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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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| 3. |
- Arshad, Salman, 1987, et al.
(författare)
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Subgrid Reaction-Diffusion Closure for Large Eddy Simulations Using the Linear-Eddy Model
- 2019
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Ingår i: Flow, Turbulence and Combustion. - : Springer Science and Business Media LLC. - 1573-1987 .- 1386-6184. ; 103:2, s. 389-416
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Tidskriftsartikel (refereegranskat)abstract
- Turbulent combustion models approximate the interaction between turbulence, molecular transport and chemical reactions. Among the many available turbulent combustion models, the present focus is the linear-eddy model (LEM) used as a subgrid combustion model for large eddy simulations. In particular this paper introduces a new LEM closure with the reaction-rate approach to close the filtered chemical source terms in the governing equations for species mass fractions and enthalpy. The new approach is tested using a non-premixed syngas flame and a bluff-body stabilized premixed flame problem. Simulation results are compared to data from a direct numerical simulation and experiments. This comparison shows that mean and rms quantities compare well with experiments and are in the range of previous simulation studies. These results are obtained with a pressure-based and unstructured computational-fluid-dynamics solver, an approach that is preferred in industry.
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| 4. |
- Gonzalez-Juez, Esteban D., et al.
(författare)
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Turbulent-combustion closure for the chemical source terms and molecular mixing using the linear-eddy model
- 2017
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Ingår i: 53rd AIAA/SAE/ASEE Joint Propulsion Conference, 2017. - 9781624105111
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Konferensbidrag (refereegranskat)abstract
- Turbulent combustion models approximate the interaction between turbulence, molecular transport and chemical reactions with the purpose of allowing computationally feasible simulations. There are many of these models and the present interest is on the lineareddy model (LEM). Specifically this paper introduces and tests a new method to use LEM to close the filtered chemical source terms in the conservation equations of the thermochemical quantities. For this purpose, this paper discusses the conceptual enhancements of this method over traditional LEM implementations, and its testing in a widely-used bluff-body-stabilized-flame problem.
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