The Replica Set method is an approach to quantitatively measure lifespan or survival of Caenorhabditis elegans nematodes in a high-throughput manner, thus allowing a single investigator to screen ...more treatments or conditions over the same amount of time without loss of data quality. The method requires common equipment found in most laboratories working with C. elegans and is thus simple to adopt. The approach centers on assaying independent samples of a population at each observation point, rather than a single sample over time as with traditional longitudinal methods. Scoring entails adding liquid to the wells of a multi-well plate, which stimulates C. elegans to move and facilitates quantifying changes in healthspan. Other major benefits of the Replica Set method include reduced exposure of agar surfaces to airborne contaminants (e.g. mold or fungus), minimal handling of animals, and robustness to sporadic mis-scoring (such as calling an animal as dead when it is still alive). To appropriately analyze and visualize the data from a Replica Set style experiment, a custom software tool was also developed. Current capabilities of the software include plotting of survival curves for both Replica Set and traditional (Kaplan-Meier) experiments, as well as statistical analysis for Replica Set. The protocols provided here describe the traditional experimental approach and the Replica Set method, as well as an overview of the corresponding data analysis.
The advent of feeding based RNAi in
Caenorhabditis elegans
led to an era of gene discovery in aging research. Hundreds of gerogenes were discovered, and many are evolutionarily conserved, raising the ...exciting possibility that the underlying genetic basis for healthy aging in higher vertebrates could be quickly deciphered. Yet, the majority of putative gerogenes have still only been cursorily characterized, highlighting the need for high-throughput, quantitative assessments of changes in aging. A widely used surrogate measure of aging is lifespan. The traditional way to measure mortality in
C. elegans
tracks the deaths of individual animals over time within a relatively small population. This traditional method provides straightforward, direct measurements of median and maximum lifespan for the sampled population. However, this method is time consuming, often underpowered, and involves repeated handling of a set of animals over time, which in turn can introduce contamination or possibly damage increasingly fragile, aged animals. We have previously developed an alternative “Replica Set” methodology, which minimizes handling and increases throughput by at least an order of magnitude. The Replica Set method allows changes in lifespan to be measured for over one hundred feeding-based RNAi clones by one investigator in a single experiment- facilitating the generation of large quantitative phenotypic datasets, a prerequisite for development of biological models at a systems level. Here, we demonstrate through analysis of lifespan experiments simulated
in silico
that the Replica Set method is at least as precise and accurate as the traditional method in evaluating and estimating lifespan, and requires many fewer total animal observations across the course of an experiment. Furthermore, we show that the traditional approach to lifespan experiments is more vulnerable than the Replica Set method to experimental and measurement error. We find no compromise in statistical power for Replica Set experiments, even for moderate effect sizes, or when simulated experimental errors are introduced. We compare and contrast the statistical analysis of data generated by the two approaches, and highlight pitfalls common with the traditional methodology. Collectively, our analysis provides a standard of measure for each method across comparable parameters, which will be invaluable in both experimental design and evaluation of published data for lifespan studies.
Atmosphere–ocean general circulation models (AOGCMs) employ very different land surface schemes (LSSs) and, as a result, their predictions of land surface quantities are often difficult to compare. ...Some of the disagreement in quantities such as soil moisture is likely due to differences in the atmospheric component; however, previous intercomparison studies have determined that different LSSs can produce very different results even when supplied with identical atmospheric forcing.
A simple off-line LSS is presented that can reproduce the soil moisture simulations of various AOGCMs, based on their modeled temperature and precipitation. The scheme makes use of the well-established Thornthwaite method for estimating potential evapotranspiration combined with a variation of the Manabe “bucket” model. The model can be tuned to reproduce the control climate soil moisture of an AOGCM by adjusting the ease with which runoff and evapotranspiration continue as the moisture level in the bucket goes down. This produces a set of parameter values that provides a good fit to each of several AOGCM control climates. In addition, the parameter values can be set to imitate the LSS from one AOGCM while the model is forced with atmospheric data from another, thus providing an estimate of the magnitude of variation caused by the differences in land surface parameterization and by differences in atmospheric forcing. In general, the authors find that differences in LSSs account for about half of the difference in soil moisture as simulated by different AOGCMs, and the differences in atmospheric forcing account for the other half of the difference. However, the LSS can be more important than differences in atmospheric forcing in some regions (such as the United States) and less important in others (such as East Africa).
The southwestern region of Hudson Bay is one of the last areas in the Hudson and James Bay lowlands region to become free of sea ice in the spring. This late breakup is due to the effects of winds ...and currents. By analyzing time series with three different statistical techniques, we found a statistically significant increase in the length of the ice-free season in this region from 1971 to 2003. Much of this increase was attributed to earlier breakup of the ice, which is consistent with increased spring temperatures in this region. The onset of breakup advanced by at least three days per decade over the study period./// La partie sud-ouest de la baie d'Hudson est l'une des dernières zones des basses terres de cette baie et de la baie James à se libérer de la banquise au printemps. Cette débâcle tardive est due aux effets des vents et des courants. En analysant des séries chronologiques à l'aide de trois techniques statistiques différentes, on a découvert que, de 1971 à 2003, la région a connu une augmentation sensible dans la durée de la saison d'eau libre. Une grande partie de cette augmentation a été attribuée à une débâcle précoce, ce qui va de pair avec une hausse des températures printanières dans la région. Le début de la débâcle a avancé d'au moins trois jours par décennie au cours de la période d'étude.
