel insights into deregulated pathways in other cancers. PMID:24223768

  6. Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis.

    PubMed

    Fertig, Elana J; Markovic, Ana; Danilova, Ludmila V; Gaykalova, Daria A; Cope, Leslie; Chung, Christine H; Ochs, Michael F; Califano, Joseph A

    2013-01-01

    Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and -negative. Global DNA methylation changes are known to drive oncogene and tumor suppressor expression in primary HNSCC of both types. However, significant heterogeneity in DNA methylation within the groups results in different transcriptional profiles and clinical outcomes. We applied a meta-pathway analysis to link gene expression changes to DNA methylation in distinguishing HNSCC subtypes. This approach isolated specific epigenetic changes controlling expression in HPV- HNSCC that distinguish it from HPV+ HNSCC. Analysis of genes identified Hedgehog pathway activation specific to HPV- HNSCC. We confirmed that GLI1, the primary Hedgehog target, showed higher expression in tumors compared to normal samples with HPV- tumors having the highest GLI1 expression, suggesting that increased expression of GLI1 is a potential driver in HPV- HNSCC. Our algorithm for integration of DNA methylation and gene expression can infer biologically significant molecular pathways that may be exploited as therapeutics targets. Our results suggest that therapeutics targeting the Hedgehog pathway may be of benefit in HPV- HNSCC. Similar integrative analysis of high-throughput coupled DNA methylation and expression datasets may yield novel insights into deregulated pathways in other cancers.

  7. Managing the Risk of Triggered Seismicity: Can We Identify (and Avoid) Potentially Active Faults? - A Practical Case Study in Oklahoma

    NASA Astrophysics Data System (ADS)

    Zoback, M. D.; Alt, R. C., II; Walsh, F. R.; Walters, R. J.

    2014-12-01

    It is well known that throughout the central and eastern U.S. there has been a marked increase in seismicity since 2009, at least some of which appears to increased wastewater injection. No area has seen a greater increase in seismicity than Oklahoma. In this paper, we utilize newly available information on in situ stress orientation and relative magnitudes, the distribution of high volume injection wells and knowledge of the intervals used for waste water disposal to identify the factors potentially contributing to the occurrence of triggered seismicity. While there are a number of sites where in situ stress data has been successfully used to identify potentially active faults, we are investigating whether this methodology can be implemented throughout a state utilizing the types of information frequently available in areas of oil and gas development. As an initial test of this concept, we have been compiling stress orientation data from wells throughout Oklahoma provided by private industry. Over fifty new high quality data points, principally drilling-induced tensile fractures observed in image logs, result in a greatly improved understanding of the stress field in much of the state. A relatively uniform ENE direction of maximum compressive stress is observed, although stress orientations (and possibly relative stress magnitudes) differ in the southern and southwestern parts of the state. The proposed methodology can be tested in the area of the NE-trending fault that produced the M 5+ earthquakes in the Prague, OK sequence in 2011, and the Meers fault in southwestern OK, that produced a M~7 reverse faulting earthquake about 1100 years ago. This methodology can also be used to essentially rule out slip on other major faults in the area, such as the ~N-S trending Nemaha fault system. Additional factors leading to the occurrence of relatively large triggered earthquakes in Oklahoma are 1) the overall increase in injection volumes throughout the state in recent

  8. Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment.

    PubMed

    Kaewseekhao, Benjawan; Naranbhai, Vivek; Roytrakul, Sittiruk; Namwat, Wises; Paemanee, Atchara; Lulitanond, Viraphong; Chaiprasert, Angkana; Faksri, Kiatichai

    2015-01-01

    Biomarkers for determining clearance of Mycobacterium tuberculosis (Mtb) infection during anti-tuberculosis therapy or following exposure could facilitate enhanced monitoring and treatment. We screened for biomarkers indicating clearance of Mtb infection in vitro. A comparative proteomic analysis was performed using GeLC MSI/MS. Intracellular and secreted proteomes from activated THP-1 cells infected with the Mtb H37Rv strain (MOI = 1) and treated with isoniazid and rifampicin for 1 day (infection stage) and 5 days (clearance stage) were analyzed. Host proteins associated with early infection (n = 82), clearance (n = 121), sustained in both conditions (n = 34) and suppressed by infection (n = 46) were elucidated. Of the potential clearance markers, SSFA2 and CAECAM18 showed the highest and lowest protein intensities, respectively. A western blot of CAECAM18 validated the LC MS/MS result. For three clearance markers (SSFA2, PARP14 and PSME4), in vivo clinical validation was concordantly reported in previous patient cohorts. A network analysis revealed that clearance markers were enriched amongst four protein interaction networks centered on: (i) CD44/CCND1, (ii) IFN-β1/NF-κB, (iii) TP53/TGF-β and (iv) IFN-γ/CCL2. After infection, proteins associated with proliferation, and recruitment of immune cells appeared to be enriched possibly reflecting recruitment of defense mechanisms. Counteracting proteins (CASP3 vs. Akt and NF-κB vs. TP53) associated with apoptosis regulation and its networks were enriched among the early and sustained infection biomarkers, indicating host-pathogen competition. The BRCA1/2 network was suppressed during infection, suggesting that cell proliferation suppression is a feature of Mtb survival. Our study provides insights into the mechanisms of host-Mtb interaction by comparing the stages of infection clearance. The identified clearance biomarkers may be useful in monitoring tuberculosis treatment.

  9. Cloning and expression of a transcription factor activator protein-1 (AP-1) member identified from manila clam Venerupis philippinarum.

    PubMed

    Wu, Luning; Zhang, Lei; Zhao, Jianmin; Ning, Xuanxuan; Mu, Changkao; Wang, Chunlin

    2015-02-15

    The transcription factor activator protein-1 (AP-1) proteins are implicated to play a major role in the regulation of numerous genes involved in the function and development of the immune system, cell differentiation, proliferation, apoptosis, etc. It can bind to promoter of its target genes in a sequence-specific manner to transactivate or repress them. In this study, the full-length cDNA of an AP-1 was identified from Venerupis philippinarum (denoted as VpAP-1) by EST analysis and RACE approaches. Phylogenetic analysis indicated that VpAP-1 had higher evolutional conservation to invertebrate than vertebrate counterparts and should be a new member of the AP-1 protein family. Spatial expression analysis found that VpAP-1 transcript was most abundantly expressed in the hemocytes and hepatopancreas, weakly expressed in the tissues of the gills, mantle and muscle. After Vibrio anguillarum challenge, the expression of VpAP-1 transcript in overall hemocyte population was up-regulated in the first 6h, and then decreased to 1.5-fold of the control group at 12h. As time progressed, a second peak of VpAP-1 expression was detected at 24h post-infection, which was 5-fold compared with that of the control group (P<0.01). After that, the expression level was sharply decreased and dropped to 0.5-fold of the control at 96h. The above results indicated that VpAP-1 was perhaps involved in the immune responses against microbe infection and might be contributed to the clearance of bacterial pathogens.

  10. Structural and functional assays of AtTLP18.3 identify its novel acid phosphatase activity in thylakoid lumen.

    PubMed

    Wu, Hsin-Yi; Liu, Mao-Sen; Lin, Tsan-Piao; Cheng, Yi-Sheng

    2011-11-01

    The membrane protein AtTLP18.3 of Arabidopsis (Arabidopsis thaliana) contains a domain of unknown function, DUF477; it forms a polysome with photosynthetic apparatuses in the thylakoid lumen. To explore the molecular function of AtTLP18.3, we resolved its crystal structures with residues 83 to 260, the DUF477 only, and performed a series of biochemical analyses to discover its function. The gene expression of AtTLP18.3 followed a circadian rhythm. X-ray crystallography revealed the folding of AtTLP18.3 as a three-layer sandwich with three α-helices in the upper layer, four β-sheets in the middle layer, and two α-helices in the lower layer, which resembles a Rossmann fold. Structural comparison suggested that AtTLP18.3 might be a phosphatase. The enzymatic activity of AtTLP18.3 was further confirmed by phosphatase assay with various substrates (e.g. p-nitrophenyl phosphate, 6,8-difluoro-4-methylumbelliferyl phosphate, O-phospho-L-serine, and several synthetic phosphopeptides). Furthermore, we obtained the structure of AtTLP18.3 in complex with O-phospho-L-serine to identify the binding site of AtTLP18.3. Our structural and biochemical studies revealed that AtTLP18.3 has the molecular function of a novel acid phosphatase in the thylakoid lumen. DUF477 is accordingly renamed the thylakoid acid phosphatase domain.

  11. Identifying Effective Strategies for Climate Change Education: The Coastal Areas Climate Change Education (CACCE) Partnership Audiences and Activities

    NASA Astrophysics Data System (ADS)

    Ryan, J. G.; Feldman, A.; Muller-Karger, F. E.; Gilbes, F.; Stone, D.; Plank, L.; Reynolds, C. J.

    2011-12-01

    Many past educational initiatives focused on global climate change have foundered on public skepticism and disbelief. Some key reasons for these past failures can be drawn directly from recognized best practices in STEM education - specifically, the necessity to help learners connect new knowledge with their own experiences and perspectives, and the need to create linkages with issues or concerns that are both important for and relevant to the audiences to be educated. The Coastal Areas Climate Change Education (CACCE) partnership has sought to follow these tenets as guiding principles in identifying critical audiences and developing new strategies for educating the public living in the low-lying coastal areas of Florida and the Caribbean on the realities, risks, and adaptation and mitigation strategies for dealing with the regional impacts of global climate change. CACCE is currently focused on three key learner audiences: a) The formal education spectrum, targeting K-12 curricula through middle school marine science courses, and student and educator audiences through coursework and participatory research strategies engaging participants in a range of climate-related investigations. b) Informal science educators and outlets, in particular aquaria and nature centers, as an avenue toward K-12 teacher professional development as well as for public education. c) Regional planning, regulatory and business professionals focused on the built environment along the coasts, many of whom require continuing education to maintain licensing and/or other professional certifications. Our current activities are focused on bringing together an effective set of educational, public- and private-sector partners to target the varied needs of these audiences in Florida and the U.S. Caribbean, and tailoring an educational plan aimed at these stakeholder audiences that starts with the regionally and topically relevant impacts of climate change, and strategies for effective adaptation and

  12. What Would You Like? Identifying the Required Characteristics of an Industry-Wide Incident Reporting and Learning System for the Led Outdoor Activity Sector

    ERIC Educational Resources Information Center

    Goode, Natassia; Finch, Caroline F.; Cassell, Erin; Lenne, Michael G.; Salmon, Paul M.

    2014-01-01

    The aim of this study was to identify the characteristics that led outdoor activity providers agree are necessary for the development of a new industry-wide incident reporting and learning system (UPLOADS). The study involved: 1) a literature review to identify a set of characteristics that are considered to be hallmarks of successful reporting…

  13. Identifying cold-water coral ecosystem by using benthic foraminiferal indicators: from active reefs to the geological record

    NASA Astrophysics Data System (ADS)

    Margreth, Stephan; Rüggeberg, Andres; Gennari, Giordana; Spezzaferri, Silvia

    2010-05-01

    Cold-water coral ecosystems dominated by the species Lophelia pertusa and Madrepora oculata, as well as cold-water coral carbonate mounds (fossils and/or active) occur worldwide and are especially developed along the European margin, from northern Norway to the Gulf of Cadiz and into the Alboran Sea. Their discovery is a major achievement of the last few decades and their widespread occurrence presents a challenge to understand their development, preservation and possible importance in the geologic record. On the Norwegian shelf active/living reefs are developed on elevated hard substrata. Along the Irish margin L. pertusa builds large fossil and/or active carbonate mounds. In the Gulf of Cadiz and in the Alboran Sea buried reefs and patch reefs are generally found in association with mud volcanoes. In modern oceans, they provide important ecological niches for the marine benthic fauna in the deep-sea. In comparison to the macrofauna the microfauna, particularly the foraminifera associated to these systems, are poorly known. We present here a detailed study based on quantitative analyses of benthic and planktonic foraminifera together with the statistical treatment of assemblage data collected along the Norwegian margin, in the Porcupine-Rockall region and in the Alboran Sea. The three regions were and/or are site of cold-water coral ecosystems settlements. Our study reveals that in the Porcupine/Rockall region benthic foraminiferal assemblages are strictly related to the distribution of facies. On the Norwegian margin, benthic foraminiferal habitats are weakly defined and grade one into the other preventing the sharp facies separation observed along the Irish margin (Margreth et al., 2009). In the Alboran Sea cold-water coral ecosystems and cold-water carbonate mounds are presently buried and corals are generally fragmented. However, benthic assemblages from coral-rich layers in the Alboran Sea and those from Porcupine/Rockall and Norway show remarkable

  14. Response to dietary tannin challenges in view of the browser/grazer dichotomy in an Ethiopian setting: Bonga sheep versus Kaffa goats.

    PubMed

    Yisehak, Kechero; Kibreab, Yoseph; Taye, Tolemariam; Lourenço, Marta Ribeiro Alves; Janssens, Geert Paul Jules

    2016-01-01

    It has been suggested that goats (typical browser) are better adapted to digest tannin-rich diets than sheep (typical grazer). To evaluate this, Bonga sheep and Kaffa goats were used in a 2 × 3 randomized crossover design with two species, three diets, and three periods (15-day adaptation + 7-day collection). The dietary treatments consisted of grass-based hay only (tannin-free diet = FT), a high-tannin diet (36% Albizia schimperiana (AS) + 9% Ficus elastica (FE) + 55% FT (HT)), and HT + polyethylene glycol 6000 (PEG). Animals were individually fed at 50 g dry matter (DM)/kg body weight (BW) and had free access to clean drinking water and mineralized salt licks. Nutrient intake, apparent nutrient digestibility, nutrient conversion ratios, and live weight changes were determined. Condensed tannin concentrations in AS and FE were 110 and 191 g/kg DM, respectively. Both sheep and goats ate 47% more of HT than FT, and dry matter intake further increased by 9% when PEG was added, with clear difference in effect size between goats and sheep (P < 0.001). The effects of the tannin-rich diet and PEG addition were similarly positive for DM digestibility between sheep and goats, but crude protein (CP) digestibility was higher in HT + PEG-fed goats than in sheep fed the same diet. However, PEG addition induced a larger improvement in growth performance and feed efficiency ratio in sheep than in goat (P < 0.001). The addition of PEG as a tannin binder improved digestion and performance in both species, but with the highest effect size in sheep.

  15. Re‐constructing nutritional history of Serengeti wildebeest from stable isotopes in tail hair: seasonal starvation patterns in an obligate grazer

    PubMed Central

    Rysava, K.; McGill, R. A. R.; Matthiopoulos, J.

    2016-01-01

    Rationale Nutritional bottlenecks often limit the abundance of animal populations and alter individual behaviours; however, establishing animal condition over extended periods of time using non‐invasive techniques has been a major limitation in population ecology. We test if the sequential measurement of δ15N values in a continually growing tissue, such as hair, can be used as a natural bio‐logger akin to tree rings or ice cores to provide insights into nutritional stress. Methods Nitrogen stable isotope ratios were measured by continuous‐flow isotope‐ratio mass spectrometry (IRMS) from 20 sequential segments along the tail hairs of 15 migratory wildebeest. Generalized Linear Models were used to test for variation between concurrent segments of hair from the same individual, and to compare the δ15N values of starved and non‐starved animals. Correlations between δ15N values in the hair and periods of above‐average energy demand during the annual cycle were tested using Generalized Additive Mixed Models. Results The time series of nitrogen isotope ratios in the tail hair are comparable between strands from the same individual. The most likely explanation for the pattern of 15N enrichment between individuals is determined by life phase, and especially the energetic demands associated with reproduction. The mean δ15N value of starved animals was greater than that of non‐starved animals, suggesting that higher δ15N values correlate with periods of nutritional stress. Conclusions High δ15N values in the tail hair of wildebeest are correlated with periods of negative energy balance, suggesting they may be used as a reliable indicator of the animal's nutritional history. This technique might be applicable to other obligate grazers. Most importantly, the sequential isotopic analysis of hair offers a continuous record of the chronic condition of wildebeest (effectively converting point data into time series) and allows researchers to establish the animal

  16. Using videography to quantify landscape-level availability of habitat for grazers: An example with emperor geese in western Alaska

    USGS Publications Warehouse

    Lake, B.C.; Lindberg, M.S.; Schmutz, J.A.; Anthony, R. Michael; Broerman, F.J.

    2006-01-01

    We present a videography approach to estimating large-scale availability of grazing lawns, an important food resource used by broods of emperor geese (Chen canagica) on the Yukon-Kuskokwim Delta, Alaska. Sampling was conducted in 1999, 2003, and 2004 at six locations that encompassed ???40% of the North American population of breeding emperor geese. We conducted ground truthing in 2003 and 2004 to estimate how accurately grazing lawn was classified. Overall, classification accuracy for grazing lawn and non-grazing lawn habitat was greater than 91%. Availability of grazing lawns was stable among years, but varied both among and within locations. Some locations have up to three times as much available grazing lawn, which in combination with densities of geese, likely represents dramatic variation in per capita food availability. Our results suggest that videography is a useful way to sample quickly across a large region and accurately identify fine-scale habitats. We present its use for estimating the availability of a preferred food resource for emperor geese, but the method could be applied to many other cases.

  17. Native and domestic browsers and grazers reduce fuels, fire temperatures, and acacia ant mortality in an African savanna.

    PubMed

    Kimuyu, Duncan M; Sensenig, Ryan L; Riginos, Corinna; Veblen, Kari E; Young, Truman P

    2014-06-01

    Despite the importance of fire and herbivory in structuring savanna systems, few replicated experiments have examined the interactive effects of herbivory and fire on plant dynamics. In addition, the effects of fire on associated ant-tree mutualisms have been largely unexplored. We carried out small controlled burns in each of 18 herbivore treatment plots of the Kenya Long-term Exclosure Experiment (KLEE), where experimentally excluding elephants has resulted in 42% greater tree densities. The KLEE design includes six different herbivore treatments that allowed us to examine how different combinations of megaherbivore wildlife, mesoherbivore wildlife, and cattle affect fire temperatures and subsequent loss of ant symbionts from Acacia trees. Before burning, we quantified herbaceous fuel loads and plant community composition. We tagged all trees, measured their height and basal diameter, and identified the resident ant species on each. We recorded weather conditions during the burns and used ceramic tiles painted with fire-sensitive paints to estimate fire temperatures at different heights and in different microsites (under vs. between trees). Across all treatments, fire temperatures were highest at 0-50 cm off the ground and hotter in the grass under trees than in the grassy areas between trees. Plots with more trees burned hotter than plots with fewer trees, perhaps because of greater fine woody debris. Plots grazed by wildlife and by cattle prior to burning had lower herbaceous fuel loads and experienced lower burn temperatures than ungrazed plots. Many trees lost their ant colonies during the burns. Ant survivorship differed by ant species and at the plot level was positively associated with previous herbivory (and lower fire temperatures). Across all treatments, ant colonies on taller trees were more likely to survive, but even some of the tallest trees lost their ant colonies. Our study marks a significant step in understanding the mechanisms that underlie the

  18. Relevance of macrozoobenthic grazers to understand the dynamic behaviour of sediment erodibility and microphytobenthos resuspension in sunny summer conditions

    NASA Astrophysics Data System (ADS)

    Orvain, Francis; Guizien, Katell; Lefebvre, Sébastien; Bréret, Martine; Dupuy, Christine

    2014-09-01

    The quantification of overall microphytobenthos productivity should include the export of biomass from the intertidal zone during high tides, which implies refined estimates and concepts of erosion parameters. For the first time, the export of microphytobenthic cells was assessed over an intertidal mudflat in the Marennes-Oléron Bay, France, during a complete spring/neap tide modulation. In the summer of 2008, resuspension rates of chl-a exported only reached 2.5% of the standing stock of benthic diatoms on each day. Sedimentary factors failed to explain any variation regarding bed and microphytobenthos erodibility. During the early fluff layer erosion phase, there were negative effects of grazing activities exerted by motile infauna (Peringia ulvae) on erosion fluxes of chl-a, while there was a related positive correlation with pheopigment proportion. The erosion process plays an important role in this vegetal-herbivore interaction by reinforcing the decline of the microphytobenthic biomass and provoking a catastrophic shift to mass erosion after a sequence of several days of co-occurring intense grazing by snails and chl-a decline. During mass erosion, the biofilm decline explained the variations of sediment erodibility, with a marked negative correlation between bound extracellular polymeric substance (EPS) proteins and critical threshold for bed erosion, in contrast with the commonly observed positive influence of EPS secretion on bed resistance. The complex nature of the effects of EPS by microphytobenthos must be further investigated to unravel their complex role in bioengineering sediments. The increase of protein proportion in EPS could provide specific properties related to hydrophilic features. Nevertheless, the level of grazing pressure by P. ulvae should be so intense that the top-down control must explain this original finding, since there was a positive correlation of proteins in EPS and snail density that could be related to mucus secretion (as a

  19. Identifying Chronic Conditions and Other Selected Factors That Motivate Physical Activity in World Senior Games Participants and the General Population

    PubMed Central

    Bowen, Elise; Hager, Ron L.

    2015-01-01

    This study assesses chronic disease or disease-related conditions as motivators of physical activity. It also compares these and other motivators of physical activity between Senior Games participants (SGPs) and the general population. Analyses are based on an anonymous cross-sectional survey conducted among 666 SGPs and 177 individuals from the general population. SGPs experienced better general health and less obesity, diabetes, and depression, as well as an average of 14.7 more years of regular physical activity (p < .0001), 130.8 more minutes per week of aerobic activity (p < .0001), and 42.7 more minutes of anaerobic activity per week (p < .0001). Among those previously told they had diabetes, high blood pressure, high cholesterol, or depression, 74.2%, 72.2%, 70.4%, and 60.6%, respectively, said that it motivated them to increase their physical activity. Percentages were similar between SGPs and the general population. SGPs were more likely motivated to be physically active to improve physical and mental health in the present, to prevent physical and cognitive decline in the future, and to increase social opportunities. The Senior Games reinforces extrinsic motivators to positively influence intrinsic promoters such as skill development, satisfaction of learning, enjoyment, and fun. PMID:28138459

  20. Identifying the number and location of body worn sensors to accurately classify walking, transferring and sedentary activities.

    PubMed

    Aziz, Omar; Robinovitch, Stephen N; Park, Edward J

    2016-08-01

    In order to perform fall risk assessments using wearable inertial sensors in older adults in their natural settings where falls are likely to occur, a first step is to automatically segment and classify sensor signals of human movements into the known `activities of interest'. Sensor data from such activities can later be used through quantitative and qualitative analysis for differentiating fallers from non-fallers. In this study, ten young adults participated in experimental trials involving several variations of walking, transferring and sedentary activities. Data from tri-axial accelerometers and gyroscopes were used to classify the aforementioned three categories using a multiclass support vector machine algorithm. Our results showed 100% accuracy in distinguishing walking, transferring and sedentary activities using data from a three-sensor combination of sternum and both ankles.

  1. In Vitro Activity of Ceftolozane-Tazobactam against Anaerobic Organisms Identified during the ASPECT-cIAI Study

    PubMed Central

    Farrell, David J.; Palchak, Melissa; Steenbergen, Judith N.

    2015-01-01

    The in vitro activities of ceftolozane-tazobactam, meropenem, and metronidazole were determined against anaerobic organisms isolated from patients with complicated intraabdominal infections (cIAI) in global phase III studies. Ceftolozane-tazobactam activity was highly variable among different species of the Bacteroides fragilis group, with MIC90 values ranging from 2 to 64 μg/ml. More-potent in vitro activity was observed against selected Gram-positive anaerobic organisms; however, small numbers of isolates were available, and, therefore, the clinical significance of these results is unknown. Variable activity of ceftolozane-tazobactam against anaerobic organisms necessitates use in combination with metronidazole for the treatment of cIAI. PMID:26552971

  2. Identifying the role of N-heteroatom location in the activity of metal catalysts for alcohol oxidation

    SciTech Connect

    Chan-Thaw, Carine E.; Veith, Gabriel M.; Villa, Alberto; Prati, Laura

    2015-04-02

    Here, this work focuses on understanding how the bonding of nitrogen heteroatoms contained on/in a activated carbon support influence the stability and reactivity of a supported Pd catalyst for the oxidation of alcohols in solution. The results show that simply adding N groups via solution chemistry is insufficient to improve catalytic properties. Instead a strongly bound N moiety is required to activate the catalyst and stabilize the metal particles.

  3. Novel spinal pathways identified by neuronal c-Fos expression after urethrogenital reflex activation in female guinea pigs.

    PubMed

    Yuan, S Y; Vilimas, P I; Zagorodnyuk, V P; Gibbins, I L

    2015-03-12

    Pudendal nerve-spinal pathways are involved in urethrogenital sensation, pain and sexual activity. However, details of these pathways and their modulation are unclear. We examined spinal pathways activated by the urethrogenital reflex (UGR) and visualized by c-Fos immunoreactivity in reflexly activated neurons within spinal cord. In anesthetized female guinea pigs, a balloon was inserted into the urethra and inflated with short-repeat or long-continuous distension to activate the UGR. A second balloon recorded reflex contractions of the vagina and uterus. Two control groups had either no balloon or a vaginal balloon (VB) only. Ninety minutes after UGR activation, c-Fos immunoreactivity in L3 and S2 spinal segments was examined. Reflex activated c-Fos immunoreactivity also was investigated in some animals with acute spinal transections at either L4 or T12 levels. There was no significant difference in spinal c-Fos expression between the control groups. Short-repeat distension reliably induced a UGR and a two- to threefold increase in c-Fos-expressing neurons throughout dorsal, intermediate and lateral spinal gray matter at S2 and about twofold increase in superficial dorsal horn at L3. T12 transection had little effect on c-Fos expression at either spinal level. However, after L4 transection, UGR generation was associated with a four- to sixfold increase in c-Fos-expressing neurons in lateral horn (LH) and central canal areas at S2, and but only 20-30% increase at L3. Thus, UGR activates preganglionic neurons projecting to pelvic viscera in both sacral and lumbar spinal cord. The reflex also must activate ascending and descending spinal inhibitory circuits that suppress c-Fos-expression in neurons at both sacral and lumbar spinal levels.

  4. Genetic and biochemical dissection of a HisKA domain identifies residues required exclusively for kinase and phosphatase activities.

    PubMed

    Willett, Jonathan W; Kirby, John R

    2012-01-01

    Two-component signal transduction systems, composed of histidine kinases (HK) and response regulators (RR), allow bacteria to respond to diverse environmental stimuli. The HK can control both phosphorylation and subsequent dephosphorylation of its cognate RR. The majority of HKs utilize the HisKA subfamily of dimerization and histidine phosphotransfer (DHp) domains, which contain the phospho-accepting histidine and directly contact the RR. Extensive genetics, biochemistry, and structural biology on several prototypical TCS systems including NtrB-NtrC and EnvZ-OmpR have provided a solid basis for understanding the function of HK-RR signaling. Recently, work on NarX, a HisKA_3 subfamily protein, indicated that two residues in the highly conserved region of the DHp domain are responsible for phosphatase activity. In this study we have carried out both genetic and biochemical analyses on Myxococcus xanthus CrdS, a member of the HisKA subfamily of bacterial HKs. CrdS is required for the regulation of spore formation in response to environmental stress. Following alanine-scanning mutagenesis of the α1 helix of the DHp domain of CrdS, we determined the role for each mutant protein for both kinase and phosphatase activity. Our results indicate that the conserved acidic residue (E372) immediately adjacent to the site of autophosphorylation (H371) is specifically required for kinase activity but not for phosphatase activity. Conversely, we found that the conserved Thr/Asn residue (N375) was required for phosphatase activity but not for kinase activity. We extended our biochemical analyses to two CrdS homologs from M. xanthus, HK1190 and HK4262, as well as Thermotoga maritima HK853. The results were similar for each HisKA family protein where the conserved acidic residue is required for kinase activity while the conserved Thr/Asn residue is required for phosphatase activity. These data are consistent with conserved mechanisms for kinase and phosphatase activities in the

  5. ISD97, a computer program to analyze data from a series of in situ measurements on a grid and identify potential localized areas of elevated activity

    SciTech Connect

    Reginatto, M.; Shebell, P.; Miller, K.M.

