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- 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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| 2. |
- Mottram, J. C., et al.
(författare)
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Water in star-forming regions with Herschel (WISH)
- 2014
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 572
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Tidskriftsartikel (refereegranskat)abstract
- Context. Outflows are an important part of the star formation process as both the result of ongoing active accretion and one of the main sources of mechanical feedback on small scales. Water is the ideal tracer of these effects because it is present in high abundance for the conditions expected in various parts of the protostar, particularly the outflow. Aims. We constrain and quantify the physical conditions probed by water in the outflow-jet system for Class 0 and I sources. Methods. We present velocity-resolved Herschel HIFI spectra of multiple water-transitions observed towards 29 nearby Class 0/I protostars as part of the WISH guaranteed time key programme. The lines are decomposed into different Gaussian components, with each component related to one of three parts of the protostellar system; quiescent envelope, cavity shock and spot shocks in the jet and at the base of the outflow. We then use non-LTE radex models to constrain the excitation conditions present in the two outflow-related components. Results. Water emission at the source position is optically thick but effectively thin, with line ratios that do not vary with velocity, in contrast to CO. The physical conditions of the cavity and spot shocks are similar, with post-shock H-2 densities of order 10(5) -10(8) cm(-3) and H2O column densities of order 10(16) -10(18) cm(-2). H2O emission originates in compact emitting regions: for the spot shocks these correspond to point sources with radii of order 10-200 AU, while for the cavity shocks these come from a thin layer along the outflow cavity wall with thickness of order 1-30 AU. Conclusions. Water emission at the source position traces two distinct kinematic components in the outflow; J shocks at the base of the outflow or in the jet, and C shocks in a thin layer in the cavity wall. The similarity of the physical conditions is in contrast to off-source determinations which show similar densities but lower column densities and larger filling factors. We propose that this is due to the differences in shock properties and geometry between these positions. Class I sources have similar excitation conditions to Class 0 sources, but generally smaller line-widths and emitting region sizes. We suggest that it is the velocity of the wind driving the outflow, rather than the decrease in envelope density or mass, that is the cause of the decrease in H2O intensity between Class 0 and I sources.
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| 3. |
- Santangelo, G., et al.
(författare)
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Water distribution in shocked regions of the NGC 1333-IRAS 4A protostellar outflow
- 2014
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 568, s. Article no. A125-
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Tidskriftsartikel (refereegranskat)abstract
- Context. Water is a key molecule in protostellar environments because its line emission is very sensitive to both the chemistry and the physical conditions of the gas. Observations of H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observatory have highlighted the complexity of H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ line profiles, in which different kinematic components can be distinguished. Aims. The goal is to study the spatial distribution of H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ, in particular of the different kinematic components detected in H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ emission, at two bright shocked regions along IRAS 4A, one of the strongest H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ emitters among the Class 0 outflows. Methods. We obtained Herschel-PACS maps of the IRAS 4A outflow and HIFI observations of two shocked positions. The largest HIFI beam of 38'' at 557 GHz was mapped in several key water lines with different upper energy levels, to reveal possible spatial variations of the line profiles. A large velocity gradient (LVG) analysis was performed to determine the excitation conditions of the gas. Results. We detect four H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ lines and CO (16-15) at the two selected shocked positions. In addition, transitions from related outflow and envelope tracers are detected. Different gas components associated with the shock are identified in the H2O emission. In particular, at the head of the red lobe of the outflow, two distinct gas components with different excitation conditions are distinguished in the HIFI emission maps: a compact component, detected in the ground-state water lines, and a more extended one. Assuming that these two components correspond to two different temperature components observed in previous H2O and CO studies, the LVG analysis of the H2O line emission from low-mass protostars and their associated outflows performed with HIFI onboard the Herschel Space Observ emission suggests that the compact (about 32, corresponding to about 700 AU) component is associated with a hot (T similar to 1000 K) gas with densities n(H2) similar to (1-4) x 10(5) cm(-3), whereas the extended (10 ''-17 '', corresponding to 2400-4000 AU) one traces a warm (T similar to 300-500 K) and dense gas (n(H2) similar to (3-5) x 10(7) cm(-3)). Finally, using the CO (16-15) emission observed at R2 and assuming a typical CO/H-2 abundance of 10(-4), we estimate the H2O/H-2 abundance of the warm and hot components to be (7-10) x 10(-7) and (3-7) x 10(-5). Conclusions. Our data allowed us, for the first time, to resolve spatially the two temperature components previously observed with HIFI and PACS. We propose that the compact hot component may be associated with the jet that impacts the surrounding material, whereas the warm, dense, and extended component originates from the compression of the ambient gas by the propagating flow.
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