bluuebunny/crossref_metadata_2025_split huggingface dataset:
Method to Detect the Cellular Source of Over‐Activated NADPH Oxidases Using NAD(P)H Fluorescence Lifetime Imaging
Authors: Bremer Daniel , Leben Ruth , Mothes Ronja , Radbruch Helena , Niesner Raluca 
Published: April 2017

AbstractFluorescence‐lifetime imaging microscopy (FLIM) is a technique to generate images, in which the contrast is obtained by the excited‐state lifetime of fluorescent molecules instead of their intensity and emission spectrum. The ubiquitous coenzymes NADH and NADPH, hereafter NAD(P)H, in cells show a short fluorescence lifetime ≈︀400 psec in the free‐state and a longer fluorescence lifetime when bound to enzymes. The fluorescence lifetime of NAD(P)H in this state depends on the binding‐site on the specific enzyme. In the case of NADPH bound to members of the NADPH oxidases family we measured a fluorescence lifetime of 3650 psec as compared to enzymes typically active in cells, in which case fluorescence lifetimes of ∼2000 psec are measured. Here we present a robust protocol based on NAD(P)H fluorescence lifetime imaging in isolated cells to distinguish between normally active enzymes and NADPH oxidases, mainly responsible for oxidative stress. © 2017 by John Wiley & Sons, Inc.
Mapping Transposon Insertions in Bacterial Genomes by Arbitrarily Primed PCR
Authors: Saavedra José T. , Schwartzman Julia A. , Gilmore Michael S. 
Published: April 2017

AbstractTransposons can be used to easily generate and label the location of mutations throughout bacterial and other genomes. Transposon insertion mutants may be screened for a phenotype as individual isolates, or by selection applied to a pool of thousands of mutants. Identifying the location of a transposon insertion is critical for connecting phenotype to the genetic lesion. In this unit, we present an easy and detailed approach for mapping transposon insertion sites using arbitrarily‐primed PCR (AP‐PCR). Two rounds of PCR are used to (1) amplify DNA spanning the transposon insertion junction, and (2) increase the specific yield of transposon insertion junction fragments for sequence analysis. The resulting sequence is mapped to a bacterial genome to identify the site of transposon insertion. In this protocol, AP‐PCR as it is routinely used to map sites of transposon insertion within Staphylococcus aureus, is used to illustrate the principle. Guidelines are provided for adapting this protocol for mapping insertions in other bacterial genomes. Mapping transposon insertions using this method is typically achieved in 2 to 3 days if starting from a culture of the transposon insertion mutant. © 2017 by John Wiley & Sons, Inc.
Bioluminescence Resonance Energy Transfer (BRET)‐Based Synthetic Sensor Platform for Drug Discovery
Authors: Woo Jongchan , Hong Jason , Dinesh‐Kumar Savithramma P. 
Published: April 2017

AbstractBioluminescence resonance energy transfer (BRET) is a technique that analyzes protein‐protein interactions (PPIs). The unique feature of BRET delineates that the resonance energy is generated by the resonance energy donor, Renilla luciferase by the oxidative decarboxylation of coelenterazine substrate. BRET is superior to FRET where issues such as autofluorescence, photobleaching, and light scattering can occur. Recently, BRET has been applied to design synthetic biosensors for monitoring autophagy in vivo and in vitro. Here, we report the methods for constructing a biosensor of human HsLC3a as a probe for autophagy biogenesis and the optimization of the intramolecular BRET assay that allows for high‐throughput screening of chemical modulators of autophagy. User‐friendly working interface with the BRET‐based synthetic sensor of HsLC3a makes drug discovery easy and amenable for high‐throughput. The BRET protocol described here could be easily applicable to generate other biosensors for monitoring PPIs by measurement of intermolecular BRET. © 2017 by John Wiley & Sons, Inc.
Quantitative analysis of cell proliferation by a dye dilution assay: Application to cell lines and cocultures
Authors: Chung Soobin , Kim Seol‐Hee , Seo Yuri , Kim Sook‐Kyung , Lee Ji Youn 
Published: April 2017