    1997-10-01

    A computer program, ISD97, was developed to analyze data from a series of in situ measurements on a grid and identify potential localized areas of elevated activity. The ISD97 code operates using a two-step process. A deconvolution of the data is carried out using the maximum entropy method, and a map of activity on the ground that fits the data within experimental error is generated. This maximum entropy map is then analyzed to determine the locations and magnitudes of potential areas of elevated activity that are consistent with the data. New deconvolutions are then carried out for each potential area of elevated activity identified by the code. Properties of the algorithm are demonstrated using data from actual field measurements.

  6. Identifying Hazards

    EPA Pesticide Factsheets

    The federal government has established a system of labeling hazardous materials to help identify the type of material and threat posed. Summaries of information on over 300 chemicals are maintained in the Envirofacts Master Chemical Integrator.

  7. Structure of the active N-terminal domain of Ezrin. Conformational and mobility changes identify keystone interactions.

    PubMed

    Smith, William James; Nassar, Nicolas; Bretscher, Anthony; Cerione, Richard A; Karplus, P Andrew

    2003-02-14

    Ezrin is a member of the ERM (ezrin, radixin, moesin) family of proteins that cross-link the actin cytoskeleton to the plasma membrane and also may function in signaling cascades that regulate the assembly of actin stress fibers. Here, we report a crystal structure for the free (activated) FERM domain (residues 2-297) of recombinant human ezrin at 2.3 A resolution. Structural comparison among the dormant moesin FERM domain structure and the three known active FERM domain structures (radixin, moesin, and now ezrin) allows the clear definition of regions that undergo structural changes during activation. The key regions affected are residues 135-150 and 155-180 in lobe F2 and residues 210-214 and 235-267 in lobe F3. Furthermore, we show that a large increase in the mobilities of lobes F2 and F3 accompanies activation, suggesting that their integrity is compromised. This leads us to propose a new concept that we refer to as keystone interactions. Keystone interactions occur when one protein (or protein part) contributes residues that allow another protein to complete folding, meaning that it becomes an integral part of the structure and would rarely dissociate. Such interactions are well suited for long-lived cytoskeletal protein interactions. The keystone interactions concept leads us to predict two specific docking sites within lobes F2 and F3 that are likely to bind target proteins.

  8. Activated-ion electron transfer dissociation improves the ability of electron transfer dissociation to identify peptides in a complex mixture.

    PubMed

    Ledvina, Aaron R; Beauchene, Nicole A; McAlister, Graeme C; Syka, John E P; Schwartz, Jae C; Griep-Raming, Jens; Westphall, Michael S; Coon, Joshua J

    2010-12-15

    Using a modified electron transfer dissociation (ETD)-enabled quadrupole linear ion trap (QLT) mass spectrometer, we demonstrate the utility of IR activation concomitant with ETD ion-ion reactions (activated-ion ETD, AI-ETD). Analyzing 12 strong cation exchanged (SCX) fractions of a LysC digest of human cell protein extract using ETD, collision-activated dissociation (CAD), and AI-ETD, we find that AI-ETD generates 13 405 peptide spectral matches (PSMs) at a 1% false-discovery rate (1% FDR), surpassing both ETD (7 968) and CAD (10 904). We also analyze 12 SCX fractions of a tryptic digest of human cell protein extract and find that ETD produces 6 234 PSMs, AI-ETD 9 130 PSMs, and CAD 15 209 PSMs. Compared to ETD with supplemental collisional activation (ETcaD), AI-ETD generates ∼80% more PSMs for the whole cell lysate digested with trypsin and ∼50% more PSMs for the whole cell lysate digested with LysC.

  9. Micro-grazer biomass, composition and distribution across prey resource and dissolved oxygen gradients in the far eastern tropical north Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Brady Olson, M.; Daly, Kendra L.

    2013-05-01

    The ecology of micro-grazers (Mg) was investigated across prey and dissolved oxygen (DO) gradients in the eastern tropical north Pacific Ocean (ETNP) during October-November 2007. Surface (<200 m) chlorophyll a (Chl a) across a ˜1700 km north-south transect ranged between the seasonal average of 0.2 μg Chl a L-1 to 1.8 μg Chl a L-1 in an extensive Chl a-rich patch in the center of the transect. Limiting (<20 μmol kg-1 O2) DO concentrations were encountered as shallow as 24 m. Biomass of Mg in waters above the upper oxycline (UO) ranged between 5.6 μg C L-1 and 36.6 μg C L-1, with highest Mg biomass observed in locations with highest Chl a. Heterotrophic dinoflagellates contributed most, on average, to Mg biomass (41% to 53%), followed by aloricate spirotrich ciliates (24% to 29%) and heterotrophic nanoflagellates (11% to 33%). Biomass of Mg decreased, on average, over 96% in waters below the UO, but this decrease did not appear to be regulated by DO; Mg biomass more strongly correlated with Chl a (r=0.83, P<0.001) and temperature (r=0.76, P<0.001) at discrete depths than with DO (r=0.67, P<0.001). Using a multiple stepwise regression model, Chl a alone accounted for 68% Mg biomass variability, whereas Chl a and temperature combined accounted for 84%. In two Mg grazing experiments we found that Mg removed 33% and 108% of surface primary production in the upper mixed layer. These estimates of Mg grazing, while limited in scope, fall within estimates from other regions of the equatorial Pacific Ocean, and help reinforce the paradigm that Mg are influential in regulating organic carbon dynamics in the eastern tropical Pacific. A primary finding from this study was that observations of Mg biomass are higher than previously reported for the ETNP. This observation suggests that the region's complex air-sea interactions and the resultant positive influence on primary production and phytoplankton biomass can episodically support high biomass of a diverse Mg community.

  10. Water-borne cues of a non-indigenous seaweed mediate grazer-deterrent responses in native seaweeds, but not vice versa.

    PubMed

    Yun, Hee Young; Engelen, Aschwin H; Santos, Rui O; Molis, Markus

    2012-01-01

    Plants optimise their resistance to herbivores by regulating deterrent responses on demand. Induction of anti-herbivory defences can occur directly in grazed plants or from emission of risk cues to the environment, which modifies interactions of adjacent plants with, for instance, their consumers. This study confirmed the induction of anti-herbivory responses by water-borne risk cues between adjoining con-specific seaweeds and firstly examined whether plant-plant signalling also exists among adjacent hetero-specific seaweeds. Furthermore, differential abilities and geographic variation in plant-plant signalling by a non-indigenous seaweed as well as native seaweeds were assessed. Twelve-day induction experiments using the non-indigenous seaweed Sargassum muticum were conducted in the laboratory in Portugal and Germany with one local con-familiar (Portugal: Cystoseira humilis, Germany: Halidrys siliquosa) and hetero-familiar native species (Portugal: Fucus spiralis, Germany: F. vesiculosus). All seaweeds were grazed by a local isopod species (Portugal: Stenosoma nadejda, Germany: Idotea baltica) and were positioned upstream of con- and hetero-specific seaweeds. Grazing-induced modification in seaweed traits were tested in three-day feeding assays between cue-exposed and cue-free ( = control) pieces of both fresh and reconstituted seaweeds. Both Fucus species reduced their palatability when positioned downstream of isopod-grazed con-specifics. Yet, the palatability of non-indigenous S. muticum remained constant in the presence of upstream grazed con-specifics and native hetero-specifics. In contrast, both con-familiar (but neither hetero-familiar) native species reduced palatability when located downstream of grazed S. muticum. Similar patterns of grazer-deterrent responses to water-borne cues were observed on both European shores, and were almost identical between assays using fresh and reconstituted seaweeds. Hence, seaweeds may use plant-plant signalling to

  11. Identifying Drug (Cocaine) Intake Events from Acute Physiological Response in the Presence of Free-living Physical Activity.

    PubMed

    Hossain, Syed Monowar; Ali, Amin Ahsan; Rahman, Mahbubur; Ertin, Emre; Epstein, David; Kennedy, Ashley; Preston, Kenzie; Umbricht, Annie; Chen, Yixin; Kumar, Santosh

    2014-01-01

    A variety of health and behavioral states can potentially be inferred from physiological measurements that can now be collected in the natural free-living environment. The major challenge, however, is to develop computational models for automated detection of health events that can work reliably in the natural field environment. In this paper, we develop a physiologically-informed model to automatically detect drug (cocaine) use events in the free-living environment of participants from their electrocardiogram (ECG) measurements. The key to reliably detecting drug use events in the field is to incorporate the knowledge of autonomic nervous system (ANS) behavior in the model development so as to decompose the activation effect of cocaine from the natural recovery behavior of the parasympathetic nervous system (after an episode of physical activity). We collect 89 days of data from 9 active drug users in two residential lab environments and 922 days of data from 42 active drug users in the field environment, for a total of 11,283 hours. We develop a model that tracks the natural recovery by the parasympathetic nervous system and then estimates the dampening caused to the recovery by the activation of the sympathetic nervous system due to cocaine. We develop efficient methods to screen and clean the ECG time series data and extract candidate windows to assess for potential drug use. We then apply our model on the recovery segments from these windows. Our model achieves 100% true positive rate while keeping the false positive rate to 0.87/day over (9+ hours/day of) lab data and to 1.13/day over (11+ hours/day of) field data.

  12. A Repurposing Approach Identifies Off-Patent Drugs with Fungicidal Cryptococcal Activity, a Common Structural Chemotype, and Pharmacological Properties Relevant to the Treatment of Cryptococcosis

    PubMed Central

    Butts, Arielle; DiDone, Louis; Koselny, Kristy; Baxter, Bonnie K.; Chabrier-Rosello, Yeissa; Wellington, Melanie

    2013-01-01

    New, more accessible therapies for cryptococcosis represent an unmet clinical need of global importance. We took a repurposing approach to identify previously developed drugs with fungicidal activity toward Cryptococcus neoformans, using a high-throughput screening assay designed to detect drugs that directly kill fungi. From a set of 1,120 off-patent medications and bioactive molecules, we identified 31 drugs/molecules with fungicidal activity, including 15 drugs for which direct antifungal activity had not previously been reported. A significant portion of the drugs are orally bioavailable and cross the blood-brain barrier, features key to the development of a widely applicable anticryptococcal agent. Structural analysis of this set revealed a common chemotype consisting of a hydrophobic moiety linked to a basic amine, features that are common to drugs that cross the blood-brain barrier and access the phagolysosome, two important niches of C. neoformans. Consistent with their fungicidal activity, the set contains eight drugs that are either additive or synergistic in combination with fluconazole. Importantly, we identified two drugs, amiodarone and thioridazine, with activity against intraphagocytic C. neoformans. Finally, the set of drugs is also enriched for molecules that inhibit calmodulin, and we have confirmed that seven drugs directly bind C. neoformans calmodulin, providing a molecular target that may contribute to the mechanism of antifungal activity. Taken together, these studies provide a foundation for the optimization of the antifungal properties of a set of pharmacologically attractive scaffolds for the development of novel anticryptococcal therapies. PMID:23243064

  13. Characterization of RAB-like4, the first identified RAB-like protein from Trypanosoma cruzi with GTPase activity.

    PubMed

    Ramos, Fabiane Pereira; Araripe, Júlia Rolão; Urményi, Turán Péter; Silva, Rosane; Cunha e Silva, Narcisa Leal; Leite Fontes, Carlos Frederico; da Silveira, José Franco; Rondinelli, Edson

    2005-08-05

    RAB proteins, which belong to the RAS superfamily, regulate exocytic and endocytic pathways of eukaryotic cells, controlling vesicle docking and fusion. Few RAB proteins have been identified in parasites. Molecular markers for cellular compartments are important to studies concerning about the protein traffic in Trypanosoma cruzi, the causal agent of Chagas disease. In this work, we describe the characterization of TcRABL4, the first RAB-like gene identified in T. cruzi (GenBank Accession No.: ), present as a single-copy gene. TcRABL4 contains all five consensus RAB motifs but lacks cysteine residues at the C terminus, which are essential to isoprenylation, an absolute prerequisite for membrane association of these proteins. TcRABL4 is a functional GTPase that is able to bind and hydrolyze GTP, and its gene is transcribed as a single 1.2 kb mRNA in epimastigotes. TcRABL4 appears to be differentially regulated in the three cell forms of the parasite, and the protein is not associated to membranes, unlike other RAB proteins. It is possible that TcRABL4 may be a member of a novel family of small GTPases.

  14. A Systematic In Silico Search for Target Similarity Identifies Several Approved Drugs with Potential Activity against the Plasmodium falciparum Apicoplast

    PubMed Central

    Bispo, Nadlla Alves; Culleton, Richard; Silva, Lourival Almeida; Cravo, Pedro

    2013-01-01

    Most of the drugs in use against Plasmodium falciparum share similar modes of action and, consequently, there is a need to identify alternative potential drug targets. Here, we focus on the apicoplast, a malarial plastid-like organelle of algal source which evolved through secondary endosymbiosis. We undertake a systematic in silico target-based identification approach for detecting drugs already approved for clinical use in humans that may be able to interfere with the P. falciparum apicoplast. The P. falciparum genome database GeneDB was used to compile a list of ≈600 proteins containing apicoplast signal peptides. Each of these proteins was treated as a potential drug target and its predicted sequence was used to interrogate three different freely available databases (Therapeutic Target Database, DrugBank and STITCH3.1) that provide synoptic data on drugs and their primary or putative drug targets. We were able to identify several drugs that are expected to interact with forty-seven (47) peptides predicted to be involved in the biology of the P. falciparum apicoplast. Fifteen (15) of these putative targets are predicted to have affinity to drugs that are already approved for clinical use but have never been evaluated against malaria parasites. We suggest that some of these drugs should be experimentally tested and/or serve as leads for engineering new antimalarials. PMID:23555651

  15. Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in Atlantic cod.

    PubMed

    Kleppe, Lene; Edvardsen, Rolf Brudvik; Furmanek, Tomasz; Taranger, Geir Lasse; Wargelius, Anna

    2014-07-01

    The molecular mechanisms underlying oogenesis and maternally controlled embryogenesis in fish are not fully understood, especially in marine species. Our aim was to study the egg and embryo transcriptome during oogenesis and early embryogenesis in Atlantic cod. Follicles from oogenesis stages (pre-, early-, and late-vitellogenic), ovulated eggs, and two embryonic stages (blastula, gastrula) were collected from broodstock fish and fertilized eggs. Gene expression profiles were measured in a 44 K oligo microarray consisting of 23,000 cod genes. Hundreds of differentially expressed genes (DEGs) were identified in the follicle stages investigated, implicating a continuous accumulation and degradation of polyadenylated transcripts throughout oogenesis. Very few DEGs were identified from ovulated egg to blastula, showing a more stable maternal RNA pool in early embryonic stages. The highest induction of expression was observed between blastula and gastrula, signifying the onset of zygotic transcription. During early vitellogenesis, several of the most upregulated genes are linked to nervous system signaling, suggesting increasing requirements for ovarian synaptic signaling to stimulate the rapid growth of oocytes. Highly upregulated genes during late vitellogenesis are linked to protein processing, fat metabolism, osmoregulation, and arrested meiosis. One of the genes with the highest upregulation in the ovulated egg is involved in oxidative phosphorylation, reflecting increased energy requirements during fertilization and the first rapid cell divisions of early embryogenesis. In conclusion, this study provides a large-scale presentation of the Atlantic cod's maternally controlled transcriptome in ovarian follicles through oogenesis, ovulated eggs, and early embryos.

  16. Activated-Ion ETD (AI-ETD) Improves the Ability of ETD to Identify Peptides in a Complex Mixture

    PubMed Central

    Ledvina, Aaron R.; Beauchene, Nicole A.; McAlister, Graeme C.; Syka, John E. P.; Schwartz, Jae C.; Griep-Raming, Jens; Westphall, Michael S.; Coon, Joshua J.

    2010-01-01

    Using a modified ETD-enabled QLT mass spectrometer, we demonstrate the utility of IR activation concomitant with ETD ion-ion reactions (activated-ion ETD, AI-ETD). Analyzing 12 SCX fractions of a LysC digest of human cells (HS) using ETD, CAD, and AI-ETD, we find that AI-ETD generates 13,405 peptide spectral matches (PSMs) at a 1% false-discovery rate (1% FDR), surpassing both ETD (7,968) and CAD (10,904). We also analyze 12 SCX fractions of a tryptic HS digest and find that ETD produces 6,234 PSMs, AI-ETD 9,130 PSMs, and CAD 15,209 PSMs. Compared to ETcaD, AI-ETD generates ~80% more PSMs for tryptic whole cell lysate and ~50% more PSMs for LysC whole cell lysate. PMID:21062032

  17. Optimal conditions for identifying 80Br and 128I in health food Angelica keiskei using rapid epithermal neutron activation analysis.

    PubMed

    Chen, Chien-Yi

    2003-04-01

    This study presents an optimal rapid epithermal neutron activation analysis (ENAA) technique, using a 1mm Cd filter in reactor neutron flux, to analyze 80Br and 128I in the roots, stems, and leaves of health food Angelica keiskei (AK). Various sample weights of lichen (IAEA-336) for each portion of AK, under various periods of irradiation and counting, were used to optimize the elemental analysis. Selecting the analytical conditions depends on the minimum detectable concentration (MDC), required sensitivities and the quantitative accuracy of Br and I elements. These findings imply that the MDCs of Br and I, measured under 10min activation and 5min counting followed by 10min decaying, using 350mg of lichen are ideal for elemental analysis. Moreover, each portions of AK were analyzed under optimal conditions. The elemental concentrations of Br, Cl, I, Mg, Mn and Na and their implications are discussed.

  18. Cu-free cycloaddition for identifying catalytic active adenylation domains of nonribosomal peptide synthetases by phage display.

    PubMed

    Zou, Yekui; Yin, Jun

    2008-10-15

    To engineer the substrate specificities of nonribosomal peptide synthetases (NRPS), we developed a method to display NRPS modules on M13 phages and select catalytically active adenylation (A) domains that would load azide functionalized substrate analogs to the neighboring peptidyl carrier protein (PCP) domains. Biotin conjugated difluorinated cyclooctyne was used for copper free cycloaddition with an azide substituted substrate attached to PCP. Biotin-labeled phages were selected by binding to streptavidin.

  19. Using community-based participatory research to identify potential interventions to overcome barriers to adolescents’ healthy eating and physical activity

    PubMed Central

    Goh, Ying-Ying; Sipple-Asher, Bessie Ko; Uyeda, Kimberly; Hawes-Dawson, Jennifer; Olarita-Dhungana, Josephina; Ryan, Gery W.; Schuster, Mark A.

    2010-01-01

    Using a community-based participatory research approach, we explored adolescent, parent, and community stakeholder perspectives on barriers to healthy eating and physical activity, and intervention ideas to address adolescent obesity. We conducted 14 adolescent focus groups (n = 119), 8 parent focus groups (n = 63), and 28 interviews with community members (i.e., local experts knowledgeable about youth nutrition and physical activity). Participants described ecological and psychosocial barriers in neighborhoods (e.g., lack of accessible nutritious food), in schools (e.g., poor quality of physical education), at home (e.g., sedentary lifestyle), and at the individual level (e.g., lack of nutrition knowledge). Participants proposed interventions such as nutrition classes for families, addition of healthy school food options that appeal to students, and non-competitive physical education activities. Participants supported health education delivered by students. Findings demonstrate that community-based participatory research is useful for revealing potentially feasible interventions that are acceptable to community members. PMID:19544091

  20. Functional Analysis of Adenovirus Protein IX Identifies Domains Involved in Capsid Stability, Transcriptional Activity, and Nuclear Reorganization

    PubMed Central

    Rosa-Calatrava, Manuel; Grave, Linda; Puvion-Dutilleul, Francine; Chatton, Bruno; Kedinger, Claude

    2001-01-01

    The product of adenovirus (Ad) type 5 gene IX (pIX) is known to actively participate in the stability of the viral icosahedron, acting as a capsid cement. We have previously demonstrated that pIX is also a transcriptional activator of several viral and cellular TATA-containing promoters, likely contributing to the transactivation of the Ad expression program. By extensive mutagenesis, we have now delineated the functional domains involved in each of the pIX properties: residues 22 to 26 of the highly conserved N-terminal domain are crucial for incorporation of the protein into the virion; specific residues of the C-terminal leucine repeat are responsible for pIX interactions with itself and possibly other proteins, a property that is critical for pIX transcriptional activity. We also show that pIX takes part in the virus-induced nuclear reorganization of late infected cells: the protein induces, most likely through self-assembly, the formation of specific nuclear structures which appear as dispersed nuclear globules by immunofluorescence staining and as clear amorphous spherical inclusions by electron microscopy. The integrity of the leucine repeat appears to be essential for the formation and nuclear retention of these inclusions. Together, our results demonstrate the multifunctional nature of pIX and provide new insights into Ad biology. PMID:11435594

  1. Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in atlantic cod

    PubMed Central

    Kleppe, Lene; Edvardsen, Rolf Brudvik; Furmanek, Tomasz; Taranger, Geir Lasse; Wargelius, Anna

    2014-01-01

    The molecular mechanisms underlying oogenesis and maternally controlled embryogenesis in fish are not fully understood, especially in marine species. Our aim was to study the egg and embryo transcriptome during oogenesis and early embryogenesis in Atlantic cod. Follicles from oogenesis stages (pre-, early-, and late-vitellogenic), ovulated eggs, and two embryonic stages (blastula, gastrula) were collected from broodstock fish and fertilized eggs. Gene expression profiles were measured in a 44 K oligo microarray consisting of 23,000 cod genes. Hundreds of differentially expressed genes (DEGs) were identified in the follicle stages investigated, implicating a continuous accumulation and degradation of polyadenylated transcripts throughout oogenesis. Very few DEGs were identified from ovulated egg to blastula, showing a more stable maternal RNA pool in early embryonic stages. The highest induction of expression was observed between blastula and gastrula, signifying the onset of zygotic transcription. During early vitellogenesis, several of the most upregulated genes are linked to nervous system signaling, suggesting increasing requirements for ovarian synaptic signaling to stimulate the rapid growth of oocytes. Highly upregulated genes during late vitellogenesis are linked to protein processing, fat metabolism, osmoregulation, and arrested meiosis. One of the genes with the highest upregulation in the ovulated egg is involved in oxidative phosphorylation, reflecting increased energy requirements during fertilization and the first rapid cell divisions of early embryogenesis. In conclusion, this study provides a large-scale presentation of the Atlantic cod's maternally controlled transcriptome in ovarian follicles through oogenesis, ovulated eggs, and early embryos. Mol. Reprod. Dev. 81: 619–635, 2014. © 2014 Wiley Periodicals, Inc. PMID:24687555

  2. Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment.

    PubMed

    Macdonald, Catriona A; Crawley, Michael J; Wright, Denis J; Kuczynski, Justin; Robinson, Lucinda; Knight, Rob; Al-Soud, Waleed Abu; Sørensen, Søren J; Deng, Ye; Zhou, Jizhong; Singh, Brajesh K

    2015-03-01

    Herbivory is an important modulator of plant biodiversity and productivity in grasslands, but our understanding of herbivore-induced changes on below-ground processes and communities is limited. Using a long-term (17 years) experimental site, we evaluated impacts of rabbit and invertebrate grazers on some soil functions involved in carbon cycling, microbial diversity, structure and functional composition. Both rabbit and invertebrate grazing impacted soil functions and microbial community structure. All functional community measures (functions, biogeochemical cycling genes, network association between different taxa) were more strongly affected by invertebrate grazers than rabbits. Furthermore, our results suggest that exclusion of invertebrate grazers decreases both microbial biomass and abundance of genes associated with key biogeochemical cycles, and could thus have long-term consequences for ecosystem functions. The mechanism behind these impacts are likely to be driven by both direct effects of grazing altering the pattern of nutrient inputs and by indirect effects through changes in plant species composition. However, we could not entirely discount that the pesticide used to exclude invertebrates may have affected some microbial community measures. Nevertheless, our work illustrates that human activity that affects grazing intensity may affect ecosystem functioning and sustainability, as regulated by multi-trophic interactions between above- and below-ground communities.

  3. HCS Campaign to Identify Selective Inhibitors of IL-6-Induced STAT3 Pathway Activation in Head and Neck Cancer Cell Lines

    PubMed Central

    Sen, Malabika; Hua, Yun; Camarco, Daniel P.; Shun, Tong Ying; Lazo, John S.; Wilson, Gabriela Mustata; Resnick, Lynn O.; LaPorte, Matthew G.; Wipf, Peter; Huryn, Donna M.; Grandis, Jennifer R.

    2015-01-01

    Abstract Signal transducer and activator of transcription factor 3 (STAT3) is hyperactivated in head and neck squamous cell carcinomas (HNSCC). Cumulative evidence indicates that IL-6 production by HNSCC cells and/or stromal cells in the tumor microenvironment activates STAT3 and contributes to tumor progression and drug resistance. A library of 94,491 compounds from the Molecular Library Screening Center Network (MLSCN) was screened for the ability to inhibit interleukin-6 (IL-6)-induced pSTAT3 activation. For contractual reasons, the primary high-content screening (HCS) campaign was conducted over several months in 3 distinct phases; 1,068 (1.1%) primary HCS actives remained after cytotoxic or fluorescent outliers were eliminated. One thousand one hundred eighty-seven compounds were cherry-picked for confirmation; actives identified in the primary HCS and compounds selected by a structural similarity search of the remaining MLSCN library using hits identified in phases I and II of the screen. Actives were confirmed in pSTAT3 IC50 assays, and an IFNγ-induced pSTAT1 activation assay was used to prioritize selective inhibitors of STAT3 activation that would not inhibit STAT1 tumor suppressor functions. Two hundred three concentration-dependent inhibitors of IL-6-induced pSTAT3 activation were identified and 89 of these also produced IC50s against IFN-γ-induced pSTAT1 activation. Forty-nine compounds met our hit criteria: they reproducibly inhibited IL-6-induced pSTAT3 activation by ≥70% at 20 μM; their pSTAT3 activation IC50s were ≤25 μM; they were ≥2-fold selective for pSTAT3 inhibition over pSTAT1 inhibition; a cross target query of PubChem indicated that they were not biologically promiscuous; and they were ≥90% pure. Twenty-six chemically tractable hits that passed filters for nuisance compounds and had acceptable drug-like and ADME-Tox properties by computational evaluation were purchased for characterization. The hit structures were distributed

  4. Identifying Effective Enzyme Activity Targets for Recombinant Class I and Class II Collagenase for Successful Human Islet Isolation

    PubMed Central

    Balamurugan, Appakalai N.; Green, Michael L.; Breite, Andrew G.; Loganathan, Gopalakrishnan; Wilhelm, Joshua J.; Tweed, Benjamin; Vargova, Lenka; Lockridge, Amber; Kuriti, Manikya; Hughes, Michael G.; Williams, Stuart K.; Hering, Bernhard J.; Dwulet, Francis E.; McCarthy, Robert C.

    2016-01-01

    Background Isolation following a good manufacturing practice-compliant, human islet product requires development of a robust islet isolation procedure where effective limits of key reagents are known. The enzymes used for islet isolation are critical but little is known about the doses of class I and class II collagenase required for successful islet isolation. Methods We used a factorial approach to evaluate the effect of high and low target activities of recombinant class I (rC1) and class II (rC2) collagenase on human islet yield. Consequently, 4 different enzyme formulations with divergent C1:C2 collagenase mass ratios were assessed, each supplemented with the same dose of neutral protease. Both split pancreas and whole pancreas models were used to test enzyme targets (n = 20). Islet yield/g pancreas was compared with historical enzymes (n = 42). Results Varying the Wunsch (rC2) and collagen degradation activity (CDA, rC1) target dose, and consequently the C1:C2 mass ratio, had no significant effect on tissue digestion. Digestions using higher doses of Wunsch and CDA resulted in comparable islet yields to those obtained with 60% and 50% of those activities, respectively. Factorial analysis revealed no significant main effect of Wunsch activity or CDA for any parameter measured. Aggregate results from 4 different collagenase formulations gave 44% higher islet yield (>5000 islet equivalents/g) in the body/tail of the pancreas (n = 12) when compared with those from the same segment using a standard natural collagenase/protease mixture (n = 6). Additionally, islet yields greater than 5000 islet equivalents/g pancreas were also obtained in whole human pancreas. Conclusions A broader C1:C2 ratio can be used for human islet isolation than has been used in the past. Recombinant collagenase is an effective replacement for the natural enzyme and we have determined that high islet yield can be obtained even with low doses of rC1:rC2, which is beneficial for the survival

  5. A postmenopause-like model of ovariectomized Wistar rats to identify active principles of Erythrina lysistemon (Fabaceae).

