| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Lee, Shan Hu, et al.
(författare)
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Isoprene suppression of new particle formation : Potential mechanisms and implications
- 2016
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Ingår i: Journal of Geophysical Research: Atmospheres. - 2169-897X. ; 121:24, s. 14-635
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Tidskriftsartikel (refereegranskat)abstract
- Secondary aerosols formed from anthropogenic pollutants and natural emissions have substantial impacts on human health, air quality, and the Earth's climate. New particle formation (NPF) contributes up to 70% of the global production of cloud condensation nuclei (CCN), but the effects of biogenic volatile organic compounds (BVOCs) and their oxidation products on NPF processes in forests are poorly understood. Observations show that isoprene, the most abundant BVOC, suppresses NPF in forests. But the previously proposed chemical mechanism underlying this suppression process contradicts atmospheric observations. By reviewing observations made in other forests, it is clear that NPF rarely takes place during the summer when emissions of isoprene are high, even though there are sufficient concentrations of monoterpenes. But at present it is not clear how isoprene and its oxidation products may change the oxidation chemistry of terpenes and how NOx and other atmospheric key species affect NPF in forest environments. Future laboratory experiments with chemical speciation of gas phase nucleation precursors and clusters and chemical composition of particles smaller than 10 nm are required to understand the role of isoprene in NPF. Our results show that climate models can overpredict aerosol's first indirect effect when not considering the absence of NPF in the southeastern U.S. forests during the summer using the current nucleation algorithm that includes only sulfuric acid and total concentrations of low-volatility organic compounds. This highlights the importance of understanding NPF processes as function of temperature, relative humidity, and BVOC compositions to make valid predictions of NPF and CCN at a wide range of atmospheric conditions.
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| 3. |
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| 4. |
- Artaxo, Paulo, et al.
(författare)
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Tropical and Boreal Forest – Atmosphere Interactions : A Review
- 2022
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Ingår i: Tellus. Series B, Chemical and physical meteorology. - : Stockholm University Press. - 0280-6509 .- 1600-0889. ; 74:1, s. 24-163
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Forskningsöversikt (refereegranskat)abstract
- This review presents how the boreal and the tropical forests affect the atmosphere, its chemical composition, its function, and further how that affects the climate and, in return, the ecosystems through feedback processes. Observations from key tower sites standing out due to their long-term comprehensive observations: The Amazon Tall Tower Observatory in Central Amazonia, the Zotino Tall Tower Observatory in Siberia, and the Station to Measure Ecosystem-Atmosphere Relations at Hyytiäla in Finland. The review is complemented by short-term observations from networks and large experiments.The review discusses atmospheric chemistry observations, aerosol formation and processing, physiochemical aerosol, and cloud condensation nuclei properties and finds surprising similarities and important differences in the two ecosystems. The aerosol concentrations and chemistry are similar, particularly concerning the main chemical components, both dominated by an organic fraction, while the boreal ecosystem has generally higher concentrations of inorganics, due to higher influence of long-range transported air pollution. The emissions of biogenic volatile organic compounds are dominated by isoprene and monoterpene in the tropical and boreal regions, respectively, being the main precursors of the organic aerosol fraction.Observations and modeling studies show that climate change and deforestation affect the ecosystems such that the carbon and hydrological cycles in Amazonia are changing to carbon neutrality and affect precipitation downwind. In Africa, the tropical forests are so far maintaining their carbon sink.It is urgent to better understand the interaction between these major ecosystems, the atmosphere, and climate, which calls for more observation sites, providing long-term data on water, carbon, and other biogeochemical cycles. This is essential in finding a sustainable balance between forest preservation and reforestation versus a potential increase in food production and biofuels, which are critical in maintaining ecosystem services and global climate stability. Reducing global warming and deforestation is vital for tropical forests.
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| 5. |
- Barkley, Michael P., et al.
