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Miniaturizing GFP
No full textThe green fluorescent protein (GFP) has enabled researchers to visualize a wide range of cellular processes, from protein expression to metastasis. However, its size (27 kDa) can disrupt localization and association of GFP-tagged proteins. Here, we aim to address this limitation by designing a miniature GFP (<20 kDa) that conserves its chromophore-forming pocket within a shortened beta-barrel fold. Using machine learning-assisted protein design, we have produced nineteen miniature GFPs, averaging 19 kDa each, that display varying levels of expression. These small GFPs display similar excitation and emission wavelengths to wild-type GFP, albeit with fluorescence reduced by four orders of magnitude due to low quantum yield and inefficient chromophore maturation. To improve brightness, we utilized random mutagenesis but were unable to isolate improved variants due to the detection limit of our selection method (FACS) being too high to distinguish miniaturized GFP fluorescence from background cellular fluorescence at the desired wavelengths. Our results show that while machine learning can be used to miniaturize GFP, this process leads to impaired function
The Role of Transcription Factor SIX1 During Macrophage Responses to Salmonella enterica Serovar Typhimurium Infection
No full textMacrophages help eliminate bacterial pathogens that otherwise deter human health. However, certain pathogens, such as Salmonella enterica serovar Typhimurium (STm), are instead able to survive and persist within macrophages. To develop the means to prevent this phenomenon, we must further our understanding of the interplay between STm and macrophages. SIX1 (sine oculis homeobox homologue 1) is a host transcription factor that is primarily active during, and studied in the context of, embryonic development. However, there has been an increase in studies suggesting that SIX1 can regulate inflammation, which is a key antibacterial response of macrophages. Furthermore, recent evidence suggests that bacterial pathogens can upregulate SIX1 expression. Taken together, this raises the question of whether SIX1 regulates macrophage responses during bacterial infections, such as STm infection, to the host's benefit or detriment. Addressing this question could enhance our understanding of pathways that contribute to promoting or preventing the resolution of infection. However, SIX1 has not previously been studied in this context. Herein, I demonstrate that SIX1 expression modulates STm intracellular survival in a pathogen specific manner. Human THP-1 macrophages that are SIX1 overexpressing (THP-SIX1++) or knockdown (THP-SIX1) had increased or decreased STm burden respectively. I demonstrated that these differences in STm burden were due to STm intracellular survival, as opposed to being the by-product of differences in bacterial uptake or macrophage cell death. To identify factors contributing to the SIX1-dependent STm survival phenotype, I evaluated macrophage antibacterial responses including cytokine/chemokine production, reactive oxygen species (ROS) production, and autophagy. Despite previous reports wherein SIX1 downregulated inflammation, I observed only a minimal impact on the macrophages' immunological profile during STm infection and no differences in ROS or autophagy levels. Although none of those pathways appeared relevant to our phenotype, I did discover that torin-1, an inducer of autophagy, could rescue THP-SIX1++ macrophages' inability to control STm survival and replication. Aside from inducing autophagy, which I previously tested, torin-1 is also known to inhibit AKT phosphorylation, which prevents AKT activation and signalling. In testing whether torin-1's impact on AKT phosphorylation could contribute to my phenotype, I discovered that THP-SIX1++ macrophages had elevated levels of phosphorylated AKT that were abolished in the presence of torin-1. Taken together, these findings suggest that perhaps AKT signalling contributes to the observed SIX1-dependent STm survival phenotype. However, further studies are required to elucidate the precise functional mechanism responsible for SIX1's modulation of STm survival. Nonetheless, this study highlights that, in the context of macrophage infection, the transcription factor SIX1 can exhibit pathogen specific, host detrimental effects
Examining the OpenAlex Concepts: A Detailed Case Study of Machine-Derived Classification
No full textMachine-learning techniques are becoming increasingly popular in metadata and classification work due to their ability to operate at scale, but insufficient consideration has been given to how effective such techniques truly are against traditional practice. This thesis adopts an approach based on Data Feminism (D'Ignazio & Klein, 2020) to analyze the machine-generated OpenAlex concept hierarchy and its associated machine-learning model in comparison to established classification standards and practices. We find that the OpenAlex concepts differ vastly from a traditional classification system, and that this difference inhibits their effectiveness in some respects, while also offering possible ways to address modern criticisms of classification (Olson, 2001; Mai, 2005). We argue that statistical, data-processing approaches to classification cannot replace the human judgment necessary for classification work, and that, to the extent that they continue to be used in this type of work, automatic techniques should be more informed by information theoretical principles and guided by human expertise
