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

[Abstract unavailable

We show that NF-κB and transcriptional targets are activated in liver by obesity and high-fat diet (HFD). We have matched this state of chronic, subacute 'inflammation' by low-level activation of NF-κB in the liver of transgenic mice, designated LIKK, by selectively expressing constitutively active IKK-β in hepatocytes. These mice exhibit a type 2 diabetes phenotype, characterized by hyperglycemia, profound hepatic insulin resistance, and moderate systemic insulin resistance, including effects in muscle. The hepatic production of proinflammatory cytokines, including IL-6, IL-1β and TNF-α, was increased in LIKK mice to a similar extent as induced by HFD in in wildtype mice. Parallel increases were observed in cytokine signaling in liver and mucscle of LIKK mice. Insulin resistance was improved by systemic neutralization of IL-6 or salicylate inhibition of IKK-β. Hepatic expression of the IκBα superrepressor (LISR) reversed the phenotype of both LIKK mice and wild-type mice fed an HFD. These findings indicate that lipid accumulation in the liver leads to subacute hepatic 'inflammation' through NF-κB activation and downstream cytokine production. This causes insulin resistance both locally in liver and systemically.Obesity is increasingly prevalent and strongly associated with the development of insulin resistance 1 , an underlying feature of both type 2 diabetes (T2D) and the metabolic syndrome 2 . Although epidemiological correlations are established, the cellular and molecular mechanisms that link obesity and insulin resistance are unknown. Increased adiposity is associated with lipid accumulation in other tissues, including muscle (intramyocellular lipid) and liver (hepatic steatosis), which has made it that much more difficult to pinpoint the primary sites responsible for initiating insulin resistance 3 . Fat accumulation in the visceral depot and liver are strongly correlated, and both are highly correlated with the development and severity of insulin resistance 4-6 .Growing evidence links a chronic, subacute inflammatory state to the development of obesity and the coexisting conditions of insulin resistance, T2D and the metabolic syndrome. Epidemiologists have consistently found elevations in markers and potential mediators of inflammation and the acute-phase response 7,8 , suggesting that low-grade inflammation precedes and predicts the development of T2D 9 . Proinflammatory cytokines can cause insulin resistance 10,11 and anti-inflammatory medications may reverse it 12,13 , suggesting that inflammation may be directly involved in its pathogenesis. Markers and mediators of inflammation that are biosynthesized in liver include CRP, PAI-1, fibrinogen and IL-6, suggesting that 'subacute inflammation' in liver, secondary to steatosis, might be involved in the development of insulin resistance, T2D and the metabolic syndrome. Because visceral adiposity and hepatic steatosis are etiologically and functionally intertwined, and both might be associated with subacute inflammation, we took a transgenic approa...

SUMMARY Overnutrition is associated with chronic inflammation in metabolic tissues; however, whether metabolic inflammation compromises the neural regulatory systems and therefore promotes overnutrition-associated diseases remains unexplored. Our results demonstrate that a mediator of metabolic inflammation, IKKβ/NF-κB, normally remains inactive although enriched in the hypothalamic neurons; however, overnutrition atypically activates hypothalamic IKKβ/NF-κB at least through elevated endoplasmic reticulum stress in the hypothalamus. While forced activation of hypothalamic IKKβ/NF-κB interrupts central insulin/leptin signaling and actions, site- or cell-specific suppression of IKKβ either broadly across the brain, or locally within the mediobasal hypothalamus, or specifically in hypothalamic AGRP neurons significantly protects against obesity and glucose intolerance. The involved molecular mechanisms include the control of IKKβ/NF-κB over SOCS3, a core inhibitor of insulin and leptin signaling. In conclusion, the hypothalamic IKKβ/NF-κB program is a general neural mechanism for energy imbalance underlying obesity; suppressing hypothalamic IKKβ/NF-κB represents a new strategy to combat obesity and related diseases.