mRNA localization in Caenorhabditis elegans embryogenesis

2021 Summer.Includes bibliographical references.From guiding cell specification to regulating protein output, post-transcriptional regulation of mRNA is essential for life. As a result, many mechanisms underlying post-transcriptional regulation are highly conserved across the kingdoms of life. As the spatial resolution of microscopy and sequencing assays has increased, mRNA localization has emerged as a prevalent form of post-transcriptional regulation directing various cellular processes. Perhaps most notably, our understanding of post-transcriptional mRNA regulation and cellular function as a whole has been revolutionized by the discovery that many well-studied mRNA foci, such as germ granules, P-bodies, and stress granules, do not follow the lock-and-key principle of stoichiometric complex formation, but are actually phase-separated, biomolecular condensates. Due to their liquid-like nature, biomolecular condensates can aggregate or disperse component transcripts and proteins with exquisite environmental and temporal sensitivity. As a result, biomolecular condensates can regulate myriad processes as varied as co-translationally organizing protein components for complex assembly (Budding yeast translation factor mRNA granules), reinforcing translation inhibition (Germ granules) or activation (Neuronal granules), and facilitating the organization of other organelles (Axonemal dynein foci/kl-bodies). While an influx of studies have provided insights into the function of well-studied and novel biomolecular condensates alike, much remains unknown. What factors govern assembly and disassembly of condensates? How do they interact with one another? Is condensation the cause or consequence of the functional regulation of any particular mRNA? To begin to answer these questions, this thesis defines Caenorhabditis elegans as a model organism for exploring mRNA localization, its mechanisms, and its functions with a focus on condensate transcripts. Thus, the discoveries made have contributed to the fields of post-transcriptional gene regulation, mRNA localization, and condensate biology by elucidating mechanisms of localization, improving on methods of observing localization patterns, and establishing C. elegans as a tractable model for exploration of mRNA localization

Geophysical response to simulated methane migration in groundwater based on a controlled injection experiment in a sandy unconfined aquifer

The final publication is available at Elsevier via https://doi.org/ 10.1016/j.jappgeo.2019.05.019. © 2019. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Geophysical methods have the capacity to detect and characterize gas-phase dynamics in groundwater. Suitable methods can be deployed at surface or within boreholes depending on the required depth of investigation, spatial/temporal resolution, and geologic conditions. While the application of geophysical methods to monitor immiscible phase contaminants in the subsurface has been extensively documented, the effects of hydraulic properties and flow system conditions on the nature of the geophysical responses used to elucidate multi-phase fluid flow remains underdeveloped. A series of numerical 2-dimensional multi-phase flow and geophysical model simulations based on a controlled methane release experiment in the Borden unconfined sand aquifer was carried out to assess the influence of porous media hydraulic properties and flow system conditions on geophysical signatures associated with transient gas-phase saturation and gas migration behaviour. Specifically, the utility of electrical resistivity tomography (ERT) and ground-penetrating radar (GPR) to monitor gas-phase plume dynamics in shallow groundwater flow systems is examined. ERT and GPR responses to gas-phase distribution and migration during a 72-day methane gas injection and subsequent recovery period was calculated using a numerical multi-phase flow model (CFbio) simulating four distinct parameterizations of the sandy aquifer system. Geophysical models showed that ERT was effective at imaging the central position of the plume but was less effective at detecting thinner lateral migration pathways extending beyond the primary high gas saturation bulb. Conversely, GPR was able to detect thin gas pools emanating from the primary gas bulb and small-scale vertical preferential pathways arising from capillary boundaries with contrasting saturations; however, gradational boundaries proved to be more difficult to resolve using GPR. This study demonstrates that ERT and GPR can be very useful tools in combination for longer-term monitoring of stray gas leakage from decommissioned hydrocarbon wells in shallow granular media freshwater aquifers, especially given the likelihood of strong lateral migration.This research was made possible through an NSERC Strategic Partnerships Grant Project (SPG-P) awarded to Drs. John Cherry and Beth Parker along with their project collaborators Drs. Aaron Cahill, Bernhard Mayer, Ulrich Mayer and Cathryn Ryan

Monitoring the evolution and migration of a methane gas plume in an unconfined sandy aquifer using time-lapse GPR and ERT

