bluuebunny/crossref_metadata_2025 huggingface dataset:
Net accumulation and flux of dissolved organic carbon and dissolved organic nitrogen in marine plankton communities
Authors: Søndergaard Morten , Williams Peter J. le B. , Cauwet Gustave , Riemann Bo , Robinson Carol , Terzic Senka , Woodward E. Malcolm S. , Worm Jakob
Published: June 2010

Marine mesocosms were manipulated with inorganic nutrients over a period of 22 d to investigate organic carbon partitioning under a variety of nutrient regimes. The chemical analyses and biotic measurements included inorganic nutrients, pigment signatures, particulate and dissolved organic species, bacterial production, and community respiration. The biodegradability of dissolved organic carbon (DOC) was investigated with in vitro decomposition experiments.

The net particulate organic carbon (POC) production was 50% of the total organic production during the initial 6 d of nutrient‐replete growth and during a major diatom bloom. In all other situations the carbon partitioning was strongly in favor of DOC, which accounted for 82 to 111% of the total production. The production of new DOC preceded new DON by about 1 week. Thus, the new dissolved organic matter (DOM) initially had an infinite C:N ratio, which fell to 11‐20 when DON started to accumulate. The highest C:N ratio was measured during a nutrient‐replete diatom bloom. Dissolved polysaccharides accounted for 50 to 70% of the new DOC, and the lowest relative amount was produced during a diatom bloom. The chemical analyses unequivocally demonstrated that carbon partitioning in favor of carbon‐rich DOM can take place during an active diatom bloom and not only during the decay of a bloom. The DOC‐producing mechanisms cannot be fully identified. However, during the different growth phases the DOC production varied, as did the speciation of DOM with respect to the C:N ratios. When net production of dissolved organic nitrogen (DON) was detected after 11 d, the DON production accounted for 25 to 50% of the daily added and assimilated inorganic nitrogen. The measurements of community respiration made it possible to calculate the maximum carbon recycling by bacteria and bacterial net DOC assimilation. These calculations showed the estimates of carbon partitioning to be very sensitive to bacterial growth yield values and the factors used to convert leucine and thymidine isotope incorporation to bacterial production.

Decomposition experiments showed that at least 35% of the new DOC was biodegradable over 10–12 d and that inorganic nutrients only marginally affected use. The calculated turnover times of new DOC were between 15 and 25 d. The semilabile nature of new DOC with respect to microbial attack is suggested as the main reason for the medium‐term accumulation of new DOC.
Substrate specificity in polysaccharide hydrolysis: Contrasts between bottom water and sediments
Authors: Arnosti C.
Published: June 2010

Six structurally distinct polysaccharides were fluorescently labeled and used to compare potential hydrolysis rates and substrate specificities of extracellular enzymes in bottom water and surface sediments. Potential hydrolysis rates differed by factors of 10–100 among the six polysaccharides. The relative order of potential hydrolysis rates in sediments was distinctly different from that of the bottom water samples. In surface sediments, pullulan hydrolysis was extremely rapid, and relative hydrolysis rates decreased in the order pullulan ≫ laminarin > chondroitin sulfate > xylan > arabinogalactan ≫ fucoidan. In bottom water, in contrast, pullulan, arabinogalactan, and fucoidan were barely hydrolyzed, whereas chondroitin sulfate, xylan, and laminarin were hydrolyzed relatively rapidly. Hydrolysis rates decreased in the order xylan > chondroitin sulfate > laminarin >>> arabinogalactan ≅ pullulan ≅ fucoidan. The differences among the relative hydrolysis rates might reflect fundamental differences in seawater and sedimentary microbial communities with disparate extracellular enzymatic capabilities. Carbohydrates are significant constituents of dissolved organic carbon in seawater and are detectable as molecularly distinct structures in sediments of significant geologic age. Slow hydrolysis may provide the time required for geochemical transformations that further increase resistance to remineralization.
Stoichiometric theory extended to micronutrients: Comparison of the roles of essential fatty acids, carbon, and nitrogen in the nutrition of marine copepods
Authors: Anderson Thomas R. , Pond David W.
Published: June 2010

Conventional stoichiometric theory, which is used to study the limitation of zooplankton production by C, N, and other elements, is extended to include the essential polyunsaturated fatty acids (PUFAs) 20:5(n−3) and 22:6(n−3). Using typical biochemical compositions of consumer (Calanus helgolandicus) and algal food (hypothetical diatom‐dinoflagellate mixtures), the analysis shows that PUFAs or macronutrients can be important in limiting zooplankton production, depending on the biochemical compositions of consumer and food and the efficiencies with which dietary components are used. Predicted limitation by fatty acids is strongest when zooplankton use a monospecific diet, indicating that such limitation may be of particular significance in laboratory zooplankton, which are often fed phytoplankton monocultures. The analysis illustrates several factors that operate to minimize the limiting potential of fatty acids to the extent that limitation by C or N could occur: selective grazing to obtain a nutritionally balanced diet, plasticity in consumer biochemical composition, and high C requirements for respiration. The possibility of macronutrient limitation is increased further if zooplankton are able to actively synthesize essential PUFAs, although this is not thought to be the case in most aquatic systems. The work highlights the need for complete data sets incorporating fatty acids and bulk elemental properties of consumers and prey, as well as an improved understanding of the roles and cycling of essential fatty acids, if we are to be able to provide a unified view of zooplankton nutrition.
Total nitrogen, total phosphorus, and nutrient limitation in lakes and oceans: Is there a common relationship?
Authors: Guildford Stephanie J. , Hecky Robert E.
Published: June 2010