All-Optical Quantum Information Processing in the Ultrafast Regime
No full textQuantum computing offers a promising pathway to solving problems that are intractable for classical computers. Despite recent progress, the development of a scalable quantum information processor remains an open challenge. Several hardware platforms remain contenders; however, photonic systems have emerged as a strong candidate due to their ability to operate at room temperature and exceptional resilience to decoherence. State-of-the-art photonic quantum processors use path encoding, which often requires an exponentially increasing number of optical components, making these schemes unavoidably large or lossy in some cases. Time-bin encoding has recently proven to be a promising method to reduce the number of optical components in a photonic quantum processor by enabling operation along a single optical path. Yet, a major barrier to the widespread adoption of time-bin encoding is the challenge of maintaining phase stability across the entire device for extended periods of time. We overcome this obstacle here, by introducing a promising new contender in the photonic quantum computing landscape: ultrafast time-bin encoding.
The architecture proposed in this thesis encodes quantum information in the arrival time of photons on ultrafast timescales, processed using optically induced nonlinearities via Kerr gating and birefringent media. A major part of this thesis is the development of the optical Kerr gating technique, which is explored in three initial studies. We first introduce a characterization method, which also happens to enable the carving of ultrashort pulses from a continuous wave laser. With this technique, we demonstrate configurable all-optical Kerr gating down to a temporal resolution of 305 fs. We next investigate translating this high temporal resolution to the frequency domain, using our Kerr gate to measure time-stretched spectra. Finally, we employ two Kerr gates for measurement of the temporal profiles of entangled photons, subsequently allowing for verification of entanglement. Each of these studies provides valuable insight into the optimal operation of the Kerr gate for quantum information processing.
The Kerr gate is then deployed for the demonstration of our ultrafast time-bin encoding scheme. Operating first in the single photon regime, we implement both a specific quantum algorithm and a more generalized, programmable circuit. Within the large multimode interferometers presented in these two implementations, we see remarkable phase stability over extended periods of time, high fidelity operation, and low loss - all key ingredients for scalability in quantum information processing. Finally, these capabilities are extended to include multiphoton operation, which is a crucial requirement for any photonic quantum information processing system. Taken together, these results demonstrate the potential of ultrafast time-bin encoding for the development of scalable photonic quantum information processing
Optimal Contracts under General Mixed Constraints: Continuity, Structure, and Applications
No full textThis paper characterizes optimal contract structures under adverse selection when the principal faces a general class of mixed (involving allocation and transfer) constraints. We establish conditions for the existence and the continuity of the optimal allocation. We show that under regularity conditions, the optimal continuous contract features at most three distinct regions: segments where the constraint is slack and the allocation follows a modified Baron-Myerson path, alternating with segments where the constraint binds. Assuming non-generic cases are excluded, the binding constraint forces a constant allocation (bunching) over a range of agent types. Our analysis demonstrates how bunching can arise endogenously from optimal design under smooth constraints, distinct from exogenously induced behavioural responses documented empirically
Migration et racialisation en temps de « crise »: La fabrique des crises et ses effets
No full textCrise sanitaire, crise migratoire, crise humanitaire, crise climatique… Le renvoi répété à l’idée de crise pour désigner nombre de bouleversements sociaux laisse à penser que nous vivons désormais dans un monde « crisogène ».
Or, l’urgence inhérente à l’idée de crise conduit souvent à légitimer la violation des droits et le renforcement de la surveillance, du profilage et des arrestations arbitraires, rendant visible le contrôle qu’exerce l’État sur les corps, et surtout sur certains corps.
