bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indicators Based on Fluorescence Resonance Energy Transfer (FRET): Figure 1.
Authors: Tsien Roger Y. 
Published: July 2009

INTRODUCTIONOne of the major new trends in the design of indicators for optically imaging biochemical and physiological functions of living cells has been the exploitation of fluorescence resonance energy transfer (FRET). FRET is a well-known spectroscopic technique for monitoring changes in the proximity and mutual orientation of pairs of chromophores. It has long been used in biochemistry and cell biology to assess distances and orientations between specific labeling sites within a single macromolecule or between two separate molecules. More recently, macromolecules or molecular pairs have been engineered to change their FRET in response to biochemical and physiological signals such as membrane potential, cyclic AMP (cAMP), protease activity, free Ca2+ and Ca2+-calmodulin (CaM) concentrations, protein-protein heterodimerization, phosphorylation, and reporter-gene expression. Because FRET is general, nondestructive, and easily imaged, it has proven to be one of the most versatile spectroscopic readouts available to the designer of new probes. FRET is particularly amenable to emission ratioing, which is more reliably quantifiable than single-wavelength monitoring and better suited than excitation ratioing to high-speed and laser-excited imaging. This article summarizes the photophysical principles of FRET and the types of indicators used.
The Maize Transcription Factor KNOTTED1 Directly Regulates the Gibberellin Catabolism Genega2ox1
Authors: Bolduc Nathalie , Hake Sarah 
Published: July 2009

AbstractKNOTTED1 (KN1)-like homeobox (KNOX) transcription factors are involved in the establishment and maintenance of plant meristems; however, few direct targets of KNOX proteins have been recognized. Using a combination of double mutant analysis and biochemistry, we found that in maize (Zea mays), KN1 negatively modulates the accumulation of gibberellin (GA) through the control of ga2ox1, which codes for an enzyme that inactivates GA. The ga2ox1 mRNA level is elevated in immature leaves of dominant KNOX mutants and downregulated in reproductive meristems of the null allele kn1-e1. KN1 binds in vivo to an intron of ga2ox1 through a cis-regulatory element containing two TGAC motifs. VP16-KN1 activates transcription in planta from a chimeric promoter containing this binding site. The domains of expression of kn1 and ga2ox1 mRNAs overlap at the base of the shoot apical meristem and the base of newly initiated leaves, suggesting that KN1-mediated activation of ga2ox1 maintains a boundary between meristem cell identity and rapidly elongating cells of the shoot. The KN1 binding site is conserved in ga2ox1 genes of different grasses, suggesting that the local regulation of bioactive GA levels through KNOX proteins is a common theme in grasses.
Common genetic variants in candidate genes and risk of familial lymphoid malignancies
Authors: Liang Xueying (Sharon) , Caporaso Neil , McMaster Mary Lou , Ng David , Landgren Ola , Yeager Meredith , Chanock Stephen , Goldin Lynn R. 
Published: July 2009

SummaryFamilial aggregation, linkage and case–control studies support the role of germline genes in the aetiology of lymphoid malignancies. To further examine the role of genetic variation underlying susceptibility, we analysed 1536 single nucleotide polymorphisms in 152 genes involved in apoptosis, DNA repair, immune response and oxidative stress pathways among a unique sample of 165 unrelated familial cases including patients with chronic lymphocytic leukaemia (CLL), Waldenström macroglobulinaemia (WM) and Hodgkin lymphoma (HL), and 107 spouse controls. We confirmed previous studies showing a polymorphism in the IL10 promoter (rs1800890/‐3575T>A) to be associated with non‐Hodgkin lymphoma, as this allele was found to be associated with both CLL and WM. We also confirmed the role of IL6 variation to be associated with HL. Polymorphisms in TNFSF10 were associated with both CLL and WM. Future replication and functional studies are needed to clarify the role of these genetic variants. Finally, our data further support the close association of WM and CLL.
Simulation of physically mediated variability in prey resources of a larval fish: a three‐dimensional NPZ model
Authors: HINCKLEY S. , NAPP J. M. , HERMANN A. J. , PARADA C. 
Published: July 2009

