ALBERT

Description: Abstract Experimental study of the effects of projected climate change on plant phenology allows us to isolate effects of warming on life history events such as leaf out. We simulated a 2°C temperature increase and 20% precipitation increase in a recently harvested temperate deciduous forest community in central Pennsylvania, USA, and observed the leaf out phenology of all species in 2009 and 2010. Over 130 plant species were monitored weekly in study plots, but due to high variability in species composition among plots, species were grouped into five functional groups: short forbs, tall forbs, shrubs, small trees, and large trees. Tall forbs and large trees, which usually emerge in the late spring, advanced leaf out 14‐18 days in response to warming. Short forbs, shrubs, and small trees emerge early in spring and did not alter their phenology in response to warming or increased precipitation treatments. Earlier leaf out of tall forbs and large trees coincided with almost three weeks of increased community‐level leaf area index (LAI), indicating greater competition and a condensed spring green‐up period. While phenology of large trees and tall forbs appears to be strongly influenced by temperature‐based growth cues, our results suggest that photoperiod and chilling cues more strongly influence the leaf out of other functional groups. Reduced freeze events and warmer temperatures from predicted climate change will interact with non‐temperature growth cues to have cascading consequences throughout the ecosystem.

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: At least half of the world's population resides in the coastal zone and the livelihoods of billions of people are affected either directly or indirectly by the production and sustainability of nearshore fisheries. Landscape change, specifically development of tree plantations, is accelerating worldwide as developing countries integrate into global markets to sell goods, offer climate-mitigation services (carbon), and/or provide renewable energy. These changes can release excess nutrients into adjacent coastal waters causing eutrophication that alters the structure and function of coastal ecosystems. This study examined the relationship between coastal drainage basin land use/ land cover change (LCLUC), specifically development of tree plantations, patterns of chlorophyll a in nearshore coastal waters, and the biological condition of commercially important shellfish, Concholepas concholepas ( loco ) in southern Chile. Locos (N= 1,374) were sampled across 13 watersheds (35,853 km 2 ) and 42 fisheries management areas (spanning 250 km of coastline). Locos harvested from management areas influenced by tree plantations had approximately 30% more endobiont (shell-boring) phoronids, almost twice as many endobiont polychaetes and twice as many epibiont (shell-attaching) barnacles than locos from areas in close proximity to watersheds dominated by native forests (15-20% of the watershed). Phoronid infested locos from coastal waters adjacent to watersheds with tree plantations were of relatively poor biological condition (smaller and narrower in width) and of reduced market value. Our study suggests that tree plantations result in indirect ecological impacts to coastal fisheries (more nutrients and higher phytoplankton biomass, resulting in smaller, low quality locos), and costs are born by coastal fishers (lower prices for locos). Increases in tree plantations could thus potentially significantly impact coastal fisheries worldwide and such problems should be managed as an interconnected network of land use change, oceanic ecosystems, and economic systems that are considered an integrated socio-ecological system.

Description: Glacial retreat creates new habitat which is colonised and developed by plants and animals during the process of primary succession. While there has been much debate about the relative role of deterministic and stochastic processes during terrestrial succession, evidence from freshwater ecosystems remains minimal and a general consensus is lacking. Using a unique 27 year record of community assembly following glacial recession in southeast Alaska, we demonstrate significant change in the trait composition of stream invertebrate communities as catchment glacial cover decreased from 〉70% to zero. Functional diversity increased significantly as glacier cover decreased and taxonomic richness increased. Null modelling approaches led to a key finding that niche filtering processes were dominant when glacial cover was extensive, reflecting water temperature and dispersal constraints. Thereafter the community shifted towards co-occurrence of stochastic and deterministic assembly processes. A further novel discovery was that intrinsic functional redundancy developed throughout the study, particularly because new colonisers possessed similar traits to taxa already present. Rapid glacial retreat is occurring in Arctic and alpine environments worldwide and the assembly processes observed in this study provide new fundamental insights into how glacially influenced stream ecosystems will respond. These findings support tolerance as a key primary successional mechanism in this system, and have broader value for developing our understanding of how biological communities in river ecosystems assemble or restructure in response to environmental change.

Description: Major sources of greenhouse gas (GHG) emissions from agricultural crop production are nitrous oxide (N 2 O) emissions resulting from the application of mineral and organic fertiliser, and carbon dioxide (CO 2 ) emissions from soil carbon losses. Consequently, choice of fertiliser type, optimising fertiliser application rates and timing, reducing microbial denitrification and improving soil carbon management are focus areas for mitigation. We have integrated separate models derived from global data on fertiliser induced soil N 2 O emissions, soil nitrification inhibitors, and the effects of tillage and soil inputs of soil C stocks into a single model in order to determine optimal mitigation options as a function of soil type, climate, and fertilisation rates. After Monte Carlo sampling of input variables we aggregated the outputs according to climate, soil and fertiliser factors to consider the benefits of several possible emissions mitigation strategies, and identified the most beneficial option for each factor class on a per hectare basis. The optimal mitigation for each soil-climate-region was then mapped to propose geographically specific optimal GHG mitigation strategies for crops with varying N requirements. The use of empirical models reduces the requirements for validation (since they are calibrated on globally or continentally observed phenomena). However, since they are relatively simple in structure, they may not be applicable for accurate site specific prediction of GHG emissions. The value of this modelling approach is for initial screening and ranking of potential agricultural mitigation options and to explore the potential impact of regional agricultural GHG abatement policies. Given the clear association between management practice and crop productivity, it is essential to incorporate characterisation of the yield effect on a given crop before recommending any mitigation practice.

Description: Biogeochemical cycles in the coastal ocean are changing and will continue to change in response to a changing climate. Effects on the oxygen and carbon cycles are particularly important, as either episodic or permanent shifts toward lower oxygen and/or higher inorganic carbon conditions can impact coastal ecosystems negatively. Here we study the sensitivity of these cycles to changes that may occur in the coastal ocean, focusing on a summer wind-driven upwelling region off southern Vancouver Island shelf. We use a quasi 2-D configuration of the Regional Ocean Modeling System (ROMS) to perform six sensitivity experiments. Results indicate that carbon and oxygen cycles in this region may be significantly affected by an altered upwelling season, a shallower offshore Oxygen Minimum Zone, and a carbon-enriched environment. Combinations of these scenarios suggest a potentially increasing risk for the development of coastal hypoxia and corrosive conditions in the region.

Description: Longitudinal and diel measurements of dual isotope composition (δ15N and δ18O) in nitrate (NO3-N) were made in the Ichetucknee River, a large (∼8 m3 s−1), entirely spring-fed river in North Florida, to determine whether isotopic variation can deconvolve assimilatory and dissimilatory removal. Comparing nitrate concentrations and isotope composition during the day and night we predicted (1) daytime declines in total fractionation due to low assimilatory fractionation and (2) diurnal variation in dual isotope coupling between 1:1 (assimilation) and 2:1 (denitrification). Five daytime longitudinal transects comprising 10 sampling stations showed consistent NO3-N removal (25–35% of inputs) and modest fractionation (15εtotal between −2 and −6‰, enriching the residual nitrate pool). Lower fractionation (by ∼1‰) during two nighttime transects, suggests higher fractionation due to assimilation than denitrification. Total fractionation was significantly negatively associated with discharge, input [NO3-N], N mass removal, and fractional water loss. Despite well-constrained mass balance estimates that denitrification dominated total N removal, isotope coupling was consistently 1:1, both for longitudinal and diel sampling. Hourly samples on two dates at the downstream location showed significant diel variation in concentration ([NO3-N] amplitude = 60 to 90 μg N L−1) and isotope composition (δ15N amplitude = −0.7‰ to −1.6‰). Total fractionation differed between day and night only on one date but estimated assimilatory fractionation assuming constant denitrification was highly variable and implausibly large (for N, 15ε = −2 to −25‰), suggesting that fractionation and removal due to denitrification is not diurnally constant. Pronounced counterclockwise hysteresis in the relationship between [NO3-N] and δ15N suggests diel variation in N isotope dynamics. Together, low fractionation, isotope versus concentration hysteresis, and consistent 1:1 isotope coupling suggests that denitrification is controlled by NO3− diffusion into the benthic sediments, the length of which is mediated by riverine oxygen dynamics. While using dual isotope behavior to deconvolve removal pathways was not possible, isotope measurements did yield valuable information about riverine N cycling and transformations.

Description: Thermokarst lakes are thought to have been an important source of methane (CH4) during the last deglaciation when atmospheric CH4 concentrations increased rapidly. Here we demonstrate that meltwater from permafrost ice serves as an H source to CH4 production in thermokarst lakes, allowing for region-specific reconstructions of δDCH4 emissions from Siberian and North American lakes. δDCH4 reflects regionally varying δD values of precipitation incorporated into ground ice at the time of its formation. Late Pleistocene-aged permafrost ground ice was the dominant H source to CH4 production in primary thermokarst lakes, whereas Holocene-aged permafrost ground ice contributed H to CH4 production in later generation lakes. We found that Alaskan thermokarst lake δDCH4 was higher (−334 ± 17‰) than Siberian lake δDCH4 (−381 ± 18‰). Weighted mean δDCH4 values for Beringian lakes ranged from −385‰ to −382‰ over the deglacial period. Bottom-up estimates suggest that Beringian thermokarst lakes contributed 15 ± 4 Tg CH4 yr−1 to the atmosphere during the Younger Dryas and 25 ± 5 Tg CH4 yr−1 during the Preboreal period. These estimates are supported by independent, top-down isotope mass balance calculations based on ice core δDCH4 and δ13CCH4 records. Both approaches suggest that thermokarst lakes and boreal wetlands together were important sources of deglacial CH4.

Description: As part of the Mercury Experiment to Assess Atmospheric Loading in Canada and the U.S. (METAALICUS), different stable Hg(II) isotope spikes were applied to the upland and wetland areas of a boreal catchment between 2001 and 2006 to examine retention of newly deposited Hg(II). In the present study, a Geographical Information Systems (GIS)-based approach was used to quantify canopy and ground vegetation pools of experimentally applied upland and wetland spike Hg within the METAALICUS watershed over the terrestrial loading phase of the experiment. A chemical kinetic model was also used to describe the changes in spike Hg concentrations of canopy and ground vegetation over time. An examination of the fate of spike Hg initially present on canopy vegetation using a mass balance approach indicated that the largest percentage flux from the canopy over one year post-spray was emission to the atmosphere (upland: 45%; wetland: 71%), followed by litterfall (upland: 14%; wetland: 10%) and throughfall fluxes (upland: 12%; wetland: 9%) and longer term retention of spike in the forest canopy (11% for both upland and wetland). Average half-lives (t1/2) of spike on deciduous (110 ± 30 days) and coniferous (180 ± 40 days) canopy and ground vegetation (890 ± 620 days) indicated that retention of new atmospheric Hg(II) on terrestrial (especially ground) vegetation delays downward transport of new atmospheric Hg(II) into the soil profile and runoff into lakes.

Description: Climate change may considerably impact the carbon (C) dynamics and C stocks of forest soils. To assess the combined effects of warming and reduced precipitation on soil CO 2 efflux, we conducted a two-way factorial manipulation experiment (4 °C soil warming + throughfall exclusion) in a temperate spruce forest from 2008 until 2010. Soil was warmed by heating cables throughout the growing seasons. Soil drought was simulated by throughfall exclusions with three 100 m 2 roofs during 25 days in July/August 2008 and 2009. Soil warming permanently increased the CO 2 efflux from soil whereas throughfall exclusion led to a sharp decrease in soil CO 2 efflux (45% and 50% reduction during roof installation in 2008 and 2009, respectively). In 2008, CO 2 efflux did not recover after natural rewetting and remained lowered until autumn. In 2009, CO 2 efflux recovered shortly after rewetting, but relapsed again for several weeks. Drought offset the increase in soil CO 2 efflux by warming in 2008 (growing season CO 2 efflux in t C ha −1 : control: 7.1 ± 1.0; warmed: 9.5 ± 1.7; warmed + roof: 7.4 ± 0.3; roof: 5.9 ± 0.4) and in 2009 (control: 7.6 ± 0.8; warmed + roof: 8.3 ± 1.0). Throughfall exclusion mainly affected the organic layer and the top 5 cm of the mineral soil. Radiocarbon data suggest that heterotrophic and autotrophic respiration were affected to the same extent by soil warming and drying. Microbial biomass in the mineral soil (0 - 5 cm) was not affected by the treatments. Our results suggest that warming causes significant C losses from the soil as long as precipitation patterns remain steady at our site. If summer droughts become more severe in the future, warming induced C losses will likely be offset by reduced soil CO 2 efflux during and after summer drought.