Total nitrogen (TN) and total phosphorus (TP) measurements and contemporaneous measurements of chlorophyll a (Chl a) and phytoplankton nutrient deficiency have been made across a broad range of lakes and ocean sites using common methods. The ocean environment was nutrient rich in terms of TN and TP when compared with most lakes in the study, although Lake Victoria had the highest values of TN and TP. TN concentrations in lakes rose rapidly with TP concentrations, from low values to TN concentrations that are similar to those associated with the ocean sites. In contrast, the TN concentrations in the oceans were relatively homogeneous and independent of TP concentrations. The hyperbolic shape of the TN:TP relationship created a broad range of TN:TP values for both lakes and oceans. The TN:TP ratios of the surface ocean sites were usually well in excess of the Redfield ratio that is noted in the deep ocean. Phytoplankton biomass, as indicated by Chl a, was strongly dependent upon TP in the lakes, and there was a weaker relationship with TN. Oceanic Chl a values showed a positive relationship with TP, but at much higher TP values than were observed in the lakes; there was no relation with TN.P‐deficient phytoplankton growth was inferred using independent indicators when TP was >0.5 µmol L−1 at both freshwater and marine sites. N‐deficiency indicators were highly variable and did not show any clear dependence on TN concentration. The TN:TP ratio was indicative of which nutrient would become limiting for growth in both lakes and oceans. When all sites are compared, N‐deficient growth was apparent at TN:TP µ 20 (molar), whereas P‐deficient growth consistently occurred when TN:TP µ 50 (molar). At intermediate TN:TP ratios, either N or P can become deficient. We conclude that N or P limitation of algal growth is a product of the TN and TP concentration and the TN:TP ratio rather than a product of whether the system of study is marine or freshwater.
The distribution of biogenic thiols in surface waters of Galveston Bay
Authors: Tang Degui , Hung Chin‐Chang , Warnken Kent W. , Santschi Peter H.
Published: June 2010

Thiolic compounds are important metal‐complexing ligands as well as important components of the global sulfur biogeochemical cycle. A lack of information on the concentration and distribution of thiols in natural waters, especially in the dissolved fraction, is still a major impediment to a complete understanding of the role of thiols in these biogeochemical processes. The concentrations of dissolved, colloidal, and particulate thiols were measured along a salinity gradient in estuarine waters off of Galveston Bay, Texas. The majority of thiols were present in the dissolved fraction, although more thiolic species were detected in the particulate phase. Dissolved glutathione was present at higher concentrations (0.23 to 6.23 nM) than was the particulate glutathione (0.094 to 0.72 nM). Most γ‐glutamylcysteine was present in the particulate phase, with concentrations as high as 2.24 nM in the middle of the estuary. Phytochelatin‐2 was ubiquitous in surface waters, with chlorophyll aa–normalized concentrations of up to 6.3 ³mol g Chl aa‐1. A major thiol peak was present in Lower Galveston Bay and a minor peak in Upper Galveston Bay, and in both regions, 5–6 mol of γ‐glutamylcysteine were produced per mole of glutathione. This bimodal distribution indicates in situ production of thiols from two different phytoplankton communities in Galveston Bay during this period.
DNA fingerprinting reveals extensive genetic diversity in a field population of the centric diatom Ditylum brightwellii
Authors: Rynearson Tatiana A. , Armbrust E. Virginia
Published: June 2010

Microsatellite markers were developed to examine the genetic diversity of field populations of the centric diatom Ditylum brightwellii. Polymerase chain reaction amplification of two dinucleotide microsatellite loci using DNA extracted from single cell isolates was sensitive enough to identify genetically distinct clones. Each of four culture collection isolates was genetically distinct. Moreover, 23 of 24 isolates obtained from the Hood Canal Basin in Puget Sound, Washington, displayed unique genotypes. The gene diversity of the field isolates is 0.88, indicating that the D. brightwellii population was composed predominantly of unrelated individuals. Maximum growth rates were measured for eight genetically distinct field isolates that were maintained at three light intensities. The growth rates of the isolates differed significantly, indicating that high levels of physiological variability also existed within the population. The results of this study indicate that both extensive genetic and physiological diversity can exist within diatom populations isolated from a single geographical locale at a single time. The observed high levels of diversity are hypothesized to result from the exposure of individual diatom cells to a constantly changing environment and thus to changing selection pressures. The extensive physiological and genetic diversity documented here may help explain how diatoms are able to bloom under a wide range of environmental conditions.
Reconstructing the history of intercontinental dispersal in Daphnia lumholtzi by use of genetic markers
Authors: Havel John E. , Colbourne John K. , Hebert Paul D. N.
Published: June 2010

