Evaluating a fast headspace method for measuring DIC and subsequent calculation of pCO2 in freshwater systems

A variety of different sampling and analysis methods are found in the literature for determining carbon dioxide (CO2) in freshwaters, methods that rarely have been evaluated or compared. Here we present an evaluation of an acidified headspace method (AHS) in which the dissolved inorganic carbon (DIC) is measured from an acidified sample and the partial pressure (pCO2) is calculated from DIC using pH and water temperature. We include information on practical sampling, accuracy, and precision of the DIC/pCO2 determination and a storage test of samples. The pCO2 determined from the AHS method is compared to that obtained from the more widely used direct headspace method (DHS) in which CO2 is equilibrated between the water and gas phases at ambient pH. The method was tested under both controlled laboratory conditions as well as wintertime field sampling. The accuracy of the DIC detection was on average 99% based on prepared standard solutions. The pCO2 determination in lab, using the DHS method as a reference, showed no significant difference, although the discrepancy between the methods was larger in samples with <1000 µatm. The precision of the pCO2 determination was on average ±4.3%, which was slightly better than the DHS method (±6.7%). In the field, the AHS method determined on average 10% higher pCO2 than the DHS method, which was explained by the extreme winter conditions (below −20 °C) at sampling that affected the sampling procedure of the DHS method. Although samples were acidified to pH 2, respiration processes were still occurring (at a low rate), and we recommend that analyses are conducted within 3 days from sampling. The AHS method was found to be a robust method to determine DIC and pCO2 in acidic to pH-neutral freshwater systems. The simple and quick sampling procedure makes the method suitable for time-limited sampling campaigns and sampling in cold climate

Separation and identification of dominant mechanisms in double photoionization

Double photoionization by a single photon is often discussed in terms of two contributing mechanisms, {\it knock-out} (two-step-one) and {\it shake-off} with the latter being a pure quantum effect. It is shown that a quasi-classical description of knock-out and a simple quantum calculation of shake-off provides a clear separation of the mechanisms and facilitates their calculation considerably. The relevance of each mechanism at different photon energies is quantified for helium. Photoionization ratios, integral and singly differential cross sections obtained by us are in excellent agreement with benchmark experimental data and recent theoretical results.Comment: 4 pages, 5 figure

Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding

Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Forster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size. We capture the role of the linker in a heuristic scaling model, and we find that compression is a function of size of the probe and volume fraction of the crowder. The FRET changes observed in Escherichia collare more complicated, where FRET increases and scaling behavior are observed solely with probes that contain the helices in the linker. The probe with the highest sensitivity to crowding in vivo yields the same macromolecularvolume fractions as previously obtained from cell dry weight. The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor

Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence

International audienceThe BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen and that bio-selection and changes in BabA binding properties through mutation and recombination with babA-related genes are selected by differences among individuals and by changes in gastric acidity over time. These processes generate diverse H. pylori subpopulations, in which BabA's adaptive evolution contributes to H. pylori persistence and overt gastric disease

Production and emission of CO2 in two unproductive lakes in northern Sweden

Unproductive lakes are one of few natural landscape compartments with net release of carbon to the atmosphere. Lakes also generally decrease the net terrestrial carbon uptake, since most of the CO2 production in unproductive lakes are derived from organic carbon produced on land (e.g. in forests). High latitude lakes are predicted to be particularly affected by the global climate change. The carbon cycling in these lakes and their role in the landscape are therefore important to study. In this thesis, carbon turnover processes were studied in two lakes above the arctic circle (Lake Diktar-Erik and Lake Merasjärvi) in year 2004 and 2005. Both lakes were net heterotrophic, with large variations in CO2 concentrations both on shorter (30min) and longer (24h) time-scales. The pelagic habitat supported a major part of the net production of CO2, with larger dynamics in the CO2 production than the sediments. The CO2 variations of the surface water were related to respiration of allochthonous organic carbon, and were affected by the concentration and quality of the DOC, as well as the whole lake water temperatures, and vertical water movements. The emission of CO2 from Lake Merasjärvi was measured with the eddy covariance tech­nique. The results showed that the gas transfer rate during moderate winds were higher than expected, causing the two most commonly used models to underestimate the long term fluxes of CO2 from the lake. Taken together, the results of the thesis show that the studied lakes contributed to bring terrestrial organic carbon back into the atmosphere, driven by a substantial internal CO2 production based on mineralization of allochthonous organic carbon. Major results are that the eddy covariance technique indicated that commonly used models tend to underestimate the net release rate of CO2 from lakes to the atmosphere, and that the lake CO2 dynamics can be the results of interactions between biogeochemical and physical processes in the lake water

