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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. |
- Huang, Wencheng, et al.
(författare)
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Enhanced orbital anisotropy through the proximity to a SrTi O3 layer in the perovskite iridate superlattices
- 2021
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Ingår i: Physical Review B. - 2469-9950. ; 104:7
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Tidskriftsartikel (refereegranskat)abstract
- We have used angle-dependent soft x-ray absorption spectroscopy (XAS) at the O K edge and first-principles calculations to investigate the electronic structures of iridate-based superlattices (SrIrO3)m/(SrTiO3) (m=1, 2, 3, and ∞). We focus on the pre-edge Ir 5d t2g-O 2p orbital hybridization feature in the XAS spectra. By varying the measurement geometry relative to the incident photon polarization, we are able to extract the dichroic contrast and observe the systematic increase in the anisotropy of Ir 5d orbitals as m decreases. First-principles calculations elucidate the orbital anisotropy coming mainly from the enhanced out-of-plane compression of IrO6 octahedra in the SrIrO3 layers that are adjacent to the inserted SrTiO3 layers. As m decreases, the increased volume fraction of these interfacial SrIrO3 layers and their contact with the SrTiO3 layers within the (SrIrO3)m/(SrTiO3) supercell lead to enhanced orbital anisotropy. Furthermore, the tilt and rotation of IrO6 octahedra are shown to be essential to understand the subtle orbital anisotropy in these superlattices, and constraining these degrees of freedom will give an incorrect trend. Our results demonstrate that the structural constraint from the inserted SrTiO3 layers, in addition to other electronic means such as polar interface and charge transfer, can serve as a knob to control the orbital degree of freedom in these iridate-based superlattices.
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