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| 2. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Hallquist, Mattias, 1969, et al.
(författare)
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The formation, properties and impact of secondary organic aerosol: Current and emerging issues
- 2009
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 9:14, s. 5155-5236
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Tidskriftsartikel (refereegranskat)abstract
- Secondary organic aerosol (SOA) accounts for a significant fraction of ambient tropospheric aerosol and a detailed knowledge of the formation, properties and transformation of SOA is therefore required to evaluate its impact on atmospheric processes, climate and human health. The chemical and physical processes associated with SOA formation are complex and varied, and, despite considerable progress in recent years, a quantitative and predictive understanding of SOA formation does not exist and therefore represents a major research challenge in atmospheric science. This review begins with an update on the current state of knowledge on the global SOA budget and is followed by an overview of the atmospheric degradation mechanisms for SOA precursors, gas-particle partitioning theory and the analytical techniques used to determine the chemical composition of SOA. A survey of recent laboratory, field and modeling studies is also presented. The following topical and emerging issues are highlighted and discussed in detail: molecular characterization of biogenic SOA constituents, condensed phase reactions and oligomerization, the interaction of atmospheric organic components with sulfuric acid, the chemical and photochemical processing of organics in the atmospheric aqueous phase, aerosol formation from real plant emissions, interaction of atmospheric organic components with water, thermodynamics and mixtures in atmospheric models. Finally, the major challenges ahead in laboratory, field and modeling studies of SOA are discussed and recommendations for future research directions are proposed.
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| 5. |
- Flores, J. M., et al.
(författare)
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Evolution of the complex refractive index in the UV spectral region in ageing secondary organic aerosol
- 2014
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 14:11, s. 5793-5806
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Tidskriftsartikel (refereegranskat)abstract
- The chemical and physical properties of secondary organic aerosol (SOA) formed by the photochemical degradation of biogenic and anthropogenic volatile organic compounds (VOC) are as yet still poorly constrained. The evolution of the complex refractive index (RI) of SOA, formed from purely biogenic VOC and mixtures of biogenic and anthropogenic VOC, was studied over a diurnal cycle in the SAPHIR photochemical outdoor chamber in Julich, Germany. The correlation of RI with SOA chemical and physical properties such as oxidation level and volatility was examined. The RI was retrieved by a newly developed broadband cavity-enhanced spectrometer for aerosol optical extinction measurements in the UV spectral region (360 to 420 nm). Chemical composition and volatility of the particles were monitored by a high-resolution time-of-flight aerosol mass spectrometer, and a volatility tandem differential mobility analyzer. SOA was formed by ozonolysis of either (i) a mixture of biogenic VOC (alpha-pinene and limonene), (ii) biogenic VOC mixture with subsequent addition of an anthropogenic VOC (p-xylene-d(10)), or (iii) a mixture of biogenic and anthropogenic VOC. The SOA aged by ozone/OH reactions up to 29.5 h was found to be non-absorbing in all cases. The SOA with p-xylene-d(10) showed an increase of the scattering component of the RI correlated with an increase of the O / C ratio and with an increase in the SOA density. There was a greater increase in the scattering component of the RI when the SOA was produced from the mixture of biogenic VOCs and anthropogenic VOC than from the sequential addition of the VOCs after approximately the same ageing time. The increase of the scattering component was inversely correlated with the SOA volatility. Two RI retrievals determined for the pure biogenic SOA showed a constant RI for up to 5 h of ageing. Mass spectral characterization shows the three types of the SOA formed in this study have a significant amount of semivolatile components. The influence of anthropogenic VOCs on the oxygenated organic aerosol as well as the atmospheric implications are discussed.
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| 6. |
- Fuzzi, S., et al.
(författare)
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Particulate matter, air quality and climate : lessons learned and future needs
- 2015
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 15:14, s. 8217-8299
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Tidskriftsartikel (refereegranskat)abstract
- The literature on atmospheric particulate matter (PM), or atmospheric aerosol, has increased enormously over the last 2 decades and amounts now to some 1500-2000 papers per year in the refereed literature. This is in part due to the enormous advances in measurement technologies, which have allowed for an increasingly accurate understanding of the chemical composition and of the physical properties of atmospheric particles and of their processes in the atmosphere. The growing scientific interest in atmospheric aerosol particles is due to their high importance for environmental policy. In fact, particulate matter constitutes one of the most challenging problems both for air quality and for climate change policies. In this context, this paper reviews the most recent results within the atmospheric aerosol sciences and the policy needs, which have driven much of the increase in monitoring and mechanistic research over the last 2 decades. The synthesis reveals many new processes and developments in the science underpinning climate-aerosol interactions and effects of PM on human health and the environment. However, while airborne particulate matter is responsible for globally important influences on premature human mortality, we still do not know the relative importance of the different chemical components of PM for these effects. Likewise, the magnitude of the overall effects of PM on climate remains highly uncertain. Despite the uncertainty there are many things that could be done to mitigate local and global problems of atmospheric PM. Recent analyses have shown that reducing black carbon (BC) emissions, using known control measures, would reduce global warming and delay the time when anthropogenic effects on global temperature would exceed 2 degrees C. Likewise, cost-effective control measures on ammonia, an important agricultural precursor gas for secondary inorganic aerosols (SIA), would reduce regional eutrophication and PM concentrations in large areas of Europe, China and the USA. Thus, there is much that could be done to reduce the effects of atmospheric PM on the climate and the health of the environment and the human population. A prioritized list of actions to mitigate the full range of effects of PM is currently undeliverable due to shortcomings in the knowledge of aerosol science; among the shortcomings, the roles of PM in global climate and the relative roles of different PM precursor sources and their response to climate and land use change over the remaining decades of this century are prominent. In any case, the evidence from this paper strongly advocates for an integrated approach to air quality and climate policies.