Description: We present a lake-wide investigation of Lake Superior carbon and organic matter biogeochemistry using radiocarbon, stable isotope, and carbon concentrations. Dissolved inorganic carbon (DIC) abundance in the lake was 121–122 Tg C, with offshore concentration and δ13C values being laterally homogenous and tightly coupled to the physical and thermal regime and biochemical processes. Offshore Δ14C of DIC (50–65‰) exhibited lateral homogeneity and was more 14C enriched than co-occurring atmospheric CO2 (∼38‰); nearshore Δ14C of DIC (36–38‰) was similar to atmospheric CO2. Dissolved organic carbon (DOC) abundance was 14.2–16.4 Tg C. DOC's concentration and δ13C were homogenous in June (mixed lake), but varied laterally during August (stratification) possibly due to spatial differences in lake productivity. Throughout sampling, DOC had modern radiocarbon values (14–58‰) indicating a semilabile nature with a turnover time of ≤60 years. Lake particulate organic carbon (POC, 0.9–1.3 Tg C) was consistently 13C depleted relative to DOC. The δ15N of epilimnetic particulate organic nitrogen shifted to more negative values during stratification possibly indicating greater use of nitrate (rather than ammonium) by phytoplankton in August. POC's radiocarbon was spatially heterogeneous (Δ14C range: 58‰ to −303‰), and generally 14C depleted relative to DOC and DIC. POC 14C depletion could not be accounted for by black carbon in the lake but, because of its spatial and temporal distribution, is attributed to sediment resuspension. The presence of old POC within the epilimnion of the open lake indicates possible benthic-pelagic coupling in the lake's organic carbon cycle; the ultimate fate of this old POC bears further investigation.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: A perturbation of the global carbon cycle has often been used for interpreting the Frasnian-Famennian (F-F) mass extinction. However, the changes of atmospheric CO2 level (pCO2) during this interval are much debatable. To illustrate the carbon cycle during F-F transition, paired inorganic (δ13Ccarb) and organic (δ13Corg) carbon isotope analyses were carried out on two late Devonian carbonate sequences (Dongcun and Yangdi) from south China. The larger amplitude shift of δ13Corg compared to δ13Ccarb and its resultant Δ13C (Δ13C = δ13Ccarb − δ13Corg) decrease indicate decreased atmospheric CO2 level around the F-F boundary. The onset of pCO2 level decrease predates that of marine regressions, which coincide with the beginning of conodont extinctions, suggesting that temperature decrease induced by decreased greenhouse effect of atmospheric CO2 might have contributed to the F-F mass extinction.

Description: Question Relationships between species richness and environmental drivers such as productivity and disturbance are sensitive to the scale over which they are measured, but the extent to which this scale-dependence is important for experimental studies conducted over small scale ranges is not well known. We ask whether the response of species richness to experimental manipulation of productivity and disturbance varies across small spatial scales (0.016–4 m 2 ). We show that species–area relationships are well suited to summarize cross-scale responses of species richness, and ask whether the responses of species–area relationships to experimental manipulations are more consistent than richness at any single scale. Location Northern Californian coastal grasslands. Methods We applied disturbance and productivity reduction treatments over 4 yr at two sites. We assessed changes in species richness over five grain sizes, encompassing a 256-fold range of plot size. This allowed us to construct a species–area relationship for each experimental plot in each sampling year. We used the slope of the species–area relationship to summarize changes in species richness across multiple spatial scales. Results Richness responses were scale-dependent and complex, causing changes at any one scale to be difficult to interpret. Disturbance either increased or had no effect on richness, while reducing productivity had idiosyncratic effects among sites, scales and years. Both treatments, however, had consistent and interpretable effects on the species–area relationship. Reducing productivity increased the slope of the species–area relationship, while disturbance decreased it. Conclusions Our results suggest that the productivity–richness and disturbance–richness relationships are scale-dependent, and that improved generality could be achieved by focusing attention on the response of the species–area relationship to these factors. We showed that experimental disturbance and reverse fertilization treatments can have scale-dependent effects on grassland species richness, even at small (0.016 – 4 m 2 ) scales. Richness responses at any one scale were idiosyncratic among sites and years, but characteristics of the species-area relationship were more predictable and consistent. We recommend increased focus on responses of the species-area relationship to experimental manipulations.

Description: Ecology, Volume 93, Issue 1, Page 9-16, January 2012.

Description: Ecology, Volume 93, Issue 1, Page 111-121, January 2012.

Description: Emissions of the trace gas nitrous oxide (N 2 O) play an important role for the greenhouse effect and stratospheric ozone depletion, but the impacts of climate change on N 2 O fluxes and the underlying microbial drivers remain unclear. The aim of this study was to determine effects of sustained climate change on field N 2 O fluxes and associated microbial enzymatic activities, microbial population abundance and community diversity in an extensively managed, upland grassland. We recorded N 2 O fluxes, nitrification and denitrification, microbial population size involved in these processes and community structure of nitrite reducers ( nir K) in a grassland exposed for four years to elevated atmospheric CO 2 (+ 200 ppm), elevated temperature (+ 3.5°C) and reduction of summer precipitations (-20%) as part of a long-term, multifactor climate change experiment. Our results showed that both warming and simultaneous application of warming, summer drought and elevated CO 2 had a positive effect on N 2 O fluxes, nitrification, N 2 O release by denitrification and the population size of N 2 O reducers and NH 4 oxidizers. In situ N 2 O fluxes showed a stronger correlation with microbial population size under warmed conditions compared with the control site. Specific lineages of nir K denitrifier communities responded significantly to temperature. In addition, nir K community composition showed significant changes in response to drought. Path analysis explained more than 85% of in situ N 2 O fluxes variance by soil temperature, denitrification activity and specific denitrifying lineages. Overall, our study underlines that climate-induced changes in grassland N 2 O emissions reflect climate-induced changes in microbial community structure, which in turn modify microbial processes.

Description: Understanding how species and ecosystems respond to climate change requires spatially and temporally rich data for a diverse set of species and habitats, combined with models that test and predict responses. Yet current work is hampered by the long-known problems of inadequate management of data and insufficient description of analytical procedures, especially in the field of ecology. Despite recent institutional incentives to share data and new data archiving infrastructure, many ecologists do not archive and publish their data and code. Given current rapid rates of global change, the consequences of this are extreme: because an ecological dataset collected at a certain place and time represents an irreproducible set of observations, ecologists doing local, independent research possess, in their file cabinets and spreadsheets, a wealth of information about the natural world and how it is changing. Although large-scale initiatives will increasingly enable and reward open science, we believe that change demands action and personal commitment by individuals—from students and PIs. Here, we outline the major benefits of sharing data and analytical procedures in the context of global change ecology, and provide guidelines for overcoming common obstacles and concerns. If individual scientists and labs can embrace a culture of archiving and sharing we can accelerate the pace of the scientific method and redefine how local science can most robustly scale up to globally-relevant questions.

Description: Changes in C 4 grass distribution and abundance are frequently observed in Quaternary, Holocene and future environmental-change scenarios. However, the factors driving these dynamics are not fully understood, and conflicting theories have been reported. In this paper, we present a very large dataset of modern altitudinal distribution profiles of C 3 and C 4 grasses covering the entire Neotropical Andes, which was compared with actual climate data. The results of multivariate analysis demonstrate that, in the Neotropical Andes, mean annual temperature is the main factor governing the modern altitudinal distribution of C 3 and C 4 grass species. The C 3 and C 4 grass distributions were compared with simulations based on the Lund-Potsdam-Jena dynamic global vegetation model (LPJ-DGVM), which allowed the present grass distribution to be estimated. Finally, the DGVM was employed to simulate past and future scenarios, using the IPCC's climate projections for 2100 and PMIP2 models for the Holocene Optimum (HO, 6000 yrs BP) and the Last Glacial Maximum (LGM, 21000 yrs BP). The results were found to be significantly different to those obtained using a simple photosynthetic model. According to LPJ forced with the PMIP2 models for the LGM, during the LGM, the C 4 grasses would not have reached higher altitudes than found in the present day.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: A large increase in near-infrared (NIR) reflectance of Amazon forests during the light-rich dry season and a corresponding decrease during the light-poor wet season has been observed in satellite measurements. This increase has been variously interpreted as seasonal change in leaf area resulting from net leaf flushing in the dry season or net leaf abscission in the wet season, enhanced photosynthetic activity during the dry season from flushing new leaves and as change in leaf scattering and absorption properties between younger and older leaves covered with epiphylls. Reconciling these divergent views using theory and observations is the goal of this article. The observed changes in NIR reflectance of Amazon forests could be due to similar, but small, changes in NIR leaf albedo (reflectance plus transmittance) resulting from the exchange of older leaves for newer ones, but with the total leaf area unchanged. However, this argument ignores accumulating evidence from ground-based reports of higher leaf area in the dry season than the wet season, seasonal changes in litterfall and does not satisfactorily explain why NIR reflectance of these forests decreases in the wet season. More plausibly, the increase in NIR reflectance during the dry season and the decrease during the wet season would result from changes in both leaf area and leaf optical properties. Such change would be consistent with known phenological behavior of tropical forests, ground-based reports of seasonal changes in leaf area, litterfall, leaf optical properties and fluxes of evapotranspiration, and thus, would reconcile the various seemingly divergent views.

Description: Mechanisms to mitigate global climate change by sequestering carbon (C) in different ‘sinks’ have been proposed as at least temporary measures. Of the major global C pools, terrestrial ecosystems hold the potential to capture and store substantially increased volumes of C in soil organic matter (SOM) through changes in management that are also of benefit to the multitude of ecosystem services that soils provide. This potential can only be realised by determining the amount of SOM stored in soils now, with subsequent quantification of how this is affected by management strategies intended to increase SOM concentrations, and used in soil C models for the prediction of the roles of soils in future climate change. An apparently obvious method to increase C stocks in soils is to augment the soil C pools with the longest mean residence times (MRT). Computer simulation models of soil C dynamics, e.g. RothC and Century, partition these refractory constituents into slow and passive pools with MRTs of centuries to millennia. This partitioning is assumed to reflect (i) the average biomolecular properties of SOM in the pools with reference to their source in plant litter, (ii) the accessibility of the SOM to decomposer organisms or catalytic enzymes, or (iii) constraints imposed on decomposition by environmental conditions, including soil moisture and temperature. However, contemporary analytical approaches suggest that the chemical composition of these pools is not necessarily predictable because, despite considerable progress with understanding decomposition processes and the role of decomposer organisms, along with refinements in simulation models, little progress has been made in reconciling biochemical properties with the kinetically-defined pools. In this review, we will explore how advances in quantitative analytical technologies have redefined the new understanding of SOM dynamics and how this is impacting on the development and application of new modelling approaches to soil C.

Description: It is often assumed that daytime patterns of ecosystem carbon assimilation are mostly driven by direct physiological responses to exogenous environmental cues. Under limited environmental variability, little variation in carbon assimilation should thus be expected unless endogenous plant controls on carbon assimilation, which regulate photosynthesis in time, are active. We evaluated this assumption with eddy flux data, and we selected periods when net ecosystem exchange (NEE) was decoupled from environmental variability in seven sites from highly contrasting biomes across a 74º latitudinal gradient over a total of 36 site-years. Under relatively constant conditions of light, temperature, and other environmental factors, significant diurnal NEE oscillations were observed at six sites, where daily NEE variation was between 20% and 90% of that under variable environmental conditions. These results are consistent with fluctuations driven by the circadian clock and other endogenous processes. Our results open a promising avenue of research for a more complete understanding of ecosystem fluxes that integrates from cellular to ecosystem processes.