    PubMed

    Mvondo, M A; Njamen, D; Fomum, S Tanee; Wandji, J; Vollmer, Günter

    2011-10-01

    To determine whether the two major compounds of Erythrina lysistemon are active principles accounting for Erythrina estrogenic effects, we used a postmenopause-like model of ovariectomized Wistar rats to evaluate their effects on some menopausal problems. Ovariectomized rats were orally treated either with compound 1 or compound 2 at 1 and 10 mg/kg BW for 28 days. Estradiol valerate served as the reference substance. As results, compounds 1 and 2 displayed estrogen-like effects on the uterus and the vagina, and reduced atherogenic risks by decreasing the two assessed atherogenic parameters, the total cholesterol/HDL-cholesterol ratio and the atherogenic index of plasma.

  6. Development and application of a sensitive, phenotypic, high-throughput image-based assay to identify compound activity against Trypanosoma cruzi amastigotes

    PubMed Central

    Sykes, Melissa L.; Avery, Vicky M.

    2015-01-01

    We have developed a high content 384-well, image-based assay to estimate the effect of compound treatment on Trypanosoma cruzi amastigotes in 3T3 fibroblasts. In the same well, the effect of compound activity on host cells can also be determined, as an initial indicator of cytotoxicity. This assay has been used to identify active compounds from an in-house library of compounds with either known biological activity or that are FDA approved, and separately, from the Medicines for Malaria Venture Malaria Box collection. Active compounds were screened against T. cruzi trypomastigotes, utilising an assay developed with the viability dye resazurin. Twelve compounds with reconfirmed solid sample activity, with IC50 values of less than 10 μM and selectivity indices to T. cruzi amastigotes over 3T3 host cells of between >22 and 319 times were identified from these libraries. As 3T3 cells are contact inhibited, with limited proliferation in the assay, selective compounds of interest were profiled in a separate assay to estimate the viability of compound treated, replicating HEK293 cells. Selective compounds that were not previously reported in the literature were further profiled by extending the incubation time against amastigote infected 3T3 cells to determine if there were residual amastigotes post-treatment, important for the consideration of the exposure time required for further biological characterisation. The assay development process and the suitability of identified compounds as hit molecules for Chagas disease research are discussed. PMID:27120069

  7. Development and application of a sensitive, phenotypic, high-throughput image-based assay to identify compound activity against Trypanosoma cruzi amastigotes.

    PubMed

    Sykes, Melissa L; Avery, Vicky M

    2015-12-01

    We have developed a high content 384-well, image-based assay to estimate the effect of compound treatment on Trypanosoma cruzi amastigotes in 3T3 fibroblasts. In the same well, the effect of compound activity on host cells can also be determined, as an initial indicator of cytotoxicity. This assay has been used to identify active compounds from an in-house library of compounds with either known biological activity or that are FDA approved, and separately, from the Medicines for Malaria Venture Malaria Box collection. Active compounds were screened against T. cruzi trypomastigotes, utilising an assay developed with the viability dye resazurin. Twelve compounds with reconfirmed solid sample activity, with IC50 values of less than 10 μM and selectivity indices to T. cruzi amastigotes over 3T3 host cells of between >22 and 319 times were identified from these libraries. As 3T3 cells are contact inhibited, with limited proliferation in the assay, selective compounds of interest were profiled in a separate assay to estimate the viability of compound treated, replicating HEK293 cells. Selective compounds that were not previously reported in the literature were further profiled by extending the incubation time against amastigote infected 3T3 cells to determine if there were residual amastigotes post-treatment, important for the consideration of the exposure time required for further biological characterisation. The assay development process and the suitability of identified compounds as hit molecules for Chagas disease research are discussed.

  8. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

    PubMed Central

    Tena, Juan J.; González-Aguilera, Cristina; Fernández-Miñán, Ana; Vázquez-Marín, Javier; Parra-Acero, Helena; Cross, Joe W.; Rigby, Peter W.J.; Carvajal, Jaime J.; Wittbrodt, Joachim; Gómez-Skarmeta, José L.; Martínez-Morales, Juan R.

    2014-01-01

    The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer’s formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115–200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan. PMID:24709821

  9. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.

    PubMed

    Tena, Juan J; González-Aguilera, Cristina; Fernández-Miñán, Ana; Vázquez-Marín, Javier; Parra-Acero, Helena; Cross, Joe W; Rigby, Peter W J; Carvajal, Jaime J; Wittbrodt, Joachim; Gómez-Skarmeta, José L; Martínez-Morales, Juan R

    2014-07-01

    The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer's formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115-200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan.

  10. In Vitro Activities of Tigecycline and Eight Other Antimicrobials against Different Nocardia Species Identified by Molecular Methods▿

    PubMed Central

    Cercenado, Emilia; Marín, Mercedes; Sánchez-Martínez, Mónica; Cuevas, Oscar; Martínez-Alarcón, José; Bouza, Emilio

    2007-01-01

    The in vitro activities of tigecycline and other antimicrobials against 51 isolates of Nocardia spp. were evaluated. MIC90s and MIC ranges were as follows: tigecycline, 4 and ≤0.06 to 8 mg/liter, respectively; minocycline, 2 and ≤0.06 to 2 mg/liter, respectively; linezolid, 1 and ≤0.06 to 2 mg/liter, respectively; moxifloxacin, 2 and ≤0.06 to >64 mg/liter, respectively; ertapenem, 32 and ≤0.06->64 mg/liter, respectively; imipenem, 2 and ≤0.06 to >64 mg/liter, respectively; meropenem, 8 and ≤0.06 to >64 mg/liter, respectively; amikacin, 1 and ≤0.06 to 32 mg/liter, respectively; and trimethoprim-sulfamethoxazole, 1/19 and ≤0.5/9.5 to >2/38 mg/liter, respectively. PMID:17194827

  11. Quantitative keratinocyte assay detects two biological activities of human papillomavirus DNA and identifies viral types associated with cervical carcinoma.

    PubMed Central

    Schlegel, R; Phelps, W C; Zhang, Y L; Barbosa, M

    1988-01-01

    Keratinocytes electroporated with human papillomavirus (HPV) DNA (HPV-6, 11, 16 and 18) exhibited an increased cellular proliferation which was quantitated as microcolony and macrocolony formation. However, only macrocolonies induced by HPV-16 or HPV-18 DNA (the two viral types most commonly found in human cervical carcinomas) gave rise to proliferating, poorly-stratified colonies when grown in the presence of serum and calcium. Hydrocortisone increased the frequency of these differentiation-resistant colonies, and studies showed that they were immortalized, contained one copy of viral DNA per cell, expressed three discrete species of viral RNA and synthesized the viral E7 protein. HPV-induced cellular proliferation and altered differentiation are therefore separable events and may represent the activity of different viral genes. Images PMID:2460337

  12. Biological activities of some Acacia spp. (Fabaceae) against new clinical isolates identified by ribosomal RNA gene-based phylogenetic analysis.

    PubMed

    Mahmoud, Mahmoud Fawzy; Alrumman, Sulaiman Abdullah; Hesham, Abd El-Latif

    2016-01-01

    Nowadays,most of the pathogenic bacteria become resistant to antibiotics. Therefore,the pharmaceutical properties of the natural plant extracts have become of interest to researchers as alternative antimicrobial agents. In this study,antibacterial activities of extract gained from Acacia etbaica, Acacia laeta, Acacia origena and Acacia pycnantha have been evaluated against isolated pathogenic bacteria (Strains MFM-01, MFM-10 and AH-09) using agar well diffusion methods.The bacterial strains were isolated from infected individuals,and their exact identification was detected on the basis of 16S rRNA gene amplification and sequence determination. Alignment results and the comparison of 16 SrRN A gene sequences of the isolates to 16 SrRN A gene sequences available in Gen Bank data base as well as the phylogenetic analysis confirmed the accurate position of the isolates as Klebsiella oxytoca strain MFM-01, Staphylococcus aureus strain MFM-10 and Klebsiella pneumoniae strain AH-09. Except for cold water, all tested solvents (Chloroform, petroleum ether, methanol, diethyl ether, and acetone) showed variation in their activity against studied bacteria. GC-MS analysis of ethanol extracts showed that four investigated Acacia species have different phyto components. Eight important pharmaceutical components were found in the legume of Acacia etbaica, seven in the legume of Acacia laeta, fifteen in the legume of Acacia origena and nine in the leaves of Acacia pycnantha. A dendrogram was constructed based on chemical composition, revealed that Acacia laeta is more closely related to Acacia etbaica forming on eclade, whereas Acacia origena less similar to other species. Our results demonstrated that, investigated plants and chemical compounds present could be used as promising antibacterial agents.

  13. Transcript profiling of Paoenia ostii during artificial chilling induced dormancy release identifies activation of GA pathway and carbohydrate metabolism.

    PubMed

    Gai, Shupeng; Zhang, Yuxi; Liu, Chunying; Zhang, Yang; Zheng, Guosheng

    2013-01-01

    Endo-dormant flower buds must pass through a period of chilling to reinitiate growth and subsequent flowering, which is a major obstacle to the forcing culture of tree peony in winter. Customized cDNA microarray (8×15 K element) was used to investigate gene expression profiling in tree peony 'Feng Dan Bai' buds during 24 d chilling treatment at 0-4°C. According to the morphological changes after the whole plants were transferred to green house, endo-dormancy was released after 18 d chilling treatment, and prolonged chilling treatment increased bud break rate. Pearson correlation hierarchical clustering of sample groups was highly consistent with the dormancy transitions revealed by morphological changes. Totally 3,174 significantly differentially-expressed genes (P<0.05) were observed through endo-dormancy release process, of which the number of up-regulated (1,611) and that of down-regulated (1,563) was almost the same. Functional annotation of differentially-expressed genes revealed that cellular process, metabolic process, response to stimulus, regulation of biological process and development process were well-represented. Hierarchical clustering indicated that activation of genes involved in carbohydrate metabolism (Glycolysis, Citrate cycle and Pentose phosphate pathway), energy metabolism and cell growth. Based on the results of GO analysis, totally 51 probes presented in the microarray were associated with GA response and GA signaling pathway, and 22 of them were differently expressed. The expression profiles also revealed that the genes of GA biosynthesis, signaling and response involved in endo-dormancy release. We hypothesized that activation of GA pathway played a central role in the regulation of dormancy release in tree peony.

  14. Characterization of Escherichia coli UmuC active-site loops identifies variants that confer UV hypersensitivity.

    PubMed

    Hawver, Lisa A; Gillooly, Caitlin A; Beuning, Penny J

    2011-10-01

    DNA is constantly exposed to chemical and environmental mutagens, causing lesions that can stall replication. In order to deal with DNA damage and other stresses, Escherichia coli utilizes the SOS response, which regulates the expression of at least 57 genes, including umuDC. The gene products of umuDC, UmuC and the cleaved form of UmuD, UmuD', form the specialized E. coli Y-family DNA polymerase UmuD'2C, or polymerase V (Pol V). Y-family DNA polymerases are characterized by their specialized ability to copy damaged DNA in a process known as translesion synthesis (TLS) and by their low fidelity on undamaged DNA templates. Y-family polymerases exhibit various specificities for different types of DNA damage. Pol V carries out TLS to bypass abasic sites and thymine-thymine dimers resulting from UV radiation. Using alanine-scanning mutagenesis, we probed the roles of two active-site loops composed of residues 31 to 38 and 50 to 54 in Pol V activity by assaying the function of single-alanine variants in UV-induced mutagenesis and for their ability to confer resistance to UV radiation. We find that mutations of the N-terminal residues of loop 1, N32, N33, and D34, confer hypersensitivity to UV radiation and to 4-nitroquinoline-N-oxide and significantly reduce Pol V-dependent UV-induced mutagenesis. Furthermore, mutating residues 32, 33, or 34 diminishes Pol V-dependent inhibition of recombination, suggesting that these mutations may disrupt an interaction of UmuC with RecA, which could also contribute to the UV hypersensitivity of cells expressing these variants.

  15. A novel ranacyclin-like peptide with anti-platelet activity identified from skin secretions of the frog Amolops loloensis.

    PubMed

    Hao, Xue; Tang, Xiaopeng; Luo, Lei; Wang, Yuming; Lai, Ren; Lu, Qiumin

    2016-01-15

    Albeit many bioactive peptides have been reported from amphibian skins, no anti-platelet peptide has been identified till to date. Here, an anti-platelet peptide, namely Zongdian platelet inhibitor (ZDPI), with the molecular weight of 1798.6 Da, was purified and characterized from skin secretions of the frog, Amolops loloensis. The amino acid sequence of ZDPI was determined as FRGCWLKNYSPRGCL-NH2 by combination methods of Edman degradation, mass spectrometry analysis and carboxypeptidase Y treatment revealing that it is composed of 15 amino acid residues with two cysteines formed an intra-molecular disulfide bridge and C-terminal amidation. cDNA encoding ZDPI precursor was cloned from skin cDNA library of A. loloensis. The precursor is composed of 63 amino acid (aa) residues including the predicted signal peptide (22 aa), an acidic spacer peptide (19 aa), and mature ZDPI. BLAST search indicates that ZDPI belongs to antimicrobial peptide family of ranacyclin, peptide leucine arginine or odorranain. It was found to inhibit ADP-induced platelet aggregation in a dose-dependent manner. At the concentration of 32 μg/ml, ZDPI completely inhibited platelet aggregation induced by ADP. To the best of our knowledge, this is the first report about an anti-platelet peptide from amphibian skin secretions. Considering its strong inhibitory ability on platelets and simple structure, ZDPI might be an excellent candidate or template to develop anti-thrombosis agent. In addition, the discovery of anti-platelet peptide in the frog skin increases biological function spectrum of amphibian skin peptides.

  16. Use of thermal desorption gas chromatography-olfactometry/mass spectrometry for the comparison of identified and unidentified odor active compounds emitted from building products containing linseed oil.

    PubMed

    Clausen, P A; Knudsen, H N; Larsen, K; Kofoed-Sørensen, V; Wolkoff, P; Wilkins, C K

    2008-11-14

    The emission of odor active volatile organic compounds (VOCs) from a floor oil based on linseed oil, the linseed oil itself and a low-odor linseed oil was investigated by thermal desorption gas chromatography combined with olfactometry and mass spectrometry (TD-GC-O/MS). The oils were applied to filters and conditioned in the micro emission cell, FLEC, for 1-3days at ambient temperature, an air exchange rate of 26.9h(-1) and a 30% relative humidity. These conditions resulted in dynamic headspace concentrations and composition of the odor active VOCs that may be similar to real indoor setting. Emission samples for TD-GC-O/MS analysis from the FLEC were on Tenax TA. Although many volatile VOCs were detected by MS, only the odor active VOCs are reported here. In total, 142 odor active VOCs were detected in the emissions from the oils. About 50 of the odor active VOCs were identified or tentatively identified by GC-MS. While 92 VOCs were detected from the oil used in the floor oil, only 13 were detected in the low-odor linseed oil. The major odor active VOCs were aldehydes and carboxylic acids. Spearmen rank correlation of the GC-O profiles showed that the odor profile of the linseed oil likely influenced the odor profile of the floor oil based on this linseed oil.

  17. A Drug Combination Screen Identifies Drugs Active against Amoxicillin-Induced Round Bodies of In Vitro Borrelia burgdorferi Persisters from an FDA Drug Library

    PubMed Central

    Feng, Jie; Shi, Wanliang; Zhang, Shuo; Sullivan, David; Auwaerter, Paul G.; Zhang, Ying

    2016-01-01

    Although currently recommended antibiotics for Lyme disease such as doxycycline or amoxicillin cure the majority of the patients, about 10–20% of patients treated for Lyme disease may experience lingering symptoms including fatigue, pain, or joint and muscle aches. Under experimental stress conditions such as starvation or antibiotic exposure, Borrelia burgdorferi can develop round body forms, which are a type of persister bacteria that appear resistant in vitro to customary first-line antibiotics for Lyme disease. To identify more effective drugs with activity against the round body form of B. burgdorferi, we established a round body persister model induced by exposure to amoxicillin (50 μg/ml) and then screened the Food and Drug Administration drug library consisting of 1581 drug compounds and also 22 drug combinations using the SYBR Green I/propidium iodide viability assay. We identified 23 drug candidates that have higher activity against the round bodies of B. burgdorferi than either amoxicillin or doxycycline. Eleven individual drugs scored better than metronidazole and tinidazole which have been previously described to be active against round bodies. In this amoxicillin-induced round body model, some drug candidates such as daptomycin and clofazimine also displayed enhanced activity which was similar to a previous screen against stationary phase B. burgdorferi persisters not exposure to amoxicillin. Additional candidate drugs active against round bodies identified include artemisinin, ciprofloxacin, nifuroxime, fosfomycin, chlortetracycline, sulfacetamide, sulfamethoxypyridazine and sulfathiozole. Two triple drug combinations had the highest activity against amoxicillin-induced round bodies and stationary phase B. burgdorferi persisters: artemisinin/cefoperazone/doxycycline and sulfachlorpyridazine/daptomycin/doxycycline. These findings confirm and extend previous findings that certain drug combinations have superior activity against B. burgdorferi

  18. Antiviral Activity and Possible Mechanism of Action of Constituents Identified in Paeonia lactiflora Root toward Human Rhinoviruses

    PubMed Central

    Ngan, Luong Thi My; Jang, Myeong Jin; Kwon, Min Jung; Ahn, Young Joon

    2015-01-01

    Human rhinoviruses (HRVs) are responsible for more than half of all cases of the common cold and cost billions of USD annually in medical visits and missed school and work. An assessment was made of the antiviral activities and mechanisms of action of paeonol (PA) and 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose (PGG) from Paeonia lactiflora root toward HRV-2 and HRV-4 in MRC5 cells using a tetrazolium method and real-time quantitative reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. Results were compared with those of a reference control ribavirin. Based on 50% inhibitory concentration values, PGG was 13.4 and 18.0 times more active toward HRV-2 (17.89 μM) and HRV-4 (17.33 μM) in MRC5 cells, respectively, than ribavirin. The constituents had relatively high selective index values (3.3–>8.5). The 100 μg/mL PA and 20 μg/mL PGG did not interact with the HRV-4 particles. These constituents inhibited HRV-4 infection only when they were added during the virus inoculation (0 h), the adsorption period of HRVs, but not after 1 h or later. Moreover, the RNA replication levels of HRVs were remarkably reduced in the MRC5 cultures treated with these constituents. These findings suggest that PGG and PA may block or reduce the entry of the viruses into the cells to protect the cells from the virus destruction and abate virus replication, which may play an important role in interfering with expressions of rhinovirus receptors (intercellular adhesion molecule-1 and low-density lipoprotein receptor), inflammatory cytokines (interleukin (IL)-6, IL-8, tumor necrosis factor, interferon beta, and IL-1β), and Toll-like receptor, which resulted in diminishing symptoms induced by HRV. Global efforts to reduce the level of synthetic drugs justify further studies on P. lactiflora root-derived materials as potential anti-HRV products or lead molecules for the prevention or treatment of HRV. PMID:25860871

  19. An HSV-based library screen identifies PP1α as a negative TRPV1 regulator with analgesic activity in models of pain

    PubMed Central

    Reinhart, Bonnie; Goins, William F; Harel, Asaff; Chaudhry, Suchita; Goss, James R; Yoshimura, Naoki; de Groat, William C; Cohen, Justus B; Glorioso, Joseph C

    2016-01-01

    Transient receptor potential vanilloid 1 (TRPV1) is a pronociceptive cation channel involved in persistent inflammatory and neuropathic pain. Herpes simplex virus (HSV) vector expression of TRPV1 causes cell death in the presence of capsaicin, thereby completely blocking virus replication. Here we describe a selection system for negative regulators of TRPV1 based on rescue of virus replication. HSV-based coexpression of TRPV1 and a PC12 cell-derived cDNA library identified protein phosphatase 1α (PP1α) as a negative regulator of TRPV1, mimicking the activity of “poreless” (PL), a dominant-negative mutant of TRPV1. Vectors expressing PP1α or PL reduced thermal sensitivity following virus injection into rat footpads, but failed to reduce the nocifensive responses to menthol/icilin-activated cold pain or formalin, demonstrating that the activity identified in vitro is functional in vivo with a degree of specificity. This system should prove powerful for identifying other cellular factors that can inhibit ion channel activity. PMID:27382601

  20. Variability of the groundwater sulfate concentration in fractured rock slopes: a tool to identify active unstable areas

    NASA Astrophysics Data System (ADS)

    Binet, S.; Spadini, L.; Bertrand, C.; Guglielmi, Y.; Mudry, J.; Scavia, C.

    2009-12-01

    Water chemical analysis of 100 springs from the Orco and the Tinée valleys (Western Italy and Southern France) and a 7 year groundwater chemistry monitoring of the 5 main springs were performed. All these springs drain from crystalline rock slopes. Some of these drain from currently active gravitational slope deformations. All groundwaters flowing through presently unstable slopes show anomalies in the sulfate concentrations compared to stable aquifers. Particularly, an increase of sulfate concentrations was observed repeatedly after each of five consecutive landslides on the La Clapière slope, thus attesting to the mechanical deformations are at the origin of this concentration change. Significant changes in the water chemistry are produced even from slow (mm/year) and low magnitude deformations of the geological settings. Pyrite nuclei in open fractures were found to be coated by iron oxides. This suggests that the increase of dissolved sulfate relates to oxidative dissolution of Pyrite. Speciation calculations of Pyrite versus Gypsum confirmed that observed changes in the sulfate concentrations is predominantly provided from Pyrite. Calculated amounts of dissolved minerals in the springs water was obtained through inverse modelling of the major ion water analysis data. It is shown that the concentration ratio of calculated dissolved Pyrite versus calculated dissolved gneiss rock allows us to unambiguously distinguish water from stable and unstable areas. This result opens an interesting perspective for the follow-up of sliding or friction dynamic in landslides or in (a) seismic faults.

  1. Identifying the Atomic-Level Effects of Metal Composition on the Structure and Catalytic Activity of Peptide-Templated Materials.

    PubMed

    Merrill, Nicholas A; McKee, Erik M; Merino, Kyle C; Drummy, Lawrence F; Lee, Sungsik; Reinhart, Benjamin; Ren, Yang; Frenkel, Anatoly I; Naik, Rajesh R; Bedford, Nicholas M; Knecht, Marc R

    2015-12-22

    Bioinspired approaches for the formation of metallic nanomaterials have been extensively employed for a diverse range of applications including diagnostics and catalysis. These materials can often be used under sustainable conditions; however, it is challenging to control the material size, morphology, and composition simultaneously. Here we have employed the R5 peptide, which forms a 3D scaffold to direct the size and linear shape of bimetallic PdAu nanomaterials for catalysis. The materials were prepared at varying Pd:Au ratios to probe optimal compositions to achieve maximal catalytic efficiency. These materials were extensively characterized at the atomic level using transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, and atomic pair distribution function analysis derived from high-energy X-ray diffraction patterns to provide highly resolved structural information. The results confirmed PdAu alloy formation, but also demonstrated that significant surface structural disorder was present. The catalytic activity of the materials was studied for olefin hydrogenation, which demonstrated enhanced reactivity from the bimetallic structures. These results present a pathway to the bioinspired production of multimetallic materials with enhanced properties, which can be assessed via a suite of characterization methods to fully ascertain structure/function relationships.

  2. Pharmacological inhibition of nicotinamide phosphoribosyltransferase/visfatin enzymatic activity identifies a new inflammatory pathway linked to NAD.

    PubMed

    Busso, Nathalie; Karababa, Mahir; Nobile, Massimo; Rolaz, Aline; Van Gool, Frédéric; Galli, Mara; Leo, Oberdan; So, Alexander; De Smedt, Thibaut

    2008-05-21

    Nicotinamide phosphoribosyltransferase (NAMPT), also known as visfatin, is the rate-limiting enzyme in the salvage pathway of NAD biosynthesis from nicotinamide. Since its expression is upregulated during inflammation, NAMPT represents a novel clinical biomarker in acute lung injury, rheumatoid arthritis, and Crohn's disease. However, its role in disease progression remains unknown. We report here that NAMPT is a key player in inflammatory arthritis. Increased expression of NAMPT was confirmed in mice with collagen-induced arthritis, both in serum and in the arthritic paw. Importantly, a specific competitive inhibitor of NAMPT effectively reduced arthritis severity with comparable activity to etanercept, and decreased pro-inflammatory cytokine secretion in affected joints. Moreover, NAMPT inhibition reduced intracellular NAD concentration in inflammatory cells and circulating TNFalpha levels during endotoxemia in mice. In vitro pharmacological inhibition of NAMPT reduced the intracellular concentration of NAD and pro-inflammatory cytokine secretion by inflammatory cells. Thus, NAMPT links NAD metabolism to inflammatory cytokine secretion by leukocytes, and its inhibition might therefore have therapeutic efficacy in immune-mediated inflammatory disorders.

  3. Identifying Model Inaccuracies and Solution Uncertainties in Non-Invasive Activation-Based Imaging of Cardiac Excitation using Convex Relaxation

    PubMed Central

    Erem, Burak; van Dam, Peter M.; Brooks, Dana H.

    2014-01-01

    Noninvasive imaging of cardiac electrical function has begun to move towards clinical adoption. Here we consider one common formulation of the problem, in which the goal is to estimate the spatial distribution of electrical activation times during a cardiac cycle. We address the challenge of understanding the robustness and uncertainty of solutions to this formulation. This formulation poses a non-convex, non-linear least squares optimization problem. We show that it can be relaxed to be convex, at the cost of some degree of physiological realism of the solution set, and that this relaxation can be used as a framework to study model inaccuracy and solution uncertainty. We present two examples, one using data from a healthy human subject and the other synthesized with the ECGSIM software package. In the first case, we consider uncertainty in the initial guess and regularization parameter. In the second case, we mimic the presence of an ischemic zone in the heart in a way which violates a model assumption. We show that the convex relaxation allows understanding of spatial distribution of parameter sensitivity in the first case, and identification of model violation in the second. PMID:24710159

  4. Peptidomic analysis of skin secretions from the bullfrog Lithobates catesbeianus (Ranidae) identifies multiple peptides with potent insulin-releasing activity.

    PubMed

    Mechkarska, Milena; Ojo, Opeolu O; Meetani, Mohammed A; Coquet, Laurent; Jouenne, Thierry; Abdel-Wahab, Yasser H A; Flatt, Peter R; King, Jay D; Conlon, J Michael

    2011-02-01

    Using a combination of reversed-phase HPLC and electrospray mass spectrometry, peptidomic analysis of norepinephrine-stimulated skin secretions of the American bullfrog Lithobates catesbeianus Shaw, 1802 led to the identification and characterization of five newly described peptides (ranatuerin-1CBb, ranatuerin-2CBc, and -CBd, palustrin-2CBa, and temporin-CBf) together with seven peptides previously isolated on the basis of their antimicrobial activity (ranatuerin-1CBa, ranatuerin-2CBa, brevinin-1CBa, and -1CBb, temporin-CBa, -CBb, and -CBd). The abilities of the most abundant of the purified peptides to stimulate the release of insulin from the rat BRIN-BD11 clonal β cell line were evaluated. Ranatuerin-2CBd (GFLDIIKNLGKTFAGHMLDKIRCTIGTCPPSP) was the most potent peptide producing a significant stimulation of insulin release (119% of basal rate, P<0.01) from BRIN-BD11 cells at a concentration of 30nM, with a maximum response (236% of basal rate, P<0.001) at a concentration of 3μM. Ranatuerin-2CBd did not stimulate release of the cytosolic enzyme, lactate dehydrogenase at concentrations up to 3μM, indicating that the integrity of the plasma membrane had been preserved. Brevinin-1CBb (FLPFIARLAAKVFPSIICSVTKKC) produced the maximum stimulation of insulin release (285% of basal rate, P<0.001 at 3μM) but the peptide was cytotoxic at this concentration.

