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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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- Escartin, C., et al.
(författare)
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Reactive astrocyte nomenclature, definitions, and future directions
- 2021
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Ingår i: Nature Neuroscience. - : Springer Science and Business Media LLC. - 1097-6256 .- 1546-1726. ; 24, s. 312-325
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Tidskriftsartikel (refereegranskat)abstract
- Reactive astrocytes are astrocytes undergoing morphological, molecular, and functional remodeling in response to injury, disease, or infection of the CNS. Although this remodeling was first described over a century ago, uncertainties and controversies remain regarding the contribution of reactive astrocytes to CNS diseases, repair, and aging. It is also unclear whether fixed categories of reactive astrocytes exist and, if so, how to identify them. We point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic-vs-neuroprotective or A1-vs-A2. We advocate, instead, that research on reactive astrocytes include assessment of multiple molecular and functional parameters-preferably in vivo-plus multivariate statistics and determination of impact on pathological hallmarks in relevant models. These guidelines may spur the discovery of astrocyte-based biomarkers as well as astrocyte-targeting therapies that abrogate detrimental actions of reactive astrocytes, potentiate their neuro- and glioprotective actions, and restore or augment their homeostatic, modulatory, and defensive functions. Good-bad binary classifications fail to describe reactive astrocytes in CNS disorders. Here, 81 researchers reach consensus on widespread misconceptions and provide definitions and recommendations for future research on reactive astrocytes.
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- Bauch, S., et al.
(författare)
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Some Applications of Generalized Euler Characteristic of Quantum Graphs and Microwave Networks
- 2021
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Ingår i: Acta Physica Polonica. A. - 0587-4246 .- 1898-794X. ; 140:6, s. 525-531
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Tidskriftsartikel (refereegranskat)abstract
- In this article we continue to explore the possibilities offered by our discovery that one of the main graph and network characteristic, the generalized Euler characteristic iG, can be determined from a graph/network spectrum. We show that using the generalized Euler characteristic iG the number of vertices with Dirichlet |VD| boundary conditions of a family of graphs/networks created on the basis of the standard quantum graphs or microwave networks can be easily identified. We also present a new application of the generalized Euler characteristic for checking the completeness of graphs/networks spectra in the low energy range.
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- Ławniczak, M., et al.
(författare)
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Euler Characteristic of Graphs and Networks
- 2021
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Ingår i: Acta Physica Polonica. A. - 0587-4246 .- 1898-794X. ; 139:3, s. 323-327
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Tidskriftsartikel (refereegranskat)abstract
- The Euler characteristic chi = vertical bar V vertical bar - vertical bar E vertical bar is an important topological characteristic of graphs and networks. Here, vertical bar V vertical bar and vertical bar E vertical bar denote the number of vertices and edges of a graph or a network. It has been shown in [Phys. Rev. E 101, 052320 (2020)] that the Euler characteristic can be determined from a finite sequence of the lowest eigenenergies lambda(1), ..., lambda(N) of a simple quantum graph. We will test this finding numerically, using chaotic graphs with vertical bar V vertical bar = 8 vertices. We will consider complete (fully connected) and incomplete realizations of 8-vertex graphs. The properties of the Euler characteristic will also be tested experimentally using the sequence of the lowest resonances of the 5-vertex microwave network. We will show that the Euler characteristic chi can be used to reveal whether the graph is planar or not.
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