(författare)
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Assessing sources of uncertainty in formaldehyde air mass factors over tropical South America: Implications for top-down isoprene emission estimates
- 2012
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Ingår i: Journal of Geophysical Research. - 2156-2202. ; 117, s. 13304-13304
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Tidskriftsartikel (refereegranskat)abstract
- We use a nested-grid version of the GEOS-Chem chemistry transport model, constrained by isoprene emissions from the Model of Emissions of Gases and Aerosols from Nature (MEGAN), and the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) bottom-up inventories, to evaluate the impact that surface isoprene emissions have on formaldehyde (HCHO) air-mass factors (AMFs) and vertical column densities (VCDs) over tropical South America during 2006, as observed by the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI). Although the large-scale seasonal variability of monthly mean HCHO VCDs is typically unaffected by the choice of bottom-up inventory, large relative differences of up to +/- 45% in the HCHO VCD can occur for individual regions and months, but typically most VCD differences are of order +/- 20%. These relative changes are comparable to those produced by other sources of uncertainty in the AMF including aerosols and surface albedo, but less than those from clouds. In a sensitivity test, we find that top-down annual isoprene emissions inferred from SCIAMACHY and OMI HCHO vertical columns can vary by as much as +/- 30-50% for each instrument respectively, depending on the region studied and the a priori isoprene emissions used. Our analysis suggests that the influence of the a priori isoprene emissions on HCHO AMFs and VCDs is therefore non-negligible and must be carefully considered when inferring top-down isoprene emissions estimates over this, or potentially any other, region.
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| 6. |
- Barkley, Michael P., et al.
(författare)
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Can a "state of the art" chemistry transport model simulate Amazonian tropospheric chemistry?
- 2011
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Ingår i: Journal of Geophysical Research. - 2156-2202. ; 116, s. 16302-16302
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Tidskriftsartikel (refereegranskat)abstract
- We present an evaluation of a nested high-resolution Goddard Earth Observing System (GEOS)-Chem chemistry transport model simulation of tropospheric chemistry over tropical South America. The model has been constrained with two isoprene emission inventories: (1) the canopy-scale Model of Emissions of Gases and Aerosols from Nature (MEGAN) and (2) a leaf-scale algorithm coupled to the Lund-Potsdam-Jena General Ecosystem Simulator (LPJ-GUESS) dynamic vegetation model, and the model has been run using two different chemical mechanisms that contain alternative treatments of isoprene photo-oxidation. Large differences of up to 100 Tg C yr (1) exist between the isoprene emissions predicted by each inventory, with MEGAN emissions generally higher. Based on our simulations we estimate that tropical South America (30-85 degrees W, 14 degrees N-25 degrees S) contributes about 15-35% of total global isoprene emissions. We have quantified the model sensitivity to changes in isoprene emissions, chemistry, boundary layer mixing, and soil NOx emissions using ground-based and airborne observations. We find GEOS-Chem has difficulty reproducing several observed chemical species; typically hydroxyl concentrations are underestimated, whilst mixing ratios of isoprene and its oxidation products are overestimated. The magnitude of model formaldehyde (HCHO) columns are most sensitive to the choice of chemical mechanism and isoprene emission inventory. We find GEOS-Chem exhibits a significant positive bias (10-100%) when compared with HCHO columns from the Scanning Imaging Absorption Spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI) for the study year 2006. Simulations that use the more detailed chemical mechanism and/or lowest isoprene emissions provide the best agreement to the satellite data, since they result in lower-HCHO columns.
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| 7. |
- Barkley, Michael P., et al.
