A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. <it>Panagrolaimus superbus </it>is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that <it>P. superbus </it>uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.</p> <p>Results</p> <p>To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of <it>P. superbus</it>. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at <url>http://www.nematodes.org/nembase4/species_info.php?species=PSC</url>. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from <it>P. superbus</it>. Notable among those is a putative lineage expansion of the <it>lea </it>(late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific <it>sxp/ral-2 </it>family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from <it>Phytophthora infestans</it>. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This <it>P. superbus </it>sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants <it>glutathione peroxidase, dj-1 </it>and <it>1-Cys peroxiredoxin</it>, an <it>shsp </it>sequence and an <it>lea </it>gene.</p> <p>Conclusions</p> <p><it>P. superbus </it>appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of <it>lea </it>genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of <it>P. superbus</it>.</p

The project for intercomparison of land-surface parameterization schemes (PILPS) phase 2(c) Red-Arkansas River basin experiment: 2. Spatial and temporal analysis of energy fluxes

The energy components of sixteen Soil-Vegetation Atmospheric Transfer (SVAT) schemes were analyzed and intercompared using 10 years of surface meteorological and radiative forcing data from the Red-Arkansas River basin in the Southern Great Plains of the United States. Comparisons of simulated surface energy fluxes among models showed that the net radiation and surface temperature generally had the best agreement among the schemes. On an average (annual and monthly) basis, the estimated latent heat fluxes agreed (to within approximate estimation errors) with the latent heat fluxes derived from a radiosonde-based atmospheric budget method for slightly more than half of the schemes. The sensible heat fluxes had larger differences among the schemes than did the latent heat fluxes, and the model-simulated ground heat fluxes had large variations among the schemes. The spatial patterns of the model-computed net radiation and surface temperature were generally similar among the schemes, and appear reasonable and consistent with observations of related variables, such as surface air temperature. The spatial mean patterns of latent and sensible heat fluxes were less similar than for net radiation, and the spatial patterns of the ground heat flux vary greatly among the 16 schemes. Generally, there is less similarity among the models in the temporal (interannual) variability of surface fluxes and temperature than there is in the mean fields, even for schemes with similar mean fields

The project for intercomparison of land-surface parameterization schemes (PILPS) phase 2(c) Red-Arkansas River basin experiment: 2. Spatial and temporal analysis of energy fluxes

The energy components of sixteen Soil-Vegetation Atmospheric Transfer (SVAT) schemes were analyzed and intercompared using 10 years of surface meteorological and radiative forcing data from the Red-Arkansas River basin in the Southern Great Plains of the United States. Comparisons of simulated surface energy fluxes among models showed that the net radiation and surface temperature generally had the best agreement among the schemes. On an average (annual and monthly) basis, the estimated latent heat fluxes agreed (to within approximate estimation errors) with the latent heat fluxes derived from a radiosonde-based atmospheric budget method for slightly more than half of the schemes. The sensible heat fluxes had larger differences among the schemes than did the latent heat fluxes, and the model-simulated ground heat fluxes had large variations among the schemes. The spatial patterns of the model-computed net radiation and surface temperature were generally similar among the schemes, and appear reasonable and consistent with observations of related variables, such as surface air temperature. The spatial mean patterns of latent and sensible heat fluxes were less similar than for net radiation, and the spatial patterns of the ground heat flux vary greatly among the 16 schemes. Generally, there is less similarity among the models in the temporal (interannual) variability of surface fluxes and temperature than there is in the mean fields, even for schemes with similar mean fields

The project for intercomparison of land-surface parameterization schemes (PILPS) phase 2(c) Red-Arkansas River basin experiment: 1. Experiment description and summary intercomparisons

Sixteen land-surface schemes participating in the project for the Intercomparison of Land-surface Schemes (PILPS) Phase 2(c) were run using 10 years (1979-1988) of forcing data for the Red-Arkansas River basins in the Southern Great Plains region of the United States. Forcing data (precipitation, incoming radiation and surface meteorology) and land-surface characteristics (soil and vegetation parameters) were provided to each of the participating schemes. Two groups of runs are presented. (1) Calibration-validation runs, using data from six small catchments distributed across the modeling domain. These runs were designed to test the ability of the schemes to transfer information about model parameters to other catchments and to the computational grid boxes. (2) Base-runs, using data for 1979-1988, designed to evaluate the ability of the schemes to reproduce measured energy and water fluxes over multiple seasonal cycles across a climatically diverse, continental-scale basin. All schemes completed the base-runs but five schemes chose not to calibrate. Observational data (from 1980-1986) including daily river flows and monthly basin total evaporation estimated through an atmospheric budget analysis, were used to evaluate model performance. In general, the results are consistent with earlier PILPS experiments in terms of differences among models in predicted water and energy fluxes. The mean annual net radiation varied between 80 and 105 W m-2 (excluding one model). The mean annual Bowen ratio varied from 0.52 to 1.73 (also excluding one model) as compared to the data-estimated value of 0.92. The run-off ratios varied from a low of 0.02 to a high of 0.41, as compared to an observed value of 0.15. In general, those schemes that did not calibrate performed worse, not only on the validation catchments, but also at the scale of the entire modeling domain. This suggests that further PILPS experiments on the value of calibration need to be carried out

Simulations of a boreal grassland hydrology at Valdai, Russia: PILPS phase 2(d)

The Project for the Intercomparison of Land-Surface Parameterization Schemes (PILPS) aims to improve understanding and modeling of land surface processes. PILPS phase 2(d) uses a set of meteorological and hydrological data spanning 18 yr (1966-83) from a grassland catchment at the Valdai water-balance research site in Russia. A suite of stand-alone simulations is performed by 21 land surface schemes (LSSs) to explore the LSSs' sensitivity to downward longwave radiative forcing, timescales of simulated hydrologic variability, and biases resulting from single-year simulations that use recursive spinup. These simulations are the first in PILPS to investigate the performance of LSSs at a site with a well-defined seasonal snow cover and frozen soil. Considerable model scatter for the control simulations exists. However, nearly all the LSS scatter in simulated root-zone soil moisture is contained within the spatial variability observed inside the catchment. In addition, all models show a considerable sensitivity to longwave forcing for the simulation of the snowpack, which during the spring melt affects runoff, meltwater infiltration, and subsequent evapotranspiration. A greater sensitivity of the ablation, compared to the accumulation, of the winter snowpaek to the choice of snow parameterization is found. Sensitivity simulations starting at prescribed conditions with no spinup demonstrate that the treatment of frozen soil (moisture) processes can affect the long-term variability of the models. The single-year recursive runs show large biases, compared to the corresponding year of the control run, that can persist through the entire year and underscore the importance of performing multiyear simulations