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| 7. |
- Laj, P., et al.
(författare)
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Measuring Atmospheric Composition Change
- 2009
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1873-2844 .- 1352-2310. ; 43:33, s. 5351-5414
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Tidskriftsartikel (refereegranskat)abstract
- Scientific findings from the last decades have clearly highlighted the need for a more comprehensive approach to atmospheric change processes. In fact, observation of atmospheric composition variables has been an important activity of atmospheric research that has developed instrumental tools (advanced analytical techniques) and platforms (instrumented passenger aircrafts, ground-based in-situ and remote sensing stations, earth observation satellite instruments) providing essential information on the composition of the atmosphere. The variability of the atmospheric system and the extreme complexity of the atmospheric cycles for short-lived gaseous and aerosol species have led to the development of complex models to interpret observations, test our theoretical understanding of atmospheric chemistry and predict future atmospheric composition. The validation of numerical models requires accurate information concerning the variability of atmospheric composition for targeted species via comparison with observations and measurements. In this paper, we provide an overview of recent advances in instrumentation and methodologies for measuring atmospheric composition changes from space, aircraft and the surface as well as recent improvements in laboratory techniques that permitted scientific advance in the field of atmospheric chemistry. Emphasis is given to the most promising and innovative technologies that will become operational in the near future to improve knowledge of atmospheric composition. Our current observation capacity, however, is not satisfactory to understand and predict future atmospheric composition changes, in relation to predicted climate warming. Based on the limitation of the current European observing system, we address the major gaps in a second part of the paper to explain why further developments in current observation strategies are still needed to strengthen and optimise an observing system not only capable of responding to the requirements of atmospheric services but also to newly open scientific questions.
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| 8. |
- Mircea, M, et al.
(författare)
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Importance of the organic aerosol fraction for modeling aerosol hygroscopic growth and activation: a case study in the Amazon Basin
- 2005
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Ingår i: Atmospheric Chemistry and Physics. - 1680-7324. ; 5, s. 3111-3126
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Tidskriftsartikel (refereegranskat)abstract
- The aerosol in the Amazon basin is dominated throughout the year by organic matter, for the most part soluble in water. In this modeling study, we show how the knowledge of water-soluble organic compounds (WSOC) and the associated physical and chemical properties (e.g. solubility, surface tension, dissociation into ions) affect the hygroscopic growth and activation of the aerosol in this area. The study is based on data obtained during the SMOCC field experiment carried out in Rondonia, Brazil, over a period encompassing the dry (biomass burning) season to the onset of the wet season (September to mid-November, 2002). The comparison of predicted and measured cloud condensation nuclei (CCN) number concentration shows that the knowledge of aerosol WSOC composition in terms of classes of compounds and of their relative molecular weights and acidic properties may be sufficient to predict aerosol activation, without any information on solubility. Conversely, the lack of knowledge on WSOC solubility leads to a high overestimation of the observed diameter growth factors (DGF) by the theory. Moreover, the aerosol water soluble inorganic species fail to predict both DGFs and CCN number concentration. In fact, this study shows that a good reproduction of the measured DGF and CCN concentration is obtained if the chemical composition of aerosol, especially that of WSOC, is appropriately taken into account in the calculations. New parameterizations for the computed CCN spectra are also derived which take into account the variability caused by chemical effects (surface tension, molecular composition, solubility, degree of dissociation of WSOC).
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| 9. |
- Monks, P. S., et al.