Description: Question Previous studies show that large-seeded species increase their abundance in Mediterranean annual grasslands in growing seasons with dry autumns. One possible explanation is that large-seeded species have larger seedlings, which provide an advantage under drier conditions. We address the following questions: is seed mass correlated with seedling survival in annual legumes? Is this correlation influenced by the watering regime? Can seedling growth characteristics explain the differential survival of small- and large-seeded species? Location Annual Mediterranean grassland, Central Spain. Methods An experiment was conducted with six grassland legume species of different seed sizes, subjected to six different watering regimes, monitoring survival and morphological variables (shoot and root growth) for 40 d. Results Large seeds provide an advantage for seedling survival, but in extreme drought conditions, seedling survival in small-seeded species equals that of seedlings from large-seeded species. Seedlings from larger seeds are larger than those of small-seeded species, but have a lower root/shoot biomass ratio, leading to greater potential evapotranspiration, which could explain their loss of relative advantage under extreme droughts. Conclusion The hypothesis that seedlings from large-seeded species survive better than small-seeded species under drought conditions was not supported. Germination behaviour seems to be a more plausible explanation for the increased abundance in the field of large-seeded species in growing seasons with dry autumns. Large seeds provide an advantage for seedling survival, but in extreme drought conditions, seedling survival in small-seeded species equals that of seedlings from large-seeded species. Seedlings from larger seeds are larger than those of small-seeded species, but have a lower root/shoot biomass ratio, leading to greater potential evapotranspiration, which could explain their loss of relative advantage under extreme droughts.

Description: Ecological Applications, Volume 22, Issue 1, Page 119-141, January 2012.

Description: Ecological Applications, Volume 22, Issue 1, Page 374-383, January 2012.

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: The impact of climate change on the advancement of plant phenological events has been heavily studied in the last decade. While the majority of spring plant phenological events have been trending earlier, this is not universally true. Recent work has suggested that species that are not advancing in their spring phenological behavior are responding more to lack of winter chill than increased spring heat. One way to test this hypothesis is by evaluating the behavior of a species known to have a moderate to high chilling requirement and examining how it is responding to increased warming. This study used a 60-year data set for timing of leaf-out and male flowering of walnut ( Juglans regia ) cultivar ‘Payne’ to examine this issue. The spring phenological behavior of ‘Payne’ walnut differed depending on bud type. The vegetative buds, which have a higher chilling requirement, trended towards earlier leaf-out until about 1994, when they shifted to later leaf-out. The date of male bud pollen shedding advanced over the course of the whole record. Our findings suggest that many species which have exhibited earlier bud-break are responding to warmer spring temperatures, but may shift into responding more to winter temperatures (lack of adequate chilling) as warming continues. © 2012 Blackwell Publishing Ltd

Description: Mitochondrial function is achieved through the cooperative interaction of two genomes: one nuclear (nuDNA) and the other mitochondrial (mtDNA). The unusual transmission of mtDNA, predominantly maternal without recombination is predicted to affect the fitness of male offspring. Recent research suggests the strong sexual dimorphism in aging is one such fitness consequence. The uniparental inheritance of mtDNA results in a selection asymmetry; mutations that affect only males will not respond to natural selection, imposing a male-specific mitochondrial mutation load. Prior work has implicated this male-specific mutation load in disease and infertility, but new data from fruit flies suggests a prominent role for mtDNA in aging; across many taxa males almost invariably live shorter lives than females. Here we discuss this new work and identify some areas of future research that might now be encouraged to explore what may be the underpinning cause of the strong sexual dimorphism in aging. Editor's suggested further reading in BioEssays: Mitonuclear match: Optimizing fitness and fertility over generations drives ageing within generations Abstract Mitochondrial manoeuvres: Latest insights and hypotheses on mitochondrial partitioning during mitosis in Saccharomyces cerevisiae Abstract Mitochondria and the culture of the Borg Abstract The maternal inheritance of mtDNA results in a selection asymmetry; natural selection cannot act on mutations that affect only males. This asymmetry imposes a male-specific mutation load previously implicated in male disease and infertility. New work suggests this asymmetry underpins the strong sexual dimorphism in aging observed across taxa.

Description: Question Quantification of the effect of species traits on the assembly of communities is challenging from a statistical point of view. A key question is how species occurrence and abundance can be explained by the trait values of the species and the environmental values at the sites. Methods Using a sites × species abundance table, a site × environment data table and a species × trait data table, we address the above question using a novel generalized linear mixed model (GLMM) approach. The GLMM overcomes problems of pseudo-replication and heteroscedastic variance by including sites and species as random factors. The method is equally applicable to presence–absence data as to count and multinomial data. We present a tiered forward selection approach for obtaining a parsimonious model and compare the results with alternative methods (the fourth corner method and RLQ ordination). Results We illustrate the approach on a presence–absence version on two data sets. In the Dune Meadow data, species presence is parsimoniously explained by moisture and manure on the meadows in combination with seed mass and specific leaf area (SLA). In the Grazed Grassland data, species presence is parsimoniously explained by the grazing intensity and soil phosphorus in combination with the C:N ratio and flowering mode. Conclusions Our GLMM approach can be used to identify which species traits and environmental variables best explain the species distribution, and which traits are significantly correlated with environmental variables. We argue that the method is better suited for providing an interpretable and predictive model than the fourth corner method and RLQ. We propose a Generalized Linear Mixed Model (GLMM) for the functional response of species to environmental change. The model can be used to identify which functional traits and environmental variables are significantly related and which best explain the species distribution. We argue that the method is better suited for providing an interpretable model than the fourth corner method and RLQ.

Description: Alien species are considered one of the prime threats to biodiversity, driving major changes in ecosystem structure and function. Identifying the traits associated with alien introduction has been largely restricted to comparing indigenous and alien species or comparing alien species that differ in abundance or impact. However, a more complete understanding may emerge when the entire pool of potential alien species is used as a control, information that is rarely available. In the eastern Mediterranean the marine environment is undergoing an unparalleled species composition transformation, as a flood of aliens have entered from the Red Sea following the opening of the Suez Canal in 1869. In this study, we compile data on species traits, geographical distribution and environmental affinity of the entire pool of reef-associated fish species in the Red Sea and more generally across the Indo-Pacific. We use this extensive data to identify the prime characteristics separating Red Sea species that have become alien in the Mediterranean from those that have not. We find that alien species occupy a larger range of environments in their native ranges, explaining their ability to colonize the seasonal Mediterranean. Red Sea species that naturally experience high maximum temperatures in their native range have a high probability of becoming alien. Thus, contrary to predictions of an accelerating number of aliens following increased water temperatures, hotter summers in this region may prevent the establishment of many alien species. We further find that ecological trait diversity of alien species is substantially more evenly spaced and more divergent than random samples from the pool of Red Sea species, pointing at additional processes, such as competition, promoting ecological diversity among alien species. We use these results to provide a first quantitative ranking of the potential of Red Sea species to become established in the eastern Mediterranean. © 2012 Blackwell Publishing Ltd

Description: In this study, tundra N2O and CH4 fluxes were measured from one seabird sanctuary (SBT) and two non-seabird colonies (NST-I and NST-II) in Ny-Ålesund (79°55′N, 11°56′E), Svalbard during the summers of 2008 and 2009. N2O and CH4 fluxes from SBT showed large temporal and spatial variations depending on the intensity of seabird activity. High seabird activity sites showed large N2O and CH4 emissions while low N2O and CH4 emissions, even CH4 uptake occurred at medium and low seabird activity sites. Overall the mean fluxes were 18.3 ± 3.6 μg N2O m−2 h−1 and 53.5 ± 20.3 μg CH4 m−2 h−1 from tundra SBT whereas tundra NST-I and NST-II represented a relatively weak N2O source (8.3 ± 13.2 μg N2O m−2 h−1) and strong CH4 sink (−82.8 ± 22.3 μg CH4 m−2 h−1). Seabird activity was the strongest control of N2O and CH4 fluxes compared with soil temperature and moisture, and high N2O and CH4 emissions were created by soil physical and chemical processes (the sufficient supply of nutrients NH4+–N, NO3−–N, total nitrogen, total phosphorus and total carbon from seabird guano, seabird tramp and appropriate water content) related to the seabird activity. Our work suggests that tundra ecosystems impacted by seabird activity are the potential “hotspots” for N2O and CH4 emissions although these sources have been largely neglected at present. Furthermore the combination of seabird activity and warming climate will likely further enhance N2O and CH4 emissions from the High Arctic tundra.

Description: Ecological Applications, Volume 22, Issue 7, Page 2034, October 2012.

Description: Ecological Applications, Volume 22, Issue 7, Page 1865-1875, October 2012.

Description: Arctic organisms are adapted to the strong seasonality of environmental forcing. A small timing mismatch between biological processes and the environment could potentially have significant consequences for the entire food web. Climate warming causes shrinking ice coverage and earlier ice retreat in the Arctic, which is likely to change the timing of primary production. In this study, we test predictions on the interactions among sea ice phenology and production timing of ice algae and pelagic phytoplankton. We do so using 1) a synthesis of available satellite observation data; and 2) the application of a coupled ice-ocean ecosystem model. The data and model results suggest that, over a large portion of the Arctic marginal seas, the timing variability of ice retreat at a specific location has a strong impact on the timing variability of pelagic phytoplankton peaks but weak or no impact on the timing of ice-algae blooms in those regions. The model predicts latitudinal and regional differences in the timing of ice algae biomass peak (varying from April to May) and the time lags between ice algae and pelagic phytoplankton peaks (varying from 45 to 90 days). The correlation between the time lag and ice retreat is significant in areas where ice retreat has no significant impact on ice-algae peak timing, suggesting that changes in pelagic phytoplankton peak timing control the variability of time lags. Phenological variability of primary production is likely to have consequences for higher trophic levels, particularly for the zooplankton grazers, whose main food source is composed of the dually pulsed algae production of the Arctic. © 2012 Blackwell Publishing Ltd

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: Ecology, Volume 93, Issue 11, Page 2313-2320, November 2012.

Description: Osteocalcin (OC) is a non-collagenous, Vitamin K-dependent protein secreted in the late stage of osteoblasts differentiation. The presence of the three residues of γ-carbossiglutamatic acid, specific of the active form of OC protein, allows the protein to bind calcium and consequently hydroxyapatite. The osteoblastic OC protein is encoded by the bone γ-carbossiglutamate gene whose transcription is principally regulated by the Runx2/Cbfa1 regulatory element and stimulated by Vitamin D 3 through a steroid-responsive enhancer sequence. Even if data obtained in literature are controversial, the dual role of OC in bone can be presumed as follows: firstly, OC acts as a regulator of bone mineralization; secondly, OC regulates osteoblast and osteoclast activity. Recently the metabolic activity of OC, restricted to the un-carboxylated form has been demonstrated in osteoblast-specific knockout mice. This effect is mediated by the regulation of pancreatic β-cell proliferation and insulin secretion and adiponectin production by adipose tissue and leads to the regulation of glucose metabolism and fat mass. Nevertheless clinical human studies only demonstrated the correlation between OC levels and factors related to energy metabolism. Thus further investigations in humans are required to demonstrate the role of OC in the regulation of human energy metabolism. Moreover it is presumable that OC also acts on blood vessels by inducing angiogenesis and pathological mineralization. This review highlights the recent studies concerning skeletal and extra-skeletal effects of OC. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.

