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 flux 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, defined 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 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. 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 target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that 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 assays, we hope to encourage technical innovation in the field

A framework for ensemble modelling of climate change impacts on lakes worldwide: the ISIMIP Lake Sector

Empirical evidence demonstrates that lakes and reservoirs are warming across the globe. Consequently, there is an increased need to project future changes in lake thermal structure and resulting changes in lake biogeochemistry in order to plan for the likely impacts. Previous studies of the impacts of climate change on lakes have often relied on a single model forced with limited scenario-driven projections of future climate for a relatively small number of lakes. As a result, our understanding of the effects of climate change on lakes is fragmentary, based on scattered studies using different data sources and modelling protocols, and mainly focused on individual lakes or lake regions. This has precluded identification of the main impacts of climate change on lakes at global and regional scales and has likely contributed to the lack of lake water quality considerations in policy-relevant documents, such as the Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC). Here, we describe a simulation protocol developed by the Lake Sector of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) for simulating climate change impacts on lakes using an ensemble of lake models and climate change scenarios for ISIMIP phases 2 and 3. The protocol prescribes lake simulations driven by climate forcing from gridded observations and different Earth system models under various representative greenhouse gas concentration pathways (RCPs), all consistently bias-corrected on a 0.5∘ × 0.5∘ global grid. In ISIMIP phase 2, 11 lake models were forced with these data to project the thermal structure of 62 well-studied lakes where data were available for calibration under historical conditions, and using uncalibrated models for 17 500 lakes defined for all global grid cells containing lakes. In ISIMIP phase 3, this approach was expanded to consider more lakes, more models, and more processes. The ISIMIP Lake Sector is the largest international effort to project future water temperature, thermal structure, and ice phenology of lakes at local and global scales and paves the way for future simulations of the impacts of climate change on water quality and biogeochemistry in lakes

Employer Transit Subsidy Study: Main Report

This study found that the larger the transit subsidy offered, the more employees were induced to become transit riders and the more transit-only commuting increased. The increase in transit-only commuting came from a reduction in auto-only and auto-and-transit commuting. Transit subsidy acceptance and effectiveness can be dampened by factors such as the availability of cheap parking, or greater distance between the workplace and rapid transit, leading to some variability in outcomes. Transit ridership and subsidy acceptance were associated with various positive self-reported improvements to workers’ quality of life, including their health, stress levels and commute predictability. These positive quality of life outcomes were achieved without the transit subsidy having any observed effects on work schedules, turnover and performance

Employer Transit Subsidy Study: Executive Summary

This study found that the larger the transit subsidy offered, the more employees were induced to become transit riders and the more transit-only commuting increased. The increase in transit-only commuting came from a reduction in auto-only and auto-and-transit commuting. Transit subsidy acceptance and effectiveness can be dampened by factors such as the availability of cheap parking, or greater distance between the workplace and rapid transit, leading to some variability in outcomes. Transit ridership and subsidy acceptance were associated with various positive self-reported improvements to workers’ quality of life, including their health, stress levels and commute predictability. These positive quality of life outcomes were achieved without the transit subsidy having any observed effects on work schedules, turnover and performance

Evolution of Stellar-To-Halo Mass Ratio at Z = 0-7 Identified by Clustering Analysis with the Hubble Legacy Imaging and Early Subaru/Hyper Suprime-Cam Survey Data

We present clustering analysis results from 10,381 Lyman break galaxies (LBGs) at z ∼ 4-7, identified in the Hubble legacy deep imaging and new complimentary large-area Subaru/Hyper Suprime-Cam data. We measure the angular correlation functions of these LBGs at z ∼ 4, 5, 6, and 7 and fit these measurements using halo occupation distribution (HOD) models that provide an estimate of halo masses, Mh ~ (1 - 20 ) x 1011 M⊙. Our Mh estimates agree with those obtained by previous clustering studies in a UV-magnitude versus Mh plane and allow us to calculate stellar-to-halo mass ratios (SHMRs) of LBGs. By comparison with the Z ~ 0 SHMR, we identify evolution of the SHMR from z ~ 0 to z ~ 4 and from z ~ 4 to z ~ 7 at the \u3e 98% confidence levels. The SHMR decreases by a factor of ∼2 from z ~ 0 to 4 and increases by a factor of ∼4 from z ~ 4 to 7 at the dark matter halo mass of Mh ~ 1011 M⊙. We compare our SHMRs with results of a hydrodynamic simulation and a semianalytic model and find that these theoretical studies do not predict the SHMR increase from to 7. We obtain the baryon conversion efficiency (BCE) of LBGs at z ~ 4 and find that the BCE increases with increasing dark matter halo mass. Finally, we compare our clustering+HOD estimates with results from abundance matching techniques and conclude that the Mh estimates of the clustering+HOD analyses agree with those of the simple abundance matching within a factor of 3, and that the agreement improves when using more sophisticated abundance matching techniques that include subhalos, incompleteness, and/or evolution in the star formation and stellar mass functions

