Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

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. For example, 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 versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost 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 fi eld 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. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. 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. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. 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

Photoprotection in lichens: Adaptations of photobionts to high light

Lichens often grow in microhabitats where they are exposed to severe abiotic stresses such as desiccation and temperature extremes. They are also often exposed to levels of light that are greater than lichen photobionts can use in carbon fixation. Unless regulated, excess energy absorbed by the photobionts can convert ground state oxygen to reactive oxygen species (ROS). These ROS can attack the photosynthetic apparatus, causing photoinhibition and photo-oxidative stress, reducing the ability of the photobionts to fix carbon. Here, we outline our current understanding of the effects of high light on lichens and the mechanisms they use to mitigate or tolerate this stress in hydrated and desiccated states. Tolerance to high light can be achieved first by lowering ROS formation, via synthesizing light screening pigments or by thermally dissipating the excess light energy absorbed; second, by scavenging ROS once formed; or third, by repairing ROS-induced damage. While the primary focus of this review is tolerance to high light in lichen photobionts, our knowledge is rather fragmentary, and therefore we also include recent findings in free-living relatives to stimulate new lines of research in the study of high light tolerance in lichens

Innovative technologies and social inequalities in health: A scoping review of the literature

<div><p>The aim of this study was to systematically review the range, nature, and extent of current research activity exploring the influence of innovative health-related technologies on social inequalities in health, with specific focus on a deeper understanding of the variables used to measure this connection and the pathways leading to the (re)production of inequalities. A review process was conducted, based on scoping review techniques, searching literature published from January 1, 1996 to November 25, 2016 using MEDLINE, Scopus, and ISI web of science. Search, sorting, and data extraction processes were conducted by a team of researchers and experts using a dynamic, reflexive examination process. Of 4139 studies collected from the search process, a total of 33 were included in the final analysis. Results of this study include the classification of technologies based on how these technologies are accessed and used by end users. In addition to the factors and mechanisms that influence unequal <i>access</i> to technologies, the results of this study highlight the importance of variations in <i>use</i> that importantly shape social inequalities in health. Additionally, focus on health care services technologies must be accompanied by investigating emerging technologies influencing healthy lifestyle, genomics, and personalized devices in health. Findings also suggest that choosing one measure of social position over another has important implications for the interpretation of research results. Furthermore, understanding the pathways through which various innovative health technologies reduce or (re)produce social inequalities in health is context dependent. In order to better understand social inequalities in health, these contextual variations draw attention to the need for critical distinctions between technologies based on how these various technologies are accessed and used. The results of this study provide a comprehensive starting point for future research to further investigate how innovative technologies may influence the unequal distribution of health as a human right.</p></div