Influence of internal waves on primary production

Effects of vertical displacements by internal gravity wavesupon the depth distribution of horizontally averaged primaryproduction are considered. A previous analysis is extended (i)to make explicit the role of negative curvature of a P-versus-Icurve and (ii) to consider possible effects of photoadaptation.Curvature of P-versus-I is shown to yield a ‘crossoverdepth’ above which internal waves suppress mean productivityand below which internal waves enhance mean productivity. Becausecompensation depth is found to occur below crossover depth fortypical oceanic and coastal conditions, internal waves inducea deepening of the compensation depth.     

Internal waves, primary production and the compensation depth of marine phytoplankton

Internal waves increase the average light intensity experiencedby phytoplankton and augment the compensation depth below whichno net photosynthesis occurs. These effects may be quite largein eutrophic waters with moderate or high light attenuationcoefficients. Data on internal waves and light attenuation canbe used to correct standard estimates of (new) primary productionin the lower euphotic zone based on uptake rates of carbon ornitrogen isotopes.     

The significance of extracellular production and winter photosynthesis to estimates of primary production in a woodland stream community

Both winter photosynthesis and the release of extracellular DOC are commonly ignored in stream production studies. We examined these contributions in a second-order stream under a completely closed deciduous canopy. We estimate that in Sandy Run approximately 26% of the annual autochthonous particulate carbon is produced between December and March. Measured winter rates of photosynthesis were not significantly different than summertime rates. Contrary to implicit assumptions often made about stream primary productivity, winter production was as important as summer production. Highest rates of carbon assimilation, however, were measured in the spring and fall, and were significantly correlated with standing crops of stream algae as measured by chlorophyll concentration. The recovery of released DOC from stream algae indicated that this contribution was equivalent to 5% of the particulate contribution. Rates of DOC production were significantly correlated with rates of particulate production. We estimate that had winter photosynthesis and extracellular DOC production been ignored in Sandy Run, annual productivity would have been underestimated by about a third. This revised version was published online in July 2006 with corrections to the Cover Date.     

Impact of heat waves on mortality in Croatia

The aim of this work was to determine the criteria for heat loads associated with an increase in mortality in different climatic regions of Croatia. The relationship between heat stress and mortality was analysed for the period 1983–2008. The input series is excess mortality defined as the deviations of mortality from expected values determined by means of a Gaussian filter of 183 days. The assessment of the thermal environment was performed by means of physiologically equivalent temperature (PET). The curve depicting the relationship between mortality and temperature has a U shape, with increased mortality in both the cold and warm parts of the scale but more pronounced in the warm part. The threshold temperature for increased mortality was determined using a scatter plot and fitting data by means of moving average of mortality; the latter is defined as the temperature at which excess mortality becomes significant. The values are higher in the continental part of Croatia than at the coast due to the refreshing influence of the sea during the day. The same analysis on a monthly basis shows that at the beginning of the warm season increased mortality occurs at a lower temperature compared with later on in the summer, and the difference is up to 15 °C between August and April. The increase in mortality is highest during the first 3–5 days and after that it decreases and falls below the expected value. Long-lasting heat waves present an increased risk, but in very long heat waves the increase in mortality is reduced due to mortality displacement.     

Ice-covered Lake Onega: effects of radiation on convection and internal waves

The effects of river restoration on hydromorphological conditions and variability are often documented immediately following the restoration, but rarely properly monitored in the long term. This study assesses outcomes of 20 restoration projects undertaken across central and northern Europe for a comprehensive set of hydromorphological parameters, quantified at both larger and smaller spatial scales. For each project, we compared a restored river section to an upstream degraded section. Ten pairs of large projects were contrasted to ten similar but less extensive projects, to address the importance of restoration extent for the success of each project. Overall, river restoration increased habitat diversity through changes in channel morphology. Our results indicated that restoration particularly improved macro- and mesohabitat diversity, but had a limited effect on microhabitat conditions, including the diversity of substrates. We found no significant difference in effects between large and small restoration projects. Our results reveal the need to assess hydromorphological parameters which reflect processes occurring at different spatial scales, including indicators of larger-scale hydromorphological processes such as bank erosion, to monitor restoration effects effectively and accurately. Additionally, our results demonstrate the importance of developing terrestrial parameters, to assess the lateral dimension of river restoration.     

