Variation in the apparent faecal digestibility of macronutrients and urinary energy excretion for three diets varying in fat and fibre content-- assessment of the Atwater factors and related energy conversion factors : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Nutritional Science at Massey University, Palmerston North, New Zealand

Background: Current systems to estimate dietary metabolisable energy (ME), often based on Atwater factors, assume that diet ME can be accurately predicted based on a few chemical components and that the ME of components is constant across foods. Objective: Our aim was to investigate variation in apparent faecal nutrient digestibility and urinary energy excretion on different diets, and evaluate the accuracy of current systems for predicting dietary ME. Design: The ME contents of a refined (high fat, low fibre) diet and two high fibre low fat diets were determined in balance experiments on human subjects and calculated using factorial and empirical models. Apparent faecal nutrient digestibilities and urinary energy excretions were also determined. Results: The difference between calculated (Atwater factors) and determined ME values was up to 4% for the refined diet and 11% for the high fibre diets. The empirical models were generally no more accurate than the modified Atwater factorial model. Apparent faecal nutrient digestibility varied considerably among the three diets, as did urinary energy per unit urinary nitrogen. Mean digestibilities ranged from 81.4 (fruit and vegetable diet) to 90.0% (refined diet) for crude protein; 87.0 (fruit and vegetable diet) to 95.7% (refined diet) for fat; 91.1 (cereal diet) to 95.5% (fruit and vegetable diet) for total carbohydrate. Mean urinary energy per unit urinary nitrogen ranged from 33.9 (refined diet) to 44.1 KJ/gN (fruit and vegetable diet). Conclusion: Modified Atwater factors and some of the empirical models evaluated here may be suitably accurate (±5%) for use for general food labelling purposes and for determining dietary ME intakes of groups and populations, but may be inadequate for application to specialised weight-loss diets and ingredients. KEY WORDS Atwater factors, Digestibility, Energy, Metabolisable Energy, Urinary Energy Excretion

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field