This paper critically reviews and intercompares land surface schemes (LSSs) as used in atmospheric general circulation models (AGCMs) to simulate soil moisture and its response to a warmer climate, ...and potential evapotranspiration approaches as used in operational soil moisture monitoring and in predicting the response of soil moisture to a warmer climate. AGCM predictions of overall soil moisture change are in broad agreement but disagree sharply in some regions. Intercomparison projects have sought to evaluate the LSSs used by AGCMs for both accuracy and consistency. These studies have found that different LSSs can produce very different simulations even when supplied with identical atmospheric forcing. As well, LSSs that produce similar surface results from present-day or control climates often diverge when forced with climatic change data. Furthermore, no single LSS has been identified that produces an adequate simulation of all of temperature, moisture, evapotranspiration and runoff. AGCM LSSs must resolve the surface energy balance (SEB) in order to compute realistic heat fluxes between with the atmospheric model. LSSs have been used with AGCMs in both on-line (fully coupled) and off-line modes. In off-line climatic change experiments, AGCM predictions of atmospheric temperature and precipitation have been used, along with model downward radiative fluxes at the surface, to drive their own uncoupled LSS. However, there are simple non-energy-balance methods for estimating evapotranspiration that have been traditionally used in agricultural and meteorological applications. These schemes compute a potential evapotranspiration (PE) based on temperature and/or net radiation inputs, with the PE modified based on the availability of soil moisture. Operational PE approaches have also been used with AGCM data in off-line climate change experiments. The advantages of this approach are that it is simpler and requires less information, although (like the off-line SEB approach) it leaves out the simulation of feedbacks between the surface and the atmosphere.Although the SEB approach is essential for LSSs that must be coupled to AGCMs, this does not necessarily make it superior to an off-line operational PE LSS when it comes to quantities such as soil moisture. The quality of current observational data is insufficient to demonstrate that either approach is better than the other. Both approaches should continue to be used and intercompared when predicting the impacts of climatic change on soil moisture.
Genomic analyses have revealed heterogeneity among glial progenitor cells (GPCs), but the compartment selectivity of human GPCs (hGPCs) is unclear. Here, we asked if GPCs of human grey and white ...brain matter are distinct in their architecture and associated gene expression. RNA profiling of NG2‐defined hGPCs derived from adult human neocortex and white matter differed in their expression of genes involved in Wnt, NOTCH, BMP and TGFβ signaling, suggesting compartment‐selective biases in fate and self‐renewal. White matter hGPCs over‐expressed the BMP antagonists BAMBI and CHRDL1, suggesting their tonic suppression of astrocytic fate relative to cortical hGPCs, whose relative enrichment of cytoskeletal genes presaged their greater morphological complexity. In human glial chimeric mice, cortical hGPCs assumed larger and more complex morphologies than white matter hGPCs, and both were more complex than their mouse counterparts. These findings suggest that human grey and white matter GPCs comprise context‐specific pools with distinct functional biases.
Main Points
GPCs in the adult human white and gray matter are transcriptionally distinct.
GM and WM hGPCs differentially express WNT, NOTCH, BMP and TGFβ pathway genes.
The expression of BMP antagonists is significantly higher in WM hGPCs.
hGPCs in the GM are larger and more complex than in the WM.