How internal waves influence the vertical distribution of zooplankton

1. We present data with a high spatio‐temporal resolution from a 72‐h field survey in Bautzen Reservoir (Saxony, Germany). The aims of this survey were to observe hydrophysical processes during a period of unstable stratification in spring and investigate the effect of wind‐induced internal waves on the vertical distribution of zooplankton. 2. Wind velocities up to 10 m s⁻¹ caused a strong downwelling event of warm water at the sampling site and led to the generation of internal waves with an amplitude of 4 m. 3. The zooplankton community, which was dominated by Daphnia galeata, inhabited epilimnetic waters. Downwelling enlarged the thickness of the epilimnetic layer and, hence, led to high zooplankton abundances down to relatively deep water strata indicating lateral transport of zooplankton. As a consequence, area‐specific zooplankton abundances increased considerably (max. fourfold) during downwelling. 4. We conclude that classical limnological field sampling, such as for monitoring purposes, can lead to severely biased estimates of zooplankton abundance due to the interfering effects of hydrophysical processes like internal waves. 5. Backscattering strengths measured by a simultaneously deployed Acoustic Doppler Current Profiler (600 kHz) were found to be correlated with estimated zooplankton abundances based on plankton samples.     

Influence of incubation conditions on bacterial production estimates in an estuarine system

This study aimed to assess the influence of incubation conditions in the determination of bacterial production (BP). In order to achieve that goal, experimental setups were performed in situ and in the laboratory under both dark and light conditions. To test spatial and seasonal variations and the different natural light exposure of microorganisms, sampling was performed in two distinct zones of the estuary Ria de Aveiro (Portugal), typifying the marine and brackish water zones of the estuarine system. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments was used to monitor possible alterations in bacterial community composition induced by the incubation conditions. The results showed that BP determined in situ conditions significantly differed from in the laboratory. In the marine zone, a defined pattern of variation was detected, with consistent higher values of BP in laboratory dark conditions. This trend was not present in the brackish water zone. The seasonal and spatial variability of BP observed in field incubations was related to the physical–chemical proprieties of the water column, irradiance levels and the original community composition. The metabolic active profiles of bacteria were substantially different in the several incubation conditions, suggesting that methodological procedure influences the bacterial community composition, and the values of BP reported for aquatic ecosystems could be quite different from the real ones. In the light of these results, we suggest that BP determinations should be conducted under in situ conditions. However, due to execution limitations, BP needs to be frequently determined in the laboratory, and in this case, dark incubations provide more approximate values. This is the method routinely used, and although this incubation condition can cause stimulation of BP, the structure of the bacterial community is more similar to the one obtained with the in situ incubations.     

Intrinsic breaking of internal solitary waves in a deep lake

Based on simulations with the Dubreil-Jacotin-Long (DJL) equation, the limiting amplitude and the breaking mechanisms of internal solitary waves of depression (ISWs) are predicted for different background stratifications. These theoretical predictions are compared to the amplitude and the stability of the leading internal solitary waves of more than 200 trains of ISWs observed in the centre of a sub-basin of Lake Constance. The comparison of the model results with the field observations indicates that the simulated limiting amplitude of the ISWs provides an excellent prediction of the critical wave height above which ISWs break in the field. Shear instabilities and convective instabilities are each responsible for about half of the predicted wave breaking events. The data suggest the presence of core-like structures within the convectively unstable waves, but fully developed and stable cores were not observed. The lack of stable trapped cores in the field can be explained by the results from dynamic simulations of ISWs with trapped cores which demonstrate that even slight disturbances of the background stratification cause trapped cores to become unstable.     

Measuring the precision of estimates of total egg production based on plankton surveys

Methods are given to measure the effects of spatial and temporaldifferences in egg production on the precision of estimatesof total seasonal egg production derived from ichythyoplanktonsurveys. The techniques are applied to the results of largescale plankton surveys conducted in 1977 and 1979 off the northeasternUSA. For the three species analyzed (Atlantic mackerel, Scomberscombrus; silver hake, Merluccius bilinearis and yellowtailflounder, Limanda ferruginea). the surveys produced estimatesof total egg production having an average coefficient of variationequal to 31%. Estimates of spawning stock size based on theegg production estimates compared favorably with other independentassessments of stock size. ^*MARMAP Contribution MED/NEFC 83–39.     

Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates

Background

Genome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in cattle. However, the very small quantity of genomic DNA in biopsy material from early embryos poses daunting technical challenges. A reliable whole-genome amplification (WGA) procedure would greatly facilitate the procedure.

