Doctor of Philosophy

dissertationDetermining the health impacts of a nutritional regimen, suspected toxicant or other treatment is often a difficult task in both the realms of safety assessment and basic research. There are far too many examples of agents, once considered safe, found later through epidemiology (or other means) to cause adverse health effects. To prevent such experimentation on ourselves there is a great societal need for broad, sensitive assays able to detect toxicity at human-relevant exposure levels. Similarly, basic researchers often lack the experimental tools necessary to determine if a treatment adversely impacts the health of their model organism. We argue that these problems can be partially solved by using house mice in the crucible of their natural setting where they are challenged daily by the very tasks that have shaped them for millennia. Quantifying the lifelong fitness of experimentally treated animals directly competing with control individuals offers a sensitive and broad approach for detecting adverse health effects. We refer to this approach as an Organismal Performance Assay (OPA). To illustrate the effectiveness of OPAs, herein we apply them for detecting adverse health consequences of nutritional and toxic exposures. First, using OPAs we capture adverse health impacts (decreased survival, competitive ability and reproduction) from consuming 12.5% kcal of fructose; this finding now represent the lowest observed adverse effect level for dietary fructose. Next, we apply OPAs to determine if differential health impacts occur due to the consumption of one, or the other, of the two common types of added sugar, high fructose corn syrup (fructose and glucose monosaccharides) or table sugar (sucrose, which is a disaccharide of fructose and glucose), and show that the high fructose corn syrup diet increases mortality and decreases reproduction of female mice compared to sucrose, providing the first experimental evidence that the two most common forms of caloric sweeteners have differential health impacts. Next, we use OPAs to determine if an acute exposure to 3mg/kg of amine-terminated generation seven poly amido-amine dendrimers, the current maximum tolerated dose, is actually toxic and find that it is not. Finally, to address the criticism that OPAs do not lead to the underlying mechanisms of observed organismal outcomes, we illustrate the discovery of the molecular basis of the first phenomenon revealed using OPAs, major histocompatibility complex (MHC)-based mating preferences, which is done in the context of a review paper on the role of MHC during social communication

MHC signaling during social communication

Journal ArticleThe major histocompatibility complex (MHC) has been known to play a critical role in immune recognition since the 1950s. It was a surprise, then, in the 1970s when the first report appeared indicating MHC might also function in social signaling. Since this seminal discovery, MHC signaling has been found throughout vertebrates and its known functions have expanded beyond mate choice to include a suite of behaviors from kin‑biased cooperation, parent‑progeny recognition to pregnancy block. The widespread occurrence of MHC in social signaling has revealed conserved behavioral‑genetic mechanisms that span vertebrates and includes humans. The identity of the signal's chemical constituents and the receptors responsible for the perception of the signal have remained elusive, but recent advances have enabled the identification of the key components of the behavioral circuit. In this chapter we organize recent findings from the literature and discuss them in relation to four nonmutually exclusive models wherein MHC functions as a signal of (i) individuality, (ii) relatedness, (iii) genetic compatibility and (iv) quality. We also synthesize current mechanistic studies, showing how knowledge about the molecular basis of MHC signaling can lead to elegant and informative experimental manipulations. Finally, we discuss current evidence relating to the primordial functions of the MHC, including the possibility that its role in social signaling may be ancestral to its central role in adaptive immunity

Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H

Large-scale Spacecraft Fire Safety Tests

An international collaborative program is underway to address open issues in spacecraft fire safety. Because of limited access to long-term low-gravity conditions and the small volume generally allotted for these experiments, there have been relatively few experiments that directly study spacecraft fire safety under low-gravity conditions. Furthermore, none of these experiments have studied sample sizes and environment conditions typical of those expected in a spacecraft fire. The major constraint has been the size of the sample, with prior experiments limited to samples of the order of 10 cm in length and width or smaller. This lack of experimental data forces spacecraft designers to base their designs and safety precautions on 1-g understanding of flame spread, fire detection, and suppression. However, low-gravity combustion research has demonstrated substantial differences in flame behavior in low-gravity. This, combined with the differences caused by the confined spacecraft environment, necessitates practical scale spacecraft fire safety research to mitigate risks for future space missions. To address this issue, a large-scale spacecraft fire experiment is under development by NASA and an international team of investigators. This poster presents the objectives, status, and concept of this collaborative international project (Saffire). The project plan is to conduct fire safety experiments on three sequential flights of an unmanned ISS re-supply spacecraft (the Orbital Cygnus vehicle) after they have completed their delivery of cargo to the ISS and have begun their return journeys to earth. On two flights (Saffire-1 and Saffire-3), the experiment will consist of a flame spread test involving a meter-scale sample ignited in the pressurized volume of the spacecraft and allowed to burn to completion while measurements are made. On one of the flights (Saffire-2), 9 smaller (5 x 30 cm) samples will be tested to evaluate NASAs material flammability screening tests. The first flight (Saffire-1) is scheduled for July 2015 with the other two following at six-month intervals. A computer modeling effort will complement the experimental effort. Although the experiment will need to meet rigorous safety requirements to ensure the carrier vehicle does not sustain damage, the absence of a crew removes the need for strict containment of combustion products. This will facilitate the first examination of fire behavior on a scale that is relevant to spacecraft fire safety and will provide unique data for fire model validation