AbstractA three‐dimensional biophysical nutrient–phytoplankton–zooplankton model was used to investigate the spatial and temporal dynamics of food resources for young walleye pollock in the western Gulf of Alaska, to further understanding of recruitment processes for pollock. We modeled nitrogen, phytoplankton, a large herbivorous grazer parameterized as Neocalanus spp. (the biomass dominant copepod in the Gulf), and the 13 stages (egg, naupliar and copepodite) of Pseudocalanus spp. (a major constituent of the diet of pollock) so that the appropriate size class of food for each size of larval pollock was represented. Model results identified an area between the Semidi and Shumagin Islands that may not be suitable as a nursery area early in the year due to low prey abundance. Modeled mesoscale eddies, previously hypothesized to be important for larval pollock retention in Shelikof Strait, contained higher prey concentrations than the surrounding waters when they were cyclonic. This work also help to understand the consistency of pollock spawning in time and space in Shelikof Strait, by examining the timing and location of prey availability which, along with transport, narrows the window for optimal spawning.
Evaluating diel, ontogenetic and environmental effects on larval fish vertical distribution using Generalized Additive Models for Location, Scale and Shape
Authors: HERNANDEZ FRANK J. , HARE JONATHAN A. , FEY DARIUSZ P. 
Published: July 2009

AbstractChanges in ichthyoplankton vertical distributions can have important consequences with respect to larval transport and survivorship, yet determining the relative importance of environmental influences on vertical migrations in a statistically meaningful framework remains challenging. Here we use Generalized Additive Models for Location, Scale and Shape (GAMLSS) and Akaike Information Criteria (AIC) to model the vertical distribution of larval Urophycis regia collected over a 108‐h time series on the Mid‐Atlantic Bight shelf. Depth was the response variable weighted by two measures of larval abundance: concentrations (number 100 m−3) and proportions at depth. Mean and variance of depth were modeled as a function of time, wind stress, current velocity, water column stratification and ontogeny. Model results indicated a large effect of stage for both concentration‐ and proportion‐based analyses. Subsequent and separate analyses on preflexion and postflexion U. regia indicated a differential response to the environmental parameters based on ontogeny. Model results suggested preflexion U. regia do not have a diel pattern in vertical distribution, but do avoid areas of high surface turbulence related to wind stress. In contrast, postflexion larvae have a significant diel pattern of vertical distribution mediated by surface turbulence (increased variance). The statistical approaches applied here offer the potential to evaluate the effect of multiple factors on vertical distribution and have provided significant insight into the factors that influence the vertical distribution of spotted hake larvae.
Distribution and migration of age‐0 jack mackerel (Trachurus japonicus) in the East China and Yellow Seas, based on seasonal bottom trawl surveys
Authors: SASSA CHIYUKI , YAMAMOTO KEISUKE , TSUKAMOTO YOUICHI , KONISHI YOSHINOBU , TOKIMURA MUNEHARU 
Published: July 2009

AbstractWe examined the distribution and migration of age‐0 jack mackerel in the East China Sea (ECS) and Yellow Sea, based on data from seasonal bottom trawl surveys. Sampling was conducted at 79–161 stations during five cruises in spring (April–June), early summer (May–July), late summer (August–October), autumn (October–December), and winter (January–February). During early summer, jack mackerel (mean 92 mm fork length), which were estimated to have hatched in the southern East China Sea (SECS) during winter, began to occur abundantly, especially along the shelf‐break region of the central East China Sea (CECS). In late summer, the distribution center of young fish (mean 126 mm) shifted northward into the shelf region of northern East China Sea (NECS), corresponding with the rise of bottom water temperature and high prey abundance. In winter when the bottom water temperature declined in the shelf region, the distribution center of jack mackerel (mean 144 mm) shifted southward, with high densities occurring in the SECS and CECS. In spring, overwintering jack mackerel that had become age‐1 (mean 175 mm) were distributed abundantly along the shelf‐break region of the ECS. On the other hand, jack mackerel were only sporadically found, generally at low densities, in the Yellow Sea during all seasons. High densities of jack mackerel were largely restricted to areas of >15°C bottom water temperature during all seasons. Our results indicate that the seasonal shifts of the 15°C isotherm of the bottom layer and the food conditions are significant environmental factors determining the migration of jack mackerel within the ECS.
Habitat preferences of selected demersal fish species in the Bay of Biscay and Celtic Sea, North‐East Atlantic
Authors: PERSOHN CECILE , LORANCE PASCAL , TRENKEL VERENA M. 
Published: July 2009