AbstractCell proliferation represents one of the most fundamental processes in biological systems, thus the quantitative analysis of cell proliferation is important in many biological applications such as drug screening, production of biologics, and assessment of cytotoxicity. Conventional proliferation assays mainly quantify cell number based on a calibration curve of a homogeneous cell population, and therefore are not applicable for the analysis of cocultured cells. Moreover, these assays measure cell proliferation indirectly, based on cellular metabolic activity or DNA content. To overcome these shortcomings, a dye dilution assay employing fluorescent cell tracking dyes that are retained within cells was applied and was diluted proportionally by subsequent cell divisions. Here, it was demonstrated that this assay could be implemented to quantitatively analyze the cell proliferation of different types of cell lines, and to concurrently analyze the proliferation of two types of cell lines in coculture by utilizing cell tracking dyes with different spectral characteristics. The mean division time estimated by the dye dilution assay is compared with the population doubling time obtained from conventional methods and values from literature. Additionally, dye transfer between cocultured cells was investigated and it was found that it is a characteristic of the cells rather than a characteristic of the dye. It was suggested that this method can be easily combined with other flow cytometric analyses of cellular properties, providing valuable information on cell status under diverse conditions. © 2017 International Society for Advancement of Cytometry
Examining the interplay of climate and low amplitude sea‐level change on the distribution and volume of massive dolomitization: Zebbag Formation, Cretaceous, Southern Tunisia
Authors: Newport Richard , Hollis Cathy , Bodin Stéphane , Redfern Jonathan 
Published: April 2017

AbstractDuring the Cretaceous, a humid global climate, calcitic seas, high relative sea‐level and low amplitude changes in relative sea‐level largely prevented large‐scale dolomitization in many carbonate successions. However, the well‐exposed shallow‐water carbonate sediments of the Upper Albian–Lower Turonian Zebbag Formation on the Jeffara Escarpment, southern Tunisia, are pervasively dolomitized. This study considers why dolomitization was so widespread in this region during a period of Earth history when platform‐scale dolomitization is rare. Marine conditions were established in the Upper Albian, evidenced by stacked upward‐shallowing packages of shallow subtidal to peritidal carbonate sediments in the basal Rhadouane Member. A gradual increase in the volume of subtidal sediments in the Cenomanian Kerker Member, culminated in deposition of laterally extensive marls, during maximum flooding of the platform in the Lower Turonian. The overlying Gattar Member was then deposited in shallower water as relative sea‐level fell. The entire Zebbag Formation is pervasively replaced by stratabound, fabric‐retentive, dolomite, except within the marl at the top of the Kerker Member, which is only partially dolomitized. Petrographic textures indicate dolomitization largely post‐dated marine cementation and platform emergence but pre‐dated chemical compaction. Slightly more positive oxygen isotope signatures, slightly elevated concentrations of Sr and a near‐absence of evaporites are consistent with dolomitization by reflux of mesohaline sea water. An upward‐decrease in major element concentrations and higher 87Sr/86Sr compared to Upper Cretaceous sea water suggest that basal, Albian siliciclastic beds acted as aquifers facilitating dolomitization by fluxing fluids offshore. Dolomitization is interpreted to have resulted from multiple fluxes of sea water over periods of 0·5 to 2·5 Ma. The unusually high volume of dolostone for a platform of this age most probably reflects deposition within an arid climate belt, where an efficient reflux system was facilitated by basal, permeable siliciclastic strata.
Behavioral responses to encounter of fishing boats in wandering albatrosses
Authors: Collet Julien , Patrick Samantha C. , Weimerskirch Henri 
Published: April 2017