(författare)
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Top-down isoprene emissions over tropical South America inferred from SCIAMACHY and OMI formaldehyde columns
- 2013
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Ingår i: Journal of Geophysical Research: Atmospheres. - : American Geophysical Union (AGU). - 2169-8996 .- 2169-897X. ; 118:12, s. 6849-6868
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Tidskriftsartikel (refereegranskat)abstract
- We use formaldehyde (HCHO) vertical column measurements from the Scanning Imaging Absorption spectrometer for Atmospheric Chartography (SCIAMACHY) and Ozone Monitoring Instrument (OMI), and a nested-grid version of the GEOS-Chem chemistry transport model, to infer an ensemble of top-down isoprene emission estimates from tropical South America during 2006, using different model configurations and assumptions in the HCHO air-mass factor (AMF) calculation. Scenes affected by biomass burning are removed on a daily basis using fire count observations, and we use the local model sensitivity to identify locations where the impact of spatial smearing is small, though this comprises spatial coverage over the region. We find that the use of the HCHO column data more tightly constrains the ensemble isoprene emission range from 27-61TgC to 31-38TgC for SCIAMACHY, and 45-104TgC to 28-38TgC for OMI. Median uncertainties of the top-down emissions are about 60-260% for SCIAMACHY, and 10-90% for OMI. We find that the inferred emissions are most sensitive to uncertainties in cloud fraction and cloud top pressure (differences of +/- 10%), the a priori isoprene emissions (+/- 20%), and the HCHO vertical column retrieval (+/- 30%). Construction of continuous top-down emission maps generally improves GEOS-Chem's simulation of HCHO columns over the region, with respect to both the SCIAMACHY and OMI data. However, if local time top-down emissions are scaled to monthly mean values, the annual emission inferred from SCIAMACHY are nearly twice those from OMI. This difference cannot be explained by the different sampling of the sensors or uncertainties in the AMF calculation.
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| 8. |
- Bauwens, Maite, et al.
(författare)
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Recent past (1979-2014) and future (2070-2099) isoprene fluxes over Europe simulated with the MEGAN-MOHYCAN model
- 2018
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 15:12, s. 3673-3690
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Tidskriftsartikel (refereegranskat)abstract
- Isoprene is a highly reactive volatile organic compound emitted by vegetation, known to be a precursor of secondary organic aerosols and to enhance tropospheric ozone formation under polluted conditions. Isoprene emissions respond strongly to changes in meteorological parameters such as temperature and solar radiation. In addition, the increasing CO2 concentration has a dual effect, as it causes both a direct emission inhibition as well as an increase in biomass through fertilization. In this study we used the MEGAN (Model of Emissions of Gases and Aerosols from Nature) emission model coupled with the MOHYCAN (Model of HYdrocarbon emissions by the CANopy) canopy model to calculate the isoprene fluxes emitted by vegetation in the recent past (1979-2014) and in the future (2070-2099) over Europe at a resolution of 0.1° × 0.1°. As a result of the changing climate, modeled isoprene fluxes increased by 1.1%yr-1 on average in Europe over 1979-2014, with the strongest trends found over eastern Europe and European Russia, whereas accounting for the CO2 inhibition effect led to reduced emission trends (0.76%yr-1). Comparisons with field campaign measurements at seven European sites suggest that the MEGAN-MOHYCAN model provides a reliable representation of the temporal variability of the isoprene fluxes over timescales between 1h and several months. For the 1979-2014 period the model was driven by the ECMWF ERA-Interim reanalysis fields, whereas for the comparison of current with projected future emissions, we used meteorology simulated with the ALARO regional climate model. Depending on the representative concentration pathway (RCP) scenarios for greenhouse gas concentration trajectories driving the climate projections, isoprene emissions were found to increase by +7% (RCP2.6), +33% (RCP4.5), and +83% (RCP8.5), compared to the control simulation, and even stronger increases were found when considering the potential impact of CO2 fertilization: +15% (RCP2.6), +52% (RCP4.5), and +141% (RCP8.5). However, the inhibitory CO2 effect goes a long way towards canceling these increases. Based on two distinct parameterizations, representing strong or moderate inhibition, the projected emissions accounting for all effects were estimated to be 0-17% (strong inhibition) and 11-65% (moderate inhibition) higher than in the control simulation. The difference obtained using the two CO2 parameterizations underscores the large uncertainty associated to this effect.
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| 9. |
- Hartmann, Ola, et al.