Description: Invasive ductal adenocarcinoma (IDA) of the pancreas manifests poor prognosis due to the early invasion and distant metastasis. In contrast, intraductal papillary mucinous adenoma or carcinoma (IPMA or IPMC) reveals better clinical outcomes. Various molecular mechanisms contribute to these differences but entire picture is still unclear. Recent researches emphasized the important role of miRNA in biological processes including cancer invasion and metastasis. We previously described that miR-126 is down-regulated in IDA compared with IPMA or IPMC, and miR-126 regulates the expression of invasion related molecule disintegrin and metalloproteinase domain-containing protein 9 (ADAM9). Assessing the difference of miRNA expression profiles of IDA, IPMA and IPMC, we newly identified miR-197 as an up-regulated miRNA specifically in IDA. Expression of miR-197 in pancreatic cancer cells resulted in the induction of epithelial-mesenchymal transition (EMT) along with the down-regulation of p120 catenin which is a putative target of miR-197. Direct interaction between miR-197 and p120 catenin mRNA sequence was confirmed by 3'UTR assay, and knockdown of p120 catenin recapitulated EMT induction in pancreatic cancer cells. In situ hybridization of miR-197 and immunohistochemistry of p120 catenin showed mutually exclusive patterns suggesting pivotal role of miR-197 in the regulation of p120 catenin. This miR-197 / p120 catenin axis could be a novel therapeutic target. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.

Description: Riparian groundwater can exhibit considerable patchiness in the concentration and reactivity of dissolved organic matter (DOM), which ultimately shapes subsurface biogeochemical transformations. Free and combined amino acids are bioavailable constituents of DOM, and their concentration and composition can provide valuable information about the diagenetic state of DOM. Based on riparian groundwater samples and relevant DOM end-member samples, we adapted the amino-acid-based marine DOM degradation index (DI) to groundwater. The groundwater DI was applied to evaluate the spatial and temporal variability in the bioavailability and diagenetic state of riparian DOM in a restored and a channelized section of the River Thur, Switzerland. Among different indicators for DOM diagenetic state (total hydrolysable amino acid concentrations, C-normalized yields, and the contribution of nonprotein amino acids), the groundwater DI correlated best with the activity of the enzyme leucine-aminopeptidase and bacterial secondary production in riparian groundwater. The “freshest” DOM was consistently found in the channel and during high-flow conditions in the groundwater of the restored riparian section and was spatially constrained to a zone inhabited by a dense willow population. The use of amino acid data and the newly developed DI for DOM in groundwater is a promising approach for characterizing the spatial and temporal dynamics of DOM reactivity and diagenesis within riparian groundwater.

Description: Objectives The study aims to determine the distribution of candidal species in the oral cavity and differentiate the candidal species based on PCR amplification including Hinf I and Msp I digestion in order to assess the effectiveness of using the rDNA region for species identification. Methods Samples from saliva as well as the palate, tongue and cheek mucosa surfaces were collected from 45 individuals consisting of three groups: periodontal disease patients, denture wearers, and the control group. The samples were serially diluted, spread on BHI and YPD agar plates and scored for Colony-Forming Units (CFUs). Fifteen random candidal colonies were isolated and subjected to genomic DNA extraction based on glass beads disruption. Four primers were used to amplify regions in the rDNA, and the ITSI-5.8S-ITSII PCR product was digested by Hinf I and Msp I restriction enzymes. Results The microbial loads on all the sites of denture wearers was found to be significantly higher than the control, while only the microbial loads on the tongue of the periodontal disease group was significantly higher than the control. Meanwhile, there was no significant difference at other sites. The restriction fragment lengths of the clinical samples were compared to that of seven control species, allowing the differentiation of all seven species and the identification of fourteen species from the clinical samples. The Msp I restriction digest was not able to distinguish between C. albicans and C. dubliniensis , whereas the Hinf I digest could not distinguish between C. tropicalis and C. parapsilosis . Conclusion PCR-RFLP of the candidal rDNA region has potential for species identification. Copyright © 2012 John Wiley & Sons, Ltd.

Description: The responses of soil methane (CH4) net fluxes to nitrogen (N) addition in a N-fixing tree species (Acacia auriculiformis (AA)) and a non-N-fixing tree species (Eucalyptus citriodora (EU)) plantation were studied in southern China. Treatments were conducted at each plantation with three N levels (0, 50, and 100 kg N ha−1 yr−1 for control, medium-N, and high-N treatment, respectively, abbreviated as C, MN, and HN). From August 2010 to July 2011, CH4 flux was measured biweekly using a static chamber and gas chromatography technique. The soils of both sites acted as sink of atmospheric CH4. The CH4 uptake rate in control of the AA site (36.3 ± 3.2 μg CH4-C m−2 h−1) was greater than that of the EU plantation (29.9 ± 0.9 μg CH4-C m−2 h−1). In the AA plantation, the averaged rates of CH4 uptake for the MN (28.6 ± 2.3 μg CH4-C m−2 h−1) and HN treatment (23.8 ± 2.8 μg CH4-C m−2 h−1) were decreased by 21% and 35%, respectively, compared to the control. However, there was no change of soil CH4 uptake between N-treated plots and the controls in the EU site. Our results indicated that there might be large difference of inhibitive effect of N deposition on soil CH4 oxidation between the AA and EU plantations. The projected increase of N deposition would weaken the capability of N-fixing tree species plantations for atmospheric CH4 sink in tropical and subtropical regions.

Description: Output from an earth system model is paired with a size-based food web model to investigate the effects of climate change on the abundance of large fish over the 21 st century. The earth system model, forced by the IPCC Special Report on Emission Scenario A2, combines a coupled climate model with a biogeochemical model including major nutrients, three phytoplankton functional groups, and zooplankton grazing. The size-based food web model includes linkages between two size-structured pelagic communities: primary producers and consumers. Our investigation focuses on seven sites in the North Pacific, each highlighting a specific aspect of projected climate change, and includes top-down ecosystem depletion through fishing. We project declines in large fish abundance ranging from 0 to 75.8% in the central North Pacific and increases of up to 43.0% in the California Current region over the 21 st century in response to change in phytoplankton size structure and direct physiological effects. We find that fish abundance is especially sensitive to projected changes in large phytoplankton density and our model projects changes in the abundance of large fish being of the same order of magnitude as changes in the abundance of large phytoplankton. Thus, studies that address only climate-induced impacts to primary production without including changes to phytoplankton size structure may not adequately project ecosystem responses. © 2012 Blackwell Publishing Ltd

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: DNA replication and transcription have structural and temporal organization within the cell nucleus [Spector et al., 1993; Berezney 2002; Stein et al., 2003; Berezney et al., 2005; Cremer et al., 2006; Zaidi et al., 2007; Misteli, 2007; Lanctôt et al., 2007; Stein et al., 2008; Malyavantham et al., 2008a; Malyavantham et al. 2008b; Malyvantham et al., 2010]. Regions within the nucleus are zoned for either transcription or replication during the S phase of the cell cycle [Wei et al., 1998; Berezney, 2002; Malyavantham et al., 2008b]. Moreover these regions within the genome are temporally organized so that genes which are highly active in transcription predominantly replicate earlier than those which are not [Schübeler et al., 2002; White et al., 2004; Woodfine et al., 2004]. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: MicroRNA (miRNA) is a family of small, non-coding RNA first discovered as an important regulator of development in Caenorhabditis elegans ( C. elegans ). Numerous miRNAs have been found in C. elegans , and some of them are well conserved in many organisms. Though, the biologic function of miRNAs in C. elegans was largely unknown, more and more studies support the idea that miRNA is an important molecular for C. elegans . In this review, we revisit the research progress of miRNAs in C. elegans related with development, aging, cancer and neurodegenerative diseases and compared the function of miRNAs between C. elegans and human. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: The transcription factor Runx1 has been studied in leukemia and blood for decades, but recently it has been also implicated in epithelial biology and pathology. Particularly in mouse skin Runx1 modulates Wnt signaling levels thereby regulating timely induction of hair follicle specification, proper maturation of the emerging adult hair follicle stem cells in embryogenesis, and timely stem cell (SC) activation during adult homeostasis. Moreover, Runx1 acts as a tumor promoter in mouse skin squamous tumor formation and maintenance, likely by repressing p21 and promoting Stat3 activation. Similarly, Runx1 is essential for oral epithelium tumorigenesis mediated in mice by Ras, and for growth of three kinds of human epithelial cancer cells. In contrast, Runx1 has a tumor suppressor function in the mouse intestine and shows tumor subtype specific behavior in human breast cancer. Multiple studies revealed Runx1 SNPs to be associated with human cancers and autoimmune disease. With this information as background, the field is poised for functional and mechanistic studies to elucidate the role of Runx1 in formation and/or progression of epithelial-based human disease. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: The identification and purification of murine multipotent mesenchymal stem cells (MSCs) have been difficult due to their low frequency, the presence of contaminating cell types and lack of unambiguous markers. Using a magnetic micro-beads negative selection technique to remove hematopoietic cells from mouse bone marrow stromal cells (BMSCs), our lab recently isolated a highly purified osteoprogenitor (HipOP) population that was also enriched for other mesenchymal precursors, including MSCs [Itoh and Aubin, 2009]. We now report that HipOPs are also highly enriched in vascular endothelial cells (VECs), which we hypothesized were an accessory cell type regulating osteogenesis. However, when VECs were immunodepleted from HipOPs with anti-CD31 antibodies, the resulting CD31(-) HipOP population had equal osteogenic capacity to the HipOPs in vitro and in vivo . Analysis of gene expression of Ncad , Pth1r , Ang1 , Cxcl12 , Jag1 , Pdgfr-β , α-sma , Desmin and Ng2 suggested that both HipOPs and CD31(-) HipOPs are hemopoietic stem cell (HSC) niche populations. However, the data support the view that osteoblast differentiation and depletion of VECs modulate the HSC niche. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: The extensive applications of cerium (Ce) increased the chance of human exposure to Ce and its compounds. It was reported that Ce was mainly deposited in the bone after administration. However, the potential effect and mechanism of Ce on bone metabolism are not well-understood. In this study, we investigated the cellular effects of Ce on the differentiation of mesenchymal stem cells (MSCs) and the associated molecular mechanisms. The results indicated that Ce promoted the osteogenic differentiation and inhibited the adipogenic differentiation of MSCs at cell level. Genes involved in transforming growth factor- β /bone morphogenetic proteins (TGF- β /BMP) signaling pathway were significantly changed when the MSCs were exposed to 0.0001 µM Ce by RT 2 Profiler™ PCR Array analysis. The expression of genes and proteins related to pathways, osteogenic and adipogenic biomarkers of MSCs upon interaction with Ce was further confirmed by quantitative real-time reverse transcriptase polymerase chain reaction (Q-PCR) and western blot analysis. The results suggest that Ce exerts the effects by interacting with bone morphogenetic protein receptor (BMPR) and activates TGF- β /BMP signaling pathway, leads to the up-regulation of the osteogenic master transcription factor, runt-related transcription factor 2 (Runx 2), and the down-regulation of the adipocytic master transcription factor, peroxisome proliferator-activated receptor gamma 2 (PPARγ2). Runx2, which subsequently up-regulates osteoblast (OB) marker genes collagen I (Col I) and BMP2 at early stages, alkaline phosphatase (ALP) and osteocalcin (OCN) at later stages of differentiation, thus driving MSCs to differentiate into OBs. The results provide novel evidence to elucidate the mechanisms of bone metabolism by Ce. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: This study investigated the molecular mechanisms of liver cells with HBx expression on epithelium–mesenchymal transition (EMT) change using Western blot analysis and Transwell assay to assess EMT-related protein expression and cell mobility. Luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to test the Twist promoter containing different STAT3 binding loci. Electrophoretic mobility band-shift assay (EMSA) was used to detect Twist activity. Results showed that HBx expression affected the EMT-related protein expression and the cell mobility of liver cancer cells (MHCC97) and liver cells (HL-7702) in vitro or in vivo . These proteins exhibited reversed expression to a certain extent after Twist inhibition. In addition, the wound-healing capability and the mobility of HL-7702/HBx cells were lower than those treated with control-siRNA. The expressions of p-STAT3 and Twist were positively correlated with HBx expression. The second STAT-3 binding sequence in the Twist promoter region of the HL-7702/HBx cells was the first locus. Twist activity in the HL-7702/HBx2 cells was higher than that in HL-7702 cells. Moreover, the activity decreased when the cells were treated with HBx-siRNA to inhibit HBx expression, or with STAT3 inhibitor to reduce STAT3 activation. Therefore, Twist is essential for the regulation of the mobility of liver cells with HBx expression. HBx activates the Twist promoter by activating STAT3 and promotes EMT occurrence in liver cells. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: CXCL14 is a chemokine family member that is involved in various cellular responses in addition to immune cell activation. Although constitutive CXCL14 expression in normal epithelial cells may help protect against infection by activating immune systems, its expression in cancer cells has raised controversy regarding its possible role in tumorigenesis. However, the underlying mechanisms for this disparity remain unknown. Investigation of cellular CXCL14 binding properties might increase our understanding of the peptide's roles in tumorigenesis. In the present study, we found that CXCL14 binds to various cell types. Interestingly, binding to NCI-H460 cells was prevented by heparan sulfate and N-acetyl neuraminic acid. Next, we examined effect of CXCL14 binding in NCI-H460 and NCI-H23. CXCL14 enhanced proliferation and migration in NCI-H460 but had no effect on NCI-H23. A reporter gene assay with various transcription factor response elements revealed that only nuclear factor-κB (NF-κB) signaling was activated by CXCL14 in NCI-H460 cells, which was blocked by BAPTA-AM, TCPA, and brefeldin A. Exogenous expression of some glycoproteins such as syndecan-4, podoplanin, and CD43 in these cells enhanced CXCL14 binding and NF-κB activity. Collectively, these results demonstrate that CXCL14 binding to glycoproteins harboring heparan sulfate proteoglycans and sialic acids leads proliferation and migration of some cancer cells. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: Bone loss is a well documented phenomenon occurring in humans both in short and in long term spaceflights. This phenomenon can be also reproduced on the ground in human and animals and also modeled in cell-based analogs. Since space flights are infrequent and expensive to study the biomedical effects of microgravity on the human body, much of the known pathology of bone loss comes from experimental studies. The most commonly used in vitro simulators of microgravity are clinostats while in vivo simulators include the bed rest studies in humans and hindlimb unloading experiments in animals. Despite the numerous reports that have documented bone loss in wide ranges in multiple crew members, the pathology remains a key concern and development of effective countermeasures is still a major task. Thus far, the offered modalities did not show much success in preventing or alleviating bone loss in astronauts and cosmonauts. The objective of this review is to capture the most recent research on bone loss from spaceflights, bed rest and hindlimb unloading, as well as from in vitro studies utilizing cellular models in clinostats. Additionally, this review offers projections on where the research has to focus to ensure the most rapid development of effective countermeasures. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: Facing climate change (CC), species are prone to multiple modifications of their environment that can lead to extinction, migration or adaptation. Identifying the role and interplay of different potential stressors becomes a key question. Anadromous fishes will be exposed to both river and oceanic habitat changes. For Atlantic salmon, the river water temperature, river flow and oceanic growth conditions appear as three main stressing factors. They could act on population dynamics or as selective forces on life-history pathways. Using an individual-based demo-genetic model, we assessed the effects of these factors 1) to compare risks of extinction resulting from CC in river and ocean, 2) to assess CC effects on life-history pathways including the evolution of underlying genetic control of phenotypic plasticity. We focused on Atlantic salmon populations from Southern Europe for a time horizon of three decades. We showed that CC in river alone should not lead to extinction of Southern European salmon populations. In contrast, the reduced oceanic growth appeared as a significant threat for population persistence. An increase in river flow amplitude increased the risk of local extinction in synergy with the oceanic effects, but river temperature rise reduced this risk. In terms of life-history modifications, the reduced oceanic growth increased the age of return of individuals through plastic and genetic responses. The river temperature rise increased the proportion of sexually mature parr, but the genetic evolution of the maturation threshold lowered the maturation rate of male parr. This was identified as a case of environmentally driven plastic response that masked an underlying evolutionary response of plasticity going in the opposite direction. We concluded that to counteract oceanic effects, river flow management represented the sole potential force to reduce the extinction probability of Atlantic salmon populations in Southern Europe, although this might not impede changes in migration life-history. © 2012 Blackwell Publishing Ltd