Aging is the progressive physiological decline with advancing age that leads to the loss of vitality and an increase in risk of disease and mortality across nearly all organisms. Caenorhabditis ...elegans has been a critical model system for the study of aging mechanisms and interventions, thanks to its fast generation time, ease of laboratory propagation, a wealth of available genetic tools, and gene homology to mammals.One of the primary assays in investigation of aging is lifespan, for which C. elegans is amenable to perform at broader scale than mammals given the normally short median lifespan for wild-type animals of approximately 17-20 days, and relatively low cost. However, the majority of published lifespan experiments utilizing C. elegans employ an experimental strategy similar to those developed for mammalian studies: making repeated observations of a single population of animals of animals over time, until all animals in the starting population have died. Through simulation-based analysis, we identify the weaknesses of such a ”traditional longitudinal method” (TLM) for C. elegans lifespan experiments, and demonstrate the benefits of a new approach, the ”replica set method” (RSM) tailored to the strengths of C. elegans as a model, based on observing independent sub-populations of animals (”replicates”) that are each only scored once. We show that RSM is higher-throughput and less susceptible to some sources of possible experimental error and we further provide a framework for statistical analysis of the results from RSM experiments.Dietary restriction (DR) is a potential intervention that delays onset of symptoms of aging-associated diseases including sarcopenia and aberrant protein aggregation, and improves longevity across a broad range of evolutionarily distinct animals, from yeast to mammals. Our lab has previously shown that the Myc-family transcription factors (TFs) MXL-2 (Mlx) and MML-1 (MondoA/ChREBP) are necessary for the full extent of the benefits of DR in the C. elegans eat-2 genetic model of DR. Like their mammalian counterparts, MML-1 and MXL-2 function as a heterodimeric complex in the regulation of transcription. However, the adaptive transcriptional response to DR in C. elegans, and the role of MML-1::MXL-2 therein, remains largely unclear. Utilizing RNA-Sequencing we characterize transcriptional changes in DR in adult C. elegans, and find that a majority of those changes require both MML-1::MXL-2 and the FOXA homolog TF PHA-4. While most DR-modulated genes are downregulated, strikingly, we observe an inversion of this pattern of relative expression- in many cases also statistically significant- in eat-2;mxl-2 double mutant animals compared to wild-type. In contrast, RNAi knockdown of pha-4 in eat-2 animals leads to WT-like expression levels of DR genes. This is consistent with our previous model of opposing functions of the C. elegans heterodimeric MYC-family complexes in aging, with perturbation of MML1::MXL-2 leading to progeric phenotypes, and perturbation of MDL-1::MXL-1 leading to pro-longevity phenotypes. Overall, our findings position the Myc-family member TFs MML-1::MXL-2 as key effectors of the adaptive response to DR, and point to potential direct competition at binding sites with MDL-1::MXL-1. We also posit that PHA-4 acts indirectly to promote a permissive environment for MML-1::MXL-2 binding under DR in adult C. elegans.
The First Nation communities in northern Ontario have unique energy-related challenges within an interdisciplinary context, including historical, geographic, cultural, technological, and regulatory. ...Presently, undergoing an energy systems transition from off-grid to grid-connection and scoping renewable energy options, these remote communities are exhibiting characteristics of complex adaptive system principles. This is exhibited through non-linear interactions and connectedness among agents and components in the emerging energy system. This paper explores these interfaces through a case study of Poplar Hill First Nation, an Independent Power Authority community. The potentials of the complexity science through a community engagement process is used to encode and enhance understanding of the "contextual" complexities in the development of local economies, adapting to technology advancement, and social changes. The findings will help better appreciate the efforts made by Poplar Hill in their transition to self-sufficient systems with deliberations that may provide practical outcomes. This paper reflects on the deeper trajectories of the human elements embedded within the energy transition process. In conclusion, the paper adds to the academic dialogue on energy system transition adaptations in marginalised Indigenous communities in rural and remote locations.
Subpopulation growth rates and the probability of decline at current harvest levels were determined for 13 subpopulations of polar bears (Ursus maritimus) that are within or shared with Canada based ...on mark–recapture estimates of population numbers and vital rates, and harvest statistics using population viability analyses (PVA). Aboriginal traditional ecological knowledge (TEK) on subpopulation trend agreed with the seven stable/increasing results and one of the declining results, but disagreed with PVA status of five other declining subpopulations. The decline in the Baffin Bay subpopulation appeared to be due to over‐reporting of harvested numbers from outside Canada. The remaining four disputed subpopulations (Southern Beaufort Sea, Northern Beaufort Sea, Southern Hudson Bay, and Western Hudson Bay) were all incompletely mark–recapture (M‐R) sampled, which may have biased their survival and subpopulation estimates. Three of the four incompletely sampled subpopulations were PVA identified as nonviable (i.e., declining even with zero harvest mortality). TEK disagreement was nonrandom with respect to M‐R sampling protocols. Cluster analysis also grouped subpopulations with ambiguous demographic and harvest rate estimates separately from those with apparently reliable demographic estimates based on PVA probability of decline and unharvested subpopulation growth rate criteria. We suggest that the correspondence between TEK and scientific results can be used to improve the reliability of information on natural systems and thus improve resource management. Considering both TEK and scientific information, we suggest that the current status of Canadian polar bear subpopulations in 2013 was 12 stable/increasing and one declining (Kane Basin). We do not find support for the perspective that polar bears within or shared with Canada are currently in any sort of climate crisis. We suggest that monitoring the impacts of climate change (including sea ice decline) on polar bear subpopulations should be continued and enhanced and that adaptive management practices are warranted.
Status for 13 Canadian subpopulations of polar bears is examined through aboriginal traditional ecological knowledge (TEK) and population viability analysis (PVA) based on the most recent demographic and harvest statistics. A comparison of PVA simulation results and TEK perspectives on subpopulation status suggests TEK disagreement is nonrandom with respect to mark–recapture (M‐R) sampling protocols. We suggest that the lack of correspondence between PVA simulations results based on M‐R studies, TEK, and recent aerial survey results causes trend estimates for subpopulations that were partially M‐R sampled to be unreliable and negatively biased.
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