  5. Identifying the redox activity of cation-disordered Li-Fe-V-Ti oxide cathodes for Li-ion batteries.

    PubMed

    Chen, Ruiyong; Witte, Ralf; Heinzmann, Ralf; Ren, Shuhua; Mangold, Stefan; Hahn, Horst; Hempelmann, Rolf; Ehrenberg, Helmut; Indris, Sylvio

    2016-03-21

    Cation-disordered oxides have recently shown promising properties on the way to explore high-performance intercalation cathode materials for rechargeable Li-ion batteries. Here, stoichiometric cation-disordered Li2FeVyTi1-yO4 (y = 0, 0.2, 0.5) nanoparticles are studied. The substitution of V for Ti in Li2FeVyTi1-yO4 increases the content of active transition metals (Fe and V) and accordingly the amount of Li(+) (about (1 + y)Li(+) capacity per formula unit) that can be reversibly intercalated. It is found that Fe(3+)/Fe(2+) and V(4+)/V(3+) redox couples contribute to the overall capacity performance, whereas Ti(4+) remains mainly inert. There is no evidence for the presence of Fe(4+) species after charging to 4.8 V, as confirmed from the ex situ(57)Fe Mössbauer spectroscopy and the Fe K-edge absorption spectra. The redox couple reactions for iron and vanadium are examined by performing in situ synchrotron X-ray absorption spectroscopy. During charging/discharging, the spectral evolution of the K-edges for Fe and V confirms the reversible Fe(3+)/Fe(2+) and V(4+)/V(3+) redox reactions during cycling between 1.5 and 4.8 V.

  6. A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity.

    PubMed

    Dusonchet, Julien; Li, Hu; Guillily, Maria; Liu, Min; Stafa, Klodjan; Derada Troletti, Claudio; Boon, Joon Y; Saha, Shamol; Glauser, Liliane; Mamais, Adamantios; Citro, Allison; Youmans, Katherine L; Liu, LiQun; Schneider, Bernard L; Aebischer, Patrick; Yue, Zhenyu; Bandopadhyay, Rina; Glicksman, Marcie A; Moore, Darren J; Collins, James J; Wolozin, Benjamin

    2014-09-15

    Mutations in LRRK2 are one of the primary genetic causes of Parkinson's disease (PD). LRRK2 contains a kinase and a GTPase domain, and familial PD mutations affect both enzymatic activities. However, the signaling mechanisms regulating LRRK2 and the pathogenic effects of familial mutations remain unknown. Identifying the signaling proteins that regulate LRRK2 function and toxicity remains a critical goal for the development of effective therapeutic strategies. In this study, we apply systems biology tools to human PD brain and blood transcriptomes to reverse-engineer a LRRK2-centered gene regulatory network. This network identifies several putative master regulators of LRRK2 function. In particular, the signaling gene RGS2, which encodes for a GTPase-activating protein (GAP), is a key regulatory hub connecting the familial PD-associated genes DJ-1 and PINK1 with LRRK2 in the network. RGS2 expression levels are reduced in the striata of LRRK2 and sporadic PD patients. We identify RGS2 as a novel interacting partner of LRRK2 in vivo. RGS2 regulates both the GTPase and kinase activities of LRRK2. We show in mammalian neurons that RGS2 regulates LRRK2 function in the control of neuronal process length. RGS2 is also protective against neuronal toxicity of the most prevalent mutation in LRRK2, G2019S. We find that RGS2 regulates LRRK2 function and neuronal toxicity through its effects on kinase activity and independently of GTPase activity, which reveals a novel mode of action for GAP proteins. This work identifies RGS2 as a promising target for interfering with neurodegeneration due to LRRK2 mutations in PD patients.

  7. Proteomics Analysis to Identify and Characterize the Biomarkers and Physical Activities of Non-Frail and Frail Older Adults

    PubMed Central

    Lin, Ching-Hung; Liao, Chen-Chung; Huang, Chi-Huang; Tung, Yu-Tang; Chang, Huan-Cheng; Hsu, Mei-Chich; Huang, Chi-Chang

    2017-01-01

    Globally, the proportion of older adults is increasing. Older people face chronic conditions such as sarcopenia and functional decline, which are often associated with disability and frailty. Proteomics assay of potential serum biomarkers of frailty in older adults. Older adults were divided into non-frail and frail groups (n = 6 each; 3 males in each group) in accordance with the Chinese-Canadian Study of Health and Aging Clinical Frailty Scale. Adults were measured for grip power and the 6-min walk test for physical activity, and venous blood was sampled after adults fasted for 8 h. Ultra-high-performance liquid chromatography-tandem mass spectrometry was used for proteomics assay. The groups were compared for levels of biomarkers by t test and Pearson correlation analysis. Non-frail and frail subjects had mean age 77.5±0.4 and 77.7±1.6 years, mean height 160.5±1.3 and 156.6±2.9 cm and mean weight 62.5±1.2 and 62.8±2.9 kg, respectively. Physical activity level was lower for frail than non-frail subjects (grip power: 13.8±0.4 vs 26.1±1.2 kg; 6-min walk test: 215.2±17.2 vs 438.3±17.2 m). Among 226 proteins detected, for 31, serum levels were significantly higher for frail than non-frail subjects; serum levels of Ig kappa chain V-III region WOL, COX7A2, and albumin were lower. The serum levels of ANGT, KG and AT were 2.05-, 1.76- and 2.22-fold lower (all p < 0.05; Figure 1A, 2A and 3A) for non-frail than frail subjects and were highly correlated with grip power (Figure 1B, 2B and 3B). Our study found that ANGT, KG and AT levels are known to increase with aging, so degenerated vascular function might be associated with frailty. In total, 226 proteins were revealed proteomics assay; levels of angiotensinogen (ANGT), kininogen-1 (KG) and antithrombin III (AT) were higher in frail than non-frail subjects (11.26±2.21 vs 5.09±0.74; 18.42±1.36 vs 11.64±1.36; 22.23±1.64 vs 9.52±0.95, respectively, p < 0.05). These 3 factors were highly correlated with grip

  8. Persistent Long-Term Facilitation at an Identified Synapse Becomes Labile with Activation of Short-Term Heterosynaptic Plasticity

    PubMed Central

    Schacher, Samuel

    2014-01-01

    Short-term and long-term synaptic plasticity are cellular correlates of learning and memory of different durations. Little is known, however, how these two forms of plasticity interact at the same synaptic connection. We examined the reciprocal impact of short-term heterosynaptic or homosynaptic plasticity at sensorimotor synapses of Aplysia in cell culture when expressing persistent long-term facilitation (P-LTF) evoked by serotonin [5-hydroxytryptamine (5-HT)]. Short-term heterosynaptic plasticity induced by 5-HT (facilitation) or the neuropeptide FMRFa (depression) and short-term homosynaptic plasticity induced by tetanus [post-tetanic potentiation (PTP)] or low-frequency stimulation [homosynaptic depression (HSD)] of the sensory neuron were expressed in both control synapses and synapses expressing P-LTF in the absence or presence of protein synthesis inhibitors. All forms of short-term plasticity failed to significantly affect ongoing P-LTF in the absence of protein synthesis inhibitors. However, P-LTF reversed to control levels when either 5-HT or FMRFa was applied in the presence of rapamycin. In contrast, P-LTF was unaffected when either PTP or HSD was evoked in the presence of either rapamycin or anisomycin. These results indicate that synapses expressing persistent plasticity acquire a “new” baseline and functionally express short-term changes as naive synapses, but the new baseline becomes labile following selective activations—heterosynaptic stimuli that evoke opposite forms of plasticity—such that when presented in the presence of protein synthesis inhibitors produce a rapid reversal of the persistent plasticity. Activity-selective induction of a labile state at synapses expressing persistent plasticity may facilitate the development of therapies for reversing inappropriate memories. PMID:24695698

  9. Twitter as a Potential Disaster Risk Reduction Tool. Part II: Descriptive Analysis of Identified Twitter Activity during the 2013 Hattiesburg F4 Tornado

    PubMed Central

    Cooper, Guy Paul; Yeager, Violet; Burkle, Frederick M.; Subbarao, Italo

    2015-01-01

    Background: This article describes a novel triangulation methodological approach for identifying twitter activity of regional active twitter users during the 2013 Hattiesburg EF-4 Tornado. Methodology: A data extraction and geographically centered filtration approach was utilized to generate Twitter data for 48 hrs pre- and post-Tornado. The data was further validated using six sigma approach utilizing GPS data. Results: The regional analysis revealed a total of 81,441 tweets, 10,646 Twitter users, 27,309 retweets and 2637 tweets with GPS coordinates. Conclusions: Twitter tweet activity increased 5 fold during the response to the Hattiesburg Tornado.  Retweeting activity increased 2.2 fold. Tweets with a hashtag increased 1.4 fold. Twitter was an effective disaster risk reduction tool for the Hattiesburg EF-4 Tornado 2013.  PMID:26203396

  10. Antiviral activity and possible mode of action of ellagic acid identified in Lagerstroemia speciosa leaves toward human rhinoviruses

    PubMed Central

    2014-01-01

    Background Human rhinoviruses (HRVs) are responsible for more than half of all cases of the common cold and cause billions of USD annually in medical visits and school and work absenteeism. An assessment was made of the cytotoxic and antiviral activities and possible mode of action of the tannin ellagic acid from the leaves of Lagerstroemia speciosa toward HeLa cells and three rhinoviruses, HRV-2, -3, and -4. Methods The antiviral property and mechanism of action of ellagic acid were evaluated using a sulforhodamine B assay and real-time reverse transcription-PCR (RT-PCR) with SYBR Green dye. Results were compared with those of the currently used broad-spectrum antiviral agent, ribavirin. Results As judged by 50% inhibitory concentration values, natural ellagic acid was 1.8, 2.3, and 2.2 times more toxic toward HRV-2 (38 μg/mL), HRV-3 (31 μg/mL), and HRV-4 (29 μg/mL) than ribavirin, respectively. The inhibition rate of preincubation with 50 μg/mL ellagic acid was 17%, whereas continuous presence of ellagic acid during infection led to a significant increase in the inhibition (70%). Treatment with 50 μg/mL ellagic acid considerably suppressed HRV-4 infection only when added just after the virus inoculation (0 h) (87% inhibition), but not before -1 h or after 1 h or later (<20% inhibition). These findings suggest that ellagic acid does not interact with the HRV-4 particles and may directly interact with the human cells in the early stage of HRV infections to protect the cells from the virus destruction. Furthermore, RT-PCR analysis revealed that 50 μg/mL ellagic acid strongly inhibited the RNA replication of HRV-4 in HeLa cells, suggesting that ellagic acid inhibits virus replication by targeting on cellular molecules, rather than virus molecules. Conclusions Global efforts to reduce the level of antibiotics justify further studies on L. speciosa leaf-derived materials containing ellagic acid as potential anti-HRV products or a lead molecule for the

  11. Genetic Models of Apoptosis-Induced Proliferation Decipher Activation of JNK and Identify a Requirement of EGFR Signaling for Tissue Regenerative Responses in Drosophila

    PubMed Central

    Fan, Yun; Wang, Shiuan; Hernandez, Jacob; Yenigun, Vildan Betul; Hertlein, Gillian; Fogarty, Caitlin E.; Lindblad, Jillian L.; Bergmann, Andreas

    2014-01-01

    Recent work in several model organisms has revealed that apoptotic cells are able to stimulate neighboring surviving cells to undergo additional proliferation, a phenomenon termed apoptosis-induced proliferation. This process depends critically on apoptotic caspases such as Dronc, the Caspase-9 ortholog in Drosophila, and may have important implications for tumorigenesis. While it is known that Dronc can induce the activity of Jun N-terminal kinase (JNK) for apoptosis-induced proliferation, the mechanistic details of this activation are largely unknown. It is also controversial if JNK activity occurs in dying or in surviving cells. Signaling molecules of the Wnt and BMP families have been implicated in apoptosis-induced proliferation, but it is unclear if they are the only ones. To address these questions, we have developed an efficient assay for screening and identification of genes that regulate or mediate apoptosis-induced proliferation. We have identified a subset of genes acting upstream of JNK activity including Rho1. We also demonstrate that JNK activation occurs both in apoptotic cells as well as in neighboring surviving cells. In a genetic screen, we identified signaling by the EGFR pathway as important for apoptosis-induced proliferation acting downstream of JNK signaling. These data underscore the importance of genetic screening and promise an improved understanding of the mechanisms of apoptosis-induced proliferation. PMID:24497843

  12. Genetic models of apoptosis-induced proliferation decipher activation of JNK and identify a requirement of EGFR signaling for tissue regenerative responses in Drosophila.

    PubMed

    Fan, Yun; Wang, Shiuan; Hernandez, Jacob; Yenigun, Vildan Betul; Hertlein, Gillian; Fogarty, Caitlin E; Lindblad, Jillian L; Bergmann, Andreas

    2014-01-01

    Recent work in several model organisms has revealed that apoptotic cells are able to stimulate neighboring surviving cells to undergo additional proliferation, a phenomenon termed apoptosis-induced proliferation. This process depends critically on apoptotic caspases such as Dronc, the Caspase-9 ortholog in Drosophila, and may have important implications for tumorigenesis. While it is known that Dronc can induce the activity of Jun N-terminal kinase (JNK) for apoptosis-induced proliferation, the mechanistic details of this activation are largely unknown. It is also controversial if JNK activity occurs in dying or in surviving cells. Signaling molecules of the Wnt and BMP families have been implicated in apoptosis-induced proliferation, but it is unclear if they are the only ones. To address these questions, we have developed an efficient assay for screening and identification of genes that regulate or mediate apoptosis-induced proliferation. We have identified a subset of genes acting upstream of JNK activity including Rho1. We also demonstrate that JNK activation occurs both in apoptotic cells as well as in neighboring surviving cells. In a genetic screen, we identified signaling by the EGFR pathway as important for apoptosis-induced proliferation acting downstream of JNK signaling. These data underscore the importance of genetic screening and promise an improved understanding of the mechanisms of apoptosis-induced proliferation.

  13. Application of Quantitative Structure–Activity Relationship Models of 5-HT1A Receptor Binding to Virtual Screening Identifies Novel and Potent 5-HT1A Ligands

    PubMed Central

    2015-01-01

    The 5-hydroxytryptamine 1A (5-HT1A) serotonin receptor has been an attractive target for treating mood and anxiety disorders such as schizophrenia. We have developed binary classification quantitative structure–activity relationship (QSAR) models of 5-HT1A receptor binding activity using data retrieved from the PDSP Ki database. The prediction accuracy of these models was estimated by external 5-fold cross-validation as well as using an additional validation set comprising 66 structurally distinct compounds from the World of Molecular Bioactivity database. These validated models were then used to mine three major types of chemical screening libraries, i.e., drug-like libraries, GPCR targeted libraries, and diversity libraries, to identify novel computational hits. The five best hits from each class of libraries were chosen for further experimental testing in radioligand binding assays, and nine of the 15 hits were confirmed to be active experimentally with binding affinity better than 10 μM. The most active compound, Lysergol, from the diversity library showed very high binding affinity (Ki) of 2.3 nM against 5-HT1A receptor. The novel 5-HT1A actives identified with the QSAR-based virtual screening approach could be potentially developed as novel anxiolytics or potential antischizophrenic drugs. PMID:24410373

  14. Apple peels, from seven cultivars, have lipase-inhibitory activity and contain numerous ursenoic acids as identified by LC-ESI-QTOF-HRMS.

    PubMed

    McGhie, Tony K; Hudault, Sébastien; Lunken, Rona C M; Christeller, John T

    2012-01-11

    Apple peel contains numerous phytochemicals, many of which show bioactivity. This study investigated the identity of triterpenoid compounds contained in ethanolic extracts of peel from seven apple cultivars. Using HPLC-ESI-QTOF-HRMS, accurate mass information was obtained for 43 compounds, and chemical identity was inferred from the calculated elemental composition, fragment masses, ms/ms, and a limited set of authentic standards. Compounds were identified as triterpene acids and tentatively identified as ursenoic (or oleanoic) acid derivatives containing hydroxyl, oxo, and coumaroyloxy groups. These apple skin extracts exhibited lipase-inhibitory activity, which may be linked to the ursenoic acid content. Furthermore, both triterpene content and lipase-inhibitory activity varied by cultivar.

  15. Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-α protein levels and activity.

    PubMed

    Bolt, M J; Stossi, F; Callison, A M; Mancini, M G; Dandekar, R; Mancini, M A

    2015-01-08

    Estrogen receptor-α (ERα) is a central transcription factor that regulates mammary gland physiology and a key driver in breast cancer. In the present study, we aimed to identify novel modulators of ERα-mediated transcriptional regulation via a custom-built siRNA library screen. This screen was directed against a variety of coregulators, transcription modifiers, signaling molecules and DNA damage response proteins. By utilizing a microscopy-based, multi-end point, estrogen responsive biosensor cell line platform, the primary screen identified a wide range of factors that altered ERα protein levels, chromatin remodeling and mRNA output. We then focused on UBR5, a ubiquitin ligase and known oncogene that modulates ERα protein levels and transcriptional output. Finally, we demonstrated that UBR5 also affects endogenous ERα target genes and E2-mediated cell proliferation in breast cancer cells. In conclusion, our multi-end point RNAi screen identified novel modulators of ERα levels and activity, and provided a robust systems level view of factors involved in mechanisms of nuclear receptor action and pathophysiology. Utilizing a high throughput RNAi screening approach we identified UBR5, a protein commonly amplified in breast cancer, as a novel regulator of ERα protein levels and transcriptional activity.

  16. pSer40 tyrosine hydroxylase immunohistochemistry identifies the anatomical location of C1 neurons in rat RVLM that are activated by hypotension.

    PubMed

    Nedoboy, P E; Mohammed, S; Kapoor, K; Bhandare, A M; Farnham, M M J; Pilowsky, P M

    2016-03-11

    Identification of neurons, and their phenotype, that are activated in response to specific stimuli is a critical step in understanding how neural networks integrate inputs to produce specific outputs. Here, we developed novel mouse monoclonal antibodies of different IgG isotypes that are specific to tyrosine hydroxylase (TH), and to tyrosine hydroxylase activated at its serine 40 position (pSer40TH), in order to assess changes in the activity of phenotypically identified cardiovascular neurons using fluorescence immunohistochemistry. We find that the proportion of C1 pSer40TH-positive neurons in the central and medial region of the rat rostral ventrolateral medulla (RVLM) increases dramatically following hydralazine treatment, whereas phenylephrine treatment does not significantly change the pSer40TH/TH ratio in these regions compared to control. This finding suggests that there is a mediolateral topology associated with the activation of C1 neurons following baroreceptor loading or unloading. Overall, we conclude first, that our newly characterized monoclonal antibodies are specific, and selective, against TH and pSer40TH. Secondly, that they can be used to label TH and pSer40TH immunoreactive neurons simultaneously, and thirdly that that they can be used to identify the activation state of catecholamine synthetizing neurons after physiological stimuli. Finally, we find that there is basal level of activation of TH neurons in the lateral, central and medial regions (∼ 70%, 30% and 45%, respectively) of the C1 area, but that following unloading of the baroreceptors there is a marked increase in activation of central (∼ 80%) and medial (∼ 90%) C1 neurons in the RVLM.

  17. Identifying buried segments of active faults in the northern Rio Grande Rift using aeromagnetic, LiDAR,and gravity data, south-central Colorado, USA

    USGS Publications Warehouse

    Ruleman, Cal; Grauch, V. J.

    2013-01-01

    Combined interpretation of aeromagnetic and LiDAR data builds on the strength of the aeromagnetic method to locate normal faults with significant offset under cover and the strength of LiDAR interpretation to identify the age and sense of motion of faults. Each data set helps resolve ambiguities in interpreting the other. In addition, gravity data can be used to infer the sense of motion for totally buried faults inferred solely from aeromagnetic data. Combined interpretation to identify active faults at the northern end of the San Luis Basin of the northern Rio Grande rift has confirmed general aspects of previous geologic mapping but has also provided significant improvements. The interpretation revises and extends mapped fault traces, confirms tectonic versus fluvial origins of steep stream banks, and gains additional information on the nature of active and potentially active partially and totally buried faults. Detailed morphology of surfaces mapped from the LiDAR data helps constrain ages of the faults that displace the deposits. The aeromagnetic data provide additional information about their extents in between discontinuous scarps and suggest that several totally buried, potentially active faults are present on both sides of the valley.

  18. Extreme Outlier Analysis Identifies Occult Mitogen-Activated Protein Kinase Pathway Mutations in Patients With Low-Grade Serous Ovarian Cancer

    PubMed Central

    Grisham, Rachel N.; Sylvester, Brooke E.; Won, Helen; McDermott, Gregory; DeLair, Deborah; Ramirez, Ricardo; Yao, Zhan; Shen, Ronglai; Dao, Fanny; Bogomolniy, Faina; Makker, Vicky; Sala, Evis; Soumerai, Tara E.; Hyman, David M.; Socci, Nicholas D.; Viale, Agnes; Gershenson, David M.; Farley, John; Levine, Douglas A.; Rosen, Neal; Berger, Michael F.; Spriggs, David R.; Aghajanian, Carol A.; Solit, David B.; Iyer, Gopa

    2015-01-01

    Purpose No effective systemic therapy exists for patients with metastatic low-grade serous (LGS) ovarian cancers. BRAF and KRAS mutations are common in serous borderline (SB) and LGS ovarian cancers, and MEK inhibition has been shown to induce tumor regression in a minority of patients; however, no correlation has been observed between mutation status and clinical response. With the goal of identifying biomarkers of sensitivity to MEK inhibitor treatment, we performed an outlier analysis of a patient who experienced a complete, durable, and ongoing (> 5 years) response to selumetinib, a non-ATP competitive MEK inhibitor. Patients and Methods Next-generation sequencing was used to analyze this patient's tumor as well as an additional 28 SB/LGS tumors. Functional characterization of an identified novel alteration of interest was performed. Results Analysis of the extraordinary responder's tumor identified a 15-nucleotide deletion in the negative regulatory helix of the MAP2K1 gene encoding for MEK1. Functional characterization demonstrated that this mutant induced extracellular signal-regulated kinase pathway activation, promoted anchorage-independent growth and tumor formation in mice, and retained sensitivity to selumetinib. Analysis of additional LGS/SB tumors identified mutations predicted to induce extracellular signal-regulated kinase pathway activation in 82% (23 of 28), including two patients with BRAF fusions, one of whom achieved an ongoing complete response to MEK inhibitor–based combination therapy. Conclusion Alterations affecting the mitogen-activated protein kinase pathway are present in the majority of patients with LGS ovarian cancer. Next-generation sequencing analysis revealed deletions and fusions that are not detected by older sequencing approaches. These findings, coupled with the observation that a subset of patients with recurrent LGS ovarian cancer experienced dramatic and durable responses to MEK inhibitor therapy, support additional

  19. Development of gastric cancer in nonatrophic stomach with highly active inflammation identified by serum levels of pepsinogen and Helicobacter pylori antibody together with endoscopic rugal hyperplastic gastritis.

    PubMed

    Watanabe, Mika; Kato, Jun; Inoue, Izumi; Yoshimura, Noriko; Yoshida, Takeichi; Mukoubayashi, Chizu; Deguchi, Hisanobu; Enomoto, Shotaro; Ueda, Kazuki; Maekita, Takao; Iguchi, Mikitaka; Tamai, Hideyuki; Utsunomiya, Hirotoshi; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Iwane, Masataka; Tekeshita, Tatsuya; Mohara, Osamu; Ushijima, Toshikazu; Ichinose, Masao

    2012-12-01

    This study aimed to elucidate groups at high risk of developing cancer among patients with serologically identified Helicobacter pylori infection and nonatrophic stomach. Annual endoscopy was performed for a mean of 5.4 years in 496 asymptomatic middle-aged men who were H. pylori antibody-positive and pepsinogen (PG) test-negative. Subjects were stratified according to the activity of H. pylori-associated gastritis measured by serum levels of PG and H. pylori antibody, and/or by endoscopic findings of rugal hyperplastic gastritis (RHG), and cancer development was investigated. During the study period, seven cases of cancer developed in the cohort (incidence rate, 261/100,000 person-years), with 85.7% developing in the group showing a PGI/II ratio ≤ 3.0, reflecting active inflammation-based high PGII levels. Cancer incidence was significantly higher in this group (750/100,000 person-years) than in groups with less active gastritis. Furthermore, cancer incidence for this group was significantly higher in the subgroup with high H. pylori antibody titers than in the low-titer subgroup. Meanwhile, endoscopic findings revealed that 11.7% of subjects showed RHG reflecting localized highly active inflammation, and cancer risk was significantly higher in patients with RHG than in patients without. Combining the two serum tests and endoscopic examination for RHG allowed identification of subjects with more active gastritis and higher cancer risk. No cancer development was observed in these high-risk subjects after H. pylori eradication. Subjects with highly active gastritis identified by the two serological tests and endoscopic RHG constitute a group at high risk of cancer development with H. pylori-infected nonatrophic stomach.

  20. Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development

    PubMed Central

    Ma, Jingqun; Brennan, Kaelan J.; D’Aloia, Mitch R.; Pascuzzi, Pete E.; Weake, Vikki M.

    2016-01-01

    The Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex is a transcriptional coactivator with histone acetylase and deubiquitinase activities that plays an important role in visual development and function. In Drosophila melanogaster, four SAGA subunits are required for the deubiquitination of monoubiquitinated histone H2B (ubH2B): Nonstop, Sgf11, E(y)2, and Ataxin 7. Mutations that disrupt SAGA deubiquitinase activity cause defects in neuronal connectivity in the developing Drosophila visual system. In addition, mutations in SAGA result in the human progressive visual disorder spinocerebellar ataxia type 7 (SCA7). Glial cells play a crucial role in both the neuronal connectivity defect in nonstop and sgf11 flies, and in the retinal degeneration observed in SCA7 patients. Thus, we sought to identify the gene targets of SAGA deubiquitinase activity in glia in the Drosophila larval central nervous system. To do this, we enriched glia from wild-type, nonstop, and sgf11 larval optic lobes using affinity-purification of KASH-GFP tagged nuclei, and then examined each transcriptome using RNA-seq. Our analysis showed that SAGA deubiquitinase activity is required for proper expression of 16% of actively transcribed genes in glia, especially genes involved in proteasome function, protein folding and axon guidance. We further show that the SAGA deubiquitinase-activated gene Multiplexin (Mp) is required in glia for proper photoreceptor axon targeting. Mutations in the human ortholog of Mp, COL18A1, have been identified in a family with a SCA7-like progressive visual disorder, suggesting that defects in the expression of this gene in SCA7 patients could play a role in the retinal degeneration that is unique to this ataxia. PMID:27261002

  1. Ligand-activated PPARγ downregulates CXCR4 gene expression through a novel identified PPAR response element and inhibits breast cancer progression

    PubMed Central

    Rovito, Daniela; Gionfriddo, Giulia; Barone, Ines; Giordano, Cinzia; Grande, Fedora; De Amicis, Francesca; Lanzino, Marilena; Catalano, Stefania

    2016-01-01

    Stromal Derived Factor-1α (SDF-1α) and its cognate receptor CXCR4 play a key role in mediating breast cancer cell invasion and metastasis. Therefore, drugs able to inhibit CXCR4 activation may add critical tools to reduce tumor progression, especially in the most aggressive form of the breast cancer disease. Peroxisome Proliferator-Activated Receptor (PPAR) γ, a member of the nuclear receptor superfamily, has been found to downregulate CXCR4 gene expression in different cancer cells, however the molecular mechanism underlying this effect is not fully understood. Here, we identified a novel PPARγ-mediated mechanism that negatively regulates CXCR4 expression in both epithelial and stromal breast cancer cells. We found that ligand-activated PPARγ downregulated CXCR4 transcriptional activity through the recruitment of the silencing mediator of retinoid and thyroid hormone receptor (SMRT) corepressor onto a newly identified PPAR response element (PPRE) within the CXCR4 promoter in breast cancer cell lines. As a consequence, the PPARγ agonist rosiglitazone (BRL) significantly inhibited cell migration and invasion and this effect was PPARγ-mediated, since it was reversed in the presence of the PPARγ antagonist GW9662. According to the ability of cancer-associated fibroblasts (CAFs), the most abundant component of breast cancer stroma, to secrete high levels of SDF-1α, BRL reduced migratory promoting activities induced by conditioned media (CM) derived from CAFs and affected CXCR4 downstream signaling pathways activated by CAF-CM. In addition, CAFs exposed to BRL showed a decreased expression of CXCR4, a reduced motility and invasion along with a phenotype characterized by an altered morphology. Collectively, our findings provide novel insights into the role of PPARγ in inhibiting breast cancer progression and further highlight the utility of PPARγ ligands for future therapies aimed at targeting both cancer and surrounding stromal cells in breast cancer patients

  2. Investigating mitochondrial metabolism in contracting HL-1 cardiomyocytes following hypoxia and pharmacological HIF activation identifies HIF-dependent and independent mechanisms of regulation.

