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| 3. |
- 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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- D'Ambro, E. L., et al.
(författare)
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Molecular composition and volatility of isoprene photochemical oxidation secondary organic aerosol under low- and high-NOx conditions
- 2017
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 17:1, s. 159-174
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of secondary organic aerosol (SOA) formation from isoprene photochemical oxidation in an environmental simulation chamber at a variety of oxidant conditions and using dry neutral seed particles to suppress acid-catalyzed multiphase chemistry. A high-resolution time-of-flight chemical ionization mass spectrometer (HR-ToF-CIMS) utilizing iodide-adduct ionization coupled to the Filter Inlet for Gases and Aerosols (FIGAERO) allowed for simultaneous online sampling of the gas and particle composition. Under high-HO2 and low-NO conditions, highly oxygenated (O : C >= 1) C-5 compounds were major components (similar to 50 %) of SOA. The SOA composition and effective volatility evolved both as a function of time and as a function of input NO concentrations. Organic nitrates increased in both the gas and particle phases as input NO increased, but the dominant non-nitrate particle-phase components monotonically decreased. We use comparisons of measured and predicted gas-particle partitioning of individual components to assess the validity of literature-based group-contribution methods for estimating saturation vapor concentrations. While there is evidence for equilibrium partitioning being achieved on the chamber residence timescale (5.2 h) for some individual components, significant errors in group-contribution methods are revealed. In addition, >30% of the SOA mass, detected as low-molecular-weight semivolatile compounds, cannot be reconciled with equilibrium partitioning. These compounds desorb from the FIGAERO at unexpectedly high temperatures given their molecular composition, which is indicative of thermal decomposition of effectively lower-volatility components such as larger molecular weight oligomers.
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| 5. |
- Lopez-Hilfiker, F. D., et al.
(författare)
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A novel method for on-line analysis of gas and particle composition: description and evaluation of a Filter Inlet for Gases and AEROsols (FIGAERO)
- 2013
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Ingår i: Atmospheric Measurement Techniques Discussions. - : Copernicus Publications. - 1867-8610. ; 6:5, s. 9347-9395
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Tidskriftsartikel (refereegranskat)abstract
- We describe a novel inlet that allows measurement of both gas and particle molecular composition when coupled to mass spectrometric, chromatographic, or optical sensors: the Filter Inlet for Gas and AEROsol (FIGAERO). The design goals for the FIGAERO are to allow unperturbed observation of ambient air while simultaneously analyzing gases and collecting particulate matter on a Teflon filter via an entirely separate sampling port. The filter is analyzed periodically by the same sensor on hourly or faster timescales using temperature-programmed thermal desorption. We assess the performance of the FIGAERO by coupling it to a high-resolution time-of-flight chemical-ionization mass spectrometer (HRToF-CIMS) in laboratory chamber studies of α-pinene oxidation and field measurements at a boreal forest location. Low instrument backgrounds give detection limits of ppt or lower for compounds in the gas-phase and in the pg m−3 range for particle phase compounds. The FIGAERO-HRToF-CIMS provides molecular information about both gases and particle composition on the 1 Hz and hourly timescales, respectively for hundreds of compounds. The FIGAERO thermal desorptions are highly reproducible (better than 10%), allowing a calibrated assessment of the effective volatility of desorbing compounds and the role of thermal decomposition during the desorption process. We show that the often multi-modal desorption thermograms arising from secondary organic aerosol (SOA) provide additional insights into molecular composition and/or particle morphology, and exhibit changes with changes in SOA formation or aging pathways.
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- Lopez-Hilfiker, F. D., et al.
(författare)
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A novel method for online analysis of gas and particle composition: description and evaluation of a Filter Inlet for Gases and AEROsols (FIGAERO)
- 2014
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Ingår i: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 7:4, s. 983-1001
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Tidskriftsartikel (refereegranskat)abstract
- We describe a novel inlet that allows measurement of both gas and particle molecular composition when coupled to mass spectrometric, chromatographic, or optical sensors: the Filter Inlet for Gases and AEROsols (FIGAERO). The design goals for the FIGAERO are to allow unperturbed observation of ambient air while simultaneously analyzing gases and collecting particulate matter on a Teflon® (hereafter Teflon) filter via an entirely separate sampling port. The filter is analyzed periodically by the same sensor on hourly or faster timescales using temperature-programmed thermal desorption. We assess the performance of the FIGAERO by coupling it to a high-resolution time-of-flight chemical-ionization mass spectrometer (HRToF-CIMS) in laboratory chamber studies of α-pinene oxidation and field measurements at a boreal forest location. Low instrument backgrounds give detection limits of ppt or lower for compounds in the gas-phase and in the picogram m−3 range for particle phase compounds. The FIGAERO-HRToF-CIMS provides molecular information about both gases and particle composition on the 1 Hz and hourly timescales, respectively for hundreds of compounds. The FIGAERO thermal desorptions are highly reproducible (better than 10%), allowing a calibrated assessment of the effective volatility of desorbing compounds and the role of thermal decomposition during the desorption process. We show that the often multi-modal desorption thermograms arising from secondary organic aerosol (SOA) provide additional insights into molecular composition and/or particle morphology, and exhibit changes with changes in SOA formation or aging pathways.
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| 7. |
- Lopez-Hilfiker, F D, et al.
(författare)
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Molecular Composition and Volatility of Organic Aerosol in the Southeastern U.S.: Implications for IEPOX Derived SOA.