Description: Evasion of gaseous carbon (C) from streams is often poorly quantified in landscape C budgets. Even though the potential importance of the capillary network of streams as C conduits across the land-water-atmosphere interfaces is sometimes mentioned, low-order streams are often left out of budget estimates due to being poorly characterized in terms of gas exchange and even areal surface coverage. We show that evasion of C is greater than all the total dissolved C (both organic and inorganic) exported downstream in the waters of a boreal landscape. In this study evasion of carbon dioxide (CO 2 ) from running waters within a 67 km 2 boreal catchment was studied. During a four year period (2006-2009) 13 streams were sampled on 104 different occasions for dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC). From a locally determined model of gas exchange properties, we estimated the daily CO 2 evasion with a high-resolution (5×5 m) grid based stream evasion model comprising the entire ~100 km stream network. Despite the low areal coverage of stream surface the evasion of CO 2 from the stream network constituted 53% (5.0 (±1.8) g C m −2 yr −1 ) of the entire stream C flux (9.6 (±2.4) g C m −2 yr −1 ) (lateral as DIC, DOC and vertical as CO 2 ). In addition, 72% of the total CO 2 loss took place already in the 1 st and 2 nd order streams. This study demonstrates the importance of including CO 2 evasion from low-order boreal streams into landscape C budgets since it more than doubled the magnitude of the aquatic conduit for C from this landscape. Neglecting this term will consequently result in an overestimation of the terrestrial C sink strength in the boreal landscape. © 2012 Blackwell Publishing Ltd

Description: Climate change is expected to impact the amount and distribution of precipitation in the arid southwestern U.S. In addition, nitrogen (N) deposition is increasing in these regions due to increased urbanization. Responses of belowground plant activity to increases in soil water content and N have shown inconsistent patterns between biomes. In arid lands, plant productivity is limited by water and N availability so it is expected that changes in these factors will affect fine root dynamics. The objectives of this study were to quantify the effects of increased summer precipitation and N deposition on fine root dynamics in a Mojave Desert ecosystem during a two-year field experiment using minirhizotron measurements. Root length density, production, and mortality were measured in field plots in the Mojave Desert receiving three 25 mm summer rain events and/or 40 kg N ha -1 yr -1 . Increased summer precipitation and N additions did not have an overall significant effect on any of the measured root parameters. However, differences in winter precipitation resulting from interannual variability in rainfall appeared to affect root parameters with root production and turnover increasing following a wet winter most likely due to stimulation of annual grasses. In addition, roots were distributed more deeply in the soil following the wet winter. Root length density was initially higher under canopies compared to canopy interspaces but converged towards the end of the study. In addition, roots tended to be distributed more deeply into the soil in canopy interspace areas. Results from this study indicated that increased summer precipitation and N deposition in response to climate change and urbanization are not likely to affect fine root dynamics in these Mojave Desert ecosystems, despite studies showing aboveground plant physiological responses to these environmental perturbations. However, changes in the amount and possibly distribution of winter precipitation may affect fine root dynamics. © 2012 Blackwell Publishing Ltd

Description: In a global change context, the intensity and the frequency of drastic low flow periods or drought events will most likely increase to a substantial extent over the coming decades, leading to a modification of the abiotic characteristics of wetlands. This change in environmental parameters may induce severe shifts in plant and animal communities and the functioning of ecosystems. In this study, we experimentally estimated the effect of drought and the accumulation of ammonia (NH 3 ) on the feeding activities of three generalist macroinvertebrates (i.e., Gammarus pulex , Gammarus roeselii and Asellus aquaticus ) on three types of organic matter: leaves of Berula erecta growing in submerged conditions, leaves of the same species growing in emerged conditions, and dead leaves of Alnus glutinosa . We observed a modification of the biomechanical and stoichiometric characteristics of the plants as a result of the emersion of the aquatic plants. This shift produced a substantial decrease in organic matter recycling by invertebrates and in their associated physiological ability (i.e., the energy stores of the animals) to face conditions associated with environmental change. Moreover, the accumulation of NH 3 amplified the negative effect of emersion. This snowball effect on invertebrates may profoundly modify the functioning of ecosystems, particularly in terms of organic matter production/degradation and carbon mineralisation. © 2012 Blackwell Publishing Ltd

Description: The occurrence of summer heat waves is predicted to increase in amplitude and frequency in the near future, but the consequences of such extreme events are largely unknown, especially for belowground organisms. Soil organisms usually exhibit strong vertical stratification, resulting in more frequent exposure to extreme temperatures for surface-dwelling species than for soil-dwelling species. Therefore soil-dwelling species are expected to have poor acclimation responses to cope with temperature changes. We used five species of surface-dwelling and four species of soil-dwelling Collembola that habituate different depths in the soil. We tested for differences in tolerance to extreme temperatures after acclimation to warm and cold conditions. We also tested for differences in acclimation of the underlying physiology by looking at changes in membrane lipid composition. Chill coma recovery time, heat knockdown time, and fatty acid profiles were determined after one week of acclimation to either 5°C or 20°C. Our results showed that surface-dwelling Collembola better maintained increased heat tolerance across acclimation temperatures, but no such response was found for cold tolerance. Concordantly, four of the five surface-dwelling Collembola showed up to 4-fold changes in relative abundance of fatty acids after one week of acclimation, whereas none of the soil-dwelling species showed a significant adjustment in fatty acid composition. Strong physiological responses to temperature fluctuations may have become redundant in soil-dwelling species due to the relative thermal stability of their subterranean habitat. Based on the results of the four species studied, we expect that unless soil-dwelling species can temporarily retreat to avoid extreme temperatures, the predicted increase in heat waves under climatic change renders these soil-dwelling species more vulnerable to extinction than species with better physiological capabilities. Being able to act under a larger thermal range is probably costly and could reduce maximum performance at the optimal temperature. © 2012 Blackwell Publishing Ltd

Description: More than 50% of the word's population feeds on rice. Soils used for rice production are mostly managed under submerged conditions (paddy soils). This management, which favors carbon sequestration, potentially decouples surface from subsurface carbon cycling. The objective of this study was to elucidate the long-term rates of carbon accrual in surface and subsurface soil horizons relative to that of soils under non-paddy management. We assessed changes in total soil organic as well as of inorganic carbon stocks along a 2000-year chronosequence of soils under paddy and adjacent non-paddy management in the Yangtze delta, China. The initial organic carbon accumulation phase lasts much longer and is more intensive than previously assumed, e.g., by the Intergovernmental Panel on Climate Change (IPCC). Paddy topsoils accumulated 170–178 kg organic carbon ha –1 a –1 in the first 300 years; subsoils lost 29–84 kg organic carbon ha –1 a –1 during this period of time. Subsoil carbon losses were largest during the first 50 years after land embankment and again large beyond 700 years of cultivation, due to inorganic carbonate weathering and the lack of organic carbon replenishment. Carbon losses in subsoils may therefore offset soil carbon gains or losses in the surface soils. We strongly recommend including subsoils into global carbon accounting schemes, particularly for paddy fields. © 2012 Blackwell Publishing Ltd

Description: Understanding spring phenology changes in response to the rapid climate change at biome-level is crucial for projecting regional ecosystem carbon exchange and climate–biosphere interactions. In this study, we assessed the long–term changes and responses to changing climate of the spring phenology in six temperate biomes of China by analyzing the GIMMS NOAA/AVHRR Normalized Difference Vegetation Index (NDVI) and concurrent mean temperature and precipitation data for 1982–2006. Results show that the spring phenology trends in the six temperate biomes are not continuous throughout the 25-year period. The spring phenology in most areas of the six biomes showed obvious advancing trends (ranging from -0.09 to -0.65 day year -1 ) during the 1980s and early 1990s, but has subsequently suffered consistently delaying trends (ranging from 0.22 to 1.22 day year –1 ). Changes in spring (February–April) temperature are the dominating factor governing the pattern of spring vegetation phenology in the temperate biomes of China. The recently delayed spring phenology in these temperate biomes has been mainly triggered by the stalling or reversal of the warming trend in spring temperatures. Results in this study also reveal that precipitation during November–January can explain 16.1% ( p 〈 0.05), 20.9% ( p 〈 0.05) and 14.2% ( p 〈 0.05) of the variations in temperate deciduous forest, temperate steppe and temperate desert, respectively, highlighting the important role of winter precipitation in regulating changes in the spring vegetation phenology of water–limited biomes. © 2012 Blackwell Publishing Ltd

