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The photosynthetic carbon metabolism, including the Calvin-Benson cycle, is the primary pathway in C-3-plants, producing starch and sucrose from CO2. Understanding the interplay between regulation and efficiency of this pathway requires the development of mathematical models which would explain the observed dynamics of metabolic transformations. Here, we address this question by casting the existing models of Calvin-Benson cycle and the end-product processes into an analysis framework which not only facilitates the comparison of the different models, but also allows for their ranking with respect to chosen criteria, including stability, sensitivity, robustness and/or compliance with experimental data. The importance of the photosynthetic carbon metabolism for the increase of plant biomass has resulted in many models with various levels of detail. We provide the largest compendium of 15 existing, well-investigated models together with a comprehensive classification as well as a ranking framework to determine the best-performing models for metabolic engineering and planning of in silica experiments. The classification can be additionally used, based on the model structure, as a tool to identify the models which match best the experimental design. The provided ranking is just one alternative to score models and, by changing the weighting factor, this framework also could be applied for selection of other criteria of interest.
We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance.
On Earth, chemolithoautothrophic and anaerobic microorganisms such as methanogenic archaea are regarded as model organisms for possible subsurface life on Mars. For this reason, the methanogenic strain Methanosarcina soligelidi (formerly called Methanosarcina spec. SMA-21), isolated from permafrost-affected soil in northeast Siberia, has been tested under Martian thermo-physical conditions. In previous studies under simulated Martian conditions, high survival rates of these microorganisms were observed. In our study we present a method to measure methane production as a first attempt to study metabolic activity of methanogenic archaea during simulated conditions approaching conditions of Mars-like environments. To determine methanogenic activity, a measurement technique which is capable to measure the produced methane concentration with high precision and with high temporal resolution is needed. Although there are several methods to detect methane, only a few fulfill all the needed requirements to work within simulated extraterrestrial environments. We have chosen laser spectroscopy, which is a non-destructive technique that measures the methane concentration without sample taking and also can be run continuously. In our simulation, we detected methane production at temperatures down to -5 degrees C, which would be found on Mars either temporarily in the shallow subsurface or continually in the deep subsurface. The pressure of 50 kPa which we used in our experiments, corresponds to the expected pressure in the Martian near subsurface. Our new device proved to be fully functional and the results indicate that the possible existence of methanogenic archaea in Martian subsurface habitats cannot be ruled out. (C) 2013 Published by Elsevier Ltd.
We used inverse modelling techniques and soil moisture measured by the cosmic-ray neutron sensing (CRS) to estimate root-zone soil hydraulic properties at the field scale. A HYDRUS-1D model was developed for inverse modelling and calibrated with parameter estimation software (PEST) using a global optimizer. Integral CRS measurements recorded from a sunflower farm in Germany comprised the model input. Data were transformed to soil water storage to enable direct model calibration with a HYDRUS soil-water balance. Effective properties at the CRS scale were compared against local measurements and other inversely estimated soil properties from independent soil moisture profiles. Moreover, CRS-scale soil properties were tested on the basis of how field soil moisture (vertical distribution) and soil water storage were reproduced. This framework provided good estimates of effective soil properties at the CRS scale. Simulated soil moisture at different depths at the CRS scale agreed with field observations. Moreover, simulated soil water storage at the CRS scale compared well with calculations from point-scale profiles, despite their different support volumes. The CRS-scale soil properties estimated with the inverse model were within the range of variation of properties identified from all inverse simulations at the local scale. This study demonstrates the potential of CRS for inverse estimation of soil hydraulic properties.
Injection of nanoscale zero-valent iron (nZVI) has recently gained great interest as emerging technology for in-situ remediation of chlorinated organic compounds from groundwater systems. Zero-valent iron (ZVI) is able to reduce organic compounds and to render it to less harmful substances. The use of nanoscale particles instead of granular or microscale particles can increase dechlorination rates by-orders of magnitude due to its high surface area. However, classical nZVI appears to be hampered in its environmental application by its limited mobility. One approach is colloid supported transport of nZVI, where the nZVI gets transported by a Mobile colloid. In this study transport properties of activated carbon colloid supported nZVI (c-nZVI; d(50) = 2.4 mu m) are investigated in column tests using columns of 40 cm length, which were filled with porous media. A suspension was pumped through the column under different physicochemical conditions (addition of a polyanionic stabilizer and changes in pH and ionic strength). Highest observed breakthrough was 62% of the injected concentration in glass beads with addition of stabilizer. Addition of mono- and bivalent salt, e.g. more than 0.5 mM/L CaCl2, can decrease mobility and changes in pH to values below six can inhibit mobility at all. Measurements of colloid sizes and zeta potentials show changes in the mean particle size by a factor of ten and an increase of zeta potential from -62 mV to -80 mV during the transport experiment. However, results suggest potential applicability of c-nZVI under field conditions. (C) 2014 Elsevier B.V. All rights reserved.
Nanoscale zero-valent iron (nZVI) has recently gained great interest in the scientific community as in situ reagent for installation of permeable reactive barriers in aquifer systems, since nZVI is highly reactive with chlorinated compounds and may render them to harmless substances. However, nZVI has a high tendency to agglomerate and sediment; therefore it shows very limited transport ranges. One new approach to overcome the limited transport of nZVI in porous media is using a suited carrier colloid. In this study we tested mobility of a carbon colloid supported nZVI particle "Carbo-Iron Colloids" (CIC) with a mean size of 0.63 mu m in a column experiment of 40 cm length and an experiment in a two-dimensional (2D) aquifer test system with dimensions of 110x40x5 cm. Results show a breakthrough maximum of 82 % of the input concentration in the column experiment and 58 % in the 2D-aquifer test system. Detected residuals in porous media suggest a strong particle deposition in the first centimeters and few depositions in the porous media in the further travel path. Overall, this suggests a high mobility in porous media which might be a significant enhancement compared to bare or polyanionic stabilized nZVI.