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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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- 2019
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Tidskriftsartikel (refereegranskat)
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- Rhodes, Emma, 1990-, et al.
(författare)
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Textural Insights Into the Evolving Lava Dome Cycles at Santiaguito Lava Dome, Guatemala
- 2018
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Ingår i: Frontiers in Earth Science. - : Frontiers Media SA. - 2296-6463. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- The structures and textures preserved in lava domes reflect underlying magmatic and eruptive processes, and may provide evidence of how eruptions initiate and evolve. This study explores the remarkable cycles in lava extrusion style produced between 1922 and 2012 at the Santiaguito lava dome complex, Guatemala. By combining an examination of eruptive lava morphologies and textures with a review of historical records, we aim to constrain the processes responsible for the range of erupted lava type and morphologies. The Santiaguito lava dome complex is divided into four domes (El Caliente, La Mitad, El Monje, El Brujo), containing a range of proximal structures (e.g., spines) from which a series of structurally contrasting lava flows originate. Vesicular lava flows (with a'a like, yet non-brecciated flow top) have the highest porosity with interconnected spheroidal pores and may transition into blocky lava flows. Blocky lava flows are high volume and texturally variable with dense zones of small tubular aligned pore networks and more porous zones of spheroidal shaped pores. Spines are dense and low volume and contain small skeletal shaped pores, and subvertical zones of sigmoidal pores. We attribute the observed differences in pore shapes to reflect shallow inflation, deflation, flattening, or shearing of the pore fraction. Effusion rate and duration of the eruption define the amount of time available for heating or cooling, degassing and outgassing prior to and during extrusion, driving changes in pore textures and lava type. Our new textural data when reviewed with all the other published data allow a cyclic model to be developed. The cyclic eruption models are influenced by viscosity changes resulting from (1) initial magmatic composition and temperature, and (2) effusion rate which in turn affects degassing, outgassing and cooling time in the conduit. Each lava type presents a unique set of hazards and understanding the morphologies and dome progression is useful in hazard forecasting.
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- Rhodes, Olin E., et al.
(författare)
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Integration of ecosystem science into radioecology : A consensus perspective
- 2020
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 740
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Tidskriftsartikel (refereegranskat)abstract
- In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This paper is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.
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- Schipper, C. Ian, et al.
(författare)
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Silicic conduits as supersized tuffisites : Clastogenic influences on shifting eruption styles at Cordon Caulle volcano (Chile)
- 2021
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Ingår i: Bulletin of Volcanology. - : Springer Nature. - 0258-8900 .- 1432-0819. ; 83:2
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the processes that drive explosive-effusive transitions during large silicic eruptions is crucial to hazard mitigation. Conduit models usually treat magma ascent and degassing as a gradual, unidirectional progression from bubble nucleation through magmatic fragmentation. However, there is growing evidence for the importance of bi-directional clastogenic processes that sinter fragmented materials into coherent clastogenic magmas. Bombs that were ejected immediately before the first emergence of lava in the 2011-2012 eruption at Cordon Caulle volcano (Chile) are texturally heterogeneous composite assemblages of welded pyroclastic material. Although diverse in density and appearance, SEM and X-ray tomographic analysis show them all to have been formed by multi-generational viscous sintering of fine ash. Sintering created discrete clasts ranging from obsidian to pumice and formed a pervasive clast-supporting matrix that assembled these clasts into a conduit-sealing plug. An evaluation of sintering timescales reveals texturally disparate bomb components to represent only minutes of difference in residence time within the conduit. Permeability modelling indicates that the plug was an effective conduit seal, with outgassing potential-even from high-porosity regions-being limited by the inability of gas to flow across tendrils of densely sintered inter-clast matrix. Contrary to traditional perspectives, declining expressions of explosivity at the surface need not be preceded or accompanied by a decline in fragmentation efficiency. Instead, they result from tips in balance between the opposing processes of fragmentation and sintering that occur in countless cycles within volcanic conduits. These processes may be particularly enhanced at silicic fissure volcanoes, which have laterally extensive subsurface plumbing systems that require complex magma ascent pathways. The textures investigated here reveal the processes occurring within silicic fissures to be phenomenologically identical to those that have been inferred to occur in tuffisite veins: silicic conduits are essentially supersized examples of edifice-penetrating tuffisites.
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