Migration et racialisation en temps de « crise » explore les ressorts coloniaux, racistes et sexistes au fondement de diverses déclarations de crise, ainsi que leurs effets. L’ensemble des contributions montre que l’état de crise apparaît comme une condition pour le maintien d’un capitalisme racial et patriarcal.Liste des figures et des tableaux
Introduction
Leila Benhadjoudja, Christina Clark-Kazak et Stéphanie Garneau
CHAPITRE 1
Une crise de panique raciale dans le monde universitaire québécois
Vincent Romani
CHAPITRE 2
De l’Autre à l’autre : instrumentalisation chronotopique et évolution des dynamiques d’altérisation lors de crises épidémiques
Mélissa Roy
CHAPITRE 3
Gestion de crise et colonialité du pouvoir : réhumaniser nos relations avec le monde ?
Jeanne-Marie Rugira et Maïka Sondarjee
CHAPITRE 4
Entrechoc ontologique et épistémologique des « mises en crise » de la société haïtienne
Magalie Civil et Philippe Couton
CHAPITRE 5
Fabrique idéologique de « crises », colonialisme et résurgence socio‑identitaire : neuf femmes innues se racontent
Karine Croteau
CHAPITRE 6
La CAQ et les « anges gardiens » pendant la « crise » de la COVID‑19 : prendre soin d’en prendre moins ?
Handy Leroy et Stéphanie Garneau
CHAPITRE 7
Essentiels mais temporaires ? La médiatisation des travailleurs agricoles mexicains et guatémaltèques au Canada en temps de crise de la COVID-19
Guadalupe Escalante Rengifo et Jorge Pantaleó
When the decision to die interferes with the duty to heal
No full textAbstract Background This commentary was inspired by an encounter M. M. experienced while shadowing a physician in 2024. The physician referred an otherwise healthy patient between 64 and 74 years old for a routine colonoscopy due to relevant risk factors. However, instead of the anticipated report, they received a letter from the specialist stating their refusal to complete the procedure. The reason cited for refusal: medical assistance in dying (MAiD). In the meeting with the specialist, the patient mentioned that they were considering pursuing MAiD for depression in 2026 - a choice that, notably, would not be available for solely mental health conditions until March 17, 2027. Results/Conclusion Here, we consider multiple angles centred around how we should treat MAiD, particularly when it intersects with decisions related to life expectancy. Policy reform is necessary to address this potential form of discrimination across all subspecialties in medicine, advocating instead for collaborative, case-by-case decision-making between physicians and patients to discuss their goals of care and risks. To this end, we propose a four-pronged approach, including guidelines, medical ethics training, patient-targeted education, and further research
Investigating the Role of Chronic OPA1 Loss in Muscle Stem Cell Maintenance and Activity
No full textAdult muscle stem cells (MuSCs) play a crucial role in tissue regeneration, yet the mechanisms governing their dysfunction and depletion during aging remain unclear. However, during aging, regulators of mitochondrial dynamics, a key regulator of MuSC activity and fate, decline in expression. This loss of mitochondrial fission and fusion modulators has been associated with premature aging phenotypes in whole muscle and MuSC dysregulation with age. To date, how mitochondrial dynamics contribute to senescent and aged-like phenotypes in MuSCs has not been fully described. Our lab has previously implemented a Pax7CreERT2 inducible system to conditionally knock-out the mitochondrial fusion protein OPA1 specifically within MuSCs (OPA1-KO) and found that with chronic loss of OPA1, MuSCs have enhanced activation kinetics, significant proliferation defects, and evidence of mitochondrial dysfunction. In this current work, we sought to address the role of chronic OPA1 loss in MuSCs, particularly in the contexts of aging and senescence. We found that with chronic loss of OPA1, MuSCs accumulate biomarkers of senescence, experience cell cycle dysregulation at the transcriptional level, and have a dysregulated metabolome. However, the proliferative defects associated with chronic OPA1 ablation may be partially mitigated via supplementation of exogenous metabolites. Notably, at 9 months of OPA1 loss, the phenotype of MuSC dysfunction was found to progress to the extent of stem cell depletion basally. Further, whole-muscle defects were observed at this time, including the onset of a muscle wasting phenotype (with a reduction in the myofiber cross-sectional area and the number of myonuclei per myofiber) and increased fatiguability of the muscle. These findings suggest that mitochondrial dynamics are a critical regulator of MuSC activity and maintenance in an aging context, and that whole muscle health during aging is dependent on the presence of functional MuSCs. This research offers novel therapeutic insight that may be leveraged to improve muscle stem cell health and function with age
Using an Accelerated Aging Model and an Optimised Proteomic Approach to Identify Extracellular Vesicle-Associated Proteins in Inflammaging
No full textSenescent cells contribute to inflammaging through the senescence-associated secretory phenotype (SASP). While the SASP has traditionally been identified by the release of soluble protein factors such as cytokines, extracellular vesicles (EVs) have recently emerged as important components of the SASP due to their cargo of diverse bioactive molecules. Individuals with early or accelerated aging often exhibit an increased burden of senescent cells. Hutchinson-Gilford Progeria Syndrome (HGPS), a rare and fatal genetic disorder, serves as a valuable model for studying accelerated biological aging and has played a pivotal role in elucidating SASP mechanisms. However, the composition and functional roles of EVs in HGPS remain poorly understood.
