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The endoplasmic reticulum (ER) is the site of co- and post-translational modification for secretory proteins. In order to prevent vesicular transport and secretion of misfolded or misassembled proteins, a highly regulated mechanism called ER-associated degradation (ERAD) is employed. This pathway recognizes misfolded proteins in the ER lumen and targets them to the cytosol for ubiquitination and subsequent degradation via the 26S proteasome. Sec61 and Derlin-1 are ER pores through which export occurs. AB-type protein toxins such as cholera toxin (CT), Shiga toxin (ST), exotoxin A (ETA), and ricin have evolved means of exploiting the ERAD pathway in order to reach their cytosolic targets. AB-type protein toxins consist of a catalytic A-subunit and a cell-binding B-subunit. The B-subunit recognizes cell surface receptors for the toxin. This begins a series of vesicle trafficking events, collectively termed retrograde trafficking, that lead to the ER. Dissociation of the A and B subunits occurs in the ER, and only the A subunit enters the cytosol. The exact mechanism of A subunit translocation from the ER to the cytosol is unknown. Toxin translocation occurs through a pore in the ER membrane. Exit through the pore requires the toxin to be in an unfolded conformation. The current model for toxin translocation proposes that ER chaperones actively unfold the toxin A chain for translocation. After the translocation event, the toxin spontaneously refolds to an active conformation. Our model suggests that unfolding in the ER is spontaneous and refolding in the cytosol is dependent upon cytosolic chaperones. Based on our model, we hypothesize that blockage of the A subunit unfolding and/or the ERAD translocation step will confer a phenotype of non-harmful multi-toxin resistance to cells. In support of this model, we have shown that, at 37[degrees]C, the isolated catalytic subunit of cholera toxin (CTA1) is in an unfolded and protease sensitive confirmation that identifies the toxin as misfolded by the ERAD pathway. Stabilization of CTA1 via glycerol inhibits the loss of its tertiary structure. This stabilization results in decreased translocation from the ER to the cytosol and increased secretion of CTA1 to the extracellular medium. Treatment with glycerol also prevents CTA1 degradation by the 20S proteasome in vitro. These data indicate that the thermal stability of CTA1 plays an important role in intoxication. These data also suggest that stabilization of CTA1 tertiary structure is a potential target for therapeutic agents. Our model asserts that CTA1 behaves as a normal ERAD substrate upon dissociation from the holotoxin. In support of this model, we have shown that the ER luminal protein HEDJ, known to be involved in ERAD, interacts with CTA1. The interactions between HEDJ and CTA1 occur only at temperatures in which the toxin is in an unfolded conformation. We have also shown that HEDJ does not affect the thermally stability of CTA1 since there is no alteration in its pattern of temperature-dependent protease sensitivity. Alteration of the normal HEDJ-CTA1 interaction via a dominant-negative HEDJ construct resulted in decreased translocation from the ER to the cytosol and, as a result, decreased intoxication. Our work demonstrated toxin resistance can result through effects on toxin structure or ERAD chaperones. To identify other potential inhibitors, we developed a novel assay to detect the activity of other AB toxins and compared it with an established toxicity assay. We generated a Vero cell line that expressed a destabilized variant of enