Ozone in the Tropical Troposphere

The aim of the research presented here is to acquire knowledge of the past, present, and future composition, stability, sensitivity, and variability of the troposphere. We focus mostly on the tropical regions because it has received little attention so far, measurements here are scarce, and large changes are expected to occur in the future. Special attention is given to ozone as it plays a key role in tropospheric photochemistry. Not only is it a greenhouse gas, it is also the most important precursor of the hydroxyl radical (OH) which is responsible for the removal of many trace gases from the troposphere. Furthermore, ozone is an important indicator for atmospheric transport and photochemistry. The involvement of ozone in many different processes also renders it an excellent compound to test our knowledge of coupled transport-chemistry systems. In Chapter 2, we present the measurements of ozone performed since the inauguration (1999) of a new ozone monitoring station in Paramaribo, Suriname. This station was started under the Research on Atmospheric Dynamics and Chemistry in Suriname (RADCHiS) project. The choice for this location was partly due to the historical ties with Suriname, but also because of the unique location of Paramaribo with respect to the Atlantic Ocean, the equator (northern hemisphere), and the Inter Tropical Convergence Zone (ITCZ). Because the ITCZ passes Suriname twice per year the station samples both the meteorological northern and southern hemispheres. This leads to strong contrast with nearby southern hemisphere stations (Ascension and Natal) during February and March. Chapter 3 describes the variability of ozone in the tropics, and our ability to reproduce this variability (on time scales of months to years). For that purpose we use a model simulation that spans the period 1979-1993, and that includes trends of anthropogenic emissions, and day-to-day variability of meteorology. The model calculated seasonal cycle of ozone in the tropics shows that we are able to reproduce observations for stations in the remote Pacific Ocean quite well, but that the more polluted Atlantic Ocean is more problematic. At times, the model underestimates ozone by more than 30%. Furthermore, our results show that the model realistically reproduces the changing convection patterns in the Walker circulation during the positive phase of the El Niño-Southern Oscillation (ENSO). These results are in good agreement with satellite observations, even though other influences on ozone that change during ENSO (e.g. biomass burning in dry areas) were not included in our model simulation. This work presents the first ENSO signal in a multi-year model simulation of ozone. To better understand, and possibly solve, the large underestimate of ozone over the Atlantic Ocean we have investigated the zonal distribution of ozone in more detail in Chapter 4. Since ozone monitoring stations in the tropics are not abundant, and usually only span a few years, we have used satellite observations of ozone (1979-1992) to compare our model to. We introduce a method to compare model and measurements quantitatively and systematically, and then use this method to identify times and regions where model underestimates are largest. Chapter 5 treats the stability of photochemistry in the tropics, and the largely unchanged levels of OH since industrialization. We focus specifically on OH levels, which are strongly coupled to ozone levels because together with water vapor and sunlight, they determine OH production rates. Our calculations show that global OH has remained constant through a 50% increase in primary OH production, and a 75% increase in secondary production. Locally, the OH distribution has changed substantially since industrialization with increases of more than 200% in urban areas, and decreases of more than 30% in remote marine areas

A view of the European carbon flux landscape through the lens of the ICOS atmospheric observation network