AbstractAccording to the Ideal Free Distribution theory, individual fish are distributed where environmental conditions are optimal, and the occupied area may vary with population abundance. Thus, observed distributions are a combination of habitat suitability and density‐dependent effects. Data from an annual bottom trawl survey taking place in autumn were used to assess associations between the distributions of eight demersal fish species, separately for juveniles and adults, and habitat characteristics (depth, temperature and salinity) in the Bay of Biscay and Celtic Sea. Cumulative distribution functions were used to describe the general frequency distributions of environmental variables and their relationships with fish density. During the period 1992–2006, observed bottom temperatures fluctuated with no time trend (ΔT = 8°C in the first 80 m) and population abundances varied significantly. Juvenile hake, poor cod, blue whiting, adult red gurnard, adult megrim, and lesser‐spotted dogfish were found to be significantly associated with specific depth ranges. Associations with bottom temperature and salinity were weaker. For some species, preferred environmental conditions changed over time, independently of variations in environmental conditions. In general, most species seemed to be able to cope with the experienced range of conditions. Habitat associations were not influenced by abundance variations. Fluctuating abundances had an impact on spatial occupation only for red gurnard adults, lesser‐spotted dogfish and blue whiting juveniles, independent of absolute densities.
A new method to measure carbon isotope composition of CO2 respired by trees: stem CO2 equilibration
Authors: Ubierna Nerea , Marshall John D. , Cernusak Lucas A. 
Published: July 2009

Summary 1. Applying Keeling plot techniques to derive δ13C of respiratory input in a closed non‐equilibrated chamber can lead to large errors because steady‐state diffusion rules are violated in a non‐steady‐state environment. To avoid these errors, respiratory δ13C can be derived using equilibrated closed chambers. 2. We introduce a new method to obtain stem respired CO2δ13C (δst‐r) with closed equilibrated stem chambers (E‐SC). We present a theoretical model describing the equilibration process, test the model against field data and find excellent agreement. The method is further tested by comparing it with closed non‐equilibrated stem chambers (NE‐SC); we found no difference between these methods. 3. Our theoretical model to describe CO2 diffusion from the respiratory pool into the chamber and the equation to derive the δ13C of the efflux are general. They could be applied to other ecosystem components (e.g. soils). 4. Our method is easy to implement, cost effective, minimizes sources of error and allows for rigorous leak detection. One major limitation is its inability to detect rapid change; the equilibration process requires 15 ± 2 h. A second limitation is that it cannot be used for species that produce abundant pitch at sites of stem wounding (e.g. Pseudotsuga menziesii). 5. Investigating δ13C of CO2 respired by different ecosystem components is necessary to interpret δ13C of ecosystem respiration. This parameter has major implications with respect to global carbon cycle science.
Altitudinal and environmental variation in lifespan in the Copper butterfly Lycaena tityrus
Authors: Karl Isabell , Fischer Klaus 
Published: July 2009

Summary 1. Variation in longevity within and between natural populations is widespread, and understanding the relative importance of environmental and genetic factors as well as their interactions in mediating such variation is crucial in longevity research. 2. In this study lifespan of adult copper butterflies was examined in relation to altitude, temperature (20 and 27 °C), sex and adult feeding. 3. As expected, longevity increased with decreasing temperature, and sucrose‐fed butterflies had longer lifespans compared to water‐fed and finally non‐fed individuals. The impact of feeding, especially of having access to water or not, was larger at the higher compared to the lower temperature. 4. Regarding altitudinal patterns, increased lifespan in high‐altitude populations was largely restricted to beneficial feeding conditions, while under carbohydrate deprivation low‐altitude animals lived longer, suggesting that low‐altitude butterflies do better under food stress. 5. Differences in longevity between sexes were small at 20 °C, while females lived substantially longer than males at the higher temperature. Consequently, females may be less susceptible to high temperature stress than males. Further, males suffered more from food stress than females, suggesting that females are generally more stress resistant than males. 6. Using a full factorial design, this study demonstrates that variation in longevity is caused by several factors, and additionally by substantial interactive effects. Consequently, patterns of variation in longevity are complex, and one needs to be cautious when neglecting this source of variation, by focussing on individual factors only.
When fathers make the difference: efficacy of male sexually selected antimicrobial glands in enhancing fish hatching success
Authors: Pizzolon Matteo , Giacomello Eva , Marri Laura , Marchini Daniela , Pascoli Francesco , Mazzoldi Carlotta , Rasotto Maria Berica 
Published: July 2009