Description: Question Recent studies revealed by indirect evidence that lichen–spruce woodlands in the closed-crown boreal forest are an alternative stable state of black spruce–feathermoss stands. This paper aims to demonstrate and quantify black spruce forest cover regression following successive wildfire events in the closed-crown forest zone during the 20th century. A case study in north-eastern North American closed-crown forest zone is presented. Location The study area is at the centre of the closed-crown boreal forest zone of eastern Canada (49°59′ N, 71°59′ W). Methods A burned area of 25 ha was selected in which three tree cohorts were visible. The first cohort contains partly buried trunks and stumps of a stand destroyed by a forest fire in 1920, the second contains standing dead trees from a 1995 forest fire and the third contains seedlings established after the 1995 fire. Fires were dated by scar analyses of living trees at the edge of the site. An array of sample plots was established in autumn 1997 to evaluate each cohort in terms of stocking and tree density. Results Black spruce stocking decreased significantly between cohorts, from 43.5% in Cohort 1 (all coniferous trees) to 25.6% in Cohort 2 and 11.5% in Cohort 3 (2011). Jack pine showed an inverse tendency, from 0% in Cohort 1 (not determined) to 0% in Cohort 2 and 3.8% in Cohort 3. Black spruce stems per hectare also dropped significantly from a minimum of 1322 in Cohort 1 to 1088 in Cohort 2 and 976 in Cohort 3. Conclusions This study is the first quantitative demonstration that lichen–spruce woodlands in the closed-crown boreal forest zone are an alternative stable state of black spruce–feathermoss stands. Stocking levels and densities markedly declined after each of the two fires (1920 and 1995) that both occurred after spruce budworm outbreaks (1910 and 1980) and are most likely responsible for the shift from a closed-crown to an open woodland. This paper presents a case study of a natural shift of vegetation communities after compounded disturbances in the closed-crown boreal forest. Due to a combination of short fire interval and insect outbreak, resilience of the spruce forest decreased over the last century. Our case study showed that the transformation of a closed forest into open woodland was fast and naturally irreversible.

Description: Questions What is the spatial range of regeneration of the fleshy-fruited tree Sorbus aucuparia (rowan) in a coarse-grained spruce stand on a large landscape scale? Does the spatial distribution and size of stands of different ages affect the probability of rowan regeneration? What are the consequences of the dynamics of dominant coniferous tree species for the dynamics of admixture rowan? Location A sub-alpine spruce forest in the Tatra Mountains, Poland. Methods We mapped all mature rowans in a 203-ha area and counted the rowan seedlings and saplings on a grid of evenly distributed plots. In plots, the age and diameter of trees were measured. Patches of homogenous stands were distinguished and each rowan tree and each plot was assigned to one of four stand categories: dense small-crowned stands, dense large-crowned stands, sparse large-crowned stands and sparse stands near the upper forest limit. Areas above the upper forest limit formed a separate fifth category. Results The distribution of rowan trees was clumped. Most of them grew in dense spruce stands up to 135 yr old and near the upper forest limit. Substantially fewer rowan trees were in sparse spruce stands of nearly 200 yr old. Seedlings and saplings occurred at high density (mean 24.8 individuals 100 m −2 ) only up to 40 m from trees bearing fruits, and at much lower density at longer distances. In consequence of the clumped distribution of adult trees and the short range of seed dispersal, most of the old spruce stands were outside the range of abundant regeneration of rowan. Conclusions The presence of fine- vs coarse-grained mosaics of coniferous stands of different ages can strongly influence population processes in a rowan population on a large landscape scale. Extensive disturbances resulting in large homogenous patches of coniferous stands, the long lifespan of a single generation of spruce and spatial limitation of rowan seed dispersal seem responsible for the small contribution this broad-leaved species makes to sub-alpine forests. A high share of rowan can be expected in forests with fine-grained mosaics of stands, where small patches of young and old stands are inter-mixed, assuring delivery of seeds to stands of each category. Density of rowan seedlings and saplings (mean ± SD) in plots at different distances fromthe nearest rowan tree. In a subalpine forest the distribution of rowan trees was clumped. Most of them grew in young dense spruce stands. Seedlings occurred at high density up to 40 m from rowan trees. In consequence of the clumped distribution of trees and the range of seed dispersal, most of the old spruce stands were outside the range of abundant rowan regeneration.

Description: While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact of modern technologies is influenced not only by further hard- and software developments, but also by the availability and suitability of protein-engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. Fluorescence technologies provide key to study molecular structure and dynamics with super spatial and temporal resolution. We discuss how synergistic developments of novel labeling technologies combined with optical engineering can make the biggest contribution to advance state of the art tools for both, in vitro and non-invasive in vivo measurements.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: Low spring temperatures have been found to benefit mobile herbivores by reducing the rate of spring-flush, while high rainfall increases forage availability. Cold winters prove detrimental, by increasing herbivore thermoregulatory burdens. Here we examine the effects of temperature and rainfall variability on a temperate sedentary herbivore, the Eurasian beaver, Castor fiber , in terms of inter-annual variation in mean body weight and per territory offspring production. Data pertain to 198 individuals, over 11 years, using capture-mark-recapture. We use plant growth (tree-cores) and fAPAR (a satellite-derived plant productivity index) to examine potential mechanisms through which weather conditions affect the availability and the seasonal phenology of beaver forage. Juvenile body weights were lighter after colder winters, while warmer spring temperatures were associated with lighter adult body weights, mediated by enhanced green-up phenology rates. Counter-intuitively, we observed a negative association between rainfall and body weight in juveniles and adults, and also with reproductive success. Alder, Alnus incana , (n=68) growth rings (principal beaver food in the study area) exhibited a positive relationship with rainfall for trees growing at elevations 〉2m above water level, but a negative relationship for trees growing 〈0.5m. We deduce that temperature influences beavers at the landscape scale via effects on spring green-up phenology and winter thermoregulation. Rainfall influences beavers at finer spatial scales, through topographical interactions with plant growth, where trees near water level, prone to water-logging, producing poorer forage in wetter years. Unlike most other herbivores, beavers are an obligate aquatic species that utilize a restricted ‘central-place’ foraging range, limiting their ability to take advantage of better forage growth further from water during wetter years. With respect to anthropogenic climate change, interactions between weather variables, plant phenology and topography on forage growth are instructive, and consequently warrant examination when developing conservation management strategies for populations of medium to large herbivores. © 2012 Blackwell Publishing Ltd

Description: This study explores effects of climate change and fuel management on unplanned fire activity in ecosystems representing contrasting extremes of the moisture availability spectrum (mesic and arid). Simulation modelling examined unplanned fire activity (fire incidence and area burned, and the area burned by large fires) for alternate climate scenarios and prescribed burning levels in: (i) a cool, moist temperate forest and wet moorland ecosystem in south-west Tasmania (mesic); and (ii) a spinifex and mulga ecosystem in central Australia (arid). Contemporary fire activity in these case study systems is limited respectively by fuel availability and fuel amount. For future climates, unplanned fire incidence and area burned increased in the mesic landscape, but decreased in the arid landscape in accordance with predictions based on these limiting factors. Area burned by large fires (greater than the 95 th percentile of historical, unplanned fire size) increased with future climates in the mesic landscape. Simulated prescribed burning was more effective in reducing unplanned fire activity in the mesic landscape. However, the inhibitory effects of prescribed burning are predicted to be outweighed by climate change in the mesic landscape, whereas in the arid landscape prescribed burning reinforced a predicted decline in fire under climate change. The potentially contrasting direction of future changes to fire will have fundamentally different consequences for biodiversity in these contrasting ecosystems, and these will need to be accommodated through contrasting, innovative management solutions. © 2012 Blackwell Publishing Ltd

Description: Although climate change is predicted to place mountain-top and other narrowly endemic species at severe risk of extinction, the ecological processes involved in such extinctions are still poorly resolved. In addition, much of this biodiversity loss will likely go unobserved, and therefore largely unappreciated. The Haleakalā silversword is restricted to a single volcano summit in Hawaiʻi, but is a highly charismatic giant rosette plant that is viewed by 1-2 million visitors annually. We link detailed local climate data to a lengthy demographic record, and combine both with a population-wide assessment of recent plant mortality and recruitment, to show that after decades of strong recovery following successful management, this iconic species has entered a period of substantial climate-associated decline. Mortality has been highest at the lower end of the distributional range, where most silverswords occur, and the strong association of annual population growth rates with patterns of precipitation suggests an increasing frequency of lethal water stress. Local climate data confirm trends towards warmer and drier conditions on the mountain, and signify a bleak outlook for silverswords if these trends continue. The silversword example foreshadows trouble for diversity in other biological hotspots, and illustrates how even well-protected and relatively abundant species may succumb to climate-induced stresses. © 2012 Blackwell Publishing Ltd

Description: The currently observed Arctic warming will increase permafrost degradation followed by mineralization of formerly frozen organic matter to carbon dioxide (CO 2 ) and methane (CH 4 ). Despite increasing awareness of permafrost carbon vulnerability the potential long-term formation of trace gases from thawing permafrost remains unclear. The objective of the current study is to quantify the potential long-term release of trace gases from permafrost organic matter. Therefore, Holocene and Pleistocene permafrost deposits were sampled in the Lena River Delta, Northeast Siberia. The sampled permafrost contained between 0.6 and 12.4% organic carbon. CO 2 and CH 4 production was measured for 1200 days in aerobic and anaerobic incubations at 4°C. The derived fluxes were used to estimate parameters of a two pool carbon degradation model. Total CO 2 production was similar in Holocene permafrost (1.3 ± 0.8 mg CO 2 -C gdw −1 aerobically, 0.25 ± 0.13 mg CO 2 -C gdw −1 anaerobically) as in 34,000 to 42,000 year old Pleistocene permafrost (1.6 ± 1.2 mg CO 2 -C gdw −1 aerobically, 0.26 ± 0.10 mg CO 2 -C gdw −1 anaerobically). The main predictor for carbon mineralization was the content of organic matter. Anaerobic conditions strongly reduced carbon mineralization since only 25% of aerobically mineralized carbon was released as CO 2 and CH 4 in the absence of oxygen. CH 4 production was low or absent in most of the Pleistocene permafrost and always started after a significant delay. After 1200 days on average 3.1% of initial carbon was mineralized to CO 2 under aerobic conditions while without oxygen 0.55% were released as CO 2 and 0.28% as CH 4 . The calibrated carbon degradation model predicted cumulative CO 2 production over a period of 100 years accounting for 15.1% (aerobic) and 1.8% (anaerobic) of initial organic carbon, which is significantly less than recent estimates. The multi-year time series from the incubation experiments helps to more reliably constrain projections of future trace gas fluxes from thawing permafrost landscapes. © 2012 Blackwell Publishing Ltd

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: Meeting the projected 50% increase in global grain demand by 2030 without further environmental degradation poses a major challenge for agricultural production. Because surface ozone (O 3 ) has a significant negative impact on crop yields, one way to increase future production is to reduce O 3 -induced agricultural losses. We present two strategies whereby O 3 damage to crops may be reduced. We first examine the potential benefits of an O 3 mitigation strategy motivated by climate change goals: gradual emission reductions of methane (CH 4 ), an important greenhouse gas and tropospheric O 3 precursor that has not yet been targeted for O 3 pollution abatement. Our second strategy focuses on adapting crops to O 3 exposure by selecting cultivars with demonstrated O 3 resistance. We find that the CH 4 reductions considered would increase global production of soybean, maize and wheat by 23-102 Mt in 2030 – the equivalent of a ~2-8% increase in year 2000 production worth $3.5-15 billion worldwide (USD 2000 ), increasing the cost-effectiveness of this CH 4 mitigation policy. Choosing crop varieties with O 3 resistance (relative to median-sensitivity cultivars) could improve global agricultural production in 2030 by over 140 Mt, the equivalent of a 12% increase in 2000 production worth ~$22 billion. Benefits are dominated by improvements for wheat in South Asia, where O 3 -induced crop losses would otherwise be severe. Combining the two strategies generates benefits that are less than fully additive given the nature of O 3 effects on crops. Our results demonstrate the significant potential to sustainably improve global agricultural production by decreasing O 3 -induced reductions in crop yields. © 2012 Blackwell Publishing Ltd

Description: Pronuclear microinjection of bacterial artificial chromosomes (BACs)is the preferred way to generate transgenic mice because the transgene accurately recapitulates expression of the endogenous gene. However, the method is demanding and the integrity and copy number of the BAC transgene is difficult to control. Here we describe a simpler pronuclear injection method that relies on transpositionto introducefull-length BACs into the mouse genome. The bacterial backbone of a hPAX6-GFP reporter BAC was retrofitted with PiggyBac transposon inverted repeats(ITRs) andco-injectedwith PiggyBac transposase mRNA. Both the frequency of transgenic founders as well as intact, full-length, single copy integrations was increased.Transposition was determined by a rapid PCR screen for a transpositional signature and confirmation by splinkerette sequencing to show that the BACs were integrated as a single copy either in one or two different genomic sites. BAC transposons displayed improved functional accuracy over random integrants as evaluated by expression of the hPAX6-GFP reporter in embryonic neural tube and absence of ectopic expression. This method involves less work to achieve increased frequencies of both transgenesis and single copy, full-length integrations. These advantages are not only relevant to rodents but also for transgenesis in all systems. © 2012 Wiley-Liss, Inc.