The ICOS (Integrated Carbon Observation System) network of atmospheric measurement stations produces standardized data on greenhouse gas concentrations at 36 stations in 14 different European countries (November 2022). The network targets a strongly heterogeneous landscape and the placement of instruments on tall towers and mountains make for large influence regions (footprints). The combined footprints for all the individual stations create the &ldquo;lens&rdquo; through which the observing network sees the European flux landscape. In this study, we summarize this view using quantitative metrics of the fluxes seen by individual stations, and by the current and future ICOS network. Results are presented both from a country-level and pan-European perspective, using open-source tools that we make available through the ICOS Carbon Portal. We target anthropogenic emissions from various sectors (e.g., energy production, industrial emissions), as well as the land-cover types found over Europe (e.g., broadleaf forests, croplands) and their spatiotemporally varying fluxes. This recognizes different interests of different ICOS stakeholders. We specifically introduce &ldquo;monitoring potential maps&rdquo;, which quantify the sensitivity of the network with regards to specific properties of each pixel compared to the averages across all pixels, to see which regions have a relative underrepresentation of land-cover, or biospheric fluxes. This potential changes with the introduction of new stations, which we investigate for the planned ICOS expansion with 20 stations over the next few years. The monitoring potential concept is novel and a useful addition to traditional quantitative network design methods. We find that the ICOS network has limited sensitivity to anthropogenic fluxes, as was intended in the current design. Its representation of biospheric fluxes follows the fractional representation of land-cover and is generally well balanced, with exceptions for a country like Norway where the southerly station Birkenes predominantly senses coniferous forest fluxes instead of the more abundant northerly grass &amp; shrublands. Grass &amp; shrubland fluxes are relatively underrepresented in ICOS, with the largest monitoring potential in Scandinavia, Croatia, and Serbia. These easterly countries similarly show a relative underrepresentation of broadleaf forest fluxes, partly due to a lack of monitoring stations, and partly due to the abundant sensitivity to broadleaf forests in the most densely monitored countries such as France and Germany. We stress that this does not imply these latter countries to be fully monitored and of lesser interest for network expansion: for example, inclusion of Schauinsland in the future network expands the network lens to mostly unmonitored mixed- and broadleaf forests which are relatively underrepresented at the national level. Such considerations demonstrate the usefulness of our analyses and can readily be re-produced for any network configuration within Europe with tools offered through the Carbon Portal.</p

Three Years of Greenhouse Gas Column-Averaged Dry Air Mole Fractions Retrieved from Satellite - Part 2: Methane

Abstract. Carbon dioxide (CO2) and methane (CH4) are the two most important anthropogenic greenhouse gases. SCIAMACHY on ENVISAT is the first satellite instrument whose measurements are sensitive to concentration changes of the two gases at all altitude levels down to the Earth's surface where the source/sink signals are largest. We have processed three years (2003-2005) of SCIAMACHY nearinfrared nadir measurements to simultaneously retrieve vertical columns of CO2 (from the 1.58µm absorption band), CH4 (1.66µm) and oxygen (O2 A-band at 0.76µm) using the scientific retrieval algorithm WFM-DOAS.We show that the latest version of WFM-DOAS, version 1.0, which is used for this study, has been significantly improved with respect to its accuracy compared to the previous versions while essentially maintaining its high processing speed (1 min per orbit, corresponding to 6000 single measurements, and per gas on a standard PC). The greenhouse gas columns are converted to dry air column-averaged mole fractions, denoted XCO2 (in ppm) and XCH4 (in ppb), by dividing the greenhouse gas columns by simultaneously retrieved dry air columns. For XCO2 dry air columns are obtained from the retrieved O2 columns. For XCH4 dry air columns are obtained from the retrieved CO2 columns because of better cancellation of light path related errors compared to using O2 columns retrieved from the spectrally distant O2 Aband. Here we focus on a discussion of the XCH4 data set. The XCO2 data set is discussed in a separate paper (Part 1). For 2003 we present detailed comparisons with the TM5 model which has been optimally matched to highly accurate but sparse methane surface observations. After accounting for a systematic low bias of 2% agreement with TM5 is typically within 1¿2%. We investigated to what extent the SCIAMACHY XCH4 is influenced by the variability of atmospheric CO2 using global CO2 fields from NOAA¿s CO2 assimilation system CarbonTracker. We show that the CO2 corrected and uncorrected XCH4 spatio-temporal pattern are very similar but that agreement with TM5 is better for the CarbonTracker CO2 corrected XCH4. In line with previous studies (e.g., Frankenberg et al., 2005b) we find higher methane over the tropics compared to the model. We show that tropical methane is also higher when normalizing the CH4 columns with retrieved O2 columns instead of CO2. In consistency with recent results of Frankenberg et al. (2008b) it is shown that the magnitude of the retrieved tropical methane is sensitive to the choice of the spectroscopic line parameters of water vapour. Concerning inter-annual variability we find similar methane spatio-temporal pattern for 2003 and 2004. For 2005 the retrieved methane shows significantly higher variability compared to the two previous years, most likely due to somewhat larger noise of the spectral measurements.JRC.H.2-Air and Climat