After its appearance in 1989, the cladoceran Daphnia lumholtzi rapidly dispersed throughout the southern United States. In the current study, we used allozyme and mitochondrial deoxyribonucleic acid sequence data to infer the past dispersal of this species. Both genetic markers revealed the similarity among all U.S. populations and those from Uganda and Nepal but their divergence from Australian lineages. The extent of genetic divergence among populations, when coupled with estimates of rates of molecular evolution, suggests that the distribution of this species reflects a series of long‐distance dispersal events over the last 4 million years.
Production and consumption of methyl halides in a freshwater lake
Authors: Huang Wenlin , Bu Xin , Nguyen Lisa , Gammon Richard H. , Bullister John L.
Published: June 2010

The concentrations of the methyl halides CH3Cl and CH3Br in Lake Washington and its tributary streams were measured during the period 1994–1998. Strong seasonal variation was observed. In summer, the surface mixed layer in the middle of the lake was found to be generally undersaturated for CH3Cl but consistently supersaturated for CH3Br relative to air‐water gas equilibrium; meanwhile, the deep waters (zmax ‐ 65 m) of the summertime lake were found to be depleted to near zero levels for both compounds. In winter, the methyl halides were observed to be vertically well mixed throughout the water column and strongly undersaturated in both species. A simple mass‐balance box model indicates that the wintertime lake (T = 8°C) is a net sink for atmospheric methyl halides with estimated loss rates of ~2.6–3.2 pM d−1 for CH3Cl (1 pM = 10−12 mol L−1) and 0.09–0.13 pM d−1 for CH3Br, probably because of unspecified microbiological processes. In summer, the mass balance model indicates that there is a net source of CH3Br in the surface mixed layer (0.17–0.25 pM d−1), as required to maintain the observed strong supersaturation. However, the summer surface waters are apparently a sink for CH3Cl, (1.9–2.9 pM d−1), with enhanced biological production compensated by larger combined microbial and chemical sinks terms. In summer, methyl halide concentrations in the deep waters continue to decrease exponentially at the observed wintertime rate, while both production and loss rates in the surface waters are likely much faster than in winter, resulting in much shorter turnover timescales. An order‐of‐magnitude extrapolation of these Lake Washington methyl halide fluxes to a global source/sink from freshwater lakes implies a negligible contribution (<0.05%) with respect to the currently estimated global budgets of these gases.
Diel changes in phagotrophy by Cryptomonas in Lake Biwa
Authors: Urabe Jotaro , Gurung Tek Bahadur , Yoshida Takehito , Sekino Tatsuki , Nakanishi Masami , Maruo Masahiro , Nakayama Eiichiro
Published: June 2010

Diel changes in bacterial ingestion by a mixotrophic flagellate, Cryptomonas sp., and heterotrophic nanoflagellates (HNF) were examined in situ at 4‐h intervals for 2 d in the epilimnion and metalimnion of Lake Biwa using bacteria‐sized fluorescent microspheres as a tracer food. Clearance rates of HNF for the microspheres ranged between 1.3 and 4.5 nl cell−1 h−1, but the average rate did not differ between day and night. In contrast, clear diel changes were observed in the clearance rate of Cryptomonas sp. in the epilimnion from <0.5 nl cell−1 h−1 at midnight to >3 nl cell−1 h−1 at noon. In the metalimnion where light intensity was lower, however, the clearance rate of Cryptomonas sp. was always <0.5 nl cell−1 h−1 through the study period. Thus, bacterial ingestion of Cryptomonas sp. is not to acquire supplementary energy or carbon at low phototrophic activities. During the study period, both inorganic phosphorus and nitrogen concentrations were less than or close to the detection limits (10 nM P and 1 µM N) in the epilimnion, but much higher in the metalimnion. The results strongly support the idea that Cryptomonas sp. utilizes N and P from bacteria as substitutable nutrients when photosynthesis takes place under conditions of nutrient depletion. To assess the grazing effect of mixotrophic algae on bacterial populations, it is essential to consider diel changes in their phagotrophic mode of nutrition that are induced by light regime and nutrient concentrations in ambient water.
Living in suboxia: Ecology of an Arabian Sea oxygen minimum zone copepod
Authors: Wishner Karen F. , Gowing Marcia M. , Celia Gelfman
Published: June 2010

Oxygen minimum zones (OMZs) are permanent suboxic features of the oceanic water column that strongly influence zooplankton distributions and biogeochemical cycles. The lower interface of prominent OMZs is characterized by a subsurface zooplankton biomass peak and high biological activity. The calanoid copepod Lucicutia grandis is an indicator species for this habitat. Its ecology in the Arabian Sea was studied during the U.S. Joint Global Ocean Flux Study (JGOFS) program to understand planktonic distributional and developmental adaptations to oxygen gradients in suboxic environments and the role of the OMZ zooplankton in food webs, vertical flux processes, and carbon cycles. Zooplankton samples were obtained in vertically stratified multiple opening‐closing net and environmental sensing system (MOCNESS) tows to 1,000 m during four seasonal cruises. The vertical distribution of L. grandis was associated with the steep oxygen gradient from 0.07 to 0.15 ml L−1 at the base of the OMZ about 600–1,000 m. There was a clear progression with age of the depths and oxygen levels inhabited by different developmental stages within this zone, a phenomenon attributed to both physiological constraints and ecological interactions. The seasonal and spatial pattern of reproduction and development was keyed in part to the seasonal monsoon cycle, with final maturation of young stages into reproducing adults probably triggered by the direct and indirect effects of the seasonal or episodic input to depth of sinking particles. Gut contents included surface flux material, deep‐sea detrital material, zooplankton remains, and deep‐sea aggregate material, indicating that L. grandis occupies at least four different trophic levels. This was an active, not a diapausing, population, since both adults and immature stages fed and reproduced during all seasons. In contrast to the pelagic fauna that are severely impacted by coastal episodic hypoxia, the animals of the oceanic OMZ are uniquely adapted to the very low oxygen and strong spatial and temporal patterns of this widespread suboxic environment.
Molecular and morphological identification of settlement‐stage vent mussel larvae, Bathymodiolus azoricus (Bivalvia: Mytilidae), preserved in situ at active vent fields on the Mid‐Atlantic Ridge
Authors: Dixon David R.
Published: June 2010