    PubMed

    Ambrose, Lucy J A; Abd-Jamil, Amira H; Gomes, Renata S M; Carter, Emma E; Carr, Carolyn A; Clarke, Kieran; Heather, Lisa C

    2014-11-01

    Hypoxia is a consequence of cardiac disease and downregulates mitochondrial metabolism, yet the molecular mechanisms through which this occurs in the heart are incompletely characterized. Therefore, we aimed to use a contracting HL-1 cardiomyocyte model to investigate the effects of hypoxia on mitochondrial metabolism. Cells were exposed to hypoxia (2% O2) for 6, 12, 24, and 48 hours to characterize the metabolic response. Cells were subsequently treated with the hypoxia inducible factor (HIF)-activating compound, dimethyloxalylglycine (DMOG), to determine whether hypoxia-induced mitochondrial changes were HIF dependent or independent, and to assess the suitability of this cultured cardiac cell line for cardiovascular pharmacological studies. Hypoxic cells had increased glycolysis after 24 hours, with glucose transporter 1 and lactate levels increased 5-fold and 15-fold, respectively. After 24 hours of hypoxia, mitochondrial networks were more fragmented but there was no change in citrate synthase activity, indicating that mitochondrial content was unchanged. Cellular oxygen consumption was 30% lower, accompanied by decreases in the enzymatic activities of electron transport chain (ETC) complexes I and IV, and aconitase by 81%, 96%, and 72%, relative to controls. Pharmacological HIF activation with DMOG decreased cellular oxygen consumption by 43%, coincident with decreases in the activities of aconitase and complex I by 26% and 30%, indicating that these adaptations were HIF mediated. In contrast, the hypoxia-mediated decrease in complex IV activity was not replicated by DMOG treatment, suggesting HIF-independent regulation of this complex. In conclusion, 24 hours of hypoxia increased anaerobic glycolysis and decreased mitochondrial respiration, which was associated with changes in ETC and tricarboxylic acid cycle enzyme activities in contracting HL-1 cells. Pharmacological HIF activation in this cardiac cell line allowed both HIF-dependent and independent

  3. Identifying panaxynol, a natural activator of nuclear factor erythroid-2 related factor 2 (Nrf2) from American ginseng as a suppressor of inflamed macrophage-induced cardiomyocyte hypertrophy

    PubMed Central

    Qu, Chen; Li, Bin; Lai, Yimu; Li, Hechu; Windust, Anthony; Hofseth, Lorne J.; Nagarkatti, Mitzi; Nagarkatti, Prakash; Wang, Xing Li; Tang, Dongqi; Janicki, Joseph S.; Tian, Xingsong; Cui, Taixing

    2015-01-01

    Ethnopharmacological relevance American ginseng is capable of ameliorating cardiac dysfunction and activating Nrf2, a master regulator of antioxidant defense, in the heart. This study was designed to isolate compounds from American ginseng and to determine those responsible for the Nrf2-mediated resolution of inflamed macrophage-induced cardiomyocyte hypertrophy. Materials and methods A standardized crude extract of American ginseng was supplied by the National Research Council of Canada, Institute for National Measurement Standards. A bioassay-based fractionization of American ginseng was performed to identify the putative substances which could activate Nrf2-mediated suppression of pro-inflammatory cytokine expression in macrophages and macrophage-mediated pro-hypertrophic growth in cardiomyocytes. Results A hexane fraction of an anti-inflammatory crude extract of American ginseng was found to be most effective in suppressing the inflammatory responses in macrophages. Preparative, reverse-phase HPLC and a comparative analysis by analytical scale LC–UV/MS revealed the hexane fraction contains predominantly C17 polyacetylenes and linolenic acid. Panaxynol, one of the major polyacetylenes, was found to be a potent Nrf2 activator. Panaxynol posttranscriptionally activated Nrf2 by inhibiting Kelch-like ECH-associated protein (Keap) 1-mediated degradation without affecting the binding of Keap1 and Nrf2. Moreover, panaxynol suppressed a selected set of cytokine expression via the activation of Nrf2 while minimally regulating nuclear factor-kappa B (NF-κB)-mediated cytokine expression in macrophages. It also dramatically inhibited the inflamed macrophage-mediated cardiomyocyte death and hypertrophy by activating Nrf2 in macrophages. Conclusions These results demonstrate that American ginseng-derived panaxynol is a specific Nrf2 activator and panaxynol-activated Nrf2 signaling is at least partly responsible for American ginseng-induced health benefit in the heart. PMID

  4. A presenilin-1 mutation identified in familial Alzheimer disease with cotton wool plaques causes a nearly complete loss of gamma-secretase activity.

    PubMed

    Heilig, Elizabeth A; Xia, Weiming; Shen, Jie; Kelleher, Raymond J

    2010-07-16

    Mutations in presenilin-1 and presenilin-2 (PS1 and PS2) are the most common cause of familial Alzheimer disease. PS1 and PS2 are the presumptive catalytic components of the multisubunit gamma-secretase complex, which proteolyzes a number of type I transmembrane proteins, including the amyloid precursor protein (APP) and Notch. APP processing by gamma-secretase produces beta-amyloid peptides (Abeta40 and Abeta42) that accumulate in the Alzheimer disease brain. Here we identify a pathogenic L435F mutation in PS1 in two affected siblings with early-onset familial Alzheimer disease characterized by deposition of cerebral cotton wool plaques. The L435F mutation resides in a conserved C-terminal PAL sequence implicated in active site conformation and catalytic activity. The impact of PS1 mutations in and around the PAL motif on gamma-secretase activity was assessed by expression of mutant PS1 in mouse embryo fibroblasts lacking endogenous PS1 and PS2. Surprisingly, the L435F mutation caused a nearly complete loss of gamma-secretase activity, including >90% reductions in the generation of Abeta40, Abeta42, and the APP and Notch intracellular domains. Two nonpathogenic PS1 mutations, P433L and L435R, caused essentially complete loss of gamma-secretase activity, whereas two previously identified pathogenic PS1 mutations, P436Q and P436S, caused partial loss of function with substantial reductions in production of Abeta40, Abeta42, and the APP and Notch intracellular domains. These results argue against overproduction of Abeta42 as an essential property of presenilin proteins bearing pathogenic mutations. Rather, our findings provide support for the hypothesis that pathogenic mutations cause a general loss of presenilin function.

  5. A Presenilin-1 Mutation Identified in Familial Alzheimer Disease with Cotton Wool Plaques Causes a Nearly Complete Loss of γ-Secretase Activity*

    PubMed Central

    Heilig, Elizabeth A.; Xia, Weiming; Shen, Jie; Kelleher, Raymond J.

    2010-01-01

    Mutations in presenilin-1 and presenilin-2 (PS1 and PS2) are the most common cause of familial Alzheimer disease. PS1 and PS2 are the presumptive catalytic components of the multisubunit γ-secretase complex, which proteolyzes a number of type I transmembrane proteins, including the amyloid precursor protein (APP) and Notch. APP processing by γ-secretase produces β-amyloid peptides (Aβ40 and Aβ42) that accumulate in the Alzheimer disease brain. Here we identify a pathogenic L435F mutation in PS1 in two affected siblings with early-onset familial Alzheimer disease characterized by deposition of cerebral cotton wool plaques. The L435F mutation resides in a conserved C-terminal PAL sequence implicated in active site conformation and catalytic activity. The impact of PS1 mutations in and around the PAL motif on γ-secretase activity was assessed by expression of mutant PS1 in mouse embryo fibroblasts lacking endogenous PS1 and PS2. Surprisingly, the L435F mutation caused a nearly complete loss of γ-secretase activity, including >90% reductions in the generation of Aβ40, Aβ42, and the APP and Notch intracellular domains. Two nonpathogenic PS1 mutations, P433L and L435R, caused essentially complete loss of γ-secretase activity, whereas two previously identified pathogenic PS1 mutations, P436Q and P436S, caused partial loss of function with substantial reductions in production of Aβ40, Aβ42, and the APP and Notch intracellular domains. These results argue against overproduction of Aβ42 as an essential property of presenilin proteins bearing pathogenic mutations. Rather, our findings provide support for the hypothesis that pathogenic mutations cause a general loss of presenilin function. PMID:20460383

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

    PubMed

    Heltemes-Harris, L M; Larson, J D; Starr, T K; Hubbard, G K; Sarver, A L; Largaespada, D A; Farrar, M A

    2016-06-30

    Signal transducer and activator of transcription 5 (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) with 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 Janus kinase/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, extracellular signal-regulated kinase (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 have in B-ALL.

  7. ALK1 signalling analysis identifies angiogenesis related genes and reveals disparity between TGF-β and constitutively active receptor induced gene expression

    PubMed Central

    Lux, Andreas; Salway, Fiona; Dressman, Holly K; Kröner-Lux, Gabriele; Hafner, Mathias; Day, Philip JR; Marchuk, Douglas A; Garland, John

    2006-01-01

    Background TGF-β1 is an important angiogenic factor involved in the different aspects of angiogenesis and vessel maintenance. TGF-β signalling is mediated by the TβRII/ALK5 receptor complex activating the Smad2/Smad3 pathway. In endothelial cells TGF-β utilizes a second type I receptor, ALK1, activating the Smad1/Smad5 pathway. Consequently, a perturbance of ALK1, ALK5 or TβRII activity leads to vascular defects. Mutations in ALK1 cause the vascular disorder hereditary hemorrhagic telangiectasia (HHT). Methods The identification of ALK1 and not ALK5 regulated genes in endothelial cells, might help to better understand the development of HHT. Therefore, the human microvascular endothelial cell line HMEC-1 was infected with a recombinant constitutively active ALK1 adenovirus, and gene expression was studied by using gene arrays and quantitative real-time PCR analysis. Results After 24 hours, 34 genes were identified to be up-regulated by ALK1 signalling. Analysing ALK1 regulated gene expression after 4 hours revealed 13 genes to be up- and 2 to be down-regulated. Several of these genes, including IL-8, ET-1, ID1, HPTPη and TEAD4 are reported to be involved in angiogenesis. Evaluation of ALK1 regulated gene expression in different human endothelial cell types was not in complete agreement. Further on, disparity between constitutively active ALK1 and TGF-β1 induced gene expression in HMEC-1 cells and primary HUVECs was observed. Conclusion Gene array analysis identified 49 genes to be regulated by ALK1 signalling and at least 14 genes are reported to be involved in angiogenesis. There was substantial agreement between the gene array and quantitative real-time PCR data. The angiogenesis related genes might be potential HHT modifier genes. In addition, the results suggest endothelial cell type specific ALK1 and TGF-β signalling. PMID:16594992

  8. From Drug Screening to Target Deconvolution: a Target-Based Drug Discovery Pipeline Using Leishmania Casein Kinase 1 Isoform 2 To Identify Compounds with Antileishmanial Activity

    PubMed Central

    Durieu, Emilie; Prina, Eric; Leclercq, Olivier; Oumata, Nassima; Gaboriaud-Kolar, Nicolas; Vougogiannopoulou, Konstantina; Aulner, Nathalie; Defontaine, Audrey; No, Joo Hwan; Ruchaud, Sandrine; Skaltsounis, Alexios-Leandros; Galons, Hervé; Späth, Gerald F.; Meijer, Laurent

    2016-01-01

    Existing therapies for leishmaniases present significant limitations, such as toxic side effects, and are rendered inefficient by parasite resistance. It is of utmost importance to develop novel drugs targeting Leishmania that take these two limitations into consideration. We thus chose a target-based approach using an exoprotein kinase, Leishmania casein kinase 1.2 (LmCK1.2) that was recently shown to be essential for intracellular parasite survival and infectivity. We developed a four-step pipeline to identify novel selective antileishmanial compounds. In step 1, we screened 5,018 compounds from kinase-biased libraries with Leishmania and mammalian CK1 in order to identify hit compounds and assess their specificity. For step 2, we selected 88 compounds among those with the lowest 50% inhibitory concentration to test their biological activity on host-free parasites using a resazurin reduction assay and on intramacrophagic amastigotes using a high content phenotypic assay. Only 75 compounds showed antileishmanial activity and were retained for step 3 to evaluate their toxicity against mouse macrophages and human cell lines. The four compounds that displayed a selectivity index above 10 were then assessed for their affinity to LmCK1.2 using a target deconvolution strategy in step 4. Finally, we retained two compounds, PP2 and compound 42, for which LmCK1.2 seems to be the primary target. Using this four-step pipeline, we identify from several thousand molecules, two lead compounds with a selective antileishmanial activity. PMID:26902771

  9. Complement-activated oligodendroglia: a new pathogenic entity identified by immunostaining with antibodies to human complement proteins C3d and C4d.

    PubMed

    Yamada, T; Akiyama, H; McGeer, P L

    1990-05-04

    Clusters of oligodendroglial fibers were identified immunohistochemically in human brain tissue with antibodies to the complement proteins C3d and C4d in several neurological disorders. These included Pick's, Huntington's, Parkinson's and Alzheimer's disease, amyotrophic lateral sclerosis, progressive supranuclear palsy and Shy-Drager syndrome. These complement-activated oligodendroglia occurred in selected areas of gray and white matter. They were rarely observed in control tissue. Immunogold electron microscopy established that the C4d antibody was attached to degenerating myelin sheaths. These data indicate attachment of classical complement pathway proteins to selective oligodendroglia in several neurological disorders.

  10. Identifying and applying a highly selective probe to simultaneously determine the O-glucuronidation activity of human UGT1A3 and UGT1A4

    PubMed Central

    Jiang, Li; Liang, Si-Cheng; Wang, Chao; Ge, Guang-Bo; Huo, Xiao-Kui; Qi, Xiao-Yi; Deng, Sa; Liu, Ke-Xin; Ma, Xiao-Chi

    2015-01-01

    Glucuronidation mediated by uridine 5′-diphospho (UDP)-glucuronosyltransferase is an important detoxification pathway. However, identifying a selective probe of UDP- glucuronosyltransferase is complicated because of the significant overlapping substrate specificity displayed by the enzyme. In this paper, desacetylcinobufagin (DACB) 3-O- and 16-O-glucuronidation were found to be isoform-specific probe reactions for UGT1A4 and UGT1A3, respectively. DACB was well characterized as a probe for simultaneously determining the catalytic activities of O-glucuronidation mediated by UGT1A3 and UGT1A4 from various enzyme sources, through a sensitive analysis method. PMID:25884245

  11. Aryl hydrocarbon receptor-mediated and estrogenic activities of oxygenated polycyclic aromatic hydrocarbons and azaarenes originally identified in extracts of river sediments.

    PubMed

    Machala, M; Ciganek, M; Bláha, L; Minksová, K; Vondráck, J

    2001-12-01

    Reproductive dysfunction in wildlife populations can be a result of environmental contaminants binding to aryl hydrocarbon receptor (AhR) or estrogenic receptors. Signaling by both types of receptors can be affected by polycyclic aromatic hydrocarbons (PAHs), which are potential endocrine disruptors. However, our knowledge regarding the effects of oxygenated (oxy)-PAHs and azaarenes on AhR-mediated and estrogenic activities is incomplete. In the present study, we have identified 9-fluorenone, anthrone, anthraquinone, benzanthrone, benz[a]anthracene-7,12-dione, benz[c]acridine, and dibenz[a,h]acridine as prevalent oxy-PAHs and azaarenes found in river sediments. Their concentrations in sediment samples ranged from 2.1 to 165.2 ng g(-1) for oxy-PAHs and up to 27.3 ng g(-1) for azaarenes. Their relative AhR-inducing and estrogenic potencies were quantified in vitro using two cell lines that were stably transfected with a luciferase reporter gene system and expressed as induction equivalency factors (IEFs). The only oxy-PAHs with detectable levels of in vitro AhR-mediated activity were benzanthrone and benz[a]anthracene-7,12-dione. However, their IEFs were approximately three to four orders of magnitude lower than those of benzo[a]pyrene. On the other hand, azaarenes showed a strong AhR-mediated activity, with dibenzo[a,h]acridine being a far more potent inducer of activity than benzo[a]pyrene. Benzanthrone, benz[a]anthracene-7,12-dione, anthraquinone, and benz[a]acridine were weak inducers of in vitro estrogenic activity, with IEFs similar to that of benzo[a]pyrene. Based on concentrations and relative potencies, our results suggest that dibenzo[a,h]acridine can significantly contribute to the overall AhR-mediated activity in river sediments, whereas the remaining compounds do not. No studied compound was found to contribute significantly to estrogen receptor-mediated activity in vitro.

  12. Screen of FDA-approved drug library identifies maprotiline, an antibiofilm and antivirulence compound with QseC sensor-kinase dependent activity in Francisella novicida.

    PubMed

    Dean, Scott N; van Hoek, Monique L

    2015-01-01

    Development of new therapeutics against Select Agents such as Francisella is critical preparation in the event of bioterrorism. Testing FDA-approved drugs for this purpose may yield new activities unrelated to their intended purpose and may hasten the discovery of new therapeutics. A library of 420 FDA-approved drugs was screened for antibiofilm activity against a model organism for human tularemia, Francisella (F.) novicida, excluding drugs that significantly inhibited growth. The initial screen was based on the 2-component system (TCS) dependent biofilm effect, thus, the QseC dependence of maprotiline anti-biofilm action was demonstrated. By comparing their FDA-approved uses, chemical structures, and other properties of active drugs, toremifene and polycyclic antidepressants maprotiline and chlorpromazine were identified as being highly active against F. novicida biofilm formation. Further down-selection excluded toremifene for its membrane active activity and chlorpromazine for its high antimicrobial activity. The mode of action of maprotiline against F. novicida was sought. It was demonstrated that maprotiline was able to significantly down-regulate the expression of the virulence factor IglC, encoded on the Francisella Pathogenicity Island (FPI), suggesting that maprotiline is exerting an effect on bacterial virulence. Further studies showed that maprotiline significantly rescued F. novicida infected wax worm larvae. In vivo studies demonstrated that maprotiline treatment could prolong time to disease onset and survival in F. novicida infected mice. These results suggest that an FDA-approved drug such as maprotiline has the potential to combat Francisella infection as an antivirulence agent, and may have utility in combination with antibiotics.

  13. Screen of FDA-approved drug library identifies maprotiline, an antibiofilm and antivirulence compound with QseC sensor-kinase dependent activity in Francisella novicida

    PubMed Central

    Dean, Scott N; van Hoek, Monique L

    2015-01-01

    Development of new therapeutics against Select Agents such as Francisella is critical preparation in the event of bioterrorism. Testing FDA-approved drugs for this purpose may yield new activities unrelated to their intended purpose and may hasten the discovery of new therapeutics. A library of 420 FDA-approved drugs was screened for antibiofilm activity against a model organism for human tularemia, Francisella (F.) novicida, excluding drugs that significantly inhibited growth. The initial screen was based on the 2-component system (TCS) dependent biofilm effect, thus, the QseC dependence of maprotiline anti-biofilm action was demonstrated. By comparing their FDA-approved uses, chemical structures, and other properties of active drugs, toremifene and polycyclic antidepressants maprotiline and chlorpromazine were identified as being highly active against F. novicida biofilm formation. Further down-selection excluded toremifene for its membrane active activity and chlorpromazine for its high antimicrobial activity. The mode of action of maprotiline against F. novicida was sought. It was demonstrated that maprotiline was able to significantly down-regulate the expression of the virulence factor IglC, encoded on the Francisella Pathogenicity Island (FPI), suggesting that maprotiline is exerting an effect on bacterial virulence. Further studies showed that maprotiline significantly rescued F. novicida infected wax worm larvae. In vivo studies demonstrated that maprotiline treatment could prolong time to disease onset and survival in F. novicida infected mice. These results suggest that an FDA-approved drug such as maprotiline has the potential to combat Francisella infection as an antivirulence agent, and may have utility in combination with antibiotics. PMID:26155740

  14. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7

    PubMed Central

    Ismail, Hanafy M.; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H. L.; Hemingway, Janet; Biagini, Giancarlo A.; O’Neill, Paul M.; Ward, Stephen A.

    2016-01-01

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography–MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  15. Use of DEAD-box polypeptide-4 (Ddx4) gene promoter-driven fluorescent reporter mice to identify mitotically active germ cells in post-natal mouse ovaries

    PubMed Central

    Park, Eun-Sil; Tilly, Jonathan L.

    2015-01-01

    Several laboratories have independently isolated mitotically active germ cells, termed female germline stem cells or oogonial stem cells (OSCs), from adult mouse ovaries. However, a recent study using Ddx4-Cre;Rosa26 reporter mice concluded that such germ cells do not exist. Given the disparity in conclusions drawn in this study compared with others, we felt it was important to re-assess the utility of Ddx4-Cre;Rosa26 reporter mice for identification of OSCs in adult mouse ovaries. Transgenic Ddx4-Cre mice were crossed with Rosa26tdTm/tdTm mice to drive restricted tomato red (tdTm) gene expression in cells in which the Ddx4 gene promoter has been activated. Crude dispersion of ovaries from recombined offspring generated cell fractions containing tdTm-positive immature oocytes, which are incapable of proliferation and thus probably represent the uncharacterized reporter-positive ovarian cells identified in the paper Zhang et al. (2012) as being mitotically inactive. Dispersed ovaries further subjected to fluorescence-activated cell sorting yielded a large population of non-germline tdTm-positive cells, indicative of promoter ‘leakiness’ in the Ddx4-Cre mouse line. Nonetheless, a small percentage of these tdTm-positive cells exhibited externalized (extracellular, ec) expression of Ddx4 protein (ecDdx4-positive), expressed markers of primitive germ cells but not of oocytes, and actively proliferated in culture, all of which are characteristic features of OSCs. Thus, crude dispersion of ovaries collected from Ddx4 gene promoter-driven reporter mice is not, by itself, a reliable approach to identify OSCs, whereas the same ovarian dispersates further subjected to cell sorting strategies yield purified OSCs that can be expanded in culture. PMID:25147160

  16. Use of DEAD-box polypeptide-4 (Ddx4) gene promoter-driven fluorescent reporter mice to identify mitotically active germ cells in post-natal mouse ovaries.

    PubMed

    Park, Eun-Sil; Tilly, Jonathan L

    2015-01-01

    Several laboratories have independently isolated mitotically active germ cells, termed female germline stem cells or oogonial stem cells (OSCs), from adult mouse ovaries. However, a recent study using Ddx4-Cre;Rosa26 reporter mice concluded that such germ cells do not exist. Given the disparity in conclusions drawn in this study compared with others, we felt it was important to re-assess the utility of Ddx4-Cre;Rosa26 reporter mice for identification of OSCs in adult mouse ovaries. Transgenic Ddx4-Cre mice were crossed with Rosa26(tdTm/tdTm) mice to drive restricted tomato red (tdTm) gene expression in cells in which the Ddx4 gene promoter has been activated. Crude dispersion of ovaries from recombined offspring generated cell fractions containing tdTm-positive immature oocytes, which are incapable of proliferation and thus probably represent the uncharacterized reporter-positive ovarian cells identified in the paper Zhang et al. (2012) as being mitotically inactive. Dispersed ovaries further subjected to fluorescence-activated cell sorting yielded a large population of non-germline tdTm-positive cells, indicative of promoter 'leakiness' in the Ddx4-Cre mouse line. Nonetheless, a small percentage of these tdTm-positive cells exhibited externalized (extracellular, ec) expression of Ddx4 protein (ecDdx4-positive), expressed markers of primitive germ cells but not of oocytes, and actively proliferated in culture, all of which are characteristic features of OSCs. Thus, crude dispersion of ovaries collected from Ddx4 gene promoter-driven reporter mice is not, by itself, a reliable approach to identify OSCs, whereas the same ovarian dispersates further subjected to cell sorting strategies yield purified OSCs that can be expanded in culture.

  17. Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH, an asparagine synthetase gene involved in its immune-activating capacity.

    PubMed

    Ito, Masahiro; Kim, Yun-Gi; Tsuji, Hirokazu; Takahashi, Takuya; Kiwaki, Mayumi; Nomoto, Koji; Danbara, Hirofumi; Okada, Nobuhiko

    2014-01-01

    Lactobacillus casei ATCC 27139 enhances host innate immunity, and the J1 phage-resistant mutants of this strain lose the activity. A transposon insertion mutant library of L. casei ATCC 27139 was constructed, and nine J1 phage-resistant mutants out of them were obtained. Cloning and sequencing analyses identified three independent genes that were disrupted by insertion of the transposon element: asnH, encoding asparagine synthetase, and dnaJ and dnaK, encoding the molecular chaperones DnaJ and DnaK, respectively. Using an in vivo mouse model of Listeria infection, only asnH mutant showed deficiency in their ability to enhance host innate immunity, and complementation of the mutation by introduction of the wild-type asnH in the mutant strain recovered the immuno-augmenting activity. AsnH protein exhibited asparagine synthetase activity when the lysozyme-treated cell wall extracts of L. casei ATCC 27139 was added as substrate. The asnH mutants lost the thick and rigid peptidoglycan features that are characteristic to the wild-type cells, indicating that AsnH of L. casei is involved in peptidoglycan biosynthesis. These results indicate that asnH is required for the construction of the peptidoglycan composition involved in the immune-activating capacity of L. casei ATCC 27139.

  18. Proof-of-principle results for identifying the composition of dust particles and volcanic ash samples through the technique of photon activation analysis at the IAC

    NASA Astrophysics Data System (ADS)

    Mamtimin, Mayir; Cole, Philip L.; Segebade, Christian

    2013-04-01

    Instrumental analytical methods are preferable in studying sub-milligram quantities of airborne particulates collected in dust filters. The multi-step analytical procedure used in treating samples through chemical separation can be quite complicated. Further, due to the minute masses of the airborne particulates collected on filters, such chemical treatment can easily lead to significant levels of contamination. Radio-analytical techniques, and in particular, activation analysis methods offer a far cleaner alternative. Activation methods require minimal sample preparation and provide sufficient sensitivity for detecting the vast majority of the elements throughout the periodic table. In this paper, we will give a general overview of the technique of photon activation analysis. We will show that by activating dust particles with 10- to 30-MeV bremsstrahlung photons, we can ascertain their elemental composition. The samples are embedded in dust-collection filters and are irradiated "as is" by these photons. The radioactivity of the photonuclear reaction products is measured with appropriate spectrometers and the respective analytes are quantified using multi-component calibration materials. We shall provide specific examples of identifying the elemental components of airborne dust particles and volcanic ash by making use of bremsstrahlung photons from an electron linear accelerator at the Idaho Accelerator Center in Pocatello, Idaho.

  19. Studies toward the Unique Pederin Family Member Psymberin: Structure Activity Relationships, Biochemical Studies and Genetics Identify the Mode of Action of Psymberin

    PubMed Central

    Wu, Cheng-Yang; Feng, Yu; Cardenas, Eduardo R.; Williams, Noelle; Floreancig, Paul E.; De Brabander, Jef K.; Roth, Michael G.

