Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

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

International Consensus Statement on Rhinology and Allergy: Rhinosinusitis

Background: The 5 years since the publication of the first International Consensus Statement on Allergy and Rhinology: Rhinosinusitis (ICAR‐RS) has witnessed foundational progress in our understanding and treatment of rhinologic disease. These advances are reflected within the more than 40 new topics covered within the ICAR‐RS‐2021 as well as updates to the original 140 topics. This executive summary consolidates the evidence‐based findings of the document. Methods: ICAR‐RS presents over 180 topics in the forms of evidence‐based reviews with recommendations (EBRRs), evidence‐based reviews, and literature reviews. The highest grade structured recommendations of the EBRR sections are summarized in this executive summary. Results: ICAR‐RS‐2021 covers 22 topics regarding the medical management of RS, which are grade A/B and are presented in the executive summary. Additionally, 4 topics regarding the surgical management of RS are grade A/B and are presented in the executive summary. Finally, a comprehensive evidence‐based management algorithm is provided. Conclusion: This ICAR‐RS‐2021 executive summary provides a compilation of the evidence‐based recommendations for medical and surgical treatment of the most common forms of RS

State of the commons

Collaboration, sharing, and cooperation are a driving force for human evolution. Creative Commoners have known this fact all along, and recently there has been a flurry of new research to explain why.  The online communities that we’ve created together are a global platform for sharing. If we want to live in a digital world that is fair, diverse, vibrant, serendipitous, and safe for everyone, we will have to choose to make it that way. If that world is going to be accessible, equitable, and full of innovation and opportunity, it will require our leadership to foster and defend these ideals. Founded in 2001, Creative Commons has created legal and technical infrastructure that is fundamental to the Web we know and love. Today, our work goes beyond the ubiquitous CC licenses to foster cooperation and sharing, support collaborative communities, and drive engagement across the spectrum of open knowledge and free culture. The 2015 State of the Commons report measures the immeasurable scope of the commons by looking at the CC licensed content, along with content marked as public domain, that comprise the slice of the commons powered by CC tools.&nbsp

Improved Calibration of Cutthroat Flumes

An analysis of laboratory data for a 0.914-m (3-ft) length Cutthroat flume with four different throat widths is presented. Significant differences with previously published calibration parameters were found. Special attention was given to non-hydrostatic pressures at the upstream and downstream piezometer taps, and the variations are presented in a series of three-dimensional plots. Variation in relative pressure at different tap heights was observed and was concluded to represent a shift from a concave to a convex flow profile between the 0.305- and 0.203-m throat widths. This significant alteration in the flow profile correlates with a sharp change in the nf calibration parameter, describing a non-linear relationship with flume throat width. Alternative equation forms were explored in an attempt to increase the predictive accuracy of the calculated flow rates for free- and submerged-flow regimes. The alternative equations showed a decrease in the percent error, in the submerged-flow regime, by more than 50%. Transition submergence was observed to vary not only due to flume size, but also to flow rate. An empirically fitted equation was developed to calculate the transition submergence as a function of throat width and flow rate. In addition, a separate calibration for free-flow parameters was defined based on measurements from an upstream point gauge. The flow measurement accuracy of existing Cutthroat flumes can be significantly increased, especially for submerged-flow regimes

Reversible Control of Gelatin Hydrogel Stiffness Using DNA Crosslinkers

Biomaterials with dynamically tunable properties are critical for a range of applications in regenerative medicine and basic biology. In this work, we show the reversible control of gelatin methacrylate (GelMA) hydrogel stiffness through the use of DNA crosslinkers. We replaced some of the inter-GelMA crosslinks with double-stranded DNA, allowing for their removal via toehold-mediated strand displacement. The crosslinks could be restored by adding fresh dsDNA with complementary handles to the hydrogel. The elastic modulus (G’) of the hydrogels could be tuned between 500 and 1000 Pa, reversibly, over two cycles without degradation of performance. By functionalizing the gels with a second DNA strand, it was possible to control the crosslink density and a model ligand in an orthogonal fashion with two different displacement strands. Our results demonstrate the potential for DNA to reversibly control both stiffness and ligand presentation in a protein-based hydrogel, and will be useful for teasing apart the spatiotemporal behavior of encapsulated cells

De novo Sequencing and Native Mass Spectrometry Reveals Hetero-Association of Dirigent Protein Homologs and Potential Interacting Proteins in Forsythia × intermedia

The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families. In vascular plants, DPs hypothetically function, along with other essential enzymes/proteins (e.g. oxidases), as part of lignin/lignan forming complexes (LFCs). Herein, we used an integrated bottom-up, top-down, and native mass spectrometry approach to detect potential interacting proteins in a DP-enriched solubilized protein fraction from Forsythia × intermedia, via adaptation of our initial report of DP solubilization and purification. Because this hybrid species lacks a published genome, de novo sequencing was performed using publicly available transcriptome and genomic data from closely related species. We detected and identified two new DP homologs, which appear to form hetero-trimers. Molecular dynamics simulations suggest that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarity. Other identified proteins in the DP-enriched preparation were putatively associated with DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for components of a protein complex in vivo, none were found to form stable complexes with DPs under the specific experimental conditions we have explored. Nevertheless, our integrated mass spectrometry method development helps prepare for future investigations directed to detect hypothetical LFCs and other related complexes isolated from plant biomass fractionation

Alzheimer Disease Research in the 21st Century: Past and Current Failures, New Perspectives and Funding Priorities

Much of Alzheimer disease (AD) research has been traditionally based on the use of animals, which have been extensively applied in an effort to both improve our understanding of the pathophysiological mechanisms of the disease and to test novel therapeutic approaches. However, decades of such research have not effectively translated into substantial therapeutic success for human patients. Here we critically discuss these issues in order to determine how existing human-based methods can be applied to study AD pathology and develop novel therapeutics. These methods, which include patient-derived cells, computational analysis and models, together with large-scale epidemiological studies represent novel and exciting tools to enhance and forward AD research. In particular, these methods are helping advance AD research by contributing multifactorial and multidimensional perspectives, especially considering the crucial role played by lifestyle risk factors in the determination of AD risk. In addition to research techniques, we also consider related pitfalls and flaws in the current research funding system. Conversely, we identify encouraging new trends in research and government policy. In light of these new research directions, we provide recommendations regarding prioritization of research funding. The goal of this document is to stimulate scientific and public discussion on the need to explore new avenues in AD research, considering outcome and ethics as core principles to reliably judge traditional research efforts and eventually undertake new research strategies