| 1. |
- 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. |
- Kirchner, Nina, et al.
(författare)
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Statistical modeling of a former Arctic Ocean ice shelf complex using Antarctic analogies
- 2013
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Ingår i: Journal of Geophysical Research: Earth Surface. - : American Geophysical Union (AGU). - 2169-9003. ; 118:2, s. 1105-1117
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Tidskriftsartikel (refereegranskat)abstract
- Geophysical mapping and coring of the central Arctic Ocean seafloor provide evidence for repeated occurrences of ice sheet/ice shelf complexes during previous glacial periods. Several ridges and bathymetric highs shallower than present water depths of approximate to 1000m show signs of erosion from deep-drafting (armadas of) icebergs, which originated from thick outlet glaciers and ice shelves. Mapped glacigenic landforms and dates of cored sediments suggest that the largest ice shelf complex was confined to the Amerasian sector of the Arctic Ocean during Marine Isotope Stage (MIS) 6. However, the spatial extent of ice shelves can not be well reconstructed from occasional groundings on bathymetric highs. Therefore, we apply a statistical approach to provide independent support for an extensive MIS 6 ice shelf complex, which previously was inferred only from interpretation of geophysical and geological data. Specifically, we assess whether this ice shelf complex comprises a likely source of the deep-draft icebergs responsible for the mapped scour marks. The statistical modeling is based on exploiting relations between contemporary Antarctic ice shelves and their local physical environments and the assumption that Arctic Ocean MIS6 ice shelves scale similarly. Analyzing ice thickness data along the calving front of contemporary ice shelves, a peak over threshold method is applied to determine sources of deep-drafting icebergs in the Arctic Ocean MIS6 ice shelf complex. This approach is novel to modeling Arctic paleoglacial configurations. Predicted extreme calving front drafts match observed deep-draft iceberg scours if the ice shelf complex is sufficiently large.
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