AbstractAnimals are attracted to human food subsidies worldwide. The behavioral response of individuals to these resources is rarely described in detail, beyond chances of encounters. Seabirds for instance scavenge in large numbers at fishing boats, triggering crucial conservation issues, but how the response to boats varies across encounters is poorly known. Here we examine the behavioral response of wandering albatrosses (Diomedea exulans), equipped with GPS tags, to longline fishing boats operating near their colony for which we had access to vessel monitoring system data. We distinguish between encounters (flying within 30 km of a boat) and attendance behavior (sitting on the sea within 3 km of a boat), and examine factors affecting each. In particular, we test hypotheses that the response to encountered boats should vary with sex and age in this long‐lived dimorphic species. Among the 60% trips that encountered boats at least once, 80% of them contained attendance (but attendance followed only 60% of each single encounter). Birds were more attracted and remained attending longer when boats were hauling lines, despite the measures enforced by this fleet to limit food availability during operations. Sex and age of birds had low influence on the response to boats, except the year when fewer boats came fishing in the area, and younger birds were attending further from boats compared to older birds. Net mass gain of birds was similar across sex and not affected by time spent attending boats. Our results indicate albatrosses extensively attend this fishery, with no clear advantages, questioning impacts on foraging time budgets. Factors responsible for sex foraging segregation at larger scale seem not to operate at this fleet near the colony and are not consistent with predictions of optimal foraging theory on potential individual dominance asymmetries. This approach complements studies of large‐scale overlap of animals with human subsidies.
Wolf in sheep's clothing: Model misspecification undermines tests of the neutral theory for life histories
Authors: Authier Matthieu , Aubry Lise M. , Cam Emmanuelle 
Published: April 2017

AbstractUnderstanding the processes behind change in reproductive state along life‐history trajectories is a salient research program in evolutionary ecology. Two processes, state dependence and heterogeneity, can drive the dynamics of change among states. Both processes can operate simultaneously, begging the difficult question of how to tease them apart in practice. The Neutral Theory for Life Histories (NTLH) holds that the bulk of variations in life‐history trajectories is due to state dependence and is hence neutral: Once previous (breeding) state is taken into account, variations are mostly random. Lifetime reproductive success (LRS), the number of descendants produced over an individual's reproductive life span, has been used to infer support for NTLH in natura. Support stemmed from accurate prediction of the population‐level distribution of LRS with parameters estimated from a state dependence model. We show with Monte Carlo simulations that the current reliance of NTLH on LRS prediction in a null hypothesis framework easily leads to selecting a misspecified model, biased estimates and flawed inferences. Support for the NTLH can be spurious because of a systematic positive bias in estimated state dependence when heterogeneity is present in the data but ignored in the analysis. This bias can lead to spurious positive covariance between fitness components when there is in fact an underlying trade‐off. Furthermore, neutrality implied by NTLH needs a clarification because of a probable disjunction between its common understanding by evolutionary ecologists and its translation into statistical models of life‐history trajectories. Irrespective of what neutrality entails, testing hypotheses about the dynamics of change among states in life histories requires a multimodel framework because state dependence and heterogeneity can easily be mistaken for each other.
Increasing copper alters cellular elemental composition (Mo and P) of marine diatom
Authors: Wang Deli , Xia Weiwei , Kumar K. Suresh , Gao Kunshan 
Published: April 2017

