Guidelines for the use and interpretation of assays for monitoring autophagy

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.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is 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 verify an autophagic response.

Origin and history of ureilitic material in the solar system: The view from asteroid 2008 TC3 and the Almahata Sitta meteorite

Asteroid 2008 TC3 (approximately 4m diameter) was tracked and studied in space for approximately 19h before it impacted Earth's atmosphere, shattering at 44-36km altitude. The recovered samples (>680 individual rocks) comprise the meteorite Almahata Sitta (AhS). Approximately 50-70% of these are ureilites (ultramafic achondrites). The rest are chondrites, mainly enstatite, ordinary, and Rumuruti types. The goal of this work is to understand how fragments of so many different types of parent bodies became mixed in the same asteroid. Almahata Sitta has been classified as a polymict ureilite with an anomalously high component of foreign clasts. However, we calculate that the mass of fallen material was 0.1% of the pre-atmospheric mass of the asteroid. Based on published data for the reflectance spectrum of the asteroid and laboratory spectra of the samples, we infer that the lost material was mostly ureilitic. Therefore, 2008 TC3 probably contained only a few percent nonureilitic materials, similar to other polymict ureilites except less well consolidated. From available data for the AhS meteorite fragments, we conclude that 2008 TC3 samples essentially the same range of types of ureilitic and nonureilitic materials as other polymict ureilites. We therefore suggest that the immediate parent of 2008 TC3 was the immediate parent of all ureilitic material sampled on Earth. We trace critical stages in the evolution of that material through solar system history. Based on various types of new modeling and re-evaluation of published data, we propose the following scenario. (1) The ureilite parent body (UPB) accreted 0.5-0.6Ma after formation of calcium-aluminum-rich inclusions (CAI), beyond the ice line (outer asteroid belt). Differentiation began approximately 1Ma after CAI. (2) The UPB was catastrophically disrupted by a major impact approximately 5Ma after CAI, with selective subsets of the fragments reassembling into daughter bodies. (3) Either the UPB (before breakup), or one of its daughters (after breakup), migrated to the inner belt due to scattering by massive embryos. (4) One daughter (after forming in or migrating to the inner belt) became the parent of 2008 TC3. It developed a regolith, mostly 3.8Ga ago. Clasts of enstatite, ordinary, and Rumuruti-type chondrites were implanted by low-velocity collisions. (5) Recently, the daughter was disrupted. Fragments were injected or drifted into Earth-crossing orbits. 2008 TC3 comes from outer layers of regolith, other polymict ureilites from deeper regolith, and main group ureilites from the interior of this body. In contrast to other models that have been proposed, this model invokes a stochastic history to explain the unique diversity of foreign materials in 2008 TC3 and other polymict ureilites.

Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes

Cell death is essential for a plethora of physiological processes, and its deregulation characterizes numerous human diseases. Thus, the in-depth investigation of cell death and its mechanisms constitutes a formidable challenge for fundamental and applied biomedical research, and has tremendous implications for the development of novel therapeutic strategies. It is, therefore, of utmost importance to standardize the experimental procedures that identify dying and dead cells in cell cultures and/or in tissues, from model organisms and/or humans, in healthy and/or pathological scenarios. Thus far, dozens of methods have been proposed to quantify cell death-related parameters. However, no guidelines exist regarding their use and interpretation, and nobody has thoroughly annotated the experimental settings for which each of these techniques is most appropriate. Here, we provide a nonexhaustive comparison of methods to detect cell death with apoptotic or nonapoptotic morphologies, their advantages and pitfalls. These guidelines are intended for investigators who study cell death, as well as for reviewers who need to constructively critique scientific reports that deal with cellular demise. Given the difficulties in determining the exact number of cells that have passed the point-of-no-return of the signaling cascades leading to cell death, we emphasize the importance of performing multiple, methodologically unrelated assays to quantify dying and dead cells.

Patterns and Correlates of Expressed Emotion, Perceived Criticism, and Rearing Style in First Admitted Early-Onset Schizophrenia Spectrum Disorders

The aim of this study was to assess patterns and correlates of family variables in 31 adolescents treated for their first episode of a schizophrenia spectrum disorder (early-onset schizophrenia [EOS]). Expressed emotion, perceived criticism, and rearing style were assessed. Potential correlates were patient psychopathology, premorbid adjustment, illness duration, quality of life (QoL), sociodemographic variables, patient and caregiver "illness concept," and caregiver personality traits and support. Families were rated as critical more frequently by patients than raters (55% vs. 13%). Perceived criticism was associated with worse QoL in relationship with parents and peers. An adverse rearing style was associated with a negative illness concept in patients, particularly with less trust in their physician. Future research should examine perceived criticism as a predictor of relapse and indicator of adolescents with EOS who need extended support and treatment. Rearing style should be carefully observed because of its link with patients' illness concept and, potentially, to service engagement and medication adherence