- 2016
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Ingår i: Environmental science & technology. - : American Chemical Society (ACS). - 1520-5851 .- 0013-936X. ; 50:5, s. 2200-2209
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements as part of the Southern Oxidant and Aerosol Study (SOAS) during which atmospheric aerosol particles were comprehensively characterized. We present results utilizing a Filter Inlet for Gases and AEROsol coupled to a chemical ionization mass spectrometer (CIMS). We focus on the volatility and composition of isoprene derived organic aerosol tracers and of the bulk organic aerosol. By utilizing the online volatility and molecular composition information provided by the FIGAERO-CIMS, we show that the vast majority of commonly reported molecular tracers of isoprene epoxydiol (IEPOX) derived secondary organic aerosol (SOA) is derived from thermal decomposition of accretion products or other low volatility organics having effective saturation vapor concentrations <10(-3) μg m(-3). In addition, while accounting for up to 30% of total submicrometer organic aerosol mass, the IEPOX-derived SOA has a higher volatility than the remaining bulk. That IEPOX-SOA, and more generally bulk organic aerosol in the Southeastern U.S. is comprised of effectively nonvolatile material has important implications for modeling SOA derived from isoprene, and for mechanistic interpretations of molecular tracer measurements. Our results show that partitioning theory performs well for 2-methyltetrols, once accretion product decomposition is taken into account. No significant partitioning delays due to aerosol phase or viscosity are observed, and no partitioning to particle-phase water or other unexplained mechanisms are needed to explain our results.
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| 8. |
- Pospisilova, V., et al.
(författare)
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On the fate of oxygenated organic molecules in atmospheric aerosol particles
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:11
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Tidskriftsartikel (refereegranskat)abstract
- Highly oxygenated organic molecules (HOMs) are formed from the oxidation of biogenic and anthropogenic gases and affect Earth's climate and air quality by their key role in particle formation and growth. While the formation of these molecules in the gas phase has been extensively studied, the complexity of organic aerosol (OA) and lack of suitable measurement techniques have hindered the investigation of their fate post-condensation, although further reactions have been proposed. We report here novel real-time measurements of these species in the particle phase, achieved using our recently developed extractive electrospray ionization time-of-flight mass spectrometer (EESI-TOF). Our results reveal that condensed-phase reactions rapidly alter OA composition and the contribution of HOMs to the particle mass. In consequence, the atmospheric fate of HOMs cannot be described solely in terms of volatility, but particle-phase reactions must be considered to describe HOM effects on the overall particle life cycle and global carbon budget.
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| 9. |
- Lutz, Anna, 1986, et al.
(författare)
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Gas to Particle Partitioning of Organic Acids in the Boreal Atmosphere
- 2019
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Ingår i: Acs Earth and Space Chemistry. - : American Chemical Society (ACS). - 2472-3452. ; 3:7, s. 1279-1287
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Tidskriftsartikel (refereegranskat)abstract
- Gas to particle partitioning of carboxylic acids was investigated using a high-resolution chemical ionization time-of-flight mass spectrometer (HR-CI-ToF-MS) with the filter inlet for gases and aerosol (FIGAERO). Specifically, the partitioning coefficients of 640 components with unique molecular composition were calculated from an assumed linear relationship between [particle]/[gas] versus the mass of the organic fraction (M-org) according to Raoult's law, i.e., equilibrium phase partitioning. We demonstrate that, using the full data set, most of the compounds do not follow a linear relationship. This is especially the case for low- and high-molecular-weight species. Using a subset of the data, with concurrent low sulfate ambient observations ([SO42- < 0.4 mu g m(-3)), the relationship improved significantly and K-i could be derived from the slope of a linear regression to the data. The 100 species with the highest R-2 (>= 0.7) of this regression are presented. The restrictions during high sulfate conditions can be explained by changes in either the equilibrium conditions (e.g., the activity coeffient, gamma(i)) or uptake kinetics (mass transfer limitation). This study demonstrates that partitioning of compounds in the complex ambient atmosphere follows ideal Raoult's law for some limited conditions and stresses the need for studies also in more polluted environments.
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| 10. |
- Mohr, C., et al.
(författare)
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Ambient observations of dimers from terpene oxidation in the gas phase: Implications for new particle formation and growth
- 2017
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Ingår i: Geophysical Research Letters. - 0094-8276. ; 44:6, s. 2958-2966
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Tidskriftsartikel (refereegranskat)abstract
- We present ambient observations of dimeric monoterpene oxidation products (C16-20HyO6-9) in gas and particle phases in the boreal forest in Finland in spring 2013 and 2014, detected with a chemical ionization mass spectrometer with a filter inlet for gases and aerosols employing acetate and iodide as reagent ions. These are among the first online dual-phase observations of such dimers in the atmosphere. Estimated saturation concentrations of 10(-15) to 10(-6)mu gm(-3) (based on observed thermal desorptions and group-contribution methods) and measured gas-phase concentrations of 10(-3) to 10(-2)mu gm(-3) (similar to 10(6)-10(7)moleculescm(-3)) corroborate a gas-phase formation mechanism. Regular new particle formation (NPF) events allowed insights into the potential role dimers may play for atmospheric NPF and growth. The observationally constrained Model for Acid-Base chemistry in NAnoparticle Growth indicates a contribution of similar to 5% to early stage particle growth from the similar to 60 gaseous dimer compounds. Plain Language Summary Atmospheric aerosol particles influence climate and air quality. We present new insights into how emissions of volatile organic compounds from trees are transformed in the atmosphere to contribute to the formation and growth of aerosol particles. We detected for the first time over a forest, a group of organic molecules, known to grow particles, in the gas phase at levels far higher than expected. Previous measurements had only measured them in the particles. This finding provides guidance on how models of aerosol formation and growth should describe their appearance and fate in the atmosphere.
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