Biogenic and biomass burning organic aerosol in a boreal forest at Hyytiälä, Finland, during HUMPPA-COPEC 2010

Submicron aerosol particles were collected during July and August 2010 in Hyytiälä, Finland, to determine the composition and sources of aerosol at that boreal forest site. Submicron particles were collected on Teflon filters and analyzed by Fourier transform infrared (FTIR) spectroscopy for organic functional groups (OFGs). Positive matrix factorization (PMF) was applied to aerosol mass spectrometry (AMS) measurements and FTIR spectra to identify summertime sources of submicron aerosol mass at the sampling site. The two largest sources of organic mass (OM) in particles identified at Hyytiälä were (1) biogenic aerosol from surrounding local forest and (2) biomass burning aerosol, transported 4–5 days from large wildfires burning near Moscow, Russia, and northern Ukraine. The robustness of this apportionment is supported by the agreement of two independent analytical methods for organic measurements with three statistical techniques. FTIR factor analysis was more sensitive to the chemical differences between biogenic and biomass burning organic components, while AMS factor analysis had a higher time resolution that more clearly linked the temporal behavior of separate OM factors to that of different source tracers even though their fragment mass spectrum were similar. The greater chemical sensitivity of the FTIR is attributed to the nondestructive preparation and the functional group specificity of spectroscopy. The FTIR spectra show strong similarities among biogenic and biomass burning factors from different regions as well as with reference OM (namely olive tree burning organic aerosol and α-pinene chamber secondary organic aerosol (SOA)). The biogenic factor correlated strongly with temperature and oxidation products of biogenic volatile organic compounds (BVOCs), included more than half of the oxygenated OFGs (carbonyl groups at 29% and carboxylic acid groups at 22%), and represented 35% of the submicron OM. Compared to previous studies at Hyytiälä, the summertime biogenic OM is 1.5 to 3 times larger than springtime biogenic OM (0.64 μg m^−3 and 0.4 μg m^−3, measured in 2005 and 2007, respectively), even though it contributed only 35% of OM. The biomass burning factor contributed 25% of OM on average and up to 62% of OM during three periods of transported biomass burning emissions: 26–28 July, 29–30 July, and 8–9 August, with OFG consisting mostly of carbonyl (41%) and alcohol (25%) groups. The high summertime terrestrial biogenic OM (1.7 μg m^−3) and the high biomass burning contributions (1.2 μg m^−3) were likely due to the abnormally high temperatures that resulted in both stressed boreal forest conditions with high regional BVOC emissions and numerous wildfires in upwind regions

Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. phaseolicola and Botrytis cinerea infection

Phaseolus vulgaris cv. Korona plants were inoculated with the bacteria Pseudomonas syringae pv. phaseolicola (Psp), necrotrophic fungus Botrytis cinerea (Bc) or with both pathogens sequentially. The aim of the experiment was to determine how plants cope with multiple infection with pathogens having different attack strategy. Possible suppression of the non-specific infection with the necrotrophic fungus Bc by earlier Psp inoculation was examined. Concentration of reactive oxygen species (ROS), such as superoxide anion (O2 -) and H2O2 and activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were determined 6, 12, 24 and 48 h after inoculation. The measurements were done for ROS cytosolic fraction and enzymatic cytosolic or apoplastic fraction. Infection with Psp caused significant increase in ROS levels since the beginning of experiment. Activity of the apoplastic enzymes also increased remarkably at the beginning of experiment in contrast to the cytosolic ones. Cytosolic SOD and guaiacol peroxidase (GPOD) activities achieved the maximum values 48 h after treatment. Additional forms of the examined enzymes after specific Psp infection were identified; however, they were not present after single Bc inoculation. Subsequent Bc infection resulted only in changes of H2O2 and SOD that occurred to be especially important during plant–pathogen interaction. Cultivar Korona of common bean is considered to be resistant to Psp and mobilises its system upon infection with these bacteria. We put forward a hypothesis that the extent of defence reaction was so great that subsequent infection did not trigger significant additional response

Application of a two layer model with the aid of a slope collapse model to the natural landslide dam outburst process