In this study, we optimized a workflow for isolating and characterizing EVs from HGPS fibroblasts cultured in vitro. Using liquid chromatography–tandem mass spectrometry (LC-MS/MS) in the data independent acquisition (DIA) mode, we identified over 1,500 unique proteins in EVs secreted by both HGPS and age-matched healthy control fibroblasts. Among these, we observed significant dysregulation of Major Histocompatibility Complex I (MHC-I) Human Leukocyte Antigen C (HLA-C) in EVs derived from mixed populations of replicating and senescent HGPS fibroblasts, compared to healthy controls. Notably, LNPEP (also known as IRAP), a protein involved in MHC-I antigen loading in endosomes, was upregulated in HGPS fibroblasts. CD9, a canonical EV marker implicated in inflammatory signaling was also upregulated in HGPS-derived EVs.
These findings suggest that EVs may participate in modulating immune responses to senescent cells, potentially contributing to the impaired clearance of senescent cells observed in age-related diseases. Our study provides novel insights into the EV-mediated component of the SASP in HGPS and underscores the broader relevance of EVs in diseases characterized by accelerated aging and cellular senescence
Responses of Bumblebees (Bombus) to Climate Change
No full textWith over 1 million species facing extinction due to land use intensification and changing climatic patterns, the acceleration of extinction rates of flora and fauna worldwide is projected to continue to worsen. The swift pace of climate change limits opportunities for evolutionary adaptation, exposing species to conditions that challenge their ability to survive or fulfill essential functions. Bee populations, globally dwindling due to these environmental shifts, play a crucial role as wild pollinators responsible for over 80% of global pollination services. Of particular concern are declines in bumblebees (Bombus), a group of approximately 260 species. Rapid climate changes expose Bombus species to conditions surpassing their historical tolerances, with rising temperatures challenging thermoregulation, foraging, and reproduction efficiency. While models linking climate change to species losses rely on broad-scale observations and complex models, the interaction between climatic position and land use at both continent-wide and local scales remains understudied for bumblebees. This thesis investigates patterns in Bombus persistence across North America to elucidate the impacts of climate and land use on bumblebees and inform conservation initiatives. In Chapter 2, I identify broad-scale, continent-wide mechanisms behind Bombus climate vulnerability to involve spatio-temporal shifts. I find that shifts in activity timing, not only range shifts, have contributed to climate-driven bumblebee extirpations across North America for the last three decades. I determine that mechanisms of climate change and land use intensity vulnerability observed at a macroecological scale are relevant at a community scale in Southern Ontario, demonstrating the biological relevance of such drivers (Chapter 3). Then, I demonstrate that, among bumblebee species, vulnerabilities to these stressors have a quantifiable pattern with regards to life-history traits and evolutionary histories (Chapter 4). This work will improve predictions of how bumblebee species respond to changing environments and landscape and may suggest new avenues for conservation and management of these and other important pollinator species. By improving predictions of bumblebee responses to changing environments, this research offers insights for conservation and management strategies, with broader implications for understanding climate and land use change responses across taxa