Description: In several biomes, including croplands, wooded savannas, and tropical forests, many small fires occur each year that are well below the detection limit of the current generation of global burned area products derived from moderate resolution surface reflectance imagery. Although these fires often generate thermal anomalies that can be detected by satellites, their contributions to burned area and carbon fluxes have not been systematically quantified across different regions and continents. Here we developed a preliminary method for combining 1-km thermal anomalies (active fires) and 500 m burned area observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) to estimate the influence of these fires. In our approach, we calculated the number of active fires inside and outside of 500 m burn scars derived from reflectance data. We estimated small fire burned area by computing the difference normalized burn ratio (dNBR) for these two sets of active fires and then combining these observations with other information. In a final step, we used the Global Fire Emissions Database version 3 (GFED3) biogeochemical model to estimate the impact of these fires on biomass burning emissions. We found that the spatial distribution of active fires and 500 m burned areas were in close agreement in ecosystems that experience large fires, including savannas across southern Africa and Australia and boreal forests in North America and Eurasia. In other areas, however, we observed many active fires outside of burned area perimeters. Fire radiative power was lower for this class of active fires. Small fires substantially increased burned area in several continental-scale regions, including Equatorial Asia (157%), Central America (143%), and Southeast Asia (90%) during 2001–2010. Globally, accounting for small fires increased total burned area by approximately by 35%, from 345 Mha/yr to 464 Mha/yr. A formal quantification of uncertainties was not possible, but sensitivity analyses of key model parameters caused estimates of global burned area increases from small fires to vary between 24% and 54%. Biomass burning carbon emissions increased by 35% at a global scale when small fires were included in GFED3, from 1.9 Pg C/yr to 2.5 Pg C/yr. The contribution of tropical forest fires to year-to-year variability in carbon fluxes increased because small fires amplified emissions from Central America, South America and Southeast Asia—regions where drought stress and burned area varied considerably from year to year in response to El Nino-Southern Oscillation and other climate modes.

Description: To investigate the function of adaptor protein complex-1 (AP-1) in the silkworm, we characterized AP-1 in the silkworm by RNAi technique and co-localization methods. As a result, AP-1 was found to exist as cytosolic form and membrane-bound form distinguished by phosphate status, showing molecular mass difference. There was relatively more cytosolic form of AP-1 than its membrane-bound counterpart in the silkworm. However, AP-1 distributed predominantly as cytosolic form in BmN cells. Interruption of AP-1 expression via DsRNA was more efficient in BmN cells than in the insect larval, which led to a tendency to dissociation between subcellular organelles like the Golgi apparatus and the mitochondria. Environmental condition changes like relatively higher temperature and treatment with dimethyl sulfoxide can lead to expression variance of AP-1 both in mRNA and protein level. In BmN cells, both the heavy chain γ and light chain σ could clearly co-localize with AP-1 β, mostly forming pits in cytoplasm. Two isoforms of AP-1 σ corresponded to distinct subcellular distribution pattern, possibly due to C-terminal amino acids difference.

Description: Atmospheric deposition is one of the major sources of nutrients bringing trace metals to remote marine biota. In this study, total atmospheric deposition and crustal aerosol concentrations were monitored at Kerguelen Islands (49°18′S; 70°07′E) in the Southern Ocean during a short campaign in early 2005 and then continuously for about 2 years (2009–2010). Results show very low levels of atmospheric dust and trace metals concentrations but higher deposition fluxes than expected. The averaged total dust deposition flux as derived from Al deposition measurements is 659 μg m−2 d−1. Simultaneously measured Fe and Co deposition fluxes are respectively 29 μg m−2 d−1 (520 nmol m−2 d−1) and 0.014 μg m−2 d−1 (0.24 nmol m−2 d−1), giving typically crustal elemental ratios to Al of 0.54 and 2.6 10−4. Measured dust deposition is in relatively good agreement with those simulated by current atmospheric models, but suggest that previous indirect calculations from field experiments are too low by a factor of 20. Observations and model results show that dust is transported above the marine atmospheric boundary layer to Kerguelen Islands, and thus that surface concentrations are not representative of the total dust column. Indeed, using surface concentrations leads to very large computed wet scavenging ratios, and to the conclusion that it is not appropriate to derive deposition fluxes from surface concentrations at remote ocean sites.

Description: Land cover changes may affect climate and the energy balance of the Earth through their influence on the greenhouse gas composition of the atmosphere (biogeochemical effects) but also through shifts in the physical properties of the land surface (biophysical effects). We explored how the radiation budget changes following the replacement of temperate dry forests by crops in central semi-arid Argentina and quantified the biophysical radiative forcing of this transformation. For this purpose, we computed the albedo and surface temperature for a 7-year period (2003-2009) from MODIS imagery at 70 paired sites occupied by native forests and crops and calculated the radiation budget at the tropopause and surface levels using a columnar radiation model parameterized with satellite data. Mean annual black-sky albedo and diurnal surface temperature were 50% and 2.5ºC higher in croplands than in dry forests. These contrasts increased the outgoing shortwave energy flux at the top of the atmosphere in croplands by a quarter (58.4 vs. 45.9 W m -2 ) which, together with a slight increase in the outgoing longwave flux, yielded a net cooling of -14 W m -2 . This biophysical cooling effect would be equivalent to a reduction of atmospheric CO 2 of 22 Mg C ha -1 , which involves approximately a quarter to a half of the typical carbon emissions that accompany deforestation in these ecosystems. We showed that the replacement of dry forests by crops in central Argentina has strong biophysical effects on the energy budget which could counterbalance the biogeochemical effects of deforestation. Underestimating or ignoring these biophysical consequences of land use changes on climate will certainly curtail the effectiveness of many warming mitigation actions, particularly in semi-arid regions where high radiation load and smaller active carbon pools would increase the relative importance of biophysical forcing. © 2012 Blackwell Publishing Ltd

Description: Previous studies have shown a correspondence between the abundance of particular plant species and methane flux. Here we apply multivariate analyses, including a weighted averaging approach, to assess the suitability of vegetation composition as a predictor of methane flux. We developed a functional classification of the vegetation, in terms of a number of plant traits expected to influence methane production and transport, and compared this with a purely taxonomic classification at species-level and higher. We applied both weighted averaging and indirect and direct ordination approaches to six sites in the UK, and found good relationships between methane flux and vegetation composition (classified both taxonomically and functionally). Plant species and functional groups also showed meaningful responses to management and experimental treatments. In addition to the UK, we applied the functional group classification across different geographical regions (Canada and Netherlands) to assess the generality of the method. Again, the relationship appeared good at the site level, suggesting some general applicability of the functional classification. The method seems to have the potential for incorporation into large-scale (national) greenhouse gas accounting programmes (in relation to peatland condition/management) using vegetation mapping schemes. The results presented here strongly suggest that robust predictive models can be derived using plant species data (for use in national-scale studies). For trans-national-scale studies, where the taxonomic assemblage of vegetation differs widely between study sites, a functional classification of plant species data provide an appropriate basis for predictive models of methane flux. © 2012 Blackwell Publishing Ltd

Description: The Mackenzie River Delta is a lake-rich arctic floodplain that receives high inputs of dissolved organic matter (DOM) and suspended particulates from allochthonous and autochthonous sources, and may transfer carbon from dissolved to particulate phase via in situ formation of transparent exopolymer particles (TEP). TEP provides food for grazers, surfaces for bacteria, and increased potential for aggregation and sedimentation of organic matter. During open water 2006, we tracked TEP abundances in three Delta lakes representing gradients that include declining river-to-lake connection times, increasing levels of dissolved organic carbon (DOC), and declining chromophoric-DOM (CDOM). Unexpectedly, TEP abundances were highest immediately after the flood, when autochthonous autotrophic production was at a seasonal low and CDOM a seasonal high. Moreover, the lake with the strongest riverine influence and lowest levels of autochthonous autotrophic production had the highest mean TEP-carbon (TEP-C) concentrations among the lakes. The mean proportion of particulate organic carbon (POC) represented by TEP-C increased with increasing river connection time, and appears to represent a substantial proportion of POC in Mackenzie Delta Lakes. Unexpectedly, the TEP gradient was most strongly related to CDOM (river water source) rather than overall DOC. Variations in CDOM accounted for 53% of TEP-C variation among the lakes, indicating allochthonous matter was the most important source of TEP. DOC release from in situ macrophytes during periods of high photosynthesis may contribute to TEP formation in the lake with lowest riverine influence, but pH levels 〉9.5 driven by the high photosynthetic rates complicate the interpretation of results from this lake.

Description: TGFβ1 is very important in the synthesis and degradation of extra cellular matrix (ECM), and also in the mediation of human lung fibroblasts proliferation, and miR-29 plays an important role in this process. To explore the interactions of miR-29 family members and TGFβ1, the effects of transforming growth factor TGFβ1 on the expression of miR-29 and whether miR-29 is involved in pro-survival signaling pathways mediated by TGFβ1 were examined in human lung fibroblasts. Treatment of the human embryonic lung fibroblast cell line IMR90 with TGFβ1 caused a decrease expression of miR-29a/b/c by real-time PCR analysis. TGFβ1 stimulation increased cell proliferation, colony formation and upregulated expression of COL1A1; transfecting with miR-29a/b/c mimics reverse TGFβ1-induced phenotype changes in IMR90 cells. Western blot analyses showed that TGFβ1 treatment unchanged total protein expression levels of PI3K or AKT, but the expression levels of p-PI3K, p-AKT and COL1A1 were increased; and miR-19a/b/c mimics interfering blocked phosphorylation of PI3K or AKT and decreased expression of COL1A1 after TGFβ1 treatment. The results indicate that TGFβ1 beta uses the PI3k-Akt pathway in these embryonic fibroblasts and miR29 blocks this activation pathway. It indicates a novel biological function of the PI3K-Akt pathway in IMR90. Elevated expression of miR-29 may play an important role in the pathogenesis of diseases related to fibrogenic reactions in human lung fibroblasts. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: Ecological Applications, Volume 0, Issue 0, Ahead of Print.

Description: Ecology, Volume 0, Issue 0, Ahead of Print.