This paper describes the first successful attempt to trap and identify the larvae of a deep‐sea vent organism using a combination of sediment traps and molecular analysis. During the European Union‐funded MARVEL cruise in August and September 1997, sediment traps containing a high‐salt DNA preservative were deployed around active black smoker chimneys on the newly discovered Rainbow vent field in an attempt to collect larval stages of the dominant vent bivalve Bathymodiolus azoricus. A total of 2,055 shelled mussel larvae was collected within a 2‐week period, all of which were of identical size and shell morphology that indicated that they were at the settlement, prodissoconch II stage. Scanning electron microscopy of the shell hinge indicated that they belonged to the family Mytilidae, but it required molecular analysis to confirm their species identity. Polymerase chain reaction (PCR) amplification of the ITS2 region was performed on a subset of the larvae, and the resulting PCR products were cut with diagnostic restriction endonucleases to allow comparison with a DNA database based on adult specimens. The DNA restriction patterns typifying the Rainbow larvae were identical to those of adult B. azoricus from the Menez Gwen, Lucky Strike, and Rainbow vent sites and were significantly different from those that typified Bathymodiolus thermophilus (Pacific) and Bathymodiolus puteoserpentis (Snake Pit vent field on the Mid‐Atlantic Ridge), which clearly points to the Rainbow larvae having their origin on that part of the ridge close to the Azores. These findings point to the value of sediment traps as a way to study the temporal and spatial aspects of larval settlement in deep‐sea hydrothermal vent environments.
Growth rate and potential climate record from a rhodolith using 14C accelerator mass spectrometry
Authors: Frantz Brian R. , Kashgarian Michaele , Coale Kenneth H. , Foster Michael S.
Published: June 2010

Rhodoliths, free‐living calcareous red algae, create large and diverse habitats worldwide. Although these plants are abundant and ecologically important, little is known about their growth rate. We determined the growth rate for an individual rhodolith, Lithothamnium crassiusculum, from the southern Gulf of California through 14C analysis using accelerator mass spectrometry (AMS) to be 0.6 mm yr−1. This growth rate suggests large L. crassiusculum, which have been found with radii in excess of 6 cm, may live over 100 yr. Declines in the Δ14C record associated with the large El Niño events of 1957, 1982, and 1992 indicate 14C analysis may lead to identification of important climate events in the more distant past. The ability to determine changes in past ocean circulation related to changes in past climatic conditions through AMS 14C analysis of rhodoliths would increase the geographic range of available climate records from the tropical oceans to the entire global ocean and potentially allow for the determination of past climate conditions from rhodoliths in fossil beds.
Photoacclimation in the marine diatom Skeletonema costatum
Authors: Anning Tracy , MacIntyre Hugh L. , Pratt Sandra M. , Sammes Pippa J. , Gibb Stuart , Geider Richard J.
Published: June 2010

Photoacclimation was examined in the marine diatom Skeletonema costatum, which was subjected to reciprocal shifts between irradiances of 50 (low‐light) and 1,200 (high‐light) µmol photons m−2 s−1. Cell chlorophyll a and fucoxanthin contents were higher but diadinoxanthin and diatoxanthin contents lower in cells grown at 50 µmol photons m−2 s−1 than in cells shifted to 1200 µmol photons m−2 s−1. Cell carbon contents measured at the start of the light period were similar in both high‐light an low‐light treatments. However, by 6 h into the light period, the carbon contents in the high‐light cells were about twofold higher than in the low‐light cells. Dark respiration rates, dark Chl a synthesis rates, and dark cell‐division rates were greater in the high‐light acclimated cells than in the low‐light cells. Thus, there was a greater uncoupling of carbon assimilation from cell division during the day in the high‐light cells, but pigment synthesis and cell division continued in darkness. Cell‐specific, light saturated photosynthesis rates, and chlorophyll a specific lightlimited photosynthesis rates were constant during reciprocal shifts between growth irradiances of 50 and 1200 µmol photons m−2s−1. Thus, differences of photosynthesis versus irradiance curves between cells acclimated to high‐light versus low‐light could be accounted for largely in terms of changes in cell chlorophyll a contents. Although the chlorophyll a‐specific initial slope, αchl, was constant, the chlorophyll a‐specific light absorbtion coeffecient, achl, increased and the maximum quantum efficiency of photosynthesis (φm) declined following the shift to high light. The increase of achl was most likely due to a decreased package effect. The decline of φm was most likely due to accumulation of xanthophyll cycle pigments. Carbon‐specific, light‐saturated photosynthesis rates were lower in high‐light than in low‐light cells; this observation may indicate that control of light‐saturated photosynthesis shifts from enzymes of the carbon dioxide reduction cycle (Calvin cycle) in low‐light cells to the photosynthetic electron transfer chain in high‐light cells.
Domoic acid production near California coastal upwelling zones, June 1998
Authors: Trainer Vera L. , Adams Nicolaus G. , Bill Brian D. , Stehr Carla M. , Wekell John C. , Moeller Peter , Busman Mark , Woodruff Dana
Published: June 2010