(författare)
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Magnetic properties of the multiferroic chromium thio-spinels CdCr2S4 and HgCr2S4
- 2013
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Ingår i: European Physical Journal B. - : Springer Science and Business Media LLC. - 1434-6028 .- 1434-6036. ; 86:4, s. 148-
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Tidskriftsartikel (refereegranskat)abstract
- Powder samples of CdCr2S4 and HgCr2S4 were investigated with respect to their magnetic behavior using muon spin rotation/relaxation spectroscopy (mu SR). In CdCr2S4, a second order magnetic transition at 83 +/- 1 K is confirmed. No influence on the mu SR magnetic parameters due to the simultaneous ferroelectric transition was detected. In the limit T -> 0, persistent spin fluctuation exists as a consequence of magnetic frustration. The proposed structural transition around 150 K is barely visible in the mu SR spectra, indicating that the change in local symmetry is subtle. In HgCr2S4, we see in zero field at 27 +/- 2 K a second order transition from the paramagnetic into a long-range ordered (LRO) magnetic state. This LRO state is characterized in the mu SR spectra by a spontaneous spin precession signal. Applications of moderate magnetic fields (up to 450 mT) destroy the precession signal in favor of a rapidly decaying exponential signal. It reflects short-range order (SRO) of strongly correlated dynamic spins. The magnitude of the field required to induce this change is dependent on temperature. The observation of an increase of magnetic spin fluctuations with applied field suggests that spin dynamics play a key role in the field induced changes of the magnetic properties.
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| 10. |
- Jaars, Kerneels, et al.
(författare)
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Measurements of biogenic volatile organic compounds at a grazed savannah grassland agricultural landscape in South Africa
- 2016
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 16:24, s. 15665-15688
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Tidskriftsartikel (refereegranskat)abstract
- Biogenic volatile organic compounds (BVOCs) play an important role in the chemistry of the troposphere, especially in the formation of tropospheric ozone (O3) and secondary organic aerosols (SOA). Ecosystems produce and emit a large number of BVOCs. It is estimated on a global scale that approximately 90% of annual BVOC emissions are from terrestrial sources. In this study, measurements of BVOCs were conducted at the Welgegund measurement station (South Africa), which is considered to be a regionally representative background site situated in savannah grasslands. Very few BVOC measurements exist for savannah grasslands and results presented in this study are the most extensive for this type of landscape. Samples were collected twice a week for 2h during the daytime and 2h during the night-time through two long-term sampling campaigns from February 2011 to February 2012 and from December 2013 to February 2015, respectively. Individual BVOCs were identified and quantified using a thermal desorption instrument, which was connected to a gas chromatograph and a mass selective detector. The annual median concentrations of isoprene, 2-methyl-3-butene-2-ol (MBO), monoterpene and sesquiterpene (SQT) during the first campaign were 14, 7, 120 and 8pptv, respectively, and 14, 4, 83 and 4pptv, respectively, during the second campaign. The sum of the concentrations of the monoterpenes were at least an order of magnitude higher than the concentrations of other BVOC species during both sampling campaigns, with α-pinene being the most abundant species. The highest BVOC concentrations were observed during the wet season and elevated soil moisture was associated with increased BVOC concentrations. However, comparisons with measurements conducted at other landscapes in southern Africa and the rest of the world that have more woody vegetation indicated that BVOC concentrations were, in general, significantly lower for savannah grasslands. Furthermore, BVOC concentrations were an order of magnitude lower compared to total aromatic concentrations measured at Welgegund. An analysis of concentrations by wind direction indicated that isoprene concentrations were higher from the western sector that is considered to be a relatively clean regional background region with no large anthropogenic point sources, while wind direction did not indicate any significant differences in the concentrations of the other BVOC species. Statistical analysis indicated that soil moisture had the most significant impact on atmospheric levels of MBO, monoterpene and SQT concentrations, whereas temperature had the greatest influence on isoprene levels. The combined O3 formation potentials of all the BVOCs measured calculated with maximum incremental reactivity (MIR) coefficients during the first and second campaign were 1162 and 1022pptv, respectively. α-Pinene and limonene had the highest reaction rates with O3, whereas isoprene exhibited relatively small contributions to O3 depletion. Limonene, α-pinene and terpinolene had the largest contributions to the OH reactivity of BVOCs measured at Welgegund for all of the months during both sampling campaigns.
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