(författare)
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Atmospheric composition change : global and regional air quality
- 2009
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310 .- 1873-2844. ; 43:33, s. 5268-5350
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Forskningsöversikt (refereegranskat)abstract
- Air quality transcends all scales with in the atmosphere from the local to the global with handovers and feedbacks at each scale interaction. Air quality has manifold effects on health, ecosystems heritage and, climate. In this review the state of scientific understanding in relation to global and regional air quality is outlined. The review discusses air quality, in terms of emissions, processing and transport of trace gases and aerosols. New insights into the characterization of both natural and anthropogenic emissions are reviewed looking at both natural (e.g. dust and lightning) as well as plant emissions. Trends in anthropogenic emissions both by region and globally are discussed as well as biomass burning emissions. In terms of chemical processing the major air quality elements of ozone, non-methane hydrocarbons, nitrogen oxides and aerosols are covered. A number of topics are presented as a way of integrating the process view into the atmospheric context; these include the atmospheric oxidation efficiency, halogen and HOx chemistry, nighttime chemistry, tropical chemistry, heat waves, megacities, biomass burning and the regional hot spot of the Mediterranean. New findings with respect to the transport of pollutants across the scales are discussed, in particular the move to quantify the impact of long-range transport on regional air quality. Gaps and research questions that remain intractable are identified. The review concludes with a focus of research and policy questions for the coming decade. In particular, the policy challenges for concerted air quality and climate change policy (co-benefit) are discussed.
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| 10. |
- Schkolnik, G., et al.
(författare)
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Constraining the density and complex refractive index of elemental and organic carbon in biomass burning aerosol using optical and chemical measurements
- 2007
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1352-2310. ; 41:5, s. 1107-1118
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Tidskriftsartikel (refereegranskat)abstract
- The role of biomass burning aerosols in the climate system is still poorly quantified, in part due to uncertainties regarding the optical properties of elemental and organic carbon (EC and OC, respectively), the main constituents of pyrogenic aerosols. In this study, we utilize comprehensive physical and chemical field measurements of biomass burning aerosols in Brazil to constrain the densities and refractive indices (RI) of EC and OC in these particles, by comparing their optically and chemically derived RI. The optically derived effective RI are retrieved from the measured absorption and scattering coefficients using a Mie scattering algorithm, and serve as a reference dataset, while the chemically derived effective RI are calculated from the measured chemical composition using electromagnetic mixing rules. The results are discussed in light of the observed combustion conditions, and in an effort to derive conclusions as to the chemical and optical properties of the usually less well-characterized components of biomass burning aerosols, namely, elemental carbon and organic matter. The best agreement between the optically and chemically derived RI was achieved by assigning a density of rho(EC) = 1.8 g cm(-3) and refractive index RIEC = 1.87 - 0.22i to the EC component, and rho = 0.9 g cm(-3) and RI = 1.4 - 0i to the unidentified organic matter fraction of the particles. These parameters suggest low graphitization levels for the EC, and a dominant proportion of aliphatic compounds in the unidentified organic matter. Combining the density and RI of the unidentified organic matter with the properties of the chemically characterized organic fraction yields rho = 1.1 g cm(-3) and RI = 1.3 - 0i for the total aerosol OC. (c) 2006 Elsevier Ltd. All rights reserved.
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| 11. |
- Zhao, D. F., et al.
(författare)
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Environmental conditions regulate the impact of plants on cloud formation
- 2017
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Ingår i: Nature Communications. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- The terrestrial vegetation emits large amounts of volatile organic compounds (VOC) into the atmosphere, which on oxidation produce secondary organic aerosol (SOA). By acting as cloud condensation nuclei (CCN), SOA influences cloud formation and climate. In a warming climate, changes in environmental factors can cause stresses to plants, inducing changes of the emitted VOC. These can modify particle size and composition. Here we report how induced emissions eventually affect CCN activity of SOA, a key parameter in cloud formation. For boreal forest tree species, insect infestation by aphids causes additional VOC emissions which modifies SOA composition thus hygroscopicity and CCN activity. Moderate heat increases the total amount of constitutive VOC, which has a minor effect on hygroscopicity, but affects CCN activity by increasing the particles' size. The coupling of plant stresses, VOC composition and CCN activity points to an important impact of induced plant emissions on cloud formation and climate.
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| 12. |
- Zhao, D. F., et al.
(författare)
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Size-dependent hygroscopicity parameter (κ) and chemical composition of secondary organic cloud condensation nuclei
- 2015
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Ingår i: Geophysical Research Letters. - 1944-8007. ; 42:24
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Tidskriftsartikel (refereegranskat)abstract
- Secondary organic aerosol components (SOA) contribute significantly to the activation of cloud condensation nuclei (CCN) in the atmosphere. The CCN activity of internally mixed submicron SOA particles is often parameterized assuming a size-independent single-hygroscopicity parameter κ. In the experiments done in a large atmospheric reactor (SAPHIR, Simulation of Atmospheric PHotochemistry In a large Reaction chamber, Jülich), we consistently observed size-dependent κ and particle composition for SOA from different precursors in the size range of 50nm–200nm. Smaller particles had higher κ and a higher degree of oxidation, although all particles were formed from the same reaction mixture. Since decreasing volatility and increasing hygroscopicity often covary with the degree of oxidation, the size dependence of composition and hence of CCN activity can be understood by enrichment of higher oxygenated, low-volatility hygroscopic compounds in smaller particles. Neglecting the size dependence of κ can lead to significant bias in the prediction of the activated fraction of particles during cloud formation.
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