Sea lion mortalities in central California during May and June 1998 were traced to their ingestion of sardines and anchovies that had accumulated the neurotoxin domoic acid. The detection of toxin in urine, feces, and stomach contents of several sea lions represents the first proven occurrence of domoic acid transfer through the food chain to a marine mammal. The pennate diatoms, Pseudo‐nitzschia multiseries and P. australis, were the dominant, toxin‐producing phytoplankton constituting algal blooms near Monterey Bay, Half Moon Bay, and Oceano Dunes, areas where sea lions with neurological symptoms stranded. Toxic Pseudo‐nitzschia were also found near Morro Bay Point Conception, Point Arguello, and Santa Barbara, demonstrating that these specie were widespread along the central California coast in June 1998. Measurements of domoic acid during three cruises in early June showed the highest cellular toxin levels in P. multiseries near Point A~o Nuevo at 6 pg cell−1 and in P. australis from Morro Bay at 78 pg cell−1. Maximum cellular domoic acid levels were observed within 20 km of the coast between 0 and 5 m depth, although toxin was also measured t depths of 40 m. Hydrographic data indicated that the highest toxin levels and greatest numbers of toxic cells were positioned in water masses associated with upwelling zones near coastal headlands. Nutrient levels at these sites were less than those typically measured during periods of active upwelling, due to the 1998 El Ni~o event. The flow of cells and/or nutrients from coastal headlands into embayments wher cells can multiply in a stratified environment is a possible mechanism of bloom development along the central California coast. This coupling of toxic Pseudo‐nitzschia growth near upwelling zones with physical processes involved in cell transport will be understood only when long‐term measurements are made at several key coastal locations, aiding in our capability to predict domoic‐acid producing algal blooms.
Evidence Review to Investigate the Support for Subtypes of Children With Difficulty Processing and Integrating Sensory Information
Authors: Davies Patricia L. , Tucker Rebecca
Published: June 2010

We investigated the evidence for subtypes in children with difficulty processing and integrating sensory information. Fifty-seven articles were incorporated into a systematic literature review; only 4 articles provided direct evidence for subtypes. These studies did not provide a comprehensive assessment of all sensory functions and sensory-based motor functions (i.e., praxis) and included different diagnostic groups. Therefore, generalized conclusions about subtypes could not be drawn. The other 53 studies reviewed provided meaningful information about strengths and challenges that children with difficulty processing and integrating sensory information demonstrate, but these studies were limited in scope. A principal theme was the importance of conducting comprehensive assessments of sensory-based functions, including multiple measures of sensory integrative functions such as praxis, sensory modulation, and sensory discrimination in children and adolescents with various clinical disorders. In addition, more consistency in the use of specific assessment tools will allow for synthesis of data across studies.
Impairment of Stance Control in Children With Sensory Modulation Disorder
Authors: Su Chia-Ting , Wu Meng-Yao , Yang Ai-Lun , Chen-Sea Mei-Jin , Hwang Ing-Shiou
Published: June 2010

OBJECTIVE. To compare stance control between children with sensory modulation disorder (SMD) and typically developing children in various visual and somatosensory conditions.

METHOD. Thirty-one children participated in this study, including 17 children with SMD and 14 matched typically developing children. The Sensory Profile was used to screen for sensory modulation problems, which were further confirmed by measures of electrodermal response and the Evaluation of Sensory Processing. Stance parameters for an assessment of postural stability were obtained with a dual-axis accelerometer on the lumbar area.

RESULTS. The children with SMD presented atypical sensory responses in terms of both electrophysiological and behavioral measures. The results for stance showed a greater body sway in the SMD group than in the control group (p < .05). However, the group difference was not always significant under the conditions of reliable somatosensory input and sway-referenced vision.

CONCLUSION. Our findings first confirmed impaired stance control in children with SMD.
The leaf-level emission factor of volatile isoprenoids: caveats, model algorithms, response shapes and scaling
Authors: Niinemets Ü. , Monson R. K. , Arneth A. , Ciccioli P. , Kesselmeier J. , Kuhn U. , Noe S. M. , Peñuelas J. , Staudt M.
Published: June 2010