The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry

Background The NORMAN Association (https://www.norman-network.com/) initiated the NORMAN Suspect List Exchange (NORMAN-SLE; https://www.norman-network.com/nds/SLE/) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community (https://zenodo.org/communities/norman-sle), with a total of > 40,000 unique views, > 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the US EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard/), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=101). Conclusions The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website (https://www.norman-network.com/nds/SLE/)

Hiring, Training, and Supporting Peer Research Associates: Operationalizing Community-Based Research Principles within Epidemiological Studies By, With, and For Women Living With HIV

Background A community-based research (CBR) approach is critical to redressing the exclusion of women—particularly, traditionally marginalized women including those who use substances—from HIV research participation and benefit. However, few studies have articulated their process of involving and engaging peers, particularly within large-scale cohort studies of women living with HIV where gender, cultural and linguistic diversity, HIV stigma, substance use experience, and power inequities must be navigated. Methods Through our work on the Canadian HIV Women’s Sexual and Reproductive Health Cohort Study (CHIWOS), Canada’s largest community-collaborative longitudinal cohort of women living with HIV (n = 1422), we developed a comprehensive, regionally tailored approach for hiring, training, and supporting women living with HIV as Peer Research Associates (PRAs). To reflect the diversity of women with HIV in Canada, we initially hired 37 PRAs from British Columbia, Ontario, and Quebec, prioritizing women historically under-represented in research, including women who use or have used illicit drugs, and women living with HIV of other social identities including Indigenous, racialized, LGBTQ2S, and sex work communities, noting important points of intersection between these groups. Results Building on PRAs’ lived experience, research capacity was supported through a comprehensive, multi-phase, and evidence-based experiential training curriculum, with mentorship and support opportunities provided at various stages of the study. Challenges included the following: being responsive to PRAs’ diversity; ensuring PRAs’ health, well-being, safety, and confidentiality; supporting PRAs to navigate shifting roles in their community; and ensuring sufficient time and resources for the translation of materials between English and French. Opportunities included the following: mutual capacity building of PRAs and researchers; community-informed approaches to study the processes and challenges; enhanced recruitment of harder-to-reach populations; and stronger community partnerships facilitating advocacy and action on findings. Conclusions Community-collaborative studies are key to increasing the relevance and impact potential of research. For women living with HIV to participate in and benefit from HIV research, studies must foster inclusive, flexible, safe, and reciprocal approaches to PRA engagement, employment, and training tailored to regional contexts and women’s lives. Recommendations for best practice are offered

Anthropological Contributions to Historical Ecology: 50 Questions, Infinite Prospects

This paper presents the results of a consensus-driven process identifying 50 priority research questions for historical ecology obtained through crowdsourcing, literature reviews, and in-person workshopping. A deliberative approach was designed to maximize discussion and debate with defined outcomes. Two in-person workshops (in Sweden and Canada) over the course of two years and online discussions were peer facilitated to define specific key questions for historical ecology from anthropological and archaeological perspectives. The aim of this research is to showcase the variety of questions that reflect the broad scope for historical-ecological research trajectories across scientific disciplines. Historical ecology encompasses research concerned with decadal, centennial, and millennial human-environmental interactions, and the consequences that those relationships have in the formation of contemporary landscapes. Six interrelated themes arose from our consensus-building workshop model: (1) climate and environmental change and variability; (2) multi-scalar, multi-disciplinary; (3) biodiversity and community ecology; (4) resource and environmental management and governance; (5) methods and applications; and (6) communication and policy. The 50 questions represented by these themes highlight meaningful trends in historical ecology that distill the field down to three explicit findings. First, historical ecology is fundamentally an applied research program. Second, this program seeks to understand long-term human-environment interactions with a focus on avoiding, mitigating, and reversing adverse ecological effects. Third, historical ecology is part of convergent trends toward transdisciplinary research science, which erodes scientific boundaries between the cultural and natural