Description: RGS14 is a 60 kDa protein that contains a regulator of G protein signalling (RGS) domain near its N-terminus, a central region containing a pair of tandem Ras binding domains (RBD), and a GPSM (G protein signalling modulator) domain (a.k.a. Gi/o-Loco binding (GoLoco) motif) near its C-terminus. The RGS domain of RGS14 exhibits GTPase accelerating protein (GAP) activity toward Gαi/o proteins, while its GPSM domain acts as a guanine nucleotide dissociation inhibitor (GDI) on Gαi1 and Gαi3. In the current study, we investigate the contribution of different domains of RGS14 to its biochemical functions. Here we show that the full-length protein has a greater GTPase activating activity but a weaker inhibition of nucleotide dissociation relative to its isolated RGS and GPSM regions, respectively. Our data suggest that these differences may be attributable to an inter-domain interaction within RGS14 that promotes the activity of the RGS domain, but simultaneously inhibits the activity of the GPSM domain. The RBD region seems to play an essential role in this regulatory activity. Moreover, this region of RGS14 is also able to bind to members of the B/R4 subfamily of RGS proteins and enhance their effects on GPCR-activated Gi/o proteins. Overall, our results suggest a mechanism wherein the RBD region associates with the RGS domain region, producing an intramolecular interaction within RGS14 that enhances the GTPase activating function of its RGS domain while disfavoring the negative effect of its GPSM domain on nucleotide dissociation. J. Cell. Biochem. © 2012 Wiley Periodicals, Inc.

Description: We enthusiastically read the recent manuscript by Intapad et al. from the Catravas group in the August 227 issue of Journal of Cellular Physiology entitled “ Regulation of Asthmatic Airway Relaxation by Estrogen and Heat Shock Protein 90 ” [1]. The authors show impaired relaxation of murine tracheal rings sensitized with serum from human asthmatics to nitric oxide (NO) donors, and potentiation of such relaxation upon treatment with estradiol (E 2 ), or the ERa- or ERb-selective ligands PPT and DPN, respectively [1]. They conclude that estrogens can potentiate NO-mediated bronchodilation in normal and asthmatic airways. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.

Description: We investigated here the ecdysteroid titers and the expression of six genes coding for known enzymes of the ecdysteroid biosynthesis in the testes of last instar larvae of the pest cotton leafworm, Spodoptera littoralis. We showed that the timing of the ecdysteroid profile was the same in testes and in hemolymph, with a small peak at day 2 and a large one at day 4 after ecdysis. Ecdysone and 20-hydroxyecdysone (20E) were detected in both tissues. 20E was the major ecdysteroid in testes and in hemolymph from day 4. Interestingly, the gene expression of the steroidogenetic enzymes, Neverland, and the five cytochrome P450 enzymes encoded by the Halloween genes was confirmed in the testes, and varied during the instar. However, from the data obtained so far, we cannot conclude that the measured ecdysteroids in the testes result from the activity of the genes under study. Indeed, it is suggested that the ecdysone produced centrally in the prothoracic glands, could have been transformed into 20E in the testes, where Sl-shade is well expressed.

Description: New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. Regardless of recent findings that new genes are important for human brain functions, we highlight that new genes are still generally under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes based on functional and evolutionary genomics.

Description: Question Is a lowland grassland community with a lower amount of ambient precipitation and a high abundance of subdominant species more sensitive to altered rainfall input in comparison with mountain grassland with higher ambient precipitation and a low abundance of subdominant species? Location (1) Lowland Festuca grassland characterized by dry acidophilous vegetation, low mean annual precipitation and high species richness, and (2) mountain Nardus grassland with high mean annual precipitation and low species richness in the Eastern Czech Republic. Methods We conducted a manipulative experiment with rainout shelters and gravity irrigation systems. We simulated three levels of precipitation input (50%, 100% and 150%) and examined the treatment effects on above-ground net primary productivity (ANPP) of the main plant functional groups (grasses, forbs, legumes, shrubs and mosses) and on plant species composition over three consecutive years. Results Altered rainfall input had a significant effect on total live ANPP in the drier, lowland grassland community, while no pronounced effect was observed in the mountain grassland characterized by higher ambient precipitation. In the lowland grassland, changes in total ANPP resulted primarily from enhanced growth of subdominant non-N-fixing forbs in response to the direct effect of higher artificial rainfall input and an indirect effect of reduced competition with grasses in drier treatments. Conclusions Wetter, species-poor mountain grasslands will probably show smaller changes in response to expected climate changes in ANPP, species number and abundance than lowland grasslands, characterized by dry acidophilous vegetation, with higher species richness and higher abundance of subordinate species. We conducted a manipulative experiment for simulating of three levels of precipitation input (50%, 100% and 150%) in two seminatural grassland types. Wetter, species-poor mountain grasslands will probably show smaller changes to expected climate changes in ANPP, species number and abundance than lowland grasslands, characterized by dry acidophilous vegetation, with higher species richness and higher abundance of subordinate species.

Description: This study investigates whether the anti-metastasis effect of microRNA-139 (miR-139) on hepatocellular carcinoma (HCC) is mediated through regulating c-fos expression. The expression levels of miR-139 and c-fos in human HCC cell sublines with high (MHCC97H) and low (MHCC97L) spontaneous metastatic potentials were quantified using QPCR or Western blot. miR-139 mimics was transfected into MHCC97H cells to overexpress miR-139, and miR-139 inhibitor was transfected into MHCC97L cells to down-express miR-139. The effect of overexpression or down-expression of miR-139 on c-fos expression of MHCC97H and MHCC97L cells was evaluated using QPCR and Western blot. The 3′ untranslated region segments of FOS containing the miR-139 binding sites were amplified by PCR, and the luciferase activity in the transfected cells was assayed. In comparison with the expression level of miR-139 in MHCC97L cells, the expression level in MHCC97H cells was significantly decreased, whereas c-Fos was significantly up-regulated in MHCC97H. The overexpression of miR-139 significantly inhibited the expression of c-fos in MHCC97H cells, and the down-expression of miR-139 significantly promoted the expression of c-fos in MHCC97L cells. miR-139 suppressed the luciferase activity of the pGL-FOS by approximately 40% compared with the negative control. In vitro cell migration analysis demonstrated that depletion of c-fos or overexpression of miR-139 in MHCC97H cells reduced cell migration, whereas overexpression of c-fos or depletion of miR-139 in MHCC97L cells increased cell migration. Thus, we got the conclusion that miR-139 expression is down-regulated in human HCC cell sublines with high spontaneous metastatic potentials (MHCC97H). Derepression of c-Fos caused by miR-139 down-regulation contributes to the metastasis of HCC. Copyright © 2012 John Wiley & Sons, Ltd.

Description: Sources of methane (CH 4 ) become highly variable for countries undergoing a heightened period of development due to both human activity and climate change. An urgent need therefore exists to budget key sources of CH 4 , such as wetlands (rice paddies and natural wetlands) and lakes (including reservoirs and ponds), which are sensitive to these changes. For this study, references in relation to CH 4 emissions from rice paddies, natural wetlands, and lakes in China were first reviewed and then re-estimated based upon the review itself. Total emissions from the three CH 4 sources were 11.25 Tg CH 4 yr −1 (ranging from 7.98 to 15.16 Tg CH 4 yr −1 ). Among the emissions, 8.11 Tg CH 4 yr −1 (ranging from 5.20 to 11.36 Tg CH 4 yr −1 ) derived from rice paddies, 2.69 Tg CH 4 yr −1 (ranging from 2.46 to 3.20 Tg CH 4 yr −1 ) from naturalwetlands, and 0.46 Tg CH 4 yr −1 (ranging from 0.33 to 0.59 Tg CH 4 yr −1 ) from lakes (including reservoirs and ponds). Plentiful water and warm conditions, as well as it large rice paddy area make rice paddies in southeastern China the greatest overall source of CH 4 , accounting for approximately 55% of total paddy emissions. Natural wetland estimates were slightly higher than the other estimates owing to the higher CH 4 emissions recorded within Qinghai-Tibetan Plateau peatlands. Total CH 4 emissions from lakes were estimated for the first time by this study, with three quarters from the littoral zone and one quarter from lake surfaces. Rice paddies, natural wetlands, and lakes are not constant sources of CH 4 but decreasing ones influenced by anthropogenic activity and climate change. A new progress-based model used in conjunction with more observations through model-data fusion approach could help obtain better estimates and insights with regard to CH 4 emissions deriving from wetlands and lakes in China. © 2012 Blackwell Publishing Ltd

Description: To predict the long-term effects of climate change—global warming and changes in precipitation—on the diameter (radial) growth of jack pine ( Pinus banksiana Lamb.) and black spruce ( Picea mariana [Mill.] B.S.P.) trees in boreal Ontario, we modified an existing diameter growth model to include climate variables. Diameter chronologies of 927 jack pine and 1,173 black spruce trees, growing in the area from 47° N to 50° N and 80° W to 92° W, were used to develop diameter growth models in a non-linear mixed-effects approach. Our results showed that the variables long-term average of mean growing season temperature, precipitation during wettest quarter, and total precipitation during growing season were significant (alpha = 0.05) in explaining variation in diameter growth of the sample trees. Model results indicated that higher temperatures during the growing season would increase the diameter growth of jack pine trees, but decrease that of black spruce trees. More precipitation during the wettest quarter would favor the diameter growth of both species. On the other hand, a wetter growing season, which may decrease radiation inputs, increase nutrient leaching, and reduce the decomposition rate, would reduce the diameter growth of both species. Moreover, our results indicated that future (2041-2070) diameter growth rate may differ from current (1971-2000) growth rates for both species, with conditions being more favorable for jack pine than black spruce trees. Expected future changes in the growth rate of boreal trees needs to be considered in forest management decisions. We recommend that knowledge of climate–growth relationships, as represented by models, be combined with learning from adaptive management to reduce the risks and uncertainties associated with forest management decisions. © 2012 Blackwell Publishing Ltd

Description: Colorectal cancer is one of the leading causes of tumour-related deaths. In the present study, the chemopreventive effect of green tea on 1,2-dimethylhydrazine (DMH)-induced colon carcinogenesis was studied in male Wistar rats. The DMH group received subcutaneous injections of DMH (30 mg kg −1 body weight) once a week for 30 weeks, the normal group received the vehicle of DMH, and the DMH + green tea group received DMH simultaneously with 1% green tea as their sole source of drinking fluid throughout the experimental period. In the DMH group treated with green tea, significant reductions in gene overexpressions of colonic nuclear factor κB (NF-κB), tumour necrosis factor α, inducible nitric oxide synthase and cyclooxygenase 2, and NF-κB immunostaining indicates the anti-inflammatory effect of green tea in attenuating colon cancer. Moreover, the anti-angiogenic and anti-invasiveness effects of green tea were revealed as reductions of both vascular endothelial growth factor and matrix metalloproteinase-7 mRNA expression levels. These effects were confirmed by the significant reduction of serum tumour necrosis factor α, C-reactive protein levels, inhibition of tumour incidence, and nearly normal survival rate and colonic architecture. It can be concluded that green tea exerts a potent chemopreventive effect on colon carcinogenesis possibly due to the inhibition of NF-κB. Copyright © 2012 John Wiley & Sons, Ltd.

Description: The aim of this study was to investigate the effect of isocaloric intake from a high-fat diet (HFD) on insulin resistance and inflammation in rats. Male Wistar rats were fed on an HFD ( n  = 12) or control diet ( n  = 12) for 12 weeks. Subsequently, all animals were euthanized, and blood glucose, insulin, free fatty acids, C-reactive protein, lipid profile, cytokines and hepatic-enzyme activity were determined. Carcass chemical composition was also analyzed. During the first and the twelfth weeks of the experimental protocol, the oral glucose tolerance test and insulin tolerance test were performed and demonstrated insulin resistance ( P  〈 0.05) in the HFD group. Although food intake (g) was lower ( P  〈 0.05) in the HFD group compared with the control group, the concentration of total cholesterol, low-density lipoprotein, C-reactive protein and liver weight were all significantly higher. The kinase inhibitor of κB, c-Jun N-terminal kinase and protein kinase B expressions were determined in the liver and skeletal muscle. After an insulin stimulus, the HFD group demonstrated decreased ( P  = 0.05) hepatic protein kinase B expression, whereas the kinase inhibitor of κB phospho/total ratio was elevated in the HFD muscle ( P  = 0.02). In conclusion, the isocaloric intake from the HFD induced insulin resistance, associated with impaired insulin signalling in the liver and an inflammatory response in the muscle. Copyright © 2012 John Wiley & Sons, Ltd.