    2012-01-01

    Psymberin is the only member of the pederin natural product family that contains a dihydroisocoumarin side chain. Structural modifications of psymberin uncoupled inhibition of protein translation from cytotoxicity, suggesting that psymberin has more than one bioactivity. A forward genetic screen in Caenorhabditis elegans was conducted to identify the molecular target(s) of psymberin. Multiple independent psymberin-resistant mutants were isolated, each containing the same point mutation in a gene encoding a ribosomal protein. However, a psymberin-resistant mutant strain bearing this mutation was not cross-resistant to the pederin family member mycalamide A, which binds to the archaeal form of the same protein. Thus, two pederin family members likely differ in how they bind the same molecular target. The accumulation of psymberin in cells was sensitive to the stereochemistry of the amide side chain at C4 or C8 and the presence of the dihydroisocoumarin side chain. The observation that psymberin diastereomers or dihydroisocoumarin-truncated analogs lose all cytotoxic activity while retaining the ability to inhibit protein translation in a cell-free in vitro assay can be explained in the context of these differential cell uptake issues. Finally, we also demonstrate that the blistering activity associated with pederin and other members of the family is not due to their protein synthesis inhibiting activity. Unlike pederin and mycalamide, psymberin does not display irritant or blistering activity. PMID:23088155

  20. Studies toward the unique pederin family member psymberin: structure-activity relationships, biochemical studies, and genetics identify the mode-of-action of psymberin.

    PubMed

    Wu, Cheng-Yang; Feng, Yu; Cardenas, Eduardo R; Williams, Noelle; Floreancig, Paul E; De Brabander, Jef K; Roth, Michael G

    2012-11-21

    Psymberin is the only member of the pederin natural product family that contains a dihydroisocoumarin side chain. Structural modifications of psymberin uncoupled inhibition of protein translation from cytotoxicity, suggesting that psymberin has more than one bioactivity. A forward genetic screen in Caenorhabditis elegans was conducted to identify the molecular target(s) of psymberin. Multiple independent psymberin-resistant mutants were isolated, each containing the same point mutation in a gene encoding a ribosomal protein. However, a psymberin-resistant mutant strain bearing this mutation was not cross-resistant to the pederin family member mycalamide A, which binds to the archaeal form of the same protein. Thus, two pederin family members likely differ in how they bind the same molecular target. The accumulation of psymberin in cells was sensitive to the stereochemistry of the amide side chain at C4 or C8 and the presence of the dihydroisocoumarin side chain. The observation that psymberin diastereomers or dihydroisocoumarin-truncated analogs lose all cytotoxic activity while retaining the ability to inhibit protein translation in a cell-free in vitro assay can be explained in the context of these differential cell uptake issues. Finally, we also demonstrate that the blistering activity associated with pederin and other members of the family is not due to their protein synthesis inhibiting activity. Unlike pederin and mycalamide, psymberin does not display irritant or blistering activity.

  1. Novel Inducers of Fetal Globin Identified through High Throughput Screening (HTS) Are Active In Vivo in Anemic Baboons and Transgenic Mice.

    PubMed

    Boosalis, Michael S; Sangerman, Jose I; White, Gary L; Wolf, Roman F; Shen, Ling; Dai, Yan; White, Emily; Makala, Levi H; Li, Biaoru; Pace, Betty S; Nouraie, Mehdi; Faller, Douglas V; Perrine, Susan P

    2015-01-01

    High-level fetal (γ) globin expression ameliorates clinical severity of the beta (β) hemoglobinopathies, and safe, orally-bioavailable γ-globin inducing agents would benefit many patients. We adapted a LCR-γ-globin promoter-GFP reporter assay to a high-throughput robotic system to evaluate five diverse chemical libraries for this activity. Multiple structurally- and functionally-diverse compounds were identified which activate the γ-globin gene promoter at nanomolar concentrations, including some therapeutics approved for other conditions. Three candidates with established safety profiles were further evaluated in erythroid progenitors, anemic baboons and transgenic mice, with significant induction of γ-globin expression observed in vivo. A lead candidate, Benserazide, emerged which demonstrated > 20-fold induction of γ-globin mRNA expression in anemic baboons and increased F-cell proportions by 3.5-fold in transgenic mice. Benserazide has been used chronically to inhibit amino acid decarboxylase to enhance plasma levels of L-dopa. These studies confirm the utility of high-throughput screening and identify previously unrecognized fetal globin inducing candidates which can be developed expediently for treatment of hemoglobinopathies.

  2. Novel Inducers of Fetal Globin Identified through High Throughput Screening (HTS) Are Active In Vivo in Anemic Baboons and Transgenic Mice

    PubMed Central

    Boosalis, Michael S.; Sangerman, Jose I.; White, Gary L.; Wolf, Roman F.; Shen, Ling; Dai, Yan; White, Emily; Makala, Levi H.; Li, Biaoru; Pace, Betty S.; Nouraie, Mehdi; Faller, Douglas V.; Perrine, Susan P.

    2015-01-01

    High-level fetal (γ) globin expression ameliorates clinical severity of the beta (β) hemoglobinopathies, and safe, orally-bioavailable γ-globin inducing agents would benefit many patients. We adapted a LCR-γ-globin promoter-GFP reporter assay to a high-throughput robotic system to evaluate five diverse chemical libraries for this activity. Multiple structurally- and functionally-diverse compounds were identified which activate the γ-globin gene promoter at nanomolar concentrations, including some therapeutics approved for other conditions. Three candidates with established safety profiles were further evaluated in erythroid progenitors, anemic baboons and transgenic mice, with significant induction of γ-globin expression observed in vivo. A lead candidate, Benserazide, emerged which demonstrated > 20-fold induction of γ-globin mRNA expression in anemic baboons and increased F-cell proportions by 3.5-fold in transgenic mice. Benserazide has been used chronically to inhibit amino acid decarboxylase to enhance plasma levels of L-dopa. These studies confirm the utility of high-throughput screening and identify previously unrecognized fetal globin inducing candidates which can be developed expediently for treatment of hemoglobinopathies. PMID:26713848

  3. Peptide array on cellulose support--a screening tool to identify peptides with dipeptidyl-peptidase IV inhibitory activity within the sequence of α-lactalbumin.

    PubMed

    Lacroix, Isabelle M E; Li-Chan, Eunice C Y

    2014-11-13

    The inhibition of the enzyme dipeptidyl-peptidase IV (DPP-IV) is an effective pharmacotherapeutic approach for the management of type 2 diabetes. Recent findings have suggested that dietary proteins, including bovine α-lactalbumin, could be precursors of peptides able to inhibit DPP-IV. However, information on the location of active peptide sequences within the proteins is far from being comprehensive. Moreover, the traditional approach to identify bioactive peptides from foods can be tedious and long. Therefore, the objective of this study was to use peptide arrays to screen α-lactalbumin-derived peptides for their interaction with DPP-IV. Deca-peptides spanning the entire α-lactalbumin sequence, with a frame shift of 1 amino acid between successive sequences, were synthesized on cellulose membranes using "SPOT" technology, and their binding to and inhibition of DPP-IV was studied. Among the 114 α-lactalbumin-derived decamers investigated, the peptides 60WCKDDQNPHS69 (αK(i) = 76 µM), 105LAHKALCSEK114 (K(i) = 217 µM) and 110LCSEKLDQWL119 (K(i) = 217 µM) were among the strongest DPP-IV inhibitors. While the SPOT- and traditionally-synthesized peptides showed consistent trends in DPP-IV inhibitory activity, the cellulose-bound peptides' binding behavior was not correlated to their ability to inhibit the enzyme. This research showed, for the first time, that peptide arrays are useful screening tools to identify DPP-IV inhibitory peptides from dietary proteins.

  4. A proposed approach to systematically identify and monitor the corporate political activity of the food industry with respect to public health using publicly available information.

    PubMed

    Mialon, M; Swinburn, B; Sacks, G

    2015-07-01

    Unhealthy diets represent one of the major risk factors for non-communicable diseases. There is currently a risk that the political influence of the food industry results in public health policies that do not adequately balance public and commercial interests. This paper aims to develop a framework for categorizing the corporate political activity of the food industry with respect to public health and proposes an approach to systematically identify and monitor it. The proposed framework includes six strategies used by the food industry to influence public health policies and outcomes: information and messaging; financial incentive; constituency building; legal; policy substitution; opposition fragmentation and destabilization. The corporate political activity of the food industry could be identified and monitored through publicly available data sourced from the industry itself, governments, the media and other sources. Steps for country-level monitoring include identification of key food industry actors and related sources of information, followed by systematic data collection and analysis of relevant documents, using the proposed framework as a basis for classification of results. The proposed monitoring approach should be pilot tested in different countries as part of efforts to increase the transparency and accountability of the food industry. This approach has the potential to help redress any imbalance of interests and thereby contribute to the prevention and control of non-communicable diseases.

  5. Integrated Ligand-Receptor Bioinformatic and In Vitro Functional Analysis Identifies Active TGFA/EGFR Signaling Loop in Papillary Thyroid Carcinomas

    PubMed Central

    Degl'Innocenti, Debora; Alberti, Chiara; Castellano, Giancarlo; Greco, Angela; Miranda, Claudia; Pierotti, Marco A.; Seregni, Ettore; Borrello, Maria Grazia; Canevari, Silvana; Tomassetti, Antonella

    2010-01-01

    Background Papillary thyroid carcinoma (PTCs), the most frequent thyroid cancer, is usually not life threatening, but may recur or progress to aggressive forms resistant to conventional therapies. A more detailed understanding of the signaling pathways activated in PTCs may help to identify novel therapeutic approaches against these tumors. The aim of this study is to identify signaling pathways activated in PTCs. Methodology/Principal Findings We examined coordinated gene expression patterns of ligand/receptor (L/R) pairs using the L/R database DRLP-rev1 and five publicly available thyroid cancer datasets of gene expression on a total of 41 paired PTC/normal thyroid tissues. We identified 26 (up) and 13 (down) L/R pairs coordinately and differentially expressed. The relevance of these L/R pairs was confirmed by performing the same analysis on REarranged during Transfection (RET)/PTC1-infected thyrocytes with respect to normal thyrocytes. TGFA/EGFR emerged as one of the most tightly regulated L/R pair. Furthermore, PTC clinical samples analyzed by real-time RT-PCR expressed EGFR transcript levels similar to those of 5 normal thyroid tissues from patients with pathologies other than thyroid cancer, whereas significantly elevated levels of TGFA transcripts were only present in PTCs. Biochemical analysis of PTC cell lines demonstrated the presence of EGFR on the cell membrane and TGFA in conditioned media. Moreover, conditioned medium of the PTC cell line NIM-1 activated EGFR expressed on HeLa cells, culminating in both ERK and AKT phosphorylation. In NIM-1 cells harboring BRAF mutation, TGFA stimulated proliferation, contributing to PI3K/AKT activation independent of MEK/ERK signaling. Conclusions/Significance We compiled a reliable list of L/R pairs associated with PTC and validated the biological role of one of the emerged L/R pair, the TGFA/EGFR, in this cancer, in vitro. These data provide a better understanding of the factors involved in the biology of PTCs and

  6. A Genome-wide CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Screen Identifies NEK7 as an Essential Component of NLRP3 Inflammasome Activation.

    PubMed

    Schmid-Burgk, Jonathan L; Chauhan, Dhruv; Schmidt, Tobias; Ebert, Thomas S; Reinhardt, Julia; Endl, Elmar; Hornung, Veit

    2016-01-01

    Inflammasomes are high molecular weight protein complexes that assemble in the cytosol upon pathogen encounter. This results in caspase-1-dependent pro-inflammatory cytokine maturation, as well as a special type of cell death, known as pyroptosis. The Nlrp3 inflammasome plays a pivotal role in pathogen defense, but at the same time, its activity has also been implicated in many common sterile inflammatory conditions. To this effect, several studies have identified Nlrp3 inflammasome engagement in a number of common human diseases such as atherosclerosis, type 2 diabetes, Alzheimer disease, or gout. Although it has been shown that known Nlrp3 stimuli converge on potassium ion efflux upstream of Nlrp3 activation, the exact molecular mechanism of Nlrp3 activation remains elusive. Here, we describe a genome-wide CRISPR/Cas9 screen in immortalized mouse macrophages aiming at the unbiased identification of gene products involved in Nlrp3 inflammasome activation. We employed a FACS-based screen for Nlrp3-dependent cell death, using the ionophoric compound nigericin as a potassium efflux-inducing stimulus. Using a genome-wide guide RNA (gRNA) library, we found that targeting Nek7 rescued macrophages from nigericin-induced lethality. Subsequent studies revealed that murine macrophages deficient in Nek7 displayed a largely blunted Nlrp3 inflammasome response, whereas Aim2-mediated inflammasome activation proved to be fully intact. Although the mechanism of Nek7 functioning upstream of Nlrp3 yet remains elusive, these studies provide a first genetic handle of a component that specifically functions upstream of Nlrp3.

  7. The Inhibition of Mast Cell Activation of Radix Paeoniae alba Extraction Identified by TCRP Based and Conventional Cell Function Assay Systems

    PubMed Central

    Fu, Huiying; Cheng, Hongqiang; Cao, Gang; Zhang, Xingde; Tu, Jue; Sun, Mingjiao; Mou, Xiaozhou; Shou, Qiyang; Ke, Yuehai

    2016-01-01

    Chinese herbs have long been used to treat allergic disease, but recently the development was greatly impeded by the lack of good methods to explore the mechanism of action. Here, we showed the effects of Chinese herb Radix Paeoniae alba were identified and characterized by a mast cell activation assay that involves electronic impedance readouts for dynamic monitoring of cellular responses to produce time-dependent cell responding profiles (TCRPs), and the anti-allergic activities were further confirmed with various conventional molecular and cell biology tools. We found Radix P. alba can dose-dependently inhibit TCPRs, and have anti-allergic function in vitro and in vivo. Radix P. alba suppressed mast cell degranulation not only inhibiting the translocation of granules to the plasma membrane, but also blocking membrane fusion and exocytosis; and that there may be other anti-allergic components in addition to paeoniflorin. Our results suggest that Radix P. alba regulated mast cell activation with multiple targets, and this approach is also suitable for discovering other mast cell degranulation-targeting Chinese herbs and their potential multi-target mechanisms. PMID:27195739

  8. Profound Activity of the Anti-cancer Drug Bortezomib against Echinococcus multilocularis Metacestodes Identifies the Proteasome as a Novel Drug Target for Cestodes

    PubMed Central

    Stadelmann, Britta; Aeschbacher, Denise; Huber, Cristina; Spiliotis, Markus; Müller, Joachim; Hemphill, Andrew

    2014-01-01

    A library of 426 FDA-approved drugs was screened for in vitro activity against E. multilocularis metacestodes employing the phosphoglucose isomerase (PGI) assay. Initial screening at 20 µM revealed that 7 drugs induced considerable metacestode damage, and further dose-response studies revealed that bortezomib (BTZ), a proteasome inhibitor developed for the chemotherapy of myeloma, displayed high anti-metacestodal activity with an EC50 of 0.6 µM. BTZ treatment of E. multilocularis metacestodes led to an accumulation of ubiquinated proteins and unequivocally parasite death. In-gel zymography assays using E. multilocularis extracts demonstrated BTZ-mediated inhibition of protease activity in a band of approximately 23 kDa, the same size at which the proteasome subunit beta 5 of E. multilocularis could be detected by Western blot. Balb/c mice experimentally infected with E. multilocularis metacestodes were used to assess BTZ treatment, starting at 6 weeks post-infection by intraperitoneal injection of BTZ. This treatment led to reduced parasite weight, but to a degree that was not statistically significant, and it induced adverse effects such as diarrhea and neurological symptoms. In conclusion, the proteasome was identified as a drug target in E. multilocularis metacestodes that can be efficiently inhibited by BTZ in vitro. However, translation of these findings into in vivo efficacy requires further adjustments of treatment regimens using BTZ, or possibly other proteasome inhibitors. PMID:25474446

  9. Identifying Factors Associated With Dropout During Prerandomization Run-in Period From an mHealth Physical Activity Education Study: The mPED Trial

    PubMed Central

    Gay, Caryl; Haskell, William; Arai, Shoshana; Vittinghoff, Eric

    2015-01-01

    Background The mobile phone-based physical activity education (mPED) trial is a randomized controlled trial (RCT) evaluating a mobile phone-delivered physical activity intervention for women. The study includes a run-in period to maximize the internal validity of the intervention trial, but little is known about factors related to successful run-in completion, and thus about potential threats to external validity. Objective Objectives of this study are (1) to determine the timing of dropout during the run-in period, reasons for dropout, optimum run-in duration, and relevant run-in components, and (2) to identify predictors of failure to complete the run-in period. Methods A total of 318 physically inactive women met preliminary eligibility criteria and were enrolled in the study between May 2011 and April 2014. A 3-week run-in period was required prior to randomization and included using a mobile phone app and wearing a pedometer. Cross-sectional analysis identified predictors of dropout. Results Out of 318 participants, 108 (34.0%) dropped out prior to randomization, with poor adherence using the study equipment being the most common reason. Median failure time was 17 days into the run-in period. In univariate analyses, nonrandomized participants were younger, had lower income, were less likely to drive regularly, were less likely to have used a pedometer prior to the study, were generally less healthy, had less self-efficacy for physical activity, and reported more depressive symptoms than randomized participants. In multivariate competing risks models, not driving regularly in the past month and not having used a pedometer prior to the study were significantly associated with failure to be randomized (P=.04 and .006, respectively), controlling for age, race/ethnicity, education, shift work, and use of a study-provided mobile phone. Conclusions Regular driving and past pedometer use were associated with reduced dropout during the prerandomization run-in period

  10. A functional signal profiling test for identifying a subset of HER2-negative breast cancers with abnormally amplified HER2 signaling activity

    PubMed Central

    Huang, Yao; Burns, David J; Rich, Benjamin E; MacNeil, Ian A; Dandapat, Abhijit; Soltani, Sajjad M.; Myhre, Samantha; Sullivan, Brian F; Furcht, Leo T; Lange, Carol A; Hurvitz, Sara A; Laing, Lance G

    2016-01-01

    The results of clinical trials evaluating the efficacy of HER2 inhibitors in patients with breast cancer indicate that the correlation between HER2 receptor levels and patient outcomes is as low as 50%. The relatively weak correlation between HER2 status and response to HER2-targeting drugs suggests that measurement of HER2 signaling activity, rather than absolute HER2 levels, may more accurately diagnose HER2-driven breast cancer. A new diagnostic test, the CELx HER2 Signaling Profile (CELx HSP) test, is demonstrated to measure real-time HER2 signaling function in live primary cells. In the present study, epithelial cells extracted fresh from breast cancer patient tumors classified as HER2 negative (HER2−, n = 34 of which 33 were estrogen receptor positive) and healthy subjects (n = 16) were evaluated along with reference breast cancer cell lines (n = 19). Live cell response to specific HER2 agonists (NRG1b and EGF) and antagonist (pertuzumab) was measured. Of the HER2− breast tumor cell samples tested, 7 of 34 patients (20.5%; 95% CI = 10%–37%) had HER2 signaling activity that was characterized as abnormally high. Amongst the tumor samples there was no correlation between HER2 protein status (by cell cytometry) and HER2 signaling activity (hyperactive or normal) (Regression analysis P = 0.144, R2 = 0.068). One conclusion is that measurement of HER2 signaling activity can identify a subset of breast cancers with normal HER2 receptor levels with abnormally high levels of HER2 signaling. This result constitutes a new subtype of breast cancer that should be considered for treatment with HER2 pathway inhibitors. PMID:27713176

  11. How Can We Identify the Elimination of Infectious Diseases? Experience From an Active Measles Laboratory Surveillance System in the Republic of Korea.

    PubMed

    Yang, Tae Un; Kang, Hae Ji; Eom, Hye Eun; Park, Young-Joon; Park, Ok; Kim, Su Jin; Nam, Jeong-Gu; Kim, Sung Soon; Jeong, Eun Kyeong

    2015-11-01

    Global efforts have markedly decreased the disease burden of vaccine-preventable diseases. Many countries have made considerable progress toward the elimination of measles. As elimination is approached, the very low incidence achieved by high vaccination coverage has underscored the need for a sensitive and timely surveillance system. In the Republic of Korea, an active laboratory surveillance system (ALSS) was implemented to supplement the existing passive surveillance system in 2006. The ALSS connects 5 major commercial laboratories and the national measles reference laboratory, where referred samples with positive or equivocal results are retested. Annually, from 2009 to 2013, 3714 suspected cases were detected through the ALSS, an expansion of 8- to 57-fold, compared with only the passive surveillance system. The ALSS, with its sensitivity and timeliness, is a reasonable strategy to supplement the existing measles surveillance system and to help identify the elimination of measles.

  12. Substitution of Feline Leukemia Virus Long Terminal Repeat Sequences into Murine Leukemia Virus Alters the Pattern of Insertional Activation and Identifies New Common Insertion Sites

    PubMed Central

    Johnson, Chassidy; Lobelle-Rich, Patricia A.; Puetter, Adriane; Levy, Laura S.

    2005-01-01

    The recombinant retrovirus, MoFe2-MuLV (MoFe2), was constructed by replacing the U3 region of Moloney murine leukemia virus (M-MuLV) with homologous sequences from the FeLV-945 LTR. NIH/Swiss mice neonatally inoculated with MoFe2 developed T-cell lymphomas of immature thymocyte surface phenotype. MoFe2 integrated infrequently (0 to 9%) near common insertion sites (CISs) previously identified for either parent virus. Using three different strategies, CISs in MoFe2-induced tumors were identified at six loci, none of which had been previously reported as CISs in tumors induced by either parent virus in wild-type animals. Two of the newly identified CISs had not previously been implicated in lymphoma in any retrovirus model. One of these, designated 3-19, encodes the p101 regulatory subunit of phosphoinositide-3-kinase-gamma. The other, designated Rw1, is predicted to encode a protein that functions in the immune response to virus infection. Thus, substitution of FeLV-945 U3 sequences into the M-MuLV long terminal repeat (LTR) did not alter the target tissue for M-MuLV transformation but significantly altered the pattern of CIS utilization in the induction of T-cell lymphoma. These observations support a growing body of evidence that the distinctive sequence and/or structure of the retroviral LTR determines its pattern of insertional activation. The findings also demonstrate the oligoclonal nature of retrovirus-induced lymphomas by demonstrating proviral insertions at CISs in subdominant populations in the tumor mass. Finally, the findings demonstrate the utility of novel recombinant retroviruses such as MoFe2 to contribute new genes potentially relevant to the induction of lymphoid malignancy. PMID:15596801

  13. A genomic region encompassing a newly identified exon provides enhancing activity sufficient for normal myo7aa expression in zebrafish sensory hair cells.

    PubMed

    Ernest, Sylvain; Rosa, Frédéric M

    2015-09-01

    MYO7A is an unconventional myosin involved in the structural organization of hair bundles at the apex of sensory hair cells (SHCs) where it serves mechanotransduction in the process of hearing and balance. Mutations of MYO7A are responsible for abnormal shaping of hair bundles, resulting in human deafness and murine deafness/circling behavior. Myo7aa, expressed in SHCs of the inner ear and lateral line of zebrafish, causes circling behavior and abnormal hair cell function when deficient in mariner mutant. This work identifies a new hair cell-specific enhancer, highly conserved between species, located within Intron 2-3 of zebrafish myosin 7a (myo7aa) gene. This enhancer is contained within a 761-bp DNA fragment that encompasses a newly identified Exon of myo7aa and whose activity does not depend on orientation. Compensation of mariner mutation by expression of mCherry-Myo7aa fusion protein under the control of this 761-bp DNA fragment results in recovery of balance, normal hair bundle shape and restored hair cell function. Two smaller adjacent fragments (344-bp and 431-bp), extracted from the 761-bp fragment, both show hair cell-specific enhancing activity, with apparently reduced intensity and coverage. These data should help understand the role of Myo7aa in sensory hair cell differentiation and function. They provide tools to decipher how myo7aa gene is expressed and regulated in SHCs by allowing the identification of potential transcription factors involved in this process. The discovered enhancer could represent a new target for the identification of deafness-causing mutations affecting human MYO7A.

  14. Environmental pollutants, diet, physical activity, body size, and breast cancer: where do we stand in research to identify opportunities for prevention?

    PubMed

    Brody, Julia Green; Rudel, Ruthann A; Michels, Karin B; Moysich, Kirsten B; Bernstein, Leslie; Attfield, Kathleen R; Gray, Sharon

    2007-06-15

    Breast cancer is the most common invasive cancer in women worldwide and the leading cause of death in US women in mid-life. Treatment has adverse effects, adding to the importance of finding modifiable risk factors. At the invitation of Susan G. Komen for the Cure, we reviewed studies of breast cancer and environmental pollutants, diet (assessed prospectively), body size, and physical activity, and animal studies that identify chemicals as potential mammary carcinogens. Databases developed in the review include information on 216 chemicals that increased mammary gland tumors in animal studies and 450 epidemiologic studies (accessible at www.silentspring.org/sciencereview and www.komen.org/environment). Exposure to potential mammary carcinogens is widespread from chemicals found in consumer products, air and drinking water pollution, food, and women's workplaces. Epidemiologic studies have included only a small number of chemicals identified as mammary carcinogens or as hormone disruptors, which may have implications for breast cancer; however, evidence is emerging for associations between breast cancer and polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and organic solvents. Prospective diet studies have not revealed consistent associations with breast cancer. Improved exposure assessment methods will help advance future human studies of both diet and environmental pollutants. Studies of physical activity show that it is protective. In the same vein as evidence-based medicine, messages for patients, policymakers, and the public should support decision-making based on the strength of current evidence; such messages might address exposure reduction for some pollutants. Investments in research on environmental factors in breast cancer have potentially large public health benefits.

  15. Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer.

    PubMed

    Narayanan, Sathiya Pandi; Singh, Smriti; Gupta, Amit; Yadav, Sandhya; Singh, Shree Ram; Shukla, Sanjeev

    2015-10-28

    The histone demethylase KDM1A specifically demethylates lysine residues and its deregulation has been implicated in the initiation and progression of various cancers. However, KDM1A's molecular role and its pathological consequences, and prognostic significance in oral cancer remain less understood. In the present study, we sought to investigate the expression of KDM1A and its downstream role in oral cancer pathogenesis. By comparing mRNA expression profiles, we identified an elevated KDM1A expression in oral tumors when compared to normal oral tissues. In silico pathway prediction identified the association between KDM1A and E2F1 signaling in oral cancer. Pathway scanning, functional annotation analysis and In vitro assays showed the KDM1A's involvement in oral cancer cell proliferation and the cell cycle. Moreover, real time PCR and luciferase assays confirmed KDM1A's role in regulation of E2F1 signaling activity in oral cancer. Elevated KDM1A expression is associated with poor clinical outcome in oral cancer. Our data indicate that deregulated KDM1A expression is positively associated with proliferative phenotype of oral cancer and confers poor clinical outcome. These cumulative data suggest that KDM1A might be a potential diagnostic and therapeutic target for oral cancer.

  16. Flavonoids Identified from Korean Scutellaria baicalensis Georgi Inhibit Inflammatory Signaling by Suppressing Activation of NF-κB and MAPK in RAW 264.7 Cells

    PubMed Central

    Hong, Gyeong-Eun; Kim, Jin-A.; Nagappan, Arulkumar; Yumnam, Silvia; Lee, Ho-Jeong; Kim, Eun-Hee; Lee, Won-Sup; Shin, Sung-Chul; Park, Hyeon-Soo; Kim, Gon-Sup

    2013-01-01

    Scutellaria baicalensis Georgi has been used as traditional medicine for treating inflammatory diseases, hepatitis, tumors, and diarrhea in Asia. Hence, we investigated the anti-inflammatory effect and determined the molecular mechanism of action of flavonoids isolated from Korean S. baicalensis G. in lipopolysaccharide- (LPS-) stimulated RAW 264.7 macrophages. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay was performed to examine cytotoxicity of the flavonoids at various concentrations of 10, 40, 70, and 100 µg/mL. No cytotoxicity was observed in RAW 264.7 cells at these concentrations. Furthermore, the flavonoids decreased production of inflammatory mediators such as inducible nitric oxide synthase, cyclooxygenase-2, interleukin-6, and tumor necrosis factor-alpha and inhibited phosphorylation of nuclear factor-kappa B (NF-κB) and mitogen-activated protein kinases (MAPKs) in LPS-induced RAW 264.7 cells. Moreover, to identify the differentially expressed proteins in RAW 264.7 cells of the control, LPS-treated, and flavonoid-treated groups, two-dimensional gel electrophoresis and mass spectrometry were conducted. The identified proteins were involved in the inflammatory response and included PRKA anchor protein and heat shock protein 70 kD. These findings suggest that the flavonoids isolated from S. baicalensis G. might have anti-inflammatory effects that regulate the expression of inflammatory mediators by inhibiting the NF-κB signaling pathway via the MAPK signaling pathway in RAW 264.7 cells. PMID:24348728

  17. Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors.