Abstract. In models of plant volatile isoprenoid emissions, the instantaneous compound emission rate typically scales with the plant's emission potential under specified environmental conditions, also called as the emission factor, ES. In the most widely employed plant isoprenoid emission models, the algorithms developed by Guenther and colleagues (1991, 1993), instantaneous variation of the steady-state emission rate is described as the product of ES and light and temperature response functions. When these models are employed in the atmospheric chemistry modeling community, species-specific ES values and parameter values defining the instantaneous response curves are often taken as initially defined. In the current review, we argue that ES as a characteristic used in the models importantly depends on our understanding of which environmental factors affect isoprenoid emissions, and consequently need standardization during experimental ES determinations. In particular, there is now increasing consensus that in addition to variations in light and temperature, alterations in atmospheric and/or within-leaf CO2 concentrations may need to be included in the emission models. Furthermore, we demonstrate that for less volatile isoprenoids, mono- and sesquiterpenes, the emissions are often jointly controlled by the compound synthesis and volatility. Because of these combined biochemical and physico-chemical drivers, specification of ES as a constant value is incapable of describing instantaneous emissions within the sole assumptions of fluctuating light and temperature as used in the standard algorithms. The definition of ES also varies depending on the degree of aggregation of ES values in different parameterization schemes (leaf- vs. canopy- or region-scale, species vs. plant functional type levels) and various aggregated ES schemes are not compatible for different integration models. The summarized information collectively emphasizes the need to update model algorithms by including missing environmental and physico-chemical controls, and always to define ES within the proper context of model structure and spatial and temporal resolution.
Fluxes of CO2, CH4 and N2O from soil of burned grassland savannah of central Africa
Authors: Castaldi S. , de Grandcourt A. , Rasile A. , Skiba U. , Valentini R.
Published: June 2010

Abstract. Grassland savannah ecosystems subject to frequent fires are considered to have an almost neutral carbon balance, as the C released during burning mostly balance the C fixed by the photosynthetic process. However, burning might modify the net soil-atmosphere exchange of GHGs in the post burning phase so that the radiative balance of the site might shift from neutrality. In the present study the impact of fire on soil fluxes of CO2, CH4 and N2O was investigated in a grassland savannah (Congo Brazzaville) where high frequency burning is the typical management form of the region. An area was preserved for one season from annual burning and was used as "unburned" treatment. Two field campaigns were carried on at different time length from the fire event, 1 month, in the middle of the dry season, and 8 months after, at the end of the growing season. CO2, CH4 and N2O fluxes, as well as several soil parameters, were measured in each campaign from burned and unburned plots. Rain events were simulated at each campaign to evaluate magnitude and length of the generated GHG flux pulses. In laboratory experiments, on soil samples from the two treatments, microbial biomass, net N mineralization, net nitrification, N2O, NO and CO2 emissions were analyzed in function of soil water and/or temperature variations. Results showed that fire had a significant effect on GHG fluxes but the effect was transient, as after 8 months differences between treatments were no longer significant. One month after burning CO2 soil emissions were significantly lower in the burned plots, CH4 fluxes were dominated by net emissions rather than net consumption in the unburned area and fire shifted the CH4 flux distribution towards more negative values. No significant effect of fire was observed in the field on N2O fluxes. It was assumed that the low water content was the main limiting factor as in fact laboratory data showed that only above 75% of water saturation, N2O emissions increased sharply and more strongly in the soil from burned plots. This soil water content was hardly reached in the field even in the watered plots. Burned also stimulated NO production in the laboratory, which was more evident at low water content. Differently from N2O, 25% of water saturation was sufficient to significantly stimulate CO2 production in the laboratory and rain simulation in the field stimulated soil respiration. However in the laboratory the highest fluxes were measured in burned soil whereas in the field the opposite was observed. Increasing the incubation temperature from 25 °C to 37 °C affected negatively microbial growth and activities (mineralization and nitrification) but stimulated gas production (N2O and CO2). Overall, data indicate that fire would have a reductive or null impact on soil GHG emissions in savannah sites presenting similar soil characteristics (acidic, well drained, nutrient poor) and land management (high fire frequency).
Development of an online radiative module for the computation of aerosol optical properties in 3-D atmospheric models: validation during the EUCAARI campaign
Authors: Aouizerats B. , Thouron O. , Tulet P. , Mallet M. , Gomes L. , Henzing J. S.
Published: June 2010

Abstract. Obtaining a good description of aerosol optical properties for a physically and chemically complex evolving aerosol is computationally very expensive at present. The goal of this work is to propose a new numerical module computing the optical properties for complex aerosol particles at low numerical cost so that it can be implemented in atmospheric models. This method aims to compute the optical properties online as a function of a given complex refractive index deduced from the aerosol chemical composition and the size parameters corresponding to the particles. The construction of look-up tables from the imaginary and the real part of the complex refractive index and size parameters will also be explained. This approach is validated for observations acquired during the EUCAARI campaign on the Cabauw tower during May 2008 and its computing cost is also estimated. These comparisons show that the module manages to reproduce the scattering and absorbing behaviour of the aerosol during most of the fifteen-day period of observation with a very cheap computationally cost.
Spectral-decomposition techniques for the identification of radon anomalies temporally associated with earthquakes occurring in the UK in 2002 and 2008
Authors: Crockett R. G. M. , Gillmore G. K.
Published: June 2010