A Universal Source Coding Perspective on PPM

The PPM (Prediction by Partial Matching) family of text compression algorithms has several members that have shown to be very efficient in practice. This thesis treats PPM algorithms from an information-theoretical point of view, based on results and methods from universal source coding theory. A number of source classes for modeling text-like data are developed, that are distinguished both by structural properties and by restrictions imposed on the possible combinations of parameter values. Two subproblems of PPM are studied in detail; the problem of sequential multi-alphabet coding, i.e., coding for memoryless sources with unknown alphabet, and the problem of coding for memoryless sources with side information in the form of observations from a source with similar parameters. For the multi-alphabet coding problem, several codes are presented, together with a sufficient condition for asymptotic optimality, which is satified by some of the introduced codes. Furthermore, the natural law of succession, a known solution of the underlying estimation problem, is analysed from the aspect of coding, and a method is given for calculation of the coding probabilities for a known multi-alphabet code. A code using side information from a similar source is presented and analysed, and is proved to asymptotically outperform codes not using side information if the divergence between the two sources is small. Based on the above results, modified PPM algorithms are proposed, and methods are developed for estimation of code parameters during encoding. It is experimentally verified that the introduced modifications improve the compression rate of PPM on two standard sets of test data. Several known PPM versions are shown to be characterizable in terms of the introduced source classes. The combination of PPM and MDL (minimum description length) model class estimation is investigated. Codes using this combination of estimation techniques are given for the different source structures introduced for text-like data, and the modified PPM is shown experimentally to yield an improvement when combined with MDL estimation as well

Production and emission of CO2 in two unproductive lakes in northern Sweden

Unproductive lakes are one of few natural landscape compartments with net release of carbon to the atmosphere. Lakes also generally decrease the net terrestrial carbon uptake, since most of the CO2 production in unproductive lakes are derived from organic carbon produced on land (e.g. in forests). High latitude lakes are predicted to be particularly affected by the global climate change. The carbon cycling in these lakes and their role in the landscape are therefore important to study. In this thesis, carbon turnover processes were studied in two lakes above the arctic circle (Lake Diktar-Erik and Lake Merasjärvi) in year 2004 and 2005. Both lakes were net heterotrophic, with large variations in CO2 concentrations both on shorter (30min) and longer (24h) time-scales. The pelagic habitat supported a major part of the net production of CO2, with larger dynamics in the CO2 production than the sediments. The CO2 variations of the surface water were related to respiration of allochthonous organic carbon, and were affected by the concentration and quality of the DOC, as well as the whole lake water temperatures, and vertical water movements. The emission of CO2 from Lake Merasjärvi was measured with the eddy covariance tech­nique. The results showed that the gas transfer rate during moderate winds were higher than expected, causing the two most commonly used models to underestimate the long term fluxes of CO2 from the lake. Taken together, the results of the thesis show that the studied lakes contributed to bring terrestrial organic carbon back into the atmosphere, driven by a substantial internal CO2 production based on mineralization of allochthonous organic carbon. Major results are that the eddy covariance technique indicated that commonly used models tend to underestimate the net release rate of CO2 from lakes to the atmosphere, and that the lake CO2 dynamics can be the results of interactions between biogeochemical and physical processes in the lake water