Results

Several PCR-based and non-PCR based WGA technologies, namely multiple displacement amplification, quasi-random primed library synthesis followed by PCR, ligation-mediated PCR, and single-primer isothermal amplification were tested in combination with different DNA extractions protocols for various quantities of genomic DNA inputs. The efficiency of each method was evaluated by comparing the genotypes obtained from 15 cultured cells (representative of an embryonic biopsy) to unamplified reference gDNA. The gDNA input, gDNA extraction method and amplification technology were all found to be critical for successful genome-wide genotyping. The selected WGA platform was then tested on embryo biopsies (n = 226), comparing their results to that of biopsies collected after birth. Although WGA inevitably leads to a random loss of information and to the introduction of erroneous genotypes, following genomic imputation the resulting genetic index of both sources of DNA were highly correlated (r = 0.99, P<0.001).

Conclusion

It is possible to generate high-quality DNA in sufficient quantities for successful genome-wide genotyping starting from an early embryo biopsy. However, imputation from parental and population genotypes is a requirement for completing and correcting genotypic data. Judicious selection of the WGA platform, careful handling of the samples and genomic imputation together, make it possible to perform extremely reliable genomic evaluations for pre-transfer embryos.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-889) contains supplementary material, which is available to authorized users.     

Transient exposure of root tips to primary and secondary metabolites: Impact on root growth and production of border cells

Here we describe the use of Pisum sativum L. as a model system to measure how short-term treatment of root tips with soluble metabolites can influence root growth and release of root exudates. The results revealed that even a 3-minute exposure of root tips to metabolites normally released from roots into the rhizosphere (e.g. rhamnose, ferulic acid, salicylic acid) can significantly influence root growth without affecting production of border cells and associated exudates. Conversely, products including caffeine, saccharide lactone, and pisatin alter production of border cells, without affecting root growth. Understanding how root-derived and exogenous metabolites can selectively impact root function may yield benefits in crop production, especially in greenhouse agriculture systems where growing roots can be exposed to a significant accumulation of plant exudates.     

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

Background

Dentin sialophosphoprotein (DSPP) is the largest member of the SIBLING family and is the most abundant noncollagenous protein in dentin. DSPP is also expressed in non-mineralized tissues including metabolically active ductal epithelia and some cancers. Its function, however, is poorly defined. The carboxy-terminal fragment, dentin phosphoprotein (DPP) is encoded predominantly by a large repetitive domain that requires separate cloning/sequencing reactions and is, therefore, often incomplete in genomic databases. Comparison of DPP sequences from at least one member of each major branch in the mammalian evolutionary tree (including some "toothless" mammals) as well as one reptile and bird may help delineate its possible functions in both dentin and ductal epithelia.

Results

The BMP1-cleavage and translation-termination domains were sufficiently conserved to permit amplification/cloning/sequencing of most species' DPP. While the integrin-binding domain, RGD, was present in about half of species, only vestigial remnants of this tripeptide were identified in the others. The number of tandem repeats of the nominal SerSerAsp phosphorylation motif in toothed mammals (including baleen whale and platypus which lack teeth as adults), ranged from ~75 (elephant) to >230 (human). These repeats were not perfect, however, and patterns of intervening sequences highlight the rapidity of changes among even closely related species. Two toothless anteater species have evolved different sets of nonsense mutations shortly after their BMP1 motifs suggesting that while cleavage may be important for DSPP processing in other tissues, the DPP domain itself may be required only in dentin. The lizard DSPP had an intact BMP1 site, a remnant RGD motif, as well as a distinctly different Ser/Asp-rich domain compared to mammals.

Conclusions

The DPP domain of DSPP was found to change dramatically within mammals and was lost in two truly toothless animals. The defining aspect of DPP, the long repeating phosphorylation domain, apparently undergoes frequent slip replication and recombination events that rapidly change specific patterns but not its overall biochemical character in toothed animals. Species may have to co-evolve protein processing mechanisms, however, to handle increased lengths of DSP repeats. While the RGD domain is lost in many species, some evolutionary pressure to maintain integrin binding can be observed.     