The definitive publication is available at Elsevier via http://dx.doi.org/10.1016/j.jconhyd.2017.08.011 © 2017. This version, has not been modified, and is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Fugitive methane (CH4) leakage associated with conventional and unconventional petroleum development (e.g., shale gas) may pose significant risks to shallow groundwater. While the potential threat of stray (CH4) gas in aquifers has been acknowledged, few studies have examined the nature of its migration and fate in a shallow groundwater flow system. This study examines the geophysical responses observed from surface during a 72 day field-scale simulated CH4 leak in an unconfined sandy aquifer at Canadian Forces Base Borden, Canada, to better understand the transient behaviour of fugitive CH4 gas in the subsurface. Time-lapse ground-penetrating radar (GPR) and electrical resistivity tomography (ERT) were used to monitor the distribution and migration of the gas-phase and assess any impacts to groundwater hydrochemistry. Geophysical measurements captured the transient formation of a CH4 gas plume emanating from the injector, which was accompanied by an increase in total dissolved gas pressure (PTDG). Subsequent reductions in PTDG were accompanied by reduced bulk resistivity around the injector along with an increase in the GPR reflectivity along horizontal bedding reflectors farther downgradient. Repeat temporal GPR reflection profiling identified three events with major peaks in reflectivity, interpreted to represent episodic lateral CH4 gas release events into the aquifer. Here, a gradual increase in PTDG near the injector caused a sudden lateral breakthrough of gas in the direction of groundwater flow, causing free-phase CH4 to migrate much farther than anticipated based on groundwater advection. CH4 accumulated along subtle permeability boundaries demarcated by grain-scale bedding within the aquifer characteristic of numerous Borden-aquifer multi-phase flow experiments. Diminishing reflectivity over a period of days to weeks suggests buoyancy-driven migration to the vadose zone and/or CH4 dissolution into groundwater. Lateral and vertical CH4 migration was primarily governed by subtle, yet measurable heterogeneity and anisotropy in the aquifer.NSERC Strategic Partnerships Grant Project (SPG-P)NSERC Banting Fellowshi

Characterizing model errors in chemical transport modeling of methane: impact of model resolution in versions v9-02 of GEOS-Chem and v35j of its adjoint model

The GEOS-Chem simulation of atmospheric CH$_{4}$ was evaluated against observations from the Thermal and Near Infrared Sensor for Carbon Observations Fourier Transform Spectrometer (TANSO-FTS) on the Greenhouse Gases Observing Satellite (GOSAT), the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), and the Total Carbon Column Observing Network (TCCON). We focused on the model simulations at the 4°×5° and 2°×2.5° horizontal resolutions for the period of February–May 2010. Compared to the GOSAT, TCCON, and ACE-FTS data, we found that the 2°×2.5° model produced a better simulation of CH$_{4}$, with smaller biases and a higher correlation to the independent data. We found large resolution-dependent differences such as a latitude-dependent XCH$_{4}$ bias, with higher column abundances of CH$_{4}$ at high latitudes and lower abundances at low latitudes at the 4°×5° resolution than at 2°×2.5°. We also found large differences in CH$_{4}$ column abundances between the two resolutions over major source regions such as China. These differences resulted in up to 30 % differences in inferred regional CH$_{4}$ emission estimates from the two model resolutions. We performed several experiments using 222Rn, 7Be, and CH$_{4}$ to determine the origins of the resolution-dependent errors. The results suggested that the major source of the latitude-dependent errors is excessive mixing in the upper troposphere and lower stratosphere, including mixing at the edge of the polar vortex, which is pronounced at the 4°×5° resolution. At the coarser resolution, there is weakened vertical transport in the troposphere at midlatitudes to high latitudes due to the loss of sub-grid tracer eddy mass flux in the storm track regions. The vertical air mass fluxes are calculated in the model from the degraded coarse-resolution wind fields and the model does not conserve the air mass flux between model resolutions; as a result, the low resolution does not fully capture the vertical transport. This produces significant localized discrepancies, such as much greater CH$_{4}$ abundances in the lower troposphere over China at 4°×5° than at 2°×2.5°. Although we found that the CH$_{4}$ simulation is significantly better at 2°×2.5° than at 4°×5°, biases may still be present at 2°×2.5° resolution. Their importance, particularly in regards to inverse modeling of CH$_{4}$ emissions, should be evaluated in future studies using online transport in the native general circulation model as a benchmark simulation

Investigating associations between blood metabolites, later life brain imaging measures, and genetic risk for Alzheimer’s disease