AbstractThe elemental composition (surface adsorbed and internalized fraction of Cu, Mo and P) in marine phytoplankton was first examined in cultures of the diatom Phaeodactylum tricornutum which were exposed to various levels of Cu concentrations ranging from 0.25 to 16 μmol/L with equivalent free [Cu2+] concentrations of 0.4–26 nmol/L. We observed an acceleration of algal growth rates (20–40%) with increasing ambient Cu levels, as well as slightly increased levels of internalized Cu in cells (2–13 × 10−18 mol/cell) although cellular Cu mostly accumulated onto the cell surface (>50% of the total: intracellular + surface adsorbed). In particular, we documented for the first time that the elemental composition (Mo and P) in algal cells varies dynamically in response to increased Cu levels: (1) Cellular P, predominantly in the intracellular compartment (>95%), shows with a net consumption as indicated by a gradual decrease with increasing [Cu2+] (120→50 × 10−15 mol P/cell) probably due to the fact that P, a backbone bioelement, is largely required in forming biological compartments such as cell membranes; and (2) cellular Mo, predominantly encountered in the intracellular compartment, showed up to tenfold increase in concentration in the cultures exposed to Cu, with a peak accumulation of 1.1 × 10−18 mol Mo/cell occurring in the culture exposed to [Cu2+] at 3.7 nmol/L. Such a net cellular Mo accumulation suggests that Mo might be specifically required in biological processes, probably playing a counteracting role against Cu.
A multispecies dependent double‐observer model: A new method for estimating multispecies abundance
Authors: Golding Jessie D. , Nowak J. Joshua , Dreitz Victoria J. 
Published: April 2017

AbstractConservation of biological communities requires accurate estimates of abundance for multiple species. Recent advances in estimating abundance of multiple species, such as Bayesian multispecies N‐mixture models, account for multiple sources of variation, including detection error. However, false‐positive errors (misidentification or double counts), which are prevalent in multispecies data sets, remain largely unaddressed. The dependent‐double observer (DDO) method is an emerging method that both accounts for detection error and is suggested to reduce the occurrence of false positives because it relies on two observers working collaboratively to identify individuals. To date, the DDO method has not been combined with advantages of multispecies N‐mixture models. Here, we derive an extension of a multispecies N‐mixture model using the DDO survey method to create a multispecies dependent double‐observer abundance model (MDAM). The MDAM uses a hierarchical framework to account for biological and observational processes in a statistically consistent framework while using the accurate observation data from the DDO survey method. We demonstrate that the MDAM accurately estimates abundance of multiple species with simulated and real multispecies data sets. Simulations showed that the model provides both precise and accurate abundance estimates, with average credible interval coverage across 100 repeated simulations of 94.5% for abundance estimates and 92.5% for detection estimates. In addition, 92.2% of abundance estimates had a mean absolute percent error between 0% and 20%, with a mean of 7.7%. We present the MDAM as an important step forward in expanding the applicability of the DDO method to a multispecies setting. Previous implementation of the DDO method suggests the MDAM can be applied to a broad array of biological communities. We suggest that researchers interested in assessing biological communities consider the MDAM as a tool for deriving accurate, multispecies abundance estimates.
Riparian plant composition along hydrologic gradients in a dryland river basin and implications for a warming climate
Authors: Reynolds Lindsay V. , Shafroth Patrick B. 
Published: April 2017

AbstractDroughts in dryland regions on all continents are expected to increase in severity and duration under future climate projections. In dryland regions, it is likely that minimum streamflow will decrease with some perennial streams shifting to intermittent flow under climate‐driven changes in precipitation and runoff and increases in temperature. Decreasing base flow and shifting flow regimes from perennial to intermittent could have significant implications for stream‐dependent biota, including riparian vegetation. In this study, we asked, how do riparian plant communities vary along wet‐to‐dry hydrologic gradients on small (first–third order) streams? We collected data on geomorphic, hydrologic, and plant community characteristics on 54 stream sites ranging in hydrology from intermittent to perennial flow across the Upper Colorado River Basin (284,898 km2). We found that plant communities varied along hydrologic gradients from high to low elevation between streams, and perennial to intermittent flow. We identified indicator species associated with different hydrologic conditions and suggest how plant communities may shift under warmer, drier conditions. Our results indicate that species richness and cover of total, perennial, wetland, and native plant groups will decrease while annual plants will increase under drying conditions. Understanding how plant communities respond to regional drivers such as hydroclimate requires broad‐scale approaches such as sampling across whole river basins. With increasingly arid conditions in many regions of the globe, understanding plant community shifts is key to understanding the future of riparian ecosystems.
Do benthic invertebrates use hyporheic refuges during streambed drying? A manipulative field experiment in nested hyporheic flowpaths
Authors: Maazouzi C. , Galassi D. , Claret C. , Cellot B. , Fiers F. , Martin D. , Marmonier P. , Dole‐Olivier M.‐J. 
Published: April 2017

