| 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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| 2. |
- Bian, F., et al.
(författare)
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Ultrasmall Silver Nanopores Fabricated by Femtosecond Laser Pulses
- 2011
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6992 .- 1530-6984. ; 11:8, s. 3251-3257
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Tidskriftsartikel (refereegranskat)abstract
- Ultrasmall nanopores in silver thin films with a diameter of about 2 nm have been fabricated using femtosecond laser ablation in liquid. Ultrafast laser pulse ablation generates highly nonequilibrium excitated states, from which silver thin films emerge and progressively grow with the assistance of capping agent molecules. During this growth process, capping agent molecules are enclaved within the film, leaving individual ultrasmall pores in the thin film. Our first-principles calculations show that the pore size is critically determined by the dimension of the confined molecules. Our approach advances the capability of optical methods in making nanoscale structures with potential applications in areas such as near-field aperture probes, imaging masks, magnetic plasmonic resonances, and biosensing with individual nanopores.
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| 3. |
- Tian, Rong, et al.
(författare)
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A multiresolution continuum simulation of the ductile fracture process
- 2010
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Ingår i: Journal of the mechanics and physics of solids. - : Elsevier BV. - 0022-5096 .- 1873-4782. ; 58:10, s. 1681-1700
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Tidskriftsartikel (refereegranskat)abstract
- With the advancement in computational science that is stepping into the Petascale era and experimental techniques that enable rapid reconstruction of the 3D microstructure, quantitative microstructure simulations at an unprecedented fidelity level are giving rise to new possibilities for linking microstructure to property. This paper presents recent advances in 3D computational modeling of ductile fracture in high toughness steels. Ductile fracture involves several concurrent and mutually interactive mechanisms at multiple length scales of microstructure. With serial sectioning tomographic techniques, a digital data set of microstructure features associated with the fracture process has been experimentally reconstructed. In this study, primary particles are accurately and explicitly modeled while the secondary particles are modeled by a two scale multiresolution continuum model. The present numerical simulation captures detailed characteristics of the fracture process, such as zigzag crack morphology, critical void growth ratios, local stress triaxiality variation, and intervoid ligament structure. For the first time, fracture toughness is linked to multiscale microstructures in a realistic large 3D model.
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