Exploring the potential of Δ17O in CO2 for determining mesophyll conductance

Mesophyll conductance to CO2 from the intercellular air space to the CO2–H2O exchange site has been estimated using δ18O measurements (gm18). However, the gm18 estimates are affected by the uncertainties in the δ18O of leaf water where the CO2–H2O exchange takes place and the degree of equilibration between CO2 and H2O. We show that measurements of Δ17O (i.e. Δ17O = δ17O − 0.528 × δ18O) can provide independent constraints on gm (gmΔ17) and that these gm estimates are less affected by fractionation processes during gas exchange. The gm calculations are applied to combined measurements of δ18O and Δ17O, and gas exchange in two C3 species, sunflower (Helianthus annuus L. cv. ‘sunny’) and ivy (Hedera hibernica L.), and the C4 species maize (Zea mays). The gm18 and gmΔ17 estimates agree within the combined errors (P-value, 0.876). Both approaches are associated with large errors when the isotopic composition in the intercellular air space becomes close to the CO2–H2O exchange site. Although variations in Δ17O are low, it can be measured with much higher precision compared with δ18O. Measuring gmΔ17 has a few advantages compared with gm18: (i) it is less sensitive to uncertainty in the isotopic composition of leaf water at the isotope exchange site and (ii) the relative change in the gm due to an assumed error in the equilibration fraction θeq is lower for gmΔ17 compared with gm18. Thus, using Δ17O can complement and improve the gm estimates in settings where the δ18O of leaf water varies strongly, affecting the δ18O (CO2) difference between the intercellular air space and the CO2–H2O exchange site

Leaf-scale quantification of the effect of photosynthetic gas exchange on δ ¹⁷O of atmospheric CO ₂

Understanding the processes that affect the triple oxygen isotope composition of atmospheric CO2during gas exchange can help constrain the interaction and fluxes between the atmosphere and the biosphere. We conducted leaf cuvette experiments under controlled conditions using three plant species. The experiments were conducted at two different light intensities and using CO2with different δ17O. We directly quantify the effect of photosynthesis on δ17O of atmospheric CO2for the first time. Our results demonstrate the established theory for δ18O is applicable to δ17O.CO2/at leaf level, and we confirm that the following two key factors determine the effect of photosynthetic gas exchange on the δ17O of atmospheric CO2. The relative difference between δ17O of the CO2entering the leaf and the CO2in equilibrium with leaf water and the back-diffusion flux of CO2from the leaf to the atmosphere, which can be quantified by the cm=ca ratio, where ca is the CO2mole fraction in the surrounding air and cm is the one at the site of oxygen isotope exchange between CO2and H2O. At low cm=ca ratios the discrimination is governed mainly by diffusion into the leaf, and at high cm=ca ratios it is governed by back-diffusion of CO2that has equilibrated with the leaf water. Plants with a higher cm=ca ratio modify the 117O of atmospheric CO2more strongly than plants with a lower cm=ca ratio. Based on the leaf cuvette experiments, the global value for discrimination against δ17O of atmospheric CO2during photosynthetic gas exchange is estimated to be-0:57±0:14% using cm=ca values of 0.3 and 0.7 for C4and C3plants, respectively. The main uncertainties in this global estimate arise from variation in cm=ca ratios among plants and growth conditions.</p