Abstract. During the second half of 2002, the University of Northampton Radon Research Group operated two continuous hourly-sampling radon detectors 2.25 km apart in the English East Midlands. This period included the Dudley earthquake (ML=5, 22 September 2002). Also, at various periods during 2008 the Group has operated other pairs of continuous hourly-sampling radon detectors similar distances apart in the same region. One such period included the Market Rasen earthquake (ML=5.2, 27 February 2008). Windowed cross-correlation of the paired time-series was used to identify simultaneous short-duration anomalies. In the 2002 data, only two periods of significant cross-correlation were observed, each corresponding temporally to a UK earthquake, one to the Dudley earthquake and the other to a smaller earthquake in the English Channel (ML=3, 26 August 2002). In the 2008 data, cross-correlation initially revealed little evidence of simultaneous short-duration anomalies but cross-correlation of data de-noised and de-trended using Empirical Mode Decomposition (EMD) revealed clear simultaneous short-duration anomalies which correspond temporally to the Market Rasen earthquake.
Cyclic Nucleotide Phosphodiesterase Assay Technology
Authors: MacKenzie S.J. , Hastings S.F. , Wells C.
Published: June 2010

Because of their critical role in modulating cellular cyclic nucleotide levels, phosphodiesterases (PDEs) are involved in many disease‐related signaling pathways. The PDE family is large and diverse, with members having different tissue distribution, sub‐cellular localizations, and substrate specificities. Because of these characteristics, the PDEs represent a broad group of potential drug targets. Described in the present unit are the assay development and validation procedures needed to establish a high‐throughput screening system for these important enzymes. The assays provide a structured approach for determining the kinetic parameters of related enzyme families to facilitate the characterization of PDE inhibitors. Curr. Protoc. Pharmacol. 49:3.12.1‐3.12.26. © 2010 by John Wiley & Sons, Inc.
Rodent Models of Depression: Forced Swim and Tail Suspension Behavioral Despair Tests in Rats and Mice
Authors: Castagné Vincent , Moser Paul , Roux Sylvain , Porsolt Roger D.
Published: June 2010

The development of antidepressants requires simple rodent behavioral tests for initial screening before undertaking more complex preclinical tests and clinical evaluation. Presented in the unit are two widely used screening tests used for antidepressants, the forced swim (also termed behavioral despair) test in the rat and mouse, and the tail suspension test in the mouse. These tests have good predictive validity and allow rapid and economical detection of substances with potential antidepressant‐like activity. The behavioral despair and the tail suspension tests are based on the same principle: measurement of the duration of immobility when rodents are exposed to an inescapable situation. The majority of clinically used antidepressants decrease the duration of immobility. Antidepressants also increase the latency to immobility, and this additional measure can increase the sensitivity of the behavioral despair test in the mouse for certain classes of antidepressant. Testing of new substances in the behavioral despair and tail suspension tests allows a simple assessment of their potential antidepressant activity by the measurement of their effect on immobility. Curr. Protoc. Pharmacol. 49:5.8.1‐5.8.14. © 2010 by John Wiley & Sons, Inc.
Pharmacological Applications of Baculovirus‐Mediated Protein Expression in Mammalian Cells
Authors: Condreay J. Patrick , Watson Christian A.
Published: June 2010

The development of cell‐based assays for cellular receptors, ion channels, and transporters requires the delivery and expression of transgenes. Viral‐mediated gene delivery is a particularly attractive approach for this purpose because of its efficiency and potential to deliver genes to a wide variety of cell types. Recombinant baculoviruses, long used to deliver genes to insect cells for overexpression, also effectively transfer genes to mammalian cells. The only required modification to the virus for this purpose is the addition of transgene expression cassettes controlled by mammalian cell‐active promoters. These so‐called BacMam viruses are useful for developing mammalian cell‐based assays for investigating the function of recombinant proteins and for assessing the action of pharmacological modulators of their function. The use of such viruses is gaining popularity because of the ease of optimizing assay conditions, the ability to deliver multiple gene products, and of their flexibility in terms of host cells and levels of transgene expression. BacMam‐mediated assays may be used for studying a wide variety of target proteins and assay technologies. Described in this unit is an example of BacMam‐mediated gene delivery to configure a cell‐based assay for pharmacological assessment of a G protein‐coupled receptor. A protocol is also provided describing the use of a GFP‐expressing BacMam to assess the susceptibility of new cell lines to transduction by the virus. Curr. Protoc. Pharmacol. 49:6.11.1‐6.11.12. © 2010 by John Wiley & Sons, Inc.
Overview on the Rule of Five
Authors: Pollastri Michael P.
Published: June 2010

In the mid‐ to late 1990s, because of the drug discovery paradigm shift from phenotypic screens to combinatorial chemistry and high‐throughput screening, the physicochemical properties of exploratory drug molecules displayed a dramatic shift toward higher molecular weight and lipophilicity. In response, Lipinski and coworkers reported an analysis of compounds that successfully navigated Phase I and entered into Phase II clinical studies, and correlated the computed physicochemical properties of these molecules to their aqueous solubility, permeability, and oral bioavailability. In doing so, the authors created the “Rule of Five,” a mnemonic tool for medicinal chemists to use to quickly assess compounds during the drug discovery and optimization process with respect to the compounds' likelihood to display good solubility and permeability profiles. This overview outlines the basis for the Rule of Five, the ways in which it has been applied, and its impact on drug discovery and development.Curr. Protoc. Pharmacol. 49:9.12.1‐9.12.8. © 2010 by John Wiley & Sons, Inc.
Mouse Models of Human Bladder Cancer as a Tool for Drug Discovery
Authors: Seager Catherine , Puzio‐Kuter Anna M. , Cordon‐Cardo Carlos , McKiernan James , Abate‐Shen Cory
Published: June 2010