Evaluation of Polydentate Picolinic Acid Chelating Ligands and an α-melanocyte-stimulating Hormone Derivative for Targeted Alpha Therapy Using ISOL-Produced 225Ac

Background Actinium-225 (225Ac, t1/2 = 9.9 d) is a promising candidate radionuclide for use in targeted alpha therapy (TAT), though the currently limited global supply has hindered the development of a suitable Ac-chelating ligand and 225Ac-radiopharmaceuticals towards the clinic. We at TRIUMF have leveraged our Isotope Separation On-Line (ISOL) facility to produce 225Ac and use the resulting radioactivity to screen a number of potential 225Ac-radiopharmaceutical compounds. Results MBq quantities of 225Ac and parent radium-225 (225Ra, t1/2 = 14.8 d) were produced and separated using solid phase extraction DGA resin, resulting in a radiochemically pure 225Ac product in > 98% yield and in an amenable form for radiolabeling of ligands and bioconjugates. Of the many polydentate picolinic acid (“pa”) containing ligands evaluated (H4octapa [N4O4], H4CHXoctapa [N4O4], p-NO2-Bn-H4neunpa [N5O4], and H6phospa [N4O4]), all out-performed the current gold standard, DOTA for 225Ac radiolabeling ability at ambient temperature. Moreover, a melanocortin 1 receptor-targeting peptide conjugate, DOTA-modified cyclized α-melanocyte-stimulating hormone (DOTA-CycMSH), was radiolabeled with 225Ac and proof-of-principle biodistribution studies using B16F10 tumour-bearing mice were conducted. At 2 h post-injection, tumour-to-blood ratios of 20.4 ± 3.4 and 4.8 ± 2.4 were obtained for the non-blocking (molar activity [M.A.] > 200 kBq/nmol) and blocking (M.A. = 1.6 kBq/nmol) experiment, respectively. Conclusion TRIUMF’s ISOL facility is able to provide 225Ac suitable for preclinical screening of radiopharmaceutical compounds; [225Ac(octapa)]−, [225Ac(CHXoctapa)]−, and [225Ac(DOTA-CycMSH)] may be good candidates for further targeted alpha therapy studies

Pregnancy Incidence and Intention after HIV Diagnosis among Women Living With HIV in Canada

Background Pregnancy incidence rates among women living with HIV (WLWH) have increased over time due to longer life expectancy, improved health status, and improved access to and HIV prevention benefits of combination antiretroviral therapy (cART). However, it is unclear whether intended or unintended pregnancies are contributing to observed increases. Methods We analyzed retrospective data from the Canadian HIV Women’s Sexual and Reproductive Health Cohort Study (CHIWOS). Kaplan-Meier methods and GEE Poisson models were used to measure cumulative incidence and incidence rate of pregnancy after HIV diagnosis overall, and by pregnancy intention. We used multivariable logistic regression models to examine independent correlates of unintended pregnancy among the most recent/current pregnancy. Results Of 1,165 WLWH included in this analysis, 278 (23.9%) women reported 492 pregnancies after HIV diagnosis, 60.8% of which were unintended. Unintended pregnancy incidence (24.6 per 1,000 Women-Years (WYs); 95% CI: 21.0, 28.7) was higher than intended pregnancy incidence (16.6 per 1,000 WYs; 95% CI: 13.8, 20.1) (Rate Ratio: 1.5, 95% CI: 1.2–1.8). Pregnancy incidence among WLWH who initiated cART before or during pregnancy (29.1 per 1000 WYs with 95% CI: 25.1, 33.8) was higher than among WLWH not on cART during pregnancy (11.9 per 1000 WYs; 95% CI: 9.5, 14.9) (Rate Ratio: 2.4, 95% CI: 2.0–3.0). Women with current or recent unintended pregnancy (vs. intended pregnancy) had higher adjusted odds of being single (AOR: 1.94; 95% CI: 1.10, 3.42), younger at time of conception (AOR: 0.95 per year increase, 95% CI: 0.90, 0.99), and being born in Canada (AOR: 2.76, 95% CI: 1.55, 4.92). Conclusion Nearly one-quarter of women reported pregnancy after HIV diagnosis, with 61% of all pregnancies reported as unintended. Integrated HIV and reproductive health care programming is required to better support WLWH to optimize pregnancy planning and outcomes and to prevent unintended pregnancy