Exploring the potential of Δ¹⁷O in CO₂ for determining mesophyll conductance

Mesophyll conductance to CO2 from the intercellular air space to the CO2–H2O exchange site has been estimated using δ18O measurements (gm18). However, the gm18 estimates are affected by the uncertainties in the δ18O of leaf water where the CO2–H2O exchange takes place and the degree of equilibration between CO2 and H2O. We show that measurements of Δ17O (i.e. Δ17O = δ17O − 0.528 × δ18O) can provide independent constraints on gm (gmΔ17) and that these gm estimates are less affected by fractionation processes during gas exchange. The gm calculations are applied to combined measurements of δ18O and Δ17O, and gas exchange in two C3 species, sunflower (Helianthus annuus L. cv. ‘sunny’) and ivy (Hedera hibernica L.), and the C4 species maize (Zea mays). The gm18 and gmΔ17 estimates agree within the combined errors (P-value, 0.876). Both approaches are associated with large errors when the isotopic composition in the intercellular air space becomes close to the CO2–H2O exchange site. Although variations in Δ17O are low, it can be measured with much higher precision compared with δ18O. Measuring gmΔ17 has a few advantages compared with gm18: (i) it is less sensitive to uncertainty in the isotopic composition of leaf water at the isotope exchange site and (ii) the relative change in the gm due to an assumed error in the equilibration fraction θeq is lower for gmΔ17 compared with gm18. Thus, using Δ17O can complement and improve the gm estimates in settings where the δ18O of leaf water varies strongly, affecting the δ18O (CO2) difference between the intercellular air space and the CO2–H2O exchange site.</p

Lithium ions induce prestalk-associated gene expression and inhibit prespore gene expression in Dictyostelium discoideum

We investigated the effect of Li+ on two types of cyclic AMP-regulated gene expression and on basal and cyclic AMP-stimulated inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) levels. Li+ effectively inhibits cyclic AMP-induced prespore gene expression, half-maximal inhibition occurring at about 2mM-LiCl. In contrast, Li+ (1-3 mM) promotes the cyclic AMP-induced increase of cysteine proteinase-2 mRNA levels, and induces the expression of this prestalk-associated gene in the absence of cyclic AMP stimuli. At concentrations exceeding 4-5 mM, LiCl inhibits cysteine proteinase-2 gene expression. LiCl reduces basal Ins(1,4,5)P3 levels and decreases the cyclic AMP-induced accumulation of Ins(1,4,5)P3; both effects occur half-maximally at 2-3 mM-LiCl. These results indicate that the induction of the cysteine proteinase-2 gene by Li+ is not due to elevated levels of Ins(1,4,5)P3. It is, however, possible that inhibition of prespore gene expression by Li+ is caused by Li+-induced reduction of basal and/or stimulated Ins(1,4,5)P3 levels

Quantification of Cre-mediated recombination by a novel strategy reveals a stable extra-chromosomal deletion-circle in mice

<p>Abstract</p> <p>Background</p> <p>Inducible conditional knockout animals are widely used to get insight in the function of genes and the pathogenesis of human diseases. These models frequently rely on Cre-mediated recombination of sequences flanked by Lox-P sites. To understand the consequences of gene disruption, it is essential to know the efficiency of the recombination process.</p> <p>Results</p> <p>Here, we describe a modification of the multiplex ligation-dependent probe amplification (MLPA), called extension-MLPA (eMLPA), which enables quantification of relatively small differences in DNA that are a consequence of Cre-mediated recombination. eMLPA, here applied on an inducible <it>Pkd1 </it>conditional deletion mouse model, simultaneously measures both the reduction of the floxed allele and the increase of the deletion allele in a single reaction thereby minimizing any type of experimental variation. Interestingly, with this method we were also able to observe the presence of the excised DNA fragment. This extra-chromosomal deletion-circle was detectable up to 5 months after activation of Cre.</p> <p>Conclusion</p> <p>eMLPA is a novel strategy which easily can be applied to measure the Cre-mediated recombination efficiency in each experimental case with high accuracy. In addition the fate of the deletion-circle can be followed simultaneously.</p