Summary 1. Egg and offspring resistance to pathogens is a major determinant of survival and has been mainly ascribed to maternal factors. However, paternal production of antimicrobials was recently suggested to increase offspring survival in species where males perform egg care. 2. In the peacock blenny, Salaria pavo, a demersal spawning species where males exhibit a pair of anal glands producing lysozyme‐like compounds, we tested the antimicrobial activity and the egg protection efficacy of these glands. The anal gland secretion (AGS) has an inhibitory effect on the growth of both Gram‐negative and Gram‐positive bacteria, including those causing the most severe fish diseases in marine culture. The egg clutches cared for by males deprived of anal glands have a significantly lower survival rate than those cared for by sham‐operated males and non‐viable eggs showed clear signs of bacterial infection. 3. Anal gland secretion production and its protein content are proportional to gland size. In species where male parental care plays a crucial role in offspring survival, females are expected to assess mates selecting those traits that are reliably associated with parental ability. Hence, we experimentally challenged females with dummy males differing in anal gland size. Females definitely preferred dummy males with larger anal glands, suggesting that their choice is driven by the pursuit of direct fecundity benefits. 4. These findings indicate that antimicrobial production is a crucial component of male parental care. The contribution of antimicrobials to male performance as fathers suggests that the development of traits devoted to this function may influence male attractiveness and be sexually selected.
Impact of altering the water table height of an acidic fen on N2O and NO fluxes and soil concentrations
Authors: GOLDBERG STEFANIE DANIELA , KNORR KLAUS‐HOLGER , BLODAU CHRISTIAN , LISCHEID GUNNAR , GEBAUER GERHARD 
Published: July 2009

AbstractThe impact of experimentally intensified summer drought and precipitation on N2O and NO turnover and fluxes was investigated in a minerotrophic fen over a 2‐year period. On three treatment plots, drought was induced for 6 and 10 weeks by means of roofs and drainage and decreased water table levels by 0.1–0.3 m compared with three nonmanipulated control plots. When averaged over the three treatment plots, both N2O and NO emission showed only little response to the drought. On the single plot scale, however, a clear impact of the treatment on N2O and NO fluxes could be identified. On the plot with the weakest water table reduction hardly any response could be observed, while on the plot with the greatest drainage effect, N2O and NO fluxes increased by 530% and 270%, respectively. Rewetting reduced NO emissions to background levels (0.05–0.15 μmol m−2 h−1), but heavily enhanced N2O emission (18–36 μmol m−2 h−1) for several days in the plots with largest water table reduction. These peaks contributed up to 40% to the cumulative N2O fluxes and were caused by rapid N2O production according to isotope abundance data. According to N2O concentrations and isotope abundance analysis N2O was mostly produced at depths between 0.3 and 0.5 m. During water table reduction net N2O production in 0.1 m depth steadily increased in the most effectively dried plot from 2 up to 44 pmol cm−3 day−1. Rewetting immediately increased net N2O production in the topsoil of the drought plots, showing rates of 18–174 pmol cm−3 day−1. This study demonstrates that drought and rewetting can temporarily increase N2O emission to levels that have to date only been reported from nutrient rich and degraded fens that have been drained for agricultural purposes.
Sustained predation effects of hatchery‐reared transgenic coho salmon Oncorhynchus kisutch in semi‐natural environments
Authors: Sundström L. Fredrik , Tymchuk Wendy E. , Lõhmus Mare , Devlin Robert H. 
Published: July 2009