    PubMed

    Claffey, Michelle M; Helal, Christopher J; Verhoest, Patrick R; Kang, Zhijun; Fors, Kristina S; Jung, Stanley; Zhong, Jiaying; Bundesmann, Mark W; Hou, Xinjun; Lui, Shenping; Kleiman, Robin J; Vanase-Frawley, Michelle; Schmidt, Anne W; Menniti, Frank; Schmidt, Christopher J; Hoffman, William E; Hajos, Mihaly; McDowell, Laura; O'Connor, Rebecca E; Macdougall-Murphy, Mary; Fonseca, Kari R; Becker, Stacey L; Nelson, Frederick R; Liras, Spiros

    2012-11-08

    Phosphodiesterase 9A inhibitors have shown activity in preclinical models of cognition with potential application as novel therapies for treating Alzheimer's disease. Our clinical candidate, PF-04447943 (2), demonstrated acceptable CNS permeability in rats with modest asymmetry between central and peripheral compartments (free brain/free plasma = 0.32; CSF/free plasma = 0.19) yet had physicochemical properties outside the range associated with traditional CNS drugs. To address the potential risk of restricted CNS penetration with 2 in human clinical trials, we sought to identify a preclinical candidate with no asymmetry in rat brain penetration and that could advance into development. Merging the medicinal chemistry strategies of structure-based design with parallel chemistry, a novel series of PDE9A inhibitors was identified that showed improved selectivity over PDE1C. Optimization afforded preclinical candidate 19 that demonstrated free brain/free plasma ≥ 1 in rat and reduced microsomal clearance along with the ability to increase cyclic guanosine monophosphosphate levels in rat CSF.

  18. Phage-peptide display identifies the interferon-responsive, death-activated protein kinase family as a novel modifier of MDM2 and p21WAF1.

    PubMed

    Burch, Lindsay R; Scott, Mary; Pohler, Elizabeth; Meek, David; Hupp, Ted

    2004-03-12

    Phage-peptide display is a versatile tool for identifying novel protein-protein interfaces. Our previous work highlighted the selection of phage-peptides that bind to specific isoforms of MDM2 protein and in this work we subjected the putative MDM2-binding proteins to phage-peptide display to expand further on putative protein interaction maps. One peptide that bound MDM2 had significant homology to members of the death-activated protein kinase (DAPK) family, an enzyme family of no known direct link to the p53 pathway. We examined whether a nuclear member of the DAPK family named DAPK3 or ZIP kinase had direct links to the p53 pathway. ZIP kinase was cloned, purified, and the enzyme was able to phosphorylate MDM2 at Ser166, a site previously reported to be modified by Akt kinase, thus demonstrating that ZIP kinase is a bona fide MDM2-binding protein. Native ZIP kinase fractions were then subjected to phage-peptide display and one ZIP kinase consensus peptide motif was identified in p21(WAF1). ZIP kinase phosphorylates p21(WAF1) at Thr145 and alanine-substituted mutations in the p21(WAF1) phosphorylation site alter its ability to be phosphorylated by ZIP kinase. Thus, although ZIP kinase consensus sites were then defined as containing a minimal RKKx(T/S) consensus motif, alternate contacts in ZIP kinase binding are implicated, since amino acid residues surrounding the phospho-acceptor site can effect the specific activity of the kinase. Transfected ZIPK can promote the phosphorylation of p21(WAF1) at Thr145 in vivo and can increase the half-life of p21(WAF1), while the half-life of p21(WAF1[T145A]) is not effected by ZIP kinase. Thus, phage-peptide display identified an interferon-responsive protein kinase family as a novel modifier of two components of the p53 pathway, MDM2 and p21(WAF1), and underscores the utility of phage-peptide display for gaining novel insights into biochemical pathways.

  19. A structure-activity study to identify novel and efficient substrates of the human semicarbazide-sensitive amine oxidase/VAP-1 enzyme.

    PubMed

    Bonaiuto, Emanuela; Lunelli, Michele; Scarpa, Marina; Vettor, Roberto; Milan, Gabriella; Di Paolo, Maria Luisa

    2010-07-01

    Kinetic studies were performed with various alkanamines as "substrate probes" of the properties of the active site of the human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1 (SSAO/VAP-1). We found that the enzyme-substrate recognition step is mainly controlled by apolar interactions and that a "good" substrate has a molecular structure containing a long aliphatic chain and a second positive charge at a distance greater than 12 A from the reactive amino group. In this context, we identified a novel substrate for the human SSAO/VAP-1, 1,12-diaminododecane (DIADO), which is characterised by the highest catalytic efficiency reported to date in comparison to the prototypic substrate benzylamine. Computational docking studies revealed the structural basis of this behaviour, highlighting the key role played by Lys393 in hindering substrate docking. Maximum SSAO/VAP-1 activity is reached at relatively low concentrations of DIADO (10-30 microM), and, in these conditions, it has good selectivity: it is a good substrate of SSAO/VAP-1 but not of human adipocyte monoamine oxidases or pig kidney diamine oxidase. From these findings, it appears that DIADO can be used as a new substrate for human SSAO/VAP-1 to elicit glucose transport into adipocytes, and may consequently have potential pharmacological applications in the design of anti-diabetic agents.

  20. Identifying the presence of a disulfide linkage in peptides by the selective elimination of hydrogen disulfide from collisionally activated alkali and alkaline earth metal complexes.

    PubMed

    Kim, Hugh I; Beauchamp, J L

    2008-01-30

    We report a new method for identifying disulfide linkages in peptides using mass spectrometry. This is accomplished by collisional activation of singly charged cationic alkali and alkaline earth metal complexes, which results in the highly selective elimination of hydrogen disulfide (H2S2). Complexes of peptides possessing disulfide bonds with sodium and alkaline earth metal are generated using electrospray ionization (ESI). Isolation followed by collision induced dissociation (CID) of singly charged peptide complexes results in selective elimination of H2S2 to leave newly formed dehydroalanine residues in the peptide. Further activation of the product yields sequence information in the region previously short circuited by the disulfide bond. For example, singly charged magnesium and calcium ion bound complexes of [Lys8]-vasopressin exhibit selective elimination of H2S2 via low-energy CID. Further isolation of the product followed by CID yields major b- and z-type fragments revealing the peptide sequence in the region between the newly formed dehydroalanine residues. Numerous model peptides provide mechanistic details for the selective elimination of H2S2. The process is initiated starting with a metal stabilized enolate anion at Cys, followed by cleavage of the S-C bond. An examination of the peptic digest of insulin provides an example of the application of the selective elimination of H2S2 for the identification of peptides with disulfide linkages. The energetics and mechanisms of H2S2 elimination from model compounds are investigated using density functional theory (DFT) calculations.

  1. Cell-Based Screening Identifies the Active Ingredients from Traditional Chinese Medicine Formula Shixiao San as the Inhibitors of Atherosclerotic Endothelial Dysfunction

    PubMed Central

    Wang, Xiaofan; Zhang, Ruowen; Gu, Liqiang; Zhang, Yuanyuan; Zhao, Xu; Bi, Kaishun; Chen, Xiaohui

    2015-01-01

    In this study, we performed a phenotypic screening in human endothelial cells exposed to oxidized low density lipoprotein (an in vitro model of atherosclerotic endothelial dysfunction) to identify the effective compounds in Shixiao San. After investigating the suitability and reliability of the cell-based screening method using atorvastatin as the positive control drug, this method was applied in screening Shixiao San and its extracts. The treatment of n-butanol fraction on endothelial cells exhibited stronger healing effects against oxidized low density lipoprotein-induced insult when compared with other fractions. Cell viability, the level of nitric oxide, endothelial nitric oxide synthase and endothelin-1 were measured, respectively. The assays revealed n-butanol fraction significantly elevated the survival ratio of impaired cells in culture. In parallel, n-butanol fraction exhibited the highest inhibition of inflammation. The generation of prostaglandin-2 and adhesion molecule (soluble intercellular adhesion molecule-1) was obviously declined. Furthermore, n-butanol fraction suppressed the production of reactive oxygen species and malondialdehyde, and restored the activity of superoxide dismutase. Compounds identification of the n-butanol fraction was carried out by ultra high liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry. The active ingredients including quercetin-3-O-(2G-α-l-rhamnosyl)-rutinoside, quercetin-3-O-neohesperidoside, isorhamnetin-3-O-neohesperidoside and isorhamnetin-3-O-rutinoside revealed the ability of anti-atherosclerosis after exposing on endothelial cells. The current work illustrated the pharmacology effect of Shixiao San and clearly indicated the major active components in Shixiao San. More importantly, the proposed cell-based screening method might be particularly suitable for fast evaluating the anti-atherosclerosis efficacy of Traditional Chinese Medicines and screening out the interesting

  2. Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2)

    PubMed Central

    de Jesus Cortez, Felipe; Suzawa, Miyuki; Irvy, Sam; Bruning, John M.; Sablin, Elena; Jacobson, Matthew P.; Fletterick, Robert J.; Ingraham, Holly A.

    2016-01-01

    Conventional efforts relying on high-throughput physical and virtual screening of large compound libraries have failed to yield high-efficiency chemical probes for many of the 48 human nuclear receptors. Here, we investigated whether disulfide-trapping, an approach new to nuclear receptors, would provide effective lead compounds targeting human liver receptor homolog 1 (hLRH-1, NR5A2). Despite the fact that hLRH-1 contains a large ligand binding pocket and binds phospholipids with high affinity, existing synthetic hLRH-1 ligands are of limited utility due to poor solubility, low efficacy or significant off-target effects. Using disulfide-trapping, we identified a lead compound that conjugates with remarkably high-efficiency to a native cysteine residue (Cys346) lining the hydrophobic cavity in the ligand binding domain of hLRH-1. Guided by computational modeling and cellular assays, the lead compound was elaborated into ligands PME8 and PME9 that bind hLRH-1 reversibly (no cysteine reactivity) and increase hLRH-1 activity in cells. When compared with the existing hLRH-1 synthetic agonist RJW100, both PME8 and PME9 showed comparable induction of the LRH-1 dependent target gene CYP24A1 in human HepG2 cells, beginning as early as 3 h after drug treatment. The induction is specific as siRNA-mediated knock-down of hLRH-1 renders both PME8 and PME9 ineffective. These data show that PME8 and PME9 are potent activators of hLRH-1 and suggest that with further development this lead series may yield useful chemical probes for manipulating LRH-1 activity in vivo. PMID:27467220

  3. Identifying the computational requirements of an integrated top-down-bottom-up model for overt visual attention within an active vision system.

    PubMed

    McBride, Sebastian; Huelse, Martin; Lee, Mark

    2013-01-01

    Computational visual attention systems have been constructed in order for robots and other devices to detect and locate regions of interest in their visual world. Such systems often attempt to take account of what is known of the human visual system and employ concepts, such as 'active vision', to gain various perceived advantages. However, despite the potential for gaining insights from such experiments, the computational requirements for visual attention processing are often not clearly presented from a biological perspective. This was the primary objective of this study, attained through two specific phases of investigation: 1) conceptual modeling of a top-down-bottom-up framework through critical analysis of the psychophysical and neurophysiological literature, 2) implementation and validation of the model into robotic hardware (as a representative of an active vision system). Seven computational requirements were identified: 1) transformation of retinotopic to egocentric mappings, 2) spatial memory for the purposes of medium-term inhibition of return, 3) synchronization of 'where' and 'what' information from the two visual streams, 4) convergence of top-down and bottom-up information to a centralized point of information processing, 5) a threshold function to elicit saccade action, 6) a function to represent task relevance as a ratio of excitation and inhibition, and 7) derivation of excitation and inhibition values from object-associated feature classes. The model provides further insight into the nature of data representation and transfer between brain regions associated with the vertebrate 'active' visual attention system. In particular, the model lends strong support to the functional role of the lateral intraparietal region of the brain as a primary area of information consolidation that directs putative action through the use of a 'priority map'.

  4. Evaluation of Changes in Ghanaian Students' Attitudes Towards Science Following Neuroscience Outreach Activities: A Means to Identify Effective Ways to Inspire Interest in Science Careers.

    PubMed

    Yawson, Nat Ato; Amankwaa, Aaron Opoku; Tali, Bernice; Shang, Velma Owusua; Batu, Emmanuella Nsenbah; Asiemoah, Kwame; Fuseini, Ahmed Denkeri; Tene, Louis Nana; Angaandi, Leticia; Blewusi, Isaac; Borbi, Makafui; Aduku, Linda Nana Esi; Badu, Pheonah; Abbey, Henrietta; Karikari, Thomas K

    2016-01-01

    The scientific capacity in many African countries is low. Ghana, for example, is estimated to have approximately twenty-three researchers per a million inhabitants. In order to improve interest in science among future professionals, appropriate techniques should be developed and employed to identify barriers and correlates of science education among pre-university students. Young students' attitudes towards science may affect their future career choices. However, these attitudes may change with new experiences. It is, therefore, important to evaluate potential changes in students' attitudes towards science after their exposure to experiences such as science outreach activities. Through this, more effective means of inspiring and mentoring young students to choose science subjects can be developed. This approach would be particularly beneficial in countries such as Ghana, where: (i) documented impacts of outreach activities are lacking; and (ii) effective means to develop scientist-school educational partnerships are needed. We have established an outreach scheme, aimed at helping to improve interaction between scientists and pre-university students (and their teachers). Outreach activities are designed and implemented by undergraduate students and graduate teaching assistants, with support from faculty members and technical staff. Through this, we aim to build a team of trainee scientists and graduates who will become ambassadors of science in their future professional endeavors. Here, we describe an approach for assessing changes in junior high school students' attitudes towards science following classroom neuroscience outreach activities. We show that while students tended to agree more with questions concerning their perceptions about science learning after the delivery of outreach activities, significant improvements were obtained for only two questions, namely "I enjoy science lessons" and "I want to be a scientist in the future." Furthermore, there was a

  5. Evaluation of Changes in Ghanaian Students’ Attitudes Towards Science Following Neuroscience Outreach Activities: A Means to Identify Effective Ways to Inspire Interest in Science Careers

    PubMed Central

    Yawson, Nat Ato; Amankwaa, Aaron Opoku; Tali, Bernice; Shang, Velma Owusua; Batu, Emmanuella Nsenbah; Asiemoah, Kwame; Fuseini, Ahmed Denkeri; Tene, Louis Nana; Angaandi, Leticia; Blewusi, Isaac; Borbi, Makafui; Aduku, Linda Nana Esi; Badu, Pheonah; Abbey, Henrietta; Karikari, Thomas K.

    2016-01-01

    The scientific capacity in many African countries is low. Ghana, for example, is estimated to have approximately twenty-three researchers per a million inhabitants. In order to improve interest in science among future professionals, appropriate techniques should be developed and employed to identify barriers and correlates of science education among pre-university students. Young students’ attitudes towards science may affect their future career choices. However, these attitudes may change with new experiences. It is, therefore, important to evaluate potential changes in students’ attitudes towards science after their exposure to experiences such as science outreach activities. Through this, more effective means of inspiring and mentoring young students to choose science subjects can be developed. This approach would be particularly beneficial in countries such as Ghana, where: (i) documented impacts of outreach activities are lacking; and (ii) effective means to develop scientist-school educational partnerships are needed. We have established an outreach scheme, aimed at helping to improve interaction between scientists and pre-university students (and their teachers). Outreach activities are designed and implemented by undergraduate students and graduate teaching assistants, with support from faculty members and technical staff. Through this, we aim to build a team of trainee scientists and graduates who will become ambassadors of science in their future professional endeavors. Here, we describe an approach for assessing changes in junior high school students’ attitudes towards science following classroom neuroscience outreach activities. We show that while students tended to agree more with questions concerning their perceptions about science learning after the delivery of outreach activities, significant improvements were obtained for only two questions, namely “I enjoy science lessons” and “I want to be a scientist in the future.” Furthermore

  6. Identifying Nursing's Future Leaders.

    ERIC Educational Resources Information Center

    Gunning, Carolyn S.; Hawken, Patty L.

    1990-01-01

    A study determined that encouraging and supporting students in professional activities while they were still in school would lead those students to participate in professional nursing organizations after they graduated. Organized nursing needs to identify the factors that influence nurses to join organizations and concentrate on these factors to…

  7. Genome-wide DNA methylation identifies trophoblast invasion-related genes: Claudin-4 and Fucosyltransferase IV control mobility via altering matrix metalloproteinase activity.

    PubMed

    Hu, Yuxiang; Blair, John D; Yuen, Ryan K C; Robinson, Wendy P; von Dadelszen, Peter

    2015-05-01

    Previously we showed that extravillous cytotrophoblast (EVT) outgrowth and migration on a collagen gel explant model were affected by exposure to decidual natural killer cells (dNK). This study investigates the molecular causes behind this phenomenon. Genome wide DNA methylation of exposed and unexposed EVT was assessed using the Illumina Infinium HumanMethylation450 BeadChip array (450 K array). We identified 444 differentially methylated CpG loci in dNK-treated EVT compared with medium control (P < 0.05). The genes associated with these loci had critical biological roles in cellular development, cellular growth and proliferation, cell signaling, cellular assembly and organization by Ingenuity Pathway Analysis (IPA). Furthermore, 23 mobility-related genes were identified by IPA from dNK-treated EVT. Among these genes, CLDN4 (encoding claudin-4) and FUT4 (encoding fucosyltransferase IV) were chosen for follow-up studies because of their biological relevance from research on tumor cells. The results showed that the mRNA and protein expressions of both CLDN4 and FUT4 in dNK-treated EVT were significantly reduced compared with control (P < 0.01 for both CLDN4 and FUT4 mRNA expression; P < 0.001 for CLDN4 and P < 0.01 for FUT4 protein expression), and were inversely correlated with DNA methylation. Knocking down CLDN4 and FUT4 by small interfering RNA reduced trophoblast invasion, possibly through the altered matrix metalloproteinase (MMP)-2 and/or MMP-9 expression and activity. Taken together, dNK alter EVT mobility at least partially in association with an alteration of DNA methylation profile. Hypermethylation of CLDN4 and FUT4 reduces protein expression. CLDN4 and FUT4 are representative genes that participate in modulating trophoblast mobility.

  8. Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses

    PubMed Central

    2009-01-01

    Background Optimization methods allow designing changes in a system so that specific goals are attained. These techniques are fundamental for metabolic engineering. However, they are not directly applicable for investigating the evolution of metabolic adaptation to environmental changes. Although biological systems have evolved by natural selection and result in well-adapted systems, we can hardly expect that actual metabolic processes are at the theoretical optimum that could result from an optimization analysis. More likely, natural systems are to be found in a feasible region compatible with global physiological requirements. Results We first present a new method for globally optimizing nonlinear models of metabolic pathways that are based on the Generalized Mass Action (GMA) representation. The optimization task is posed as a nonconvex nonlinear programming (NLP) problem that is solved by an outer-approximation algorithm. This method relies on solving iteratively reduced NLP slave subproblems and mixed-integer linear programming (MILP) master problems that provide valid upper and lower bounds, respectively, on the global solution to the original NLP. The capabilities of this method are illustrated through its application to the anaerobic fermentation pathway in Saccharomyces cerevisiae. We next introduce a method to identify the feasibility parametric regions that allow a system to meet a set of physiological constraints that can be represented in mathematical terms through algebraic equations. This technique is based on applying the outer-approximation based algorithm iteratively over a reduced search space in order to identify regions that contain feasible solutions to the problem and discard others in which no feasible solution exists. As an example, we characterize the feasible enzyme activity changes that are compatible with an appropriate adaptive response of yeast Saccharomyces cerevisiae to heat shock Conclusion Our results show the utility of the

  9. Quantitative High-Throughput Drug Screening Identifies Novel Classes of Drugs with Anticancer Activity in Thyroid Cancer Cells: Opportunities for Repurposing

    PubMed Central

    Zhang, Lisa; He, Mei; Zhang, Yaqin; Nilubol, Naris; Shen, Min

    2012-01-01

    Context: Despite increased understanding of the pathogenesis and targets for thyroid cancer and other cancers, developing a new anticancer chemical agent remains an expensive and long process. An alternative approach is the exploitation of clinically used and/or bioactive compounds. Objective: Our objective was to identify agents with an anticancer effect in thyroid cancer cell lines using quantitative high-throughput screening (qHTS). Design: We used the newly assembled National Institutes of Health Chemical Genomic Center's pharmaceutical collection, which contains 2816 clinically approved drugs and bioactive compounds to perform qHTS. Results: Multiple agents, across a variety of therapeutic categories and with different modes of action, were found to have an antiproliferative effect. We found the following therapeutic categories were the most enriched categories with antiproliferative activity: cardiotonic and antiobesity agents. Sixteen agents had an efficacy of greater than 60% and a 50% inhibitory concentration (IC50) in the nanomolar range. We validated the results of the qHTS using two agents (bortezomib and ouabain) in additional cell lines representing different histological subtypes of thyroid cancer and with different mutations (BRAF V600E, RET/PTC1, p53, PTEN). Both agents induced apoptosis, and ouabain also caused cell cycle arrest. Conclusions: To our knowledge, this is the first study to use qHTS of a large drug library to identify candidate drugs for anticancer therapy. Our results indicate such a screening approach can lead to the discovery of novel agents in different therapeutic categories and drugs with nonclassic chemotherapy mode of action. Our approach could lead to drug repurposing and accelerate clinical trials of compounds with well-established pharmacokinetics and toxicity profiles. PMID:22170715

  10. Development and use of a high-throughput bacterial DNA gyrase assay to identify mammalian topoisomerase II inhibitors with whole-cell anticancer activity.

    PubMed

    Roychoudhury, Siddhartha; Makin, Kelly M; Twinem, Tracy L; Stanton, David T; Nelson, Sandra L; Catrenich, Carl E

    2003-04-01

    A high-throughput screen (HTS) was developed and used to identify inhibitors of bacterial DNA gyrase. Among the validated hits were 53 compounds that also inhibited mammalian topoisomerase II with IC(50) values of <12.5 micro g/mL for 51 of them. Using computational methods, these compounds were subjected to cluster analysis to categorize them according to their chemical and structural properties. Nine compounds from different clusters were tested for their whole-cell inhibitory activity against 3 cancer cell lines-NCI-H460 (lung), MCF7 (breast), and SF-268 (CNS)-at a concentration of 100 micro M. Five compounds inhibited cell growth by >50% for all 3 cell lines tested. These compounds were tested further against a panel of 53 to 57 cell lines representing leukemia, melanoma, colon, CNS, ovarian, renal, prostate, breast, and non-small cell lung cancers. In this assay, PGE-7143417 was found to be the most potent compound, which inhibited the growth of all the cell lines by 50% at a concentration range of 0.31 to 2.58 micro M, with an average of 1.21 micro M. An additional 17 compounds were also tested separately against a panel of 10 cell lines representing melanoma, colon, lung, mammary, ovarian, prostate, and renal cancers. In this assay, 4 compounds-PGE-3782569, PGE-7411516, PGE-2908955, and PGE-3521917-were found to have activity with concentrations for 50% cell growth inhibition in the 0.59 to 3.33, 22.5 to 59.1, 7.1 to >100, and 24.7 to >100 micro M range.

  11. Time-driven activity-based costing of multivessel coronary artery bypass grafting across national boundaries to identify improvement opportunities: study protocol

    PubMed Central

    Erhun, F; Mistry, B; Platchek, T; Milstein, A; Narayanan, V G; Kaplan, R S

    2015-01-01

    Introduction Coronary artery bypass graft (CABG) surgery is a well-established, commonly performed treatment for coronary artery disease—a disease that affects over 10% of US adults and is a major cause of morbidity and mortality. In 2005, the mean cost for a CABG procedure among Medicare beneficiaries in the USA was $32 201±$23 059. The same operation reportedly costs less than $2000 to produce in India. The goals of the proposed study are to (1) identify the difference in the costs incurred to perform CABG surgery by three Joint Commission accredited hospitals with reputations for high quality and efficiency and (2) characterise the opportunity to reduce the cost of performing CABG surgery. Methods and analysis We use time-driven activity-based costing (TDABC) to quantify the hospitals’ costs of producing elective, multivessel CABG. TDABC estimates the costs of a given clinical service by combining information about the process of patient care delivery (specifically, the time and quantity of labour and non-labour resources utilised to perform each activity) with the unit cost of each resource used to provide the care. Resource utilisation was estimated by constructing CABG process maps for each site based on observation of care and staff interviews. Unit costs were calculated as a capacity cost rate, measured as a $/min, for each resource consumed in CABG production. Multiplying together the unit costs and resource quantities and summing across all resources used will produce the average cost of CABG production at each site. We will conclude by conducting a variance analysis of labour costs to reveal opportunities to bend the cost curve for CABG production in the USA. Ethics and dissemination All our methods were exempted from review by the Stanford Institutional Review Board. Results will be published in peer-reviewed journals and presented at scientific meetings. PMID:26307621

  12. Symptom screening rules to identify active pulmonary tuberculosis: Findings from the Zambian South African Tuberculosis and HIV/AIDS Reduction (ZAMSTAR) trial prevalence surveys

    PubMed Central

    Claassens, M. M.; Floyd, S.; Ayles, H.; Beyers, N.

    2017-01-01

    Background High tuberculosis (TB) burden countries should consider systematic screening among adults in the general population. We identified symptom screening rules to be used in addition to cough ≥2 weeks, in a context where X-ray screening is not feasible, aiming to increase the sensitivity of screening while achieving a specificity of ≥85%. Methods We used 2010 Zambia South Africa Tuberculosis and HIV/AIDS Reduction (ZAMSTAR) survey data: a South African (SA) training dataset, a SA testing dataset for internal validation and a Zambian dataset for external validation. Regression analyses investigated relationships between symptoms or combinations of symptoms and active disease. Sensitivity and specificity were calculated for candidate rules. Results Among all participants, the sensitivity of using only cough ≥2 weeks as a screening rule was less than 25% in both SA and Zambia. The addition of any three of six TB symptoms (cough <2 weeks, night sweats, weight loss, fever, chest pain, shortness of breath), or 2 or more of cough <2 weeks, night sweats, and weight loss, increased the sensitivity to ~38%, while reducing specificity from ~95% to ~85% in SA and ~97% to ~92% in Zambia. Among HIV-negative adults, findings were similar in SA, whereas in Zambia the increase in sensitivity was relatively small (15% to 22%). Conclusion High TB burden countries should investigate cost-effective strategies for systematic screening: one such strategy could be to use our rule in addition to cough ≥2 weeks. PMID:28257424

  13. RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters.

    PubMed

    Paul, Asosii; Jha, Ashwani; Bhardwaj, Shruti; Singh, Sewa; Shankar, Ravi; Kumar, Sanjay

    2014-08-04

    Tea [Camellia sinensis (L.) O. Kuntze] is a perennial tree which undergoes winter dormancy and unlike deciduous trees, the species does not shed its leaves during winters. The present work dissected the molecular processes operating in the leaves during the period of active growth and winter dormancy through transcriptome analysis to understand a long-standing question: why should tea be a non-deciduous species? Analyses of 24,700 unigenes obtained from 57,767 primarily assembled transcripts showed (i) operation of mechanisms of winter tolerance, (ii) down-regulation of genes involved in growth, development, protein synthesis and cell division, and (iii) inhibition of leaf abscission due to modulation of senescence related processes during winter dormancy in tea. These senescence related processes exhibited modulation to favour leaf abscission (i) in deciduous Populus tremula during winters, and (ii) also in tea but under osmotic stress during which leaves also abscise. These results validated the relevance of the identified senescence related processes for leaf abscission and suggested their operation when in need in tea.

