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

An Orientation map for height p - 1 real E theory

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, May, 2020Cataloged from the official PDF of thesis.Includes bibliographical references (pages 43-44).Let p be an odd prime and let EO = E[superscript hC] [subscript p-1] be the Cp αxed points of height p - 1 Morava E theory. We say that a spectrum X has algebraic EO theory if the splitting of K[subscript *](X) as an K[subscript *][Cp]-module lifts to a topological splitting of EO [subscript grave] X. We develop criteria to show that a spectrum has algebraic EO theory, in particular showing that any connective spectrum with mod p homology concentrated in degrees 2k(p - 1) has algebraic EO theory. As an application, we answer a question posed by Hovey and Ravenel [10] by producing a unital orientation MW [subscript 4p-4] --> EO analogous to the MSU orientation of KO at p = 2 where MW [subscript 4p-4] is the Thom spectrum of the (4p - 4)-connective Wilson space.by Hood Chatham.Ph. D.Ph.D. Massachusetts Institute of Technology, Department of Mathematic

pyodide/pyodide: 0.24.0

Pyodide is a Python distribution for the browser and Node.js based on WebAssembl

Negligible direct lactate oxidation in subsarcolemmal and intermyofibrillar mitochondria obtained from red and white rat skeletal muscle

We examined the controversial notion of whether lactate is directly oxidized by subsarcolemmal (SS) and intermyofibrillar (IMF) mitochondria obtained from red and white rat skeletal muscle. Respiratory control ratios were normal in SS and IMF mitochondria. At all concentrations (0.18–10 mm), and in all mitochondria, pyruvate oxidation greatly exceeded lactate oxidation, by 31- to 186-fold. Pyruvate and lactate oxidation were inhibited by α-cyano-4-hydroxycinnamate, while lactate oxidation was inhibited by oxamate. Excess pyruvate (10 mm) inhibited the oxidation of palmitate (1.8 mm) as well as lactate (1.8 mm). In contrast, excess lactate (10 mm) failed to inhibit the oxidation of either palmitate (1.8 mm) or pyruvate (1.8 mm). The cell-permeant adenosine analogue, AICAR, increased pyruvate oxidation; in contrast, lactate oxidation was not altered. The monocarboxylate transporters MCT1 and 4 were present on SS mitochondria, but not on IMF mitochondria, whereas, MCT2, a high-affinity pyruvate transporter, was present in both SS and IMF mitochondria. The lactate dehydrogenase (LDH) activity associated with SS and IMF mitochondria was 200- to 240-fold lower than in whole muscle. Addition of LDH increased the rate of lactate oxidation, but not pyruvate oxidation, in a dose-dependent manner, such that lactate oxidation approached the rates of pyruvate oxidation. Collectively, these studies indicate that direct mitochondrial oxidation of lactate (i.e. an intracellular lactate shuttle) does not occur within the matrix in either IMF or SS mitochondria obtained from red or white rat skeletal muscle, because of the very limited quantity of LDH within mitochondria