Site-level evaluation of satellite-based global terrestrial gross primary production and net primary production monitoring

Operational monitoring of global terrestrial gross primary production (GPP) and net primary production (NPP) is now underway using imagery from the satellite‐borne Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. Evaluation of MODIS GPP and NPP products will require site‐level studies across a range of biomes, with close attention to numerous scaling issues that must be addressed to link ground measurements to the satellite‐based carbon flux estimates. Here, we report results of a study aimed at evaluating MODIS NPP/GPP products at six sites varying widely in climate, land use, and vegetation physiognomy. Comparisons were made for twenty‐five 1 km² cells at each site, with 8‐day averages for GPP and an annual value for NPP. The validation data layers were made with a combination of ground measurements, relatively high resolution satellite data (Landsat Enhanced Thematic Mapper Plus at ～30 m resolution), and process‐based modeling. There was strong seasonality in the MODIS GPP at all sites, and mean NPP ranged from 80 g C m^?2 yr^?1 at an arctic tundra site to 550 g C m^?2 yr^?1 at a temperate deciduous forest site. There was not a consistent over‐ or underprediction of NPP across sites relative to the validation estimates. The closest agreements in NPP and GPP were at the temperate deciduous forest, arctic tundra, and boreal forest sites. There was moderate underestimation in the MODIS products at the agricultural field site, and strong overestimation at the desert grassland and at the dry coniferous forest sites. Analyses of specific inputs to the MODIS NPP/GPP algorithm – notably the fraction of photosynthetically active radiation absorbed by the vegetation canopy, the maximum light use efficiency (LUE), and the climate data – revealed the causes of the over‐ and underestimates. Suggestions for algorithm improvement include selectively altering values for maximum LUE (based on observations at eddy covariance flux towers) and parameters regulating autotrophic respiration.     

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

Background  

The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies.     

Differential effects of nutrient-limited primary production on primary, secondary or tertiary consumers

Nutritional imbalances between predator and prey are the rule rather than the exception at the lower end of food webs. We investigated the role of different grazers in the propagation of nutritionally imbalanced primary production by using the same primary producers in a three-trophic-level food chain and a four-trophic-level food chain experimental setup. The three-trophic-level food chain consisted of a classic single-cell primary producer (Rhodomonas salina), a metazoan grazer (the copepod Acartia tonsa) and a top predator (the jellyfish Gonionemus vertens), while we added a protozoan grazer (Oxyrrhis marina) as primary consumer to the food chain to establish the four-trophic-level food chain. This setup allowed us to investigate how nutrient-limitation effects change from one trophic level to another, and to investigate the performance of two components of our experimental food chains in different trophic positions. Stoichiometry and fatty acid profiles of the algae showed significant differences between the nutrient-depleted [no N and no P addition (?P), respectively] and the nutrient-replete (f/2) treatments. The differences in stoichiometry could be traced when O. marina was the first consumer. Copepods feeding on these flagellates were not affected by the nutritional imbalance of their prey in their stoichiometry, their respiration rates nor in their developmental rates. In contrast, when copepods were the primary consumer, those reared on the ?P algae showed significantly higher respiration rates along with significantly lower developmental rates. In neither of our two experimental food chains did the signals from the base of the food chains travel up to jelly fish, our top predator.     

Impact of scoring error and reproducibility RAPD data on RAPD based estimates of genetic distance

RAPD band reproducibility and scoring error were evaluated for RAPDs generated by 50 RAPD primers among ten snap bean (Phaseolus vulgaris L.) genotypes. Genetic distances based on different sets of RAPD bands were compared to evaluate the impact of scoring error, reproducibility, and differences in relative amplification strength on the reproducibility of RAPD based genetic distance estimates. The measured RAPD data scoring error was 2%. Reproducibility, expressed as the percentage of RAPD bands scored that are also scored in replicate data, was 76%. The results indicate that the probability of a scored RAPD band being scored in replicate data is strongly dependent on the uniformity of amplification conditions between experiments, as well as the relative amplification strength of the RAPD band. Significant improvement in the reproducibility of scored bands and some reduction in scoring error was achieved by reducing differences in reaction conditions between replicates. Observed primer variability for the reproducibility of scored RAPDs may also facilitate the selection of primers, resulting in dramatic improvements in the reproducibility of RAPD data used in germplasm studies. Variance of genetic distances across replicates due to sampling error was found to be more than six times greater than that due to scoring error for a set of 192 RAPD bands. Genetic distance matrices computed from the RAPD bands scored in replicated data and RAPD bands that failed to be scored in replicated data were not significantly different. Differences in the ethidium bromide staining intensity of RAPD bands were not associated with significant differences in resulting genetic distance matrices. The assumption of sampling error as the only source of error was sufficient to account for the observed variation in genetic distance estimates across independent sets of RAPD bands.     