  14. Liposomal solubilization of new 3-hydroxy-quinolinone derivatives with promising anticancer activity: a screening method to identify maximum incorporation capacity.

    PubMed

    di Cagno, Massimiliano; Styskala, Jakub; Hlaváč, Jan; Brandl, Martin; Bauer-Brandl, Annette; Skalko-Basnet, Natasa

    2011-12-01

    Four new 3-hydroxy-quinolinone derivatives with promising anticancer activity could be solubilized using liposomes as vehicle to an extent that allows their in vitro and in vivo testing without use of toxic solvent(s). A screening method to identify the maximum incorporation capacity of hydrophobic drugs within liposomes was successfully applied. The compounds and lipid(s) were dissolved in methanol, and the solvent was removed by rotary evaporation. The film was resuspended with phosphate buffer (pH 7.4), and the dispersion was sonicated to reduce vesicle size. Ultracentrifugation was used to separate liposome-associated drug from free (i.e., precipitated) drug, and the amount of drug incorporated within the liposomes was quantified using high-performance liquid chromatography. All four compounds were found to be significantly incorporated within soy phosphatidylcholine (SPC) liposomes, resulting in a 200-500-fold increase in apparent solubility. Drug-to-lipid ratios in the range of 2-5 μg/mg were obtained. Interestingly, the four quinolinone derivatives have shown different association tendencies with liposomes, probably due to the physicochemical properties of the different group bonded in position 2 of the quinolinone ring. None of the alternative lipids/lipid blends tested incorporated as much drug as SPC. Photon correlation spectroscopy analyses indicated that use of ultrasounds produced an efficient reduction in liposome size. The present approach appears suitable for incorporation capacity studies of any lipophilic drug in liposomes.

  15. Metabolomic Assessment of Induced and Activated Chemical Defence in the Invasive Red Alga Gracilaria vermiculophylla

    PubMed Central

    Nylund, Göran M.; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  16. Metabolomic assessment of induced and activated chemical defence in the invasive red alga Gracilaria vermiculophylla.

    PubMed

    Nylund, Göran M; Weinberger, Florian; Rempt, Martin; Pohnert, Georg

    2011-01-01

    In comparison with terrestrial plants the mechanistic knowledge of chemical defences is poor for marine macroalgae. This restricts our understanding in the chemically mediated interactions that take place between algae and other organisms. Technical advances such as metabolomics, however, enable new approaches towards the characterisation of the chemically mediated interactions of organisms with their environment. We address defence responses in the red alga Gracilaria vermiculophylla using mass spectrometry based metabolomics in combination with bioassays. Being invasive in the north Atlantic this alga is likely to possess chemical defences according to the prediction that well-defended exotics are most likely to become successful invaders in systems dominated by generalist grazers, such as marine macroalgal communities. We investigated the effect of intense herbivore feeding and simulated herbivory by mechanical wounding of the algae. Both processes led to similar changes in the metabolic profile. Feeding experiments with the generalist isopod grazer Idotea baltica showed that mechanical wounding caused a significant increase in grazer resistance. Structure elucidation of the metabolites of which some were up-regulated more than 100 times in the wounded tissue, revealed known and novel eicosanoids as major components. Among these were prostaglandins, hydroxylated fatty acids and arachidonic acid derived conjugated lactones. Bioassays with pure metabolites showed that these eicosanoids are part of the innate defence system of macroalgae, similarly to animal systems. In accordance with an induced defence mechanism application of extracts from wounded tissue caused a significant increase in grazer resistance and the up-regulation of other pathways than in the activated defence. Thus, this study suggests that G. vermiculophylla chemically deters herbivory by two lines of defence, a rapid wound-activated process followed by a slower inducible defence. By unravelling

  17. Identifying learning styles.

    PubMed

    Hughes, Grace

    2016-12-14

    What was the nature of the CPD activity, practice-related feedback and/or event and/or experience in your practice? The article explored different learning styles and outlined some of the models that can be used to identify them. It discussed the limitations of these models, indicating that although they can be helpful in identifying a student's preferred learning style, this is not 'fixed' and might change over time. Learning is also influenced by other factors, such as culture and age.

  18. An unusual plant triterpene synthase with predominant α-amyrin-producing activity identified by characterizing oxidosqualene cyclases from Malus × domestica.

    PubMed

    Brendolise, Cyril; Yauk, Yar-Khing; Eberhard, Ellen D; Wang, Mindy; Chagne, David; Andre, Christelle; Greenwood, David R; Beuning, Lesley L

    2011-07-01

    The pentacyclic triterpenes, in particular ursolic acid and oleanolic acid and their derivatives, exist abundantly in the plant kingdom, where they are well known for their anti-inflammatory, antitumour and antimicrobial properties. α-Amyrin and β-amyrin are the precursors of ursolic and oleanolic acids, respectively, formed by concerted cyclization of squalene epoxide by a complex synthase reaction. We identified three full-length expressed sequence tag sequences in cDNA libraries constructed from apple (Malus × domestica 'Royal Gala') that were likely to encode triterpene synthases. Two of these expressed sequence tag sequences were essentially identical (> 99% amino acid similarity; MdOSC1 and MdOSC3). MdOSC1 and MdOSC2 were expressed by transient expression in Nicotiana benthamiana leaves and by expression in the yeast Pichia methanolica. The resulting products were analysed by GC and GC-MS. MdOSC1 was shown to be a mixed amyrin synthase (a 5 : 1 ratio of α-amyrin to β-amyrin). MdOSC1 is the only triterpene synthase so far identified in which the level of α-amyrin produced is > 80% of the total product and is, therefore, primarily an α-amyrin synthase. No product was evident for MdOSC2 when expressed either transiently or in yeast, suggesting that this putative triterpene synthase is either encoded by a pseudogene or does not express well in these systems. Transcript expression analysis in Royal Gala indicated that the genes are mostly expressed in apple peel, and that the MdOSC2 expression level was much lower than that of MdOSC1 and MdOSC3 in all the tissues tested. Amyrin content analysis was undertaken by LC-MS, and demonstrated that levels and ratios differ between tissues, but that the true consequence of synthase activity is reflected in the ursolic/oleanolic acid content and in further triterpenoids derived from them. Phylogenetic analysis placed the three triterpene synthase sequences with other triterpene synthases that encoded either

  19. Critical active-site residues identified by site-directed mutagenesis in Pseudomonas aeruginosa phosphorylcholine phosphatase, a new member of the haloacid dehalogenases hydrolase superfamily.

    PubMed

    Beassoni, Paola R; Otero, Lisandro H; Massimelli, Maria J; Lisa, Angela T; Domenech, Carlos E

    2006-12-01

    Pseudomonas aeruginosa phosphorylcholine phosphatase (PChP), the product of the PA5292 gene, is synthesized when the bacteria are grown with choline, betaine, dimethylglycine, or carnitine. In the presence of Mg(2+), PChP catalyzes the hydrolysis of both phosphorylcholine (PCh) and p-nitrophenylphosphate (p-NPP). PCh saturation curve analysis of the enzyme with or without the signal peptide indicated that the peptide was the fundamental factor responsible for decreasing the affinity of the second site of PChP for PCh, either at pH 5.0 or pH 7.4. PChP contained three conserved motifs characteristic of the haloacid dehalogenases superfamily. In the PChP without the signal peptide, motifs I, II, and III correspond to the residues (31)DMDNT(35), (166)SAA(168), and K(242)/(261)GDTPDSD(267), respectively. To determine the catalytic importance of the D31, D33, T35, S166, K242, D262, D265, and D267 on the enzyme activity, site-directed mutagenesis was performed. D31, D33, D262, and D267 were identified as the more important residues for catalysis. D265 and D267 may be involved in the stabilization of motif III, or might contribute to substrate specificity. The substitution of T35 by S35 resulted in an enzyme with a low PChP activity, but conserves the catalytic sites involved in the hydrolysis of PCh (K(m1) 0.03 mM: , K(m2) 0.5 mM: ) or p-NPP (K(m) 2.1 mM: ). Mutating either S166 or K242 revealed that these residues are also important to catalyze the hydrolysis of both substrates. The substitution of lysine by arginine or by glutamine revealed the importance of the positive charged group, either from the amino or guanidinium groups, because K242Q was inactive, whereas K242R was a functional enzyme.

  20. A bioinformatics approach identifies signal transducer and activator of transcription-3 and checkpoint kinase 1 as upstream regulators of kidney injury molecule-1 after kidney injury.

    PubMed

    Ajay, Amrendra Kumar; Kim, Tae-Min; Ramirez-Gonzalez, Victoria; Park, Peter J; Frank, David A; Vaidya, Vishal S

    2014-01-01

    Kidney injury molecule-1 (KIM-1)/T cell Ig and mucin domain-containing protein-1 (TIM-1) is upregulated more than other proteins after AKI, and it is highly expressed in renal damage of various etiologies. In this capacity, KIM-1/TIM-1 acts as a phosphatidylserine receptor on the surface of injured proximal tubular epithelial cells, mediating phagocytosis of apoptotic cells, and it may also act as a costimulatory molecule for immune cells. Despite recognition of KIM-1 as an important therapeutic target for kidney disease, the regulators of KIM-1 transcription in the kidney remain unknown. Using a bioinformatics approach, we identified upstream regulators of KIM-1 after AKI. In response to tubular injury in rat and human kidneys or oxidant stress in human proximal tubular epithelial cells (HPTECs), KIM-1 expression increased significantly in a manner that corresponded temporally and regionally with increased phosphorylation of checkpoint kinase 1 (Chk1) and STAT3. Both ischemic and oxidant stress resulted in a dramatic increase in reactive oxygen species that phosphorylated and activated Chk1, which subsequently bound to STAT3, phosphorylating it at S727. Furthermore, STAT3 bound to the KIM-1 promoter after ischemic and oxidant stress, and pharmacological or genetic induction of STAT3 in HPTECs increased KIM-1 mRNA and protein levels. Conversely, inhibition of STAT3 using siRNAs or dominant negative mutants reduced KIM-1 expression in a kidney cancer cell line (769-P) that expresses high basal levels of KIM-1. These observations highlight Chk1 and STAT3 as critical upstream regulators of KIM-1 expression after AKI and may suggest novel approaches for therapeutic intervention.

  1. KV1 channels identified in rodent myelinated axons, linked to Cx29 in innermost myelin: support for electrically active myelin in mammalian saltatory conduction

    PubMed Central

    Vanderpool, Kimberly G.; Yasumura, Thomas; Hickman, Jordan; Beatty, Jonathan T.; Nagy, James I.

    2016-01-01

    Saltatory conduction in mammalian myelinated axons was thought to be well understood before recent discoveries revealed unexpected subcellular distributions and molecular identities of the K+-conductance pathways that provide for rapid axonal repolarization. In this study, we visualize, identify, localize, quantify, and ultrastructurally characterize axonal KV1.1/KV1.2 channels in sciatic nerves of rodents. With the use of light microscopic immunocytochemistry and freeze-fracture replica immunogold labeling electron microscopy, KV1.1/KV1.2 channels are localized to three anatomically and compositionally distinct domains in the internodal axolemmas of large myelinated axons, where they form densely packed “rosettes” of 9-nm intramembrane particles. These axolemmal KV1.1/KV1.2 rosettes are precisely aligned with and ultrastructurally coupled to connexin29 (Cx29) channels, also in matching rosettes, in the surrounding juxtaparanodal myelin collars and along the inner mesaxon. As >98% of transmembrane proteins large enough to represent ion channels in these specialized domains, ∼500,000 KV1.1/KV1.2 channels define the paired juxtaparanodal regions as exclusive membrane domains for the voltage-gated K+ conductance that underlies rapid axonal repolarization in mammals. The 1:1 molecular linkage of KV1 channels to Cx29 channels in the apposed juxtaparanodal collars, plus their linkage to an additional 250,000–400,000 Cx29 channels along each inner mesaxon in every large-diameter myelinated axon examined, supports previously proposed K+ conductance directly from juxtaparanodal axoplasm into juxtaparanodal myeloplasm in mammalian axons. With neither Cx29 protein nor myelin rosettes detectable in frog myelinated axons, these data showing axon-to-myelin linkage by abundant KV1/Cx29 channels in rodent axons support renewed consideration of an electrically active role for myelin in increasing both saltatory conduction velocity and maximum propagation frequency in

  2. A Global Genomic and Genetic Strategy to Identify, Validate and Use Gene Signatures of Xenobiotic-Responsive Transcription Factors in Prediction of Pathway Activation in the Mouse Liver

    EPA Science Inventory

    Many drugs and environmentally-relevant chemicals activate xenobiotic-responsive transcription factors. Identification of target genes of these factors would be useful in predicting pathway activation in in vitro chemical screening as well as their involvement in disease states. ...

  3. Purification of storage granule protein-23. A novel protein identified by phage display technology and interaction with type I plasminogen activator inhibitor.

    PubMed

    Lang, I M; Chuang, T L; Barbas, C F; Schleef, R R

    1996-11-22

    Type 1 plasminogen activator inhibitor (PAI-1) is a key regulator of the fibrinolytic cascade that is stored in a rapidly releasable form within platelet alpha-granules. To identify proteins that may participate in the targeting or storage of this potent inhibitor, this report investigates the applicability of utilizing filamentous bacteriophages to display proteins expressed by cells containing a regulated secretory pathway and their enrichment based upon an interaction with PAI-1. For this purpose, RNA was extracted from AtT-20 cells (i.e. a classical model cell system for intracellular protein sorting), reverse transcribed, amplified using polymerase chain reaction primers containing internal restriction sites, and cloned into the phagemid pCOMB3H for expression as fusion constructs with the bacteriophage gene III protein. Escherichia coli was transformed with the phagemids and infected with VCSM13 helper phage, and the resulting AtT-20 cDNA-bacteriophage library was enriched by panning against solid- and solution-phase PAI-1. The enriched cDNA library was subcloned into a prokaryotic expression vector system that replaces the gene III protein with a decapeptide tag for immunologic quantitation. One novel cDNA clone (i.e. A-61), which preferentially recognized solution-phase PAI-1 and reacted positively with antibodies derived from a rabbit immunized with alpha-granules, was subcloned into the prokaryotic expression vector pTrcHis to create a construct containing an N-terminal six-histidine purification tag. This construct was expressed in E. coli, purified by nickel-chelate chromatography followed by preparative SDS-polyacrylamide gel electrophoresis, and utilized for the generation of polyclonal antibodies. Immunoblotting analysis employing antibodies against the purified A-61 construct revealed a 23-kDa protein present in the regulated secretory pathway of AtT-20 cells. The 23-kDa molecule was purified from media conditioned by AtT-20 cells by ion exchange

  4. Identifying the activation motif in the N-terminal of rainbow trout and zebrafish melanocortin-2 receptor accessory protein 1 (MRAP1) orthologs.

    PubMed

    Dores, Robert M; Liang, Liang; Hollmann, Rebecca E; Sandhu, Navdeep; Vijayan, Mathilakath M

    2016-08-01

    The activation of mammalian melanocortin-2 receptor (MC2R) orthologs is dependent on a four-amino acid activation motif (LDYL/I) located in the N-terminal of mammalian MRAP1 (melanocortin-2 receptor accessory protein). Previous alanine substitution analysis had shown that the Y residue in this motif appears to be the most important for mediating the activation of mammalian MC2R orthologs. Similar, but not identical amino acid motifs were detected in rainbow trout MRAP1 (YDYL) and zebrafish MRAP1 (YDYV). To determine the importance of these residues in the putative activation motifs, rainbow trout and zebrafish MRAP1 orthologs were individually co-expressed in CHO cells with rainbow trout MC2R, and the activation of this receptor with either the wild-type MRAP1 ortholog or alanine-substituted analogs of the two teleost MRAP1s was analyzed. Alanine substitutions at all four amino acid positions in rainbow trout MRAP1 blocked activation of the rainbow trout MC2R. Single alanine substitutions of the D and Y residues in rainbow trout and zebrafish MRAP1 indicate that these two residues play a significant role in the activation of rainbow trout MC2R. These observations indicate that there are subtle differences in the way that teleost and mammalian MRAPs are involved in the activation of their corresponding MC2R orthologs.

  5. Identifying Barriers, Perceptions and Motivations Related to Healthy Eating and Physical Activity among 6th to 8th Grade, Rural, Limited-Resource Adolescents

    ERIC Educational Resources Information Center

    Kumar, Janavi; Adhikari, Koushik; Li, Yijing; Lindshield, Erika; Muturi, Nancy; Kidd, Tandalayo

    2016-01-01

    Purpose: The purpose of this paper is to enable community members to discuss their perceptions of eating habits and physical activity in relation to sixth, seventh, and eighth graders, and reveal facilitators and barriers to healthy eating behavior and physical activity engagement. Design/methodology/approach: Nine focus groups, which included six…

  6. Development and validation of a high-throughput cell-based screen to identify activators of a bacterial two-component signal transduction system.

    PubMed

    van Rensburg, Julia J; Fortney, Kate R; Chen, Lan; Krieger, Andrew J; Lima, Bruno P; Wolfe, Alan J; Katz, Barry P; Zhang, Zhong-Yin; Spinola, Stanley M

    2015-07-01

    CpxRA is a two-component signal transduction system (2CSTS) found in many drug-resistant Gram-negative bacteria. In response to periplasmic stress, CpxA autophosphorylates and donates a phosphoryl group to its cognate response regulator, CpxR. Phosphorylated CpxR (CpxR-P) upregulates genes involved in membrane repair and downregulates multiple genes that encode virulence factors, which are trafficked across the cell membrane. Mutants that constitutively activate CpxRA in Salmonella enterica serovar Typhimurium and Haemophilus ducreyi are avirulent in mice and humans, respectively. Thus, the activation of CpxRA has high potential as a novel antimicrobial/antivirulence strategy. Using a series of Escherichia coli strains containing a CpxR-P-responsive lacZ reporter and deletions in genes encoding CpxRA system components, we developed and validated a novel cell-based high-throughput screen (HTS) for CpxRA activators. A screen of 36,000 compounds yielded one hit compound that increased reporter activity in wild-type cells. This is the first report of a compound that activates, rather than inhibits, a 2CSTS. The activity profile of the compound against CpxRA pathway mutants in the presence of glucose suggested that the compound inhibits CpxA phosphatase activity. We confirmed that the compound induced the accumulation of CpxR-P in treated cells. Although the hit compound contained a nitro group, a derivative lacking this group retained activity in serum and had lower cytotoxicity than that of the initial hit. This HTS is amenable for the screening of larger libraries to find compounds that activate CpxRA by other mechanisms, and it could be adapted to find activators of other two-component systems.

  7. Combination of HPLC chromatogram and hypoglycemic effect identifies isoflavones as the principal active fraction of Belamcanda chinensis leaf extract in diabetes treatment.

    PubMed

    Chen, Yan; Wu, Chong-Ming; Dai, Rong-Ji; Li, Liang; Yu, Yu-Hong; Li, Yan; Meng, Wei-Wei; Zhang, Liang; Zhang, Yongqian; Deng, Yu-Lin

    2011-02-15

    In previous study, we demonstrated the hypoglycemic effect of aqueous extract of Belamcanda chinensis leaves in rats. Here, we separated the aqueous extract of B. chinensis leaves and investigated the spectrum-effect relationships between HPLC chromatograms and hypoglycemic activities of different isolates from B. chinensis leaf extract. Sequential solvent extraction with petroleum ether, chloroform, acetic ester and n-butanol provided several isolates showing similar hypoglycemic activities, making it difficult to discriminate the active fractions. Stepwise elution through HP20 macroporous resin by water, 40% and 95% ethanol provided isolates with distinct hypoglycemic activities, representing a simple, rapid and efficient preparative separation method. Combination of HPLC chromatogram and pharmacological effect targeted a hypoglycemic activity-related region in HPLC chromatogram. Each peak in this region was analyzed by UV spectrum scan. Most of them were flavonoids in which tectoridin and swertisin were known flavonoids with anti-diabetic activities. In together, this work provides a general model of combination of HPLC chromatography and pharmacological effect to study the spectrum-effect relationships of aqueous extract from B. chinensis leaves, which can be used to find principle components of B. chinensis on pharmacological activity.

  8. GABA(A)- and AMPA-like receptors modulate the activity of an identified neuron within the central pattern generator of the pond snail Lymnaea stagnalis.

    PubMed

    Moccia, Francesco; Di Cristo, Carlo; Winlow, William; Di Cosmo, Anna

    2009-03-01

    To examine the neurochemistry underlying the firing of the RPeD1 neuron in the respiratory central pattern generator of the pond snail, Lymnaea stagnalis, we examined electrophysiologically and pharmacologically either "active" or "silent" preparations by intracellular recording and pharmacology. GABA inhibited electrical firing by hyperpolarizing RPeD1, while picrotoxin, an antagonist of GABA(A) receptors, excited silent cells and reversed GABA-induced inhibition. Action potential activity was terminated by 1 mM glutamate (Glu) while silent cells were depolarized by the GluR agonists, AMPA, and NMDA. Kainate exerted a complex triphasic effect on membrane potential. However, only bath application of AMPA desensitized the firing. These data indicate that GABA inhibits RPeD1 via activation of GABA(A) receptors, while Glu stimulates the neuron by activating AMPA-sensitive GluRs.

  9. Functional genomics analysis of big data identifies novel peroxisome proliferator–activated receptor gamma target single nucleotide polymorphisms showing association with cardiometabolic outcomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background Cardiovascular disease and type 2 diabetes mellitus represent overlapping diseases where a large portion of the variation attributable to genetics remains unexplained. An important player in their pathogenesis is peroxisome proliferator–activated receptor gamma (PPARgamma) that is involve...

  10. A deep learning based strategy for identifying and associating mitotic activity with gene expression derived risk categories in estrogen receptor positive breast cancers.

    PubMed

    Romo-Bucheli, David; Janowczyk, Andrew; Gilmore, Hannah; Romero, Eduardo; Madabhushi, Anant

    2017-02-13

    The treatment and management of early stage estrogen receptor positive (ER+) breast cancer is hindered by the difficulty in identifying patients who require adjuvant chemotherapy in contrast to those that will respond to hormonal therapy. To distinguish between the more and less aggressive breast tumors, which is a fundamental criterion for the selection of an appropriate treatment plan, Oncotype DX (ODX) and other gene expression tests are typically employed. While informative, these gene expression tests are expensive, tissue destructive, and require specialized facilities. Bloom-Richardson (BR) grade, the common scheme employed in breast cancer grading, has been shown to be correlated with the Oncotype DX risk score. Unfortunately, studies have also shown that the BR grade determined experiences notable inter-observer variability. One of the constituent categories in BR grading is the mitotic index. The goal of this study was to develop a deep learning (DL) classifier to identify mitotic figures from whole slides images of ER+ breast cancer, the hypothesis being that the number of mitoses identified by the DL classifier would correlate with the corresponding Oncotype DX risk categories. The mitosis detector yielded an average F-score of 0.556 in the AMIDA mitosis dataset using a 6-fold validation setup. For a cohort of 174 whole slide images with early stage ER+ breast cancer for which the corresponding Oncotype DX score was available, the distributions of the number of mitoses identified by the DL classifier was found to be significantly different between the high vs low Oncotype DX risk groups (P < 0.01). Comparisons of other risk groups, using both ODX score and histological grade, were also found to present significantly different automated mitoses distributions. Additionally, a support vector machine classifier trained to separate low/high Oncotype DX risk categories using the mitotic count determined by the DL classifier yielded a 83.19% classification

  11. Anticancer activity of pyrithione zinc in oral cancer cells identified in small molecule screens and xenograft model: Implications for oral cancer therapy.

    PubMed

    Srivastava, Gunjan; Matta, Ajay; Fu, Guodong; Somasundaram, Raj Thani; Datti, Alessandro; Walfish, Paul G; Ralhan, Ranju

    2015-10-01

    Oral squamous cell carcinoma (OSCC) patients diagnosed in late stages have limited chemotherapeutic options, underscoring the great need for development of new anticancer agents for more effective disease management. We aimed to identify novel anticancer agents for OSCC using quantitative high throughput assays for screening six chemical libraries consisting of 5170 small molecule inhibitors. In depth characterization resulted in identification of pyrithione zinc (PYZ) as the most effective cytotoxic agent inhibiting cell proliferation and inducing apoptosis in OSCC cells in vitro. Further, treatment with PYZ reduced colony forming, migration and invasion potential of oral cancer cells in a dose-dependent manner. PYZ treatment also led to altered expression of several key components of the major signaling pathways including PI3K/AKT/mTOR and WNT/β-catenin in OSCC cells. In addition, treatment with PYZ also reduced expression of 14-3-3ζ, 14-3-3σ, cyclin D1, c-Myc and pyruvate kinase M2 (PKM2), proteins identified in our earlier studies to be involved in development and progression of OSCCs. Importantly, PYZ treatment significantly reduced tumor xenograft volume in immunocompromised NOD/SCID/Crl mice without causing apparent toxicity to normal tissues. Taken together, we demonstrate in vitro and in vivo efficacy of PYZ in OSCC. In conclusion, we identified PYZ in HTS assays and demonstrated in vitro and in vivo pre-clinical efficacy of PYZ as a novel anticancer therapeutic candidate in OSCC.

  12. Flip flops, dress clothes, and no coat: clothing barriers to children's physical activity in child-care centers identified from a qualitative study

    PubMed Central

    2009-01-01

    Background Three-quarters of 3-6 year-old children in the U.S. spend time in childcare; many spend most of their waking hours in these settings. Daily physical activity offers numerous health benefits, but activity levels vary widely across centers. This study was undertaken to explore reasons why physical activity levels may vary. The purpose of this paper is to summarize an unexpected finding that child-care providers cited was a key barrier to children's physical activity. Methods Nine focus groups with 49 child-care providers (55% black) from 34 centers (including inner-city, suburban, Head Start and Montessori) were conducted in Cincinnati, OH. Three independent raters analyzed verbatim transcripts for themes. Several techniques were used to increase credibility of findings, including interviews with 13 caregivers. Results Two major themes about clothing were: 1) children's clothing was a barrier to children's physical activity in child-care, and 2) clothing choices were a significant source of conflict between parents and child-care providers. Inappropriate clothing items included: no coat/hat/gloves in the wintertime, flip flops or sandals, dress/expensive clothes, jewelry, and clothes that were either too loose or too tight. Child-care providers explained that unless there were enough extra coats at the center, a single child without a coat could prevent the entire class from going outside. Caregivers suggested several reasons why parents may dress their child inappropriately, including forgetfulness, a rushed morning routine, limited income to buy clothes, a child's preference for a favorite item, and parents not understanding the importance of outdoor play. Several child-care providers favored specific policies prohibiting inappropriate clothing, as many reported limited success with verbal or written reminders to bring appropriate clothing. Conclusion Inappropriate clothing may be an important barrier to children's physical activity in child

  13. The Thief With a Thousand Faces and the Victim With None: Identifying Determinants for Online Identity Theft Victimization With Routine Activity Theory.

    PubMed

    Reyns, Bradford W; Henson, Billy

    2016-08-01

    Available evidence suggests that identity theft is a growing problem that has significant consequences for victims, not the least of which is billions of dollars in financial losses. However, very little is known about the correlates or causes of identity theft victimization. Utilizing a nationally representative sample of individuals from the Canadian General Social Survey, the current study attempts to address this deficiency by examining the link between victims' online routine activities and their online identity theft victimization. It was found that certain routine activities directly influence the likelihood of experiencing identity theft. Potential research and policy implications also are discussed.

  14. Fluoro-Jade B staining as useful tool to identify activated microglia and astrocytes in a mouse transgenic model of Alzheimer's disease.

    PubMed

    Damjanac, Milena; Rioux Bilan, Agnès; Barrier, Laurence; Pontcharraud, Raymond; Anne, Cantereau; Hugon, Jacques; Page, Guy