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

Replication data for: An Analysis of ANES Items and Their Use in the Construction of Political Knowledge Scales

Valid comparisons of group scores on additive measures such as political knowledge scales require that the conditional response probabilities for individuals on the observed items be invariant across groups after controlling for their overall level of the latent trait of interest. Using a multi-group confirmatory factor analysis of knowledge items drawn from American National Election Studies, we find that the scales used in recent research are not sufficiently invariant for valid comparisons across a host of theoretically important grouping variables. We demonstrate that it is possible to construct valid invariant scales using a subset of items and show the impact of invariance by comparing results from the valid and invalid scales. We provide an analysis of differential item functioning (DIF) based on grouping variables commonly used in political science research to explore the utility of each item in the construction of valid knowledge scales. An application of the vanishing tetrad test suggests it is more appropriate to conceive of these items as effects of a latent variable rather than cause or formative indicators. These results suggest that models attempting to explain apparent knowledge gaps between subgroups have been unsuccessful because previously constructed scales were validated by fiat

Correction to:Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities (Plant and Soil, (2018), 427, 1-2, (191-208), 10.1007/s11104-017-3391-x)

The article “Organic phosphorus in the terrestrial environment: a perspective on the state of the art and future priorities”, written by Timothy S George et al., was originally published with incorrect affiliation information for one of the co-authors, E. Klumpp