Terrestrial net primary production estimates for 0.5° grid cells from field observations—a contribution to global biogeochemical modeling

Net Primary Production (NPP) is an important component of the carbon cycle and, among the pools and fluxes that make up the cycle, it is one of the steps that are most accessible to field measurement. While easier than some other steps to measure, direct measurement of NPP is tedious and not practical for large areas and so models are generally used to study the carbon cycle at a global scale. Nevertheless these models require field measurements of NPP for parameterization, calibration and validation. Most NPP data are for relatively small field plots that cannot represent the 0.5° × 0.5° grid cells that are commonly used in global scale models. Furthermore, technical difficulties generally restrict NPP measurements to aboveground parts and sometimes do not even include all components of aboveground NPP. Thus direct inter‐comparison between field data obtained in different studies or comparison of these results with coarse resolution model outputs can be misleading. We summarize and present a series of methods that were used by original authors to estimate NPP and how and what we have done to prepare a consistent data set of NPP for 0.5 °grid cells for a range of biomes from these studies. The methods used for estimation of NPP include: (i) aggregation of fine‐scale (plot or stand‐level) vegetation inventory data to larger grid cells, (ii) mapping of grid cells and area weighting of field NPP observations in each mapped class, (iii) direct correlation of extensive data sets of ground measurements with remotely sensed spectral vegetation indices, (iv) local modeling of NPP using key independent variables, for which maps are available at the scale of the grid cell, and (v) regression analysis to link productivity with controlling environmental variables. For a few grid cells whose NPP were obtained for multiple years, temporal analysis was conducted. The grid cells are grouped to the biome level and are compared with existing compilations of field NPP and the results of the Miami potential NPP model. Mean NPP was similar to the well‐known compilation of Whittaker and Likens, except for temperate evergreen needle‐leaved forest, woodland, and shrubland. The grid cell datasets are a contribution to the International Geosphere‐Biosphere Programme (IGBP) Data and Information System (DIS) Global Primary Production Data Initiative (GPPDI). The full dataset currently contains 3654 cells (including replicate measurements) developed from 15 studies representing NPP in croplands, sparse vegetation, shrub lands, grasslands, and forests worldwide. An edited subset consists of 2335 cells in which outliers were removed and all replicate measurements were averaged for each unique geographical location. Most of the data incorporated into GPPDI were wholly or partly developed by participants in the GPPDI, in addition to the present authors. These studies are gathered together here to provide a consistent account of the grid cell component of GPPDI and an analysis of the entire data set. The datasets have been deposited in an IGBP‐DIS GPPDI database ( http://daacl.esd.ornl.gov/npq/GPPDI/Combined_GPPDI_des.html ).     

Impact of brief oxidant stress on primary adult cardiac fibroblasts

Reperfusion of ischemic myocardium (I/R) is associated with local release of a brief pulse of reactive oxygen species. The purpose of this study was to determine the effects of brief H2O2 stimulation on primary adult cardiac fibroblast phenotype. We demonstrate that brief H2O2 exposure results in transient phosphorylations of p38 and ERK which peaked by 15 min. Proliferation was minimally affected by either H2O2 or MAPK inhibition. Pretreatment with SB203580 or U0126 revealed that p38 enhances or maintains migration rates while ERK retarded migration. Peroxide exposure increased necrosis from 4% at baseline to >12% while reducing apoptosis by 3.5-fold. p38 inhibition resulted in increased necrosis and apoptosis while ERK inhibition had minimal effects. In conclusion, primary adult cardiac fibroblasts exposed to brief H2O2 exhibit an altered phenotype characterized by reduced migration and apoptosis and increased necrosis resulting, in part, from the differential effects of p38 and ERK signaling.     

Impact of Aspergillus oryzae genomics on industrial production of metabolites

Aspergillus oryzae is used extensively for the production of the traditional Japanese fermented foods sake (rice wine), shoyu (soy sauce), and miso (soybean paste). In recent years, recombinant DNA technology has been used to enhance industrial enzyme production by A. oryzae. Recently completed genomic studies using expressed sequence tag (EST) analyses and whole-genome sequencing are quickly expanding the industrial potential of the fungus in biotechnology. Genes that have been newly discovered through genome research can be used for the production of novel valuable enzymes and chemicals, and are important for designing new industrial processes. This article describes recent progress of A . oryzae genomics and its impact on industrial production of enzymes, metabolites, and bioprocesses.