Muscle‐invasive bladder cancer is a deadly condition in dire need of effective new treatments. This unit contains a description of mouse models suitable for the evaluation of potential new therapies. Included is a genetically engineered mouse model of bladder cancer generated by the delivery of an adenovirus expressing Cre recombinase into the bladder lumen. Also described is an orthotopic mouse model created by the instillation of human bladder tumor cells into the bladder lumen of immune deficient mice. Protocols are also provided on the use of these models for the preclinical evaluation of new chemical entities, with mTOR inhibitors shown as an example. Curr. Protoc. Pharmacol. 49:14.14.1‐14.14.18. © 2010 by John Wiley & Sons, Inc.
Guidelines for Animal Care and Use in Biomedical Research
Authors: Martin David P.
Published: June 2010

This appendix describes the general requirements for ethical use of animals in biomedical research. Several important Web sites are provided for further information on relevant regulations. Curr. Protoc. Pharmacol. 49:A.4.1‐A.4.2. © 2010 by John Wiley & Sons, Inc.
Synthesis of 2′‐Deoxyoxanosine from 2′‐Deoxyguanosine, Conversion to Its Phosphoramidite, and Incorporation into Oxanine‐Containing Oligodeoxynucleotides
Authors: Pack Seung Pil , Makino Keisuke
Published: June 2010

Oxanine (Oxa, O) is one of the damaged bases produced from guanine (G) through nitrosative deamination induced by nitric oxide (NO) or nitrous acid (HNO2). Large‐scale preparation of Oxa‐containing oligodeoxynucleotide (Oxa‐ODN) with the desired base sequence is a prerequisite for exploring detailed properties of Oxa in DNA. This can be accomplished by incubation of G nucleosides with NaNO2 in acetic acid buffer (pH 3.5) to produce Oxa nucleosides (e.g., 2′‐deoxyoxanosine or dOxo), conversion of dOxo to DMT‐dOxo‐amidite by tritylation and conventional phosphoramidation, and subsequent synthesis of Oxa‐ODN. The presence of Oxa in the synthetic ODN is confirmed by enzymatic digestion. Oxa‐ODN is useful for analyzing the biochemical and biophysical properties of Oxa in DNA, which is believed to be involved in NO‐induced genotoxicity and cytotoxicity. In addition, since Oxa possesses the carbodiimide‐activated carboxylate function (O‐acylisourea structure), Oxa‐ODN can be used as a functional DNA oligomer that makes covalent cross‐linkages with amine or amine‐containing biomolecules and amine‐modified solid surfaces. Curr. Protoc. Nucleic Acid Chem. 41:4.39.1‐4.39.20. © 2010 by John Wiley & Sons, Inc.
Fault‐tolerant control allocation for Mars entry vehicle using adaptive control
Authors: Marwaha Monika , Valasek John
Published: June 2010

Accurate and reliable control of planetary entry is a major challenge for planetary exploration vehicles. For Mars entry, uncertainties in atmospheric properties such as winds aloft and density pose a major problem for meeting precision landing requirements. Anticipated manned missions to Mars will also require levels of safety and fault tolerance not required during earlier robotic missions. This paper develops a nonlinear fault‐tolerant controller specifically tailored for addressing the unique environmental and mission demands of future Mars entry vehicles. The controller tracks a desired trajectory from entry interface to parachute deployment, and has an adaptation mechanism that reduces tracking errors in the presence of uncertain parameters such as atmospheric density, and vehicle properties such as aerodynamic coefficients and inertias. This nonlinear control law generates the commanded moments for a discrete control allocation algorithm, which then generates the optimal controls required to follow the desired trajectory. The reaction control system acts as a non‐uniform quantizer, which generates applied moments that approximate the desired moments generated by a continuous adaptive control law. If a fault is detected in the control jets, it reconfigures the controls and minimizes the impact of control failures or damage on trajectory tracking. It is assumed that a fault identification and isolation scheme already exists to identify failures. A stability analysis is presented, and fault tolerance performance is evaluated with non real‐time simulation for a complete Mars entry trajectory tracking scenario using various scenarios of control effector failures. The results presented in the paper demonstrate that the control algorithm has a satisfactory performance for tracking a pre‐defined trajectory in the presence of control failures, in addition to plant and environment uncertainties. Copyright © 2010 John Wiley & Sons, Ltd.
Supersensitive, Fast‐Response Nanowire Sensors by Using Schottky Contacts
Authors: Hu Youfan , Zhou Jun , Yeh Ping‐Hung , Li Zhou , Wei Te‐Yu , Wang Zhong Lin
Published: June 2010

A Schottky barrier can be formed at the interface between a metal electrode and a semiconductor. The current passing through the metal‐semiconductor contact is mainly controlled by the barrier height and barrier width. In conventional nanodevices, Schottky contacts are usually avoided in order to enhance the contribution made by the nanowires or nanotubes to the detected signal. We present a key idea of using the Schottky contact to achieve supersensitive and fast response nanowire‐based nanosensors. We have illustrated this idea on several platforms: UV sensors, biosensors, and gas sensors. The gigantic enhancement in sensitivity of up to 5 orders of magnitude shows that an effective usage of the Schottky contact can be very beneficial to the sensitivity of nanosensors.