| 1. |
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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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| 3. |
- 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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| 4. |
- 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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| 5. |
- 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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| 6. |
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| 7. |
- 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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| 8. |
- DeMott, Paul J., et al.
(författare)
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The Fifth International Workshop on Ice Nucleation phase 2 (FIN-02) : Laboratory intercomparison of ice nucleation measurements
- 2018
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 11:11, s. 6231-6257
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Tidskriftsartikel (refereegranskat)abstract
- The second phase of the Fifth International Ice Nucleation Workshop (FIN-02) involved the gathering of a large number of researchers at the Karlsruhe Institute of Technology's Aerosol Interactions and Dynamics of the Atmosphere (AIDA) facility to promote characterization and understanding of ice nucleation measurements made by a variety of methods used worldwide. Compared to the previous workshop in 2007, participation was doubled, reflecting a vibrant research area. Experimental methods involved sampling of aerosol particles by direct processing ice nucleation measuring systems from the same volume of air in separate experiments using different ice nucleating particle (INP) types, and collections of aerosol particle samples onto filters or into liquid for sharing amongst measurement techniques that post-process these samples. In this manner, any errors introduced by differences in generation methods when samples are shared across laboratories were mitigated. Furthermore, as much as possible, aerosol particle size distribution was controlled so that the size limitations of different methods were minimized. The results presented here use data from the workshop to assess the comparability of immersion freezing measurement methods activating INPs in bulk suspensions, methods that activate INPs in condensation and/or immersion freezing modes as single particles on a substrate, continuous flow diffusion chambers (CFDCs) directly sampling and processing particles well above water saturation to maximize immersion and subsequent freezing of aerosol particles, and expansion cloud chamber simulations in which liquid cloud droplets were first activated on aerosol particles prior to freezing. The AIDA expansion chamber measurements are expected to be the closest representation to INP activation in atmospheric cloud parcels in these comparisons, due to exposing particles freely to adiabatic cooling. The different particle types used as INPs included the minerals illite NX and potassium feldspar (K-feldspar), two natural soil dusts representative of arable sandy loam (Argentina) and highly erodible sandy dryland (Tunisia) soils, respectively, and a bacterial INP (Snomax®). Considered together, the agreement among post-processed immersion freezing measurements of the numbers and fractions of particles active at different temperatures following bulk collection of particles into liquid was excellent, with possible temperature uncertainties inferred to be a key factor in determining INP uncertainties. Collection onto filters for rinsing versus directly into liquid in impingers made little difference. For methods that activated collected single particles on a substrate at a controlled humidity at or above water saturation, agreement with immersion freezing methods was good in most cases, but was biased low in a few others for reasons that have not been resolved, but could relate to water vapor competition effects. Amongst CFDC-style instruments, various factors requiring (variable) higher supersaturations to achieve equivalent immersion freezing activation dominate the uncertainty between these measurements, and for comparison with bulk immersion freezing methods. When operated above water saturation to include assessment of immersion freezing, CFDC measurements often measured at or above the upper bound of immersion freezing device measurements, but often underestimated INP concentration in comparison to an immersion freezing method that first activates all particles into liquid droplets prior to cooling (the PIMCA-PINC device, or Portable Immersion Mode Cooling chAmber-Portable Ice Nucleation Chamber), and typically slightly underestimated INP number concentrations in comparison to cloud parcel expansions in the AIDA chamber; this can be largely mitigated when it is possible to raise the relative humidity to sufficiently high values in the CFDCs, although this is not always possible operationally. Correspondence of measurements of INPs among direct sampling and post-processing systems varied depending on the INP type. Agreement was best for Snomax® particles in the temperature regime colder than -10°C, where their ice nucleation activity is nearly maximized and changes very little with temperature. At temperatures warmer than -10°C, Snomax® INP measurements (all via freezing of suspensions) demonstrated discrepancies consistent with previous reports of the instability of its protein aggregates that appear to make it less suitable as a calibration INP at these temperatures. For Argentinian soil dust particles, there was excellent agreement across all measurement methods; measures ranged within 1 order of magnitude for INP number concentrations, active fractions and calculated active site densities over a 25 to 30°C range and 5 to 8 orders of corresponding magnitude change in number concentrations. This was also the case for all temperatures warmer than -25°C in Tunisian dust experiments. In contrast, discrepancies in measurements of INP concentrations or active site densities that exceeded 2 orders of magnitude across a broad range of temperature measurements found at temperatures warmer than -25°C in a previous study were replicated for illite NX. Discrepancies also exceeded 2 orders of magnitude at temperatures of -20 to -25°C for potassium feldspar (K-feldspar), but these coincided with the range of temperatures at which INP concentrations increase rapidly at approximately an order of magnitude per 2°C cooling for K-feldspar. These few discrepancies did not outweigh the overall positive outcomes of the workshop activity, nor the future utility of this data set or future similar efforts for resolving remaining measurement issues. Measurements of the same materials were repeatable over the time of the workshop and demonstrated strong consistency with prior studies, as reflected by agreement of data broadly with parameterizations of different specific or general (e.g., soil dust) aerosol types. The divergent measurements of the INP activity of illite NX by direct versus post-processing methods were not repeated for other particle types, and the Snomax° data demonstrated that, at least for a biological INP type, there is no expected measurement bias between bulk collection and direct immediately processed freezing methods to as warm as -10°C. Since particle size ranges were limited for this workshop, it can be expected that for atmospheric populations of INPs, measurement discrepancies will appear due to the different capabilities of methods for sampling the full aerosol size distribution, or due to limitations on achieving sufficient water supersaturations to fully capture immersion freezing in direct processing instruments. Overall, this workshop presents an improved picture of present capabilities for measuring INPs than in past workshops, and provides direction toward addressing remaining measurement issues.
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| 9. |
- 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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| 10. |
- 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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