Endocytosis, Phagocytosis, and Innate Immune Responses: A Dissertation

In this dissertation, the roles of endocytosis and phagocytosis pathways in a variety of clinically relevant scenarios were examined. These scenarios include antibody-mediated internalization of cell surface proteins, titanium wear-particle uptake in failed joint replacements, and polymeric microparticle uptake and immune responses for drug delivery or adjuvant use. The use of antibodies specific for cell surface proteins has become a popular method to deliver therapeutics to target cells. As such, it is imperative to fully understand the ability of antibodies to mediate internalization and endosomal trafficking of the surface protein that it recognizes, so that drug delivery can be optimized. By comparing the internalization and endosomal localization of two different antibody-bound proteins, the transferrin receptor (TfR) and rabies G, we have found that there is a specific antibody-mediated internalization pathway that occurs when an antibody binds to a cell surface protein. Interestingly, the internalization pathway induced by antibody binding is different than that seen with recycling receptor internalization after ligand binding. This may have broad implications for the future development of antibody-based therapeutics. Joint replacement failure is a major clinical problem. Studies have indicated that a large amount of metal and polyethylene wear debris is found in the synovial membrane and tissue surrounding failed replacements. Through examination of the immune response following uptake of titanium particles, our results suggest that titanium wear-particle induced inflammation and subsequent joint replacement failure may be due to activation of the NLRP3 inflammasome, leading to increased IL-1ß secretion and IL-1 associated signaling. These findings introduce IL-1 as a target for potential therapeutics for patients exhibiting significant inflammation. Polymeric microparticles have been widely used in a variety of therapeutic applications, including drug delivery and vaccine adjuvants. It is essential to understand the ability of such particles to either activate or inhibit an immune response following uptake. Through comparison of particles with varying surface morphology, we have determined that particles with regions of high surface curvature (budding) are more immunogenic than particles with low surface curvature (spherical). Budding particles were more rapidly phagocytosed and induced higher levels of the inflammasome-associated cytokine, IL-1ß, when exposed to mouse macrophages. Additionally, budding particles induced a more rapid neutrophil response in vivo, when compared to spherical particles. These findings have broad implications for the development of future targeting vehicles for delivery of vaccines, drugs, proteins, and siRNA therapeutics

LGBTTQI Communities and Home Care in Ontario: Project Report

Canadian Institutes of Health Research – Institute of Gender and Healt

Genome-wide association study in two cohorts from a multi-generational mouse advanced intercross line highlights the difficulty of replication due to study-specific heterogeneity

There has been extensive discussion of the Replication Crisis in many fields, including genome-wide association studies

Observations of fresh, anticyclonic eddies in the Hudson Strait outflow

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 88 (2011): 375-384, doi:10.1016/j.jmarsys.2010.12.004.The waters that flow out through Hudson Strait, a coastal system that connects Hudson Bay with the Labrador Sea, constitute the third largest freshwater contribution to the northern North Atlantic. Recent studies have documented the mean structure and transport of the outflow, as well as highlighting significant variability on synoptic scales (days–week). This study examines the outflow’s variability on these synoptic scales through the use of observations collected by a mooring array from 2005-2006. We focus on the mechanisms that cause the freshwater export to be concentrated in a series of discrete pulses during the fall/winter season. We find that the pulses occur once every 4.4 days on average and are associated with anticyclonic, surface-trapped eddies propagated through the strait by the mean outflow. Their occurrence is related to the passage of storms across Hudson Bay, although local instability processes also play a role in their formation. The eddies are responsible for approximately 40% of the mean volume transport and 50% of the mean freshwater transport out of the strait. We discuss the implications of this freshwater release mechanism on the delivery of nutrient-rich and highly stratified waters to the Labrador shelf, a productive region south of Hudson Strait.This work was funded by National Science Foundation grant OCE-0751554, with additional funding from the Office of Naval Research grant N00014-08-10490

On sparse regression, Lp-regularization, and automated model discovery

Sparse regression and feature extraction are the cornerstones of knowledge discovery from massive data. Their goal is to discover interpretable and predictive models that provide simple relationships among scientific variables. While the statistical tools for model discovery are well established in the context of linear regression, their generalization to nonlinear regression in material modeling is highly problem-specific and insufficiently understood. Here we explore the potential of neural networks for automatic model discovery and induce sparsity by a hybrid approach that combines two strategies: regularization and physical constraints. We integrate the concept of Lp regularization for subset selection with constitutive neural networks that leverage our domain knowledge in kinematics and thermodynamics. We train our networks with both, synthetic and real data, and perform several thousand discovery runs to infer common guidelines and trends: L2 regularization or ridge regression is unsuitable for model discovery; L1 regularization or lasso promotes sparsity, but induces strong bias; only L0 regularization allows us to transparently fine-tune the trade-off between interpretability and predictability, simplicity and accuracy, and bias and variance. With these insights, we demonstrate that Lp regularized constitutive neural networks can simultaneously discover both, interpretable models and physically meaningful parameters. We anticipate that our findings will generalize to alternative discovery techniques such as sparse and symbolic regression, and to other domains such as biology, chemistry, or medicine. Our ability to automatically discover material models from data could have tremendous applications in generative material design and open new opportunities to manipulate matter, alter properties of existing materials, and discover new materials with user-defined properties.Comment: 35 pages, 15 figures, 2 tables, 62 reference