BACKGROUND: Identifying blood-based signatures of brain health and preclinical pathology may offer insights into early disease mechanisms and highlight avenues for intervention. Here, we systematically profiled associations between blood metabolites and whole-brain volume, hippocampal volume, and amyloid-β status among participants of Insight 46-the neuroscience sub-study of the National Survey of Health and Development (NSHD). We additionally explored whether key metabolites were associated with polygenic risk for Alzheimer's disease (AD). METHODS: Following quality control, levels of 1019 metabolites-detected with liquid chromatography-mass spectrometry-were available for 1740 participants at age 60-64. Metabolite data were subsequently clustered into modules of co-expressed metabolites using weighted coexpression network analysis. Accompanying MRI and amyloid-PET imaging data were present for 437 participants (age 69-71). Regression analyses tested relationships between metabolite measures-modules and hub metabolites-and imaging outcomes. Hub metabolites were defined as metabolites that were highly connected within significant (pFDR < 0.05) modules or were identified as a hub in a previous analysis on cognitive function in the same cohort. Regression models included adjustments for age, sex, APOE genotype, lipid medication use, childhood cognitive ability, and social factors. Finally, associations were tested between AD polygenic risk scores (PRS), including and excluding the APOE region, and metabolites and modules that significantly associated (pFDR < 0.05) with an imaging outcome (N = 1638). RESULTS: In the fully adjusted model, three lipid modules were associated with a brain volume measure (pFDR < 0.05): one enriched in sphingolipids (hippocampal volume: ß = 0.14, 95% CI = [0.055,0.23]), one in several fatty acid pathways (whole-brain volume: ß =  - 0.072, 95%CI = [- 0.12, - 0.026]), and another in diacylglycerols and phosphatidylethanolamines (whole-brain volume: ß =  - 0.066, 95% CI = [- 0.11, - 0.020]). Twenty-two hub metabolites were associated (pFDR < 0.05) with an imaging outcome (whole-brain volume: 22; hippocampal volume: 4). Some nominal associations were reported for amyloid-β, and with an AD PRS in our genetic analysis, but none survived multiple testing correction. CONCLUSIONS: Our findings highlight key metabolites, with functions in membrane integrity and cell signalling, that associated with structural brain measures in later life. Future research should focus on replicating this work and interrogating causality

Aptamer-based multiplexed proteomic technology for biomarker discovery

Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma). Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding DNA aptamer concentration signature, which is then quantified with a DNA microarray. In essence, our assay takes advantage of the dual nature of aptamers as both folded binding entities with defined shapes and unique sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to discover unique protein signatures characteristic of various disease states. More generally, we describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine

The Short-Term Effect of Weight Loss Surgery on Volumetric Breast Density and Fibroglandular Volume

Purpose: Obesity and breast density are both associated with an increased risk of breast cancer and are potentially modifiable. Weight loss surgery (WLS) causes a significant reduction in the amount of body fat and a decrease in breast cancer risk. The effect of WLS on breast density and its components has not been documented. Here, we analyze the impact of WLS on volumetric breast density (VBD) and on each of its components (fibroglandular volume and breast volume) by using three-dimensional methods. Materials and Methods: Fibroglandular volume, breast volume, and their ratio, the VBD, were calculated from mammograms before and after WLS by using Volpara™ automated software. Results: For the 80 women included, average body mass index decreased from 46.0 ± 7.22 to 33.7 ± 7.06 kg/m2. Mammograms were performed on average 11.6 ± 9.4 months before and 10.1 ± 7 months after WLS. There was a significant reduction in average breast volume (39.4 % decrease) and average fibroglandular volume (15.5 % decrease), and thus, the average VBD increased from 5.15 to 7.87 % (p < 1 × 10−9) after WLS. When stratified by menopausal status and diabetic status, VBD increased significantly in all groups but only perimenopausal and postmenopausal women and non-diabetics experienced a significant reduction in fibroglandular volume. Conclusions: Breast volume and fibroglandular volume decreased, and VBD increased following WLS, with the most significant change observed in postmenopausal women and non-diabetics. Further studies are warranted to determine how physical and biological alterations in breast density components after WLS may impact breast cancer risk.ECU Open Access Publishing Support Fun

Measurement of associated Z plus charm production in proton-proton collisions at root s=8TeV

A study of the associated production of a Z boson and a charm quark jet (Z + c), and a comparison to production with a b quark jet (Z + b), in pp collisions at a centre-of-mass energy of 8 TeV are presented. The analysis uses a data sample corresponding to an integrated luminosity of 19.7 fb(-1), collected with the CMS detector at the CERN LHC. The Z boson candidates are identified through their decays into pairs of electrons or muons. Jets originating from heavy flavour quarks are identified using semileptonic decays of c or b flavoured hadrons and hadronic decays of charm hadrons. The measurements are performed in the kinematic region with two leptons with pT(l) > 20 GeV, vertical bar eta(l)vertical bar 25 GeV and vertical bar eta(jet)vertical bar Z + c + X) B(Z -> l(+)l(-)) = 8.8 +/- 0.5 (stat)+/- 0.6 (syst) pb. The ratio of the Z+c and Z+b production cross sections is measured to be sigma(pp -> Z+c+X)/sigma (pp -> Z+b+X) = 2.0 +/- 0.2 (stat)+/- 0.2 (syst). The Z+c production cross section and the cross section ratio are also measured as a function of the transverse momentum of theZ boson and of the heavy flavour jet. The measurements are compared with theoretical predictions.Peer reviewe