Cell-free (RNA) and cell-associated (DNA) HIV-1 and postnatal transmission through breastfeeding

<p>Introduction - Transmission through breastfeeding remains important for mother-to-child transmission (MTCT) in resource-limited settings. We quantify the relationship between cell-free (RNA) and cell-associated (DNA) shedding of HIV-1 virus in breastmilk and the risk of postnatal HIV-1 transmission in the first 6 months postpartum.</p> <p>Materials and Methods - Thirty-six HIV-positive mothers who transmitted HIV-1 by breastfeeding were matched to 36 non-transmitting HIV-1 infected mothers in a case-control study nested in a cohort of HIV-infected women. RNA and DNA were quantified in the same breastmilk sample taken at 6 weeks and 6 months. Cox regression analysis assessed the association between cell-free and cell-associated virus levels and risk of postnatal HIV-1 transmission.</p> <p>Results - There were higher median levels of cell-free than cell-associated HIV-1 virus (per ml) in breastmilk at 6 weeks and 6 months. Multivariably, adjusting for antenatal CD4 count and maternal plasma viral load, at 6 weeks, each 10-fold increase in cell-free or cell-associated levels (per ml) was significantly associated with HIV-1 transmission but stronger for cell-associated than cell-free levels [2.47 (95% CI 1.33–4.59) vs. aHR 1.52 (95% CI, 1.17–1.96), respectively]. At 6 months, cell-free and cell-associated levels (per ml) in breastmilk remained significantly associated with HIV-1 transmission but was stronger for cell-free than cell-associated levels [aHR 2.53 (95% CI 1.64–3.92) vs. 1.73 (95% CI 0.94–3.19), respectively].</p> <p>Conclusions - The findings suggest that cell-associated virus level (per ml) is more important for early postpartum HIV-1 transmission (at 6 weeks) than cell-free virus. As cell-associated virus levels have been consistently detected in breastmilk despite antiretroviral therapy, this highlights a potential challenge for resource-limited settings to achieve the UNAIDS goal for 2015 of eliminating vertical transmission. More studies would further knowledge on mechanisms of HIV-1 transmission and help develop more effective drugs during lactation.</p&gt

Fire safety in space – beyond flammability testing of small samples

International audienceAn international research team has been assembled to reduce the uncertainty and risk in the design of spacecraft fire safety systems by testing material samples in a series of flight experiments (Saffire 1, 2, and-3) to be conducted in an Orbital Science Corporation Cygnus vehicle after it has undocked from the International Space Station (ISS). The tests will be fully automated with the data downlinked at the conclusion of the test before the Cygnus vehicle re-enters the atmosphere. The unmanned, pressurized environment in the Saffire experiments allows for the largest sample sizes ever to be tested for material flammability in microgravity, which will be based on the characteristics of flame spread over the surface of the combustible material. Furthermore, the experiments will have a duration that is unmatched in scale compared to earth based microgravity research facilities such as drop towers (about 5 seconds) and parabolic flights (about 20 seconds). In contrast to sounding rockets, the experiments offer a much larger volume, and the reduction in the oxygen concentration during the Saffire experiments will be minimal. The selection of the experimental settings for the first three Saffire experiments has been based on existing knowledge of scenarios that are relevant, yet challenging, for a spacecraft environment. Given that there is always airflow in the space station, all the experiments are conducted with flame spread in either concurrent or opposed flow, though with the flow being stopped in some tests, to simulate the alarm mode environment in the ISS and thereby also to study extinguishment. The materials have been selected based on their known performance in NASA STD-6001Test-1, and with different materials being classified as charring, thermally thin, and thermally thick. Furthermore, materials with non-uniform surfaces will be investigated

Unmanned Vehicle Material Flammability Test

Microgravity fire behaviour remains poorly understood and a significant risk for spaceflight An experiment is under development that will provide the first real opportunity to examine this issue focussing on two objectives: a) Flame Spread. b) Material Flammability. This experiment has been shown to be feasible on both ESA's ATV and Orbital Science's Cygnus vehicles with the Cygnus as the current base-line carrier. An international topical team has been formed to develop concepts for that experiment and support its implementation: a) Pressure Rise prediction. b) Sample Material Selection. This experiment would be a landmark for spacecraft fire safety with the data and subsequent analysis providing much needed verification of spacecraft fire safety protocols for the crews of future exploration vehicles and habitats