Earthquakes and heavy rainfall result in the formation of landslide dams following a massive collapse or landslide. Landslide dams can result in catastrophic outburst floods or debris flows when the dam breaches with overtopping erosion. Therefore, it is important to determine the discharge rate and area of flooding due to overtopping erosion to mitigate disasters triggered by landslide dams. This study applied a two-layer model that incorporates a slope-collapse model to the erosion process at landslide dams. The two-layer model was proposed by Takahama and deals with the process of deposition-erosion with fully dispersed debris flow and sediment sheet flow. A two-layer model is derived to unify these two kinds of flow. Moreover, Takahama applied this model to a two-dimensional numerical simulation of debris flow, and found that the model can analyze phenomena in which the veloc- ity direction of the upper-layer water ow differs from that of the lower layer sediment-water mixture ow. Furthermore, we introduced the slope-collapse model proposed by Sekine to express gradual collapse of the slope due to erosion in the riverbed. The model shows the process that maintains a constant angle at the side bank. We examined the erosion and deposit process of a landslide dam with a numerical simulation

Ethylene Synthesis and Regulated Expression of Recombinant Protein in Synechocystis sp PCC 6803

The ethylene-forming enzyme (EFE) from Pseudomonas syringae catalyzes the synthesis of ethylene which can be easily detected in the headspace of closed cultures. A synthetic codon-optimized gene encoding N-terminal His-tagged EFE (EFEh) was expressed in Synechocystis sp. PCC 6803 (Synechocystis) and Escherichia coli (E. coli) under the control of diverse promoters in a self-replicating broad host-range plasmid. Ethylene synthesis was stably maintained in both organisms in contrast to earlier work in Synechococcus elongatus PCC 7942. The rate of ethylene accumulation was used as a reporter for protein expression in order to assess promoter strength and inducibility with the different expression systems. Several metal-inducible cyanobacterial promoters did not function in E. coli but were well-regulated in cyanobacteria, albeit at a low level of expression. The E. coli promoter P(trc) resulted in constitutive expression in cyanobacteria regardless of whether IPTG was added or not. In contrast, a Lac promoter variant, P(A1lacO-1), induced EFE-expression in Synechocystis at a level of expression as high as the Trc promoter and allowed a fine level of IPTG-dependent regulation of protein-expression. The regulation was tight at low cell density and became more relaxed in more dense cultures. A synthetic quorum-sensing promoter system was also constructed and shown to function well in E. coli, however, only a very low level of EFE-activity was observed in Synechocystis, independent of cell density

Postlimiters and Simple Dirty-Cell Detection for Three-Dimensional Unstructured (Unlimited) Aerodynamic Simulations

The postlimiter (simple a posteriori slope limiter) is an anti-slope-limiting mechanism to preserve nominal second order in space as much as possible. This technique has been demonstrated to increase resolutions of two-dimensional simulations up to four times in each dimension [Kitamura, K., and Hashimoto, A., “Simple a posteriori Slope Limiter (Post Limiter) for High Resolution and Efficient Flow Computations,” Journal of Computational Physics, Vol. 341, July 2017, pp. 313–340]. This paper extends the postlimiter to three dimensions with an emphasis on ”dirty” (meaning ill-shaped) cells, which arise in practical three-dimensional (3-D) unstructured grids over complex geometries. Gradient accuracy is known to significantly deteriorate on dirty cells, and a slope limiter needs to be applied. However, the original postlimiter does not recognize dirty cells and deactivates a slope limiter. To address this issue, a simple dirty-cell detection method is proposed and incorporated into the postlimiter. The 3-D version of postlimiter (referred to as “postlimiter 3”) is successfully incorporated into fast aerodynamic routine (FaSTAR), a 3-D unstructured grid flow solver is developed at the Japan Aerospace Exploration Agency. Postlimiter 3 can handle general 3-D unstructured grids. Numerical examples support its efficiency, accuracy, robustness, and applicability to a wide spectrum of aerodynamic problems of high engineering importance.journal articl

Organic nitrate aerosol formation via NO_3 + biogenic volatile organic compounds in the southeastern United States