AbstractThe existence of resilience mechanisms related to a disturbance, such as invertebrate migrations into the hyporheic zone (HZ, saturated subsurface interstices), promotes persistence of benthic communities in river ecosystems. Water exchanges through the HZ, which influence the distribution of biota, are heterogeneous at different scales, determining nested hyporheic flowpaths. The effect of these nested exchanges on the use of the hyporheic refuges by benthic invertebrates is still unknown. We simulated streambed drying in a stream section where hydrological exchanges were considered at riffle (upstream or downstream of riffles) and floodplain (downstream end of a floodplain) scales. Physicochemical indicators determined that local hyporheic flowpaths (up‐ and downwelling zones) were nested in a large‐scale downwelling section of the river. In this situation, the effect of 24 h of experimental drying on the distribution of invertebrates was examined at three sediment depths to follow their migrations into the HZ. Whereas invertebrate assemblages did not change in the control channel, abundance of benthic invertebrate increased in the HZ of the impact channel (up to seven‐fold). Changes occurred rapidly (15–24 h) and only upstream of riffle where surface water down‐welled. The migration was taxon‐specific and concerned the most abundant benthic taxa that temporarily colonize the HZ (“temporary hyporheos,” e.g., Leuctra cf. fusca, Baetis sp., Caenis sp., Orthocladiinae, Tanypodinae). In the context of climate change, hyporheic refuge use will promote persistence of communities facing the increasing frequency of extreme hydrological events. Improved knowledge about the distribution and function of these refuges is becoming crucial for river managers.
Soil respiration and mass balance estimation of fine root production in Fitzroya cupressoides forests of southern Chile
Authors: Urrutia‐Jalabert Rocio , Malhi Yadvinder , Lara Antonio 
Published: April 2017

AbstractThe soil carbon dynamics of southern hemisphere temperate rainforests have rarely been studied. Here, we report for the first time soil CO2 effluxes and their partitioning for medium‐age and old‐growth Fitzroya cupressoides forests growing under contrasting environmental conditions in the Coastal Range and Andean Cordillera of southern Chile. Fitzroya is a high biomass and one of the longest lived species in the world. We characterized soil respiration patterns over almost 2 yr. Annual soil respiration was slightly higher in younger forests from the Coastal Range compared with Andean forests during the first studied year (6.37–6.66 vs. 5.06–6.14 Mg C·ha−1·yr−1), and significantly higher during the second year mainly due to a warmer and drier summer (8.08–8.64 vs. 4.98–5.35 Mg C·ha−1·yr−1). Therefore, warmer and drier conditions, likely to become more common in this region under future climate change, were associated with significantly higher respiration in the shallow soils of the coast, but not in the Andes. A higher proportion of autotrophic respiration was found in the Coastal Range forest probably due to a much higher fine root biomass in this site. However, fine root productivity, an important contributor of belowground carbon fluxes, was a little lower (not significantly) in the coastal site (0.81 ± 0.60 vs. 1.50 ± 0.42 Mg C·ha−1·yr−1), indicating a longer root residence time in forests from this area. Soil CO2 effluxes from these forests and their root productivity are at the lower end of values recorded for other mature and old‐growth temperate wet forests worldwide. The intrinsic longevity and the particularly poor soils and rainy conditions where these forests grow may influence these facts. Interannual climate variability appears to be especially important for soil respiration in the Coastal Range due to the more Mediterranean climate influence and shallow, poor water retention soils in this area.