Summary 1. The potential risks of accidental or intentional introduction of transgenic organisms to nature are unknown. We have previously shown that, after being reared in the hatchery, growth hormone transgenic coho salmon Oncorhynchus kisutch can exert a stronger predation effect on natural prey under simulated natural conditions compared with hatchery‐reared genetically wild conspecifics. However, when reared in a simulated natural environment, the difference between the two genotypes was greatly reduced. 2. Here, we tested if the difference in predation rate between the two genotypes after being reared in the hatchery diminishes with time spent in a simulated natural environment. Genetically wild coho salmon reared in the hatchery were size matched to younger satiation‐fed (fast‐growing) and same age restricted‐fed (growth rates matched to wild‐type) transgenic fish. These three types of predators were released into simulated natural habitats and their effects on prey survival and growth were monitored over a 2‐month period. 3. Restricted‐fed, but not satiation‐fed, transgenic predators consumed significantly more prey (×2·7) relative to wild predators during the first month, with an increase to 3.8 times during the second period. Prey biomass decreased more in the presence of restricted‐fed predators during the first period, but a faster growth of these prey during the second period compensated for the higher predation rate resulting in no significant difference in prey biomass among predators after 2 months. Transgenic predators grew more in length than wild type, but all three types converged in weight and condition over time. 4.
Synthesis and applications. Behavioural phenotypes developed in the hatchery showed little plasticity after release. Hence, development of policy on the use of transgenic organisms must incorporate knowledge of the effect of environmental conditions, experienced by the organism prior to escape or release, on phenotype. The risk posed by culture‐reared organisms may depend on the frequency of escapes, number of individuals escaping and age of escapees. Important to note is that wild‐reared organisms may be biologically different from culture‐reared and thus require separate evaluation. Our results will be important for science policy makers and regulators to consider when deciding whether to allow commercial application of transgenic species in aquaculture.
Contemporary ecological threats from historical pollution sources: impacts of large‐scale resuspension of contaminated sediments on sessile invertebrate recruitment
Authors: Knott Nathan A. , Aulbury Joel P. , Brown Trevor H. , Johnston Emma L. 
Published: July 2009

Summary

Historical contamination continues to pose a serious ecological threat to many ecosystems across the world. Marine sediments have long acted as sinks for contaminants from surrounding industry and urbanization, and sediment‐bound contaminants are known to affect the ecology of sediment infauna. When sediments are disturbed, however, contaminants are resuspended and potentially released into the water‐column and dispersed to other environments. The threat posed by the resuspension of contaminated sediments has been a focus of substantial research in the geochemical and ecotoxicology fields, yet to date there has been no ecological assessment of the impacts of a real‐world resuspension event involving contaminated sediments.
We assessed the ecological threat posed by the resuspension of contaminated sediments by testing for impacts of a major dredging operation in an estuary with highly contaminated sediments. We sampled the recruitment of sessile invertebrates in this estuary and two external reference estuaries, before and during dredging. These invertebrates are filter‐feeders that settle and live on hard substrata above the seafloor. Impacts of the dredging‐related resuspension were tested using a Beyond BACI analysis.
Dredging activities resulted in the large‐scale resuspension of contaminated sediments. Concurrently, the recruitment of the dominant filter‐feeders (e.g. barnacles and polychaete worms) was virtually extinguished for 4 months, despite being abundant prior to dredging. This pattern contrasted with the recruitment of the same invertebrates in the reference estuaries, which showed little change over the same period.
Synthesis and applications. The severe decrease in the recruitment of sessile invertebrates within an estuary exposed to dredging and the deposition of contaminated sediments indicates that the resuspension of these sediments pose a real ecological threat to organisms in contact with the contaminated water‐column. Containment measures (e.g. silt curtains) are, therefore, essential and further engineering innovations (e.g. dredging designs and operations) are necessary to reduce resuspension during the dredging and deposition of sediments. In addition, this study demonstrates that past pollution events can cause current ecological impacts that extend well beyond those habitats recognized as being contaminated.