Gas- and aerosol-phase measurements of oxidants, biogenic volatile organic compounds (BVOCs) and organic nitrates made during the Southern Oxidant and Aerosol Study (SOAS campaign, Summer 2013) in central Alabama show that a nitrate radical (NO_3) reaction with monoterpenes leads to significant secondary aerosol formation. Cumulative losses of NO_3 to terpenes are correlated with increase in gas- and aerosol-organic nitrate concentrations made during the campaign. Correlation of NO_3 radical consumption to organic nitrate aerosol formation as measured by aerosol mass spectrometry and thermal dissociation laser-induced fluorescence suggests a molar yield of aerosol-phase monoterpene nitrates of 23–44 %. Compounds observed via chemical ionization mass spectrometry (CIMS) are correlated to predicted nitrate loss to BVOCs and show C_(10)H_(17)NO_5, likely a hydroperoxy nitrate, is a major nitrate-oxidized terpene product being incorporated into aerosols. The comparable isoprene product C_5H_9NO_5 was observed to contribute less than 1 % of the total organic nitrate in the aerosol phase and correlations show that it is principally a gas-phase product from nitrate oxidation of isoprene. Organic nitrates comprise between 30 and 45 % of the NOy budget during SOAS. Inorganic nitrates were also monitored and showed that during incidents of increased coarse-mode mineral dust, HNO_3 uptake produced nitrate aerosol mass loading at a rate comparable to that of organic nitrate produced via NO_3 + BVOCs

Single-cell RNA-sequencing resolves self-antigen expression during mTEC development

The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization. Furthermore, expression patterns of TRA genes have been suggested to change over the course of mTEC development. Herein we have used single-cell RNA-sequencing to resolve patterns of TRA expression during mTEC development. Our data indicated that mTEC development consists of three distinct stages, correlating with previously described jTEC, mTEChi and mTEClo phenotypes. For each subpopulation, we have identified marker genes useful in future studies. Aire-induced TRAs were switched on during jTEC-mTEC transition and were expressed in genomic clusters, while otherwise the subsets expressed largely overlapping sets of TRAs. Moreover, population-level analysis of TRA expression frequencies suggested that such differences might not be necessary to achieve efficient thymocyte selection.RM is supported by a PhD Fellowship from the Fundação para a Ciência e Tecnologia, Portugal (SFRH/ BD/51950/2012). XZ is supported by an Advanced Postdoc Mobility Fellowship from the Swiss National Science Foundation (SNSF, grant number P300P2_151352). Part of the work was performed during XZ’s visit to the Simons Institute for the Theory of Computing. TL is supported by the Academy of Finland (Decision 311081). The authors would like to thank Bee Ling Ng and the staff of the Cytometry Core Facility, and Stephan Lorenz and the staff of the Single Cell Genomics Core Facility for their contribution. Mark Lynch is acknowledged for technical assistance with the Fluidigm C1 platform. Mike Stubbington and Kylie James are acknowledged for revising the language of the manuscript. We thank Sarah Teichmann for help and discussions regarding the manuscript.info:eu-repo/semantics/publishedVersio

A marine biogenic source of atmospheric ice nucleating particles

The amount of ice present in clouds can affect cloud lifetime, precipitation and radiative properties1,2. The formation of ice in clouds is facilitated by the presence of airborne ice nucleating particles1,2. Sea spray is one of the major global sources of atmospheric particles, but it is unclear to what extent these particles are capable of nucleating ice3-11. Sea spray aerosol contains large amounts of organic material that is ejected into the atmosphere during bubble bursting at the organically enriched sea-air interface or sea surface microlayer12-19. Here we show that organic material in the sea surface microlayer nucleates ice under conditions relevant for mixed-phase cloud and high-altitude ice cloud formation. The ice nucleating material is likely biogenic and less than ~0.2 μm in size. We find that exudates separated from cells of the marine diatom T. Pseudonana nucleate ice and propose that organic material associated with phytoplankton cell exudates is a likely candidate for the observed ice nucleating ability of the microlayer samples. Global model simulations of marine organic aerosol in combination with our measurements suggest that marine organic material may be an important source of ice nucleating particles in remote marine environments such as the Southern Ocean, North Pacific and North Atlantic