High fracture toughness micro-architectured materials

© 2020 We investigate the possibility of achieving high fracture toughness and high strength by the design of lightweight (density below water) metallic micro-architectured materials. The micro-architectured materials were manufactured by drilling a hexagonal array of holes in plates of an aluminum alloy, and the fracture toughness was evaluated via three-point bend tests of single-edge notch specimens. The results show that the fracture toughness of micro-architectured materials increases with increasing relative density and remarkably, a micro-architectured material can be 50% lighter than the parent material but maintain the same fracture toughness. Additional tests on geometrically similar specimens revealed that the fracture toughness increases linearly with the square-root of the cell size. The experiments are complemented by finite element calculations of ductile fracture. In the calculations, the fracture toughness of single-edge notch specimens subjected to three-point bending are evaluated using both, a procedure similar to the experiments and direct computation of the J-contour integral. The fracture toughness as calculated by both methods are consistent with the experimental results. In addition, the calculations are also carried out for single-edge notch specimens subjected to tensile loading, confirming the validity of the measured fracture toughness as a useful material property independent of specimen geometry

A Synthetic Circuit for Buffering Gene Dosage Variation Between Individual Mammalian Cell

Precise control of gene expression is critical for biological research and biotechnology. However, transient plasmid transfections in mammalian cells produce a wide distribution of copy numbers per cell, and consequently, high expression heterogeneity. Here, we report plasmid-based synthetic circuits - Equalizers - that buffer copy-number variation at the single-cell level. Equalizers couple a transcriptional negative feedback loop with post-transcriptional incoherent feedforward control. Computational modeling suggests that the combination of these two topologies enables Equalizers to operate over a wide range of plasmid copy numbers. We demonstrate experimentally that Equalizers outperform other gene dosage compensation topologies and produce as low cell-to-cell variation as chromosomally integrated genes. We also show that episome-encoded Equalizers enable the rapid generation of extrachromosomal cell lines with stable and uniform expression. Overall, Equalizers are simple and versatile devices for homogeneous gene expression and can facilitate the engineering of synthetic circuits that function reliably in every cell

Osteopontin: an early innate immune marker of Escherichia coli mastitis harbors genetic polymorphisms with possible links with resistance to mastitis

<p>Abstract</p> <p>Background</p> <p>Mastitis is the most important disease in dairy cows and it causes significant lost of profit to producers. Identification of the genes, and their variants, involved in innate immune responses is essential for the understanding of this inflammatory disease and to identify potential genetic markers for resistance to mastitis. The progeny of dairy cows would benefit from receiving favourable alleles that support greater resistance to infection, thus reducing antibiotic use. This study aims to identify a key gene in the innate immune response to mastitis, led us to evaluate its genetic association with somatic cell score (SCS), which is an indicator of clinical mastitis, and to evaluate its impact on other traits related to milk production.</p> <p>Results</p> <p>The osteopontin transcript (<it>SPP1</it>) was identified in the somatic cells from cows experimentally infected with <it>Escherichia coli</it>. By selecting bulls with extreme estimated breeding values (EBVs) for SCS, which is an indicator of mammary gland health, four DNA polymorphisms in the <it>SPP1 </it>genomic sequence were found. Statistical analysis revealed that the SNP <it>SPP1c.-1301G>A </it>has an impact on EBV for SCS (<it>P </it>< 0.001) Using an allele substitution model, <it>SPP1c.-1251C>T</it>, <it>SPP1c.-430G>A</it>, and <it>SPP1c.*40A>C </it>have an impact on SCS whereas <it>SPP1c.-1301G>A </it>has an effect on the EBVs for milk yield (second and third lactations), fat and protein percentages (all three lactations). Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (<it>P </it>= 0.012), second (<it>P </it>< 0.001), and third (<it>P </it>< 0.001) lactations.</p> <p>Conclusion</p> <p>This study reports the link between DNA polymorphisms of <it>SPP1</it>, the number of milk immune cells and, potentially, the susceptibility to mastitis. These SNPs were identified by <it>in silico </it>search to be located in transcription factor recognition sites which factors are presumably involved in the Th1 immune response and in the Th2 regulation pathway. Indeed, one SNP abolished the SP1 recognition site, whereas another SNP affected the transcription binding factor IKAROS. All together, these findings support the genetic potential of these variants in terms of selection for the improvement of mastitis resistance in dairy cows.</p

Biology and Utilization of Anadromous Alosids: Annual progress report (October 1, 1971 - September 30, 1972)

Fishing effort for herring and shad has been stable for the past three years in the lower Chesapeake Bay and tributaries. River herring catch in 1972 was slightly above the 1971 landings but continued to be very low. River herring landings in U.S. waters have declined as the c.atch has been increased by non-nationals. The catch per unit of effort has decreased from 122.5 in 1965 to 30.3 in 1972 in Virginia waters. Total mortality rates for river herring were without significant trend from 1965-1971. Twice as much towing effort was expended in 1972 as in other years. The abundance of juvenile alosids was much lower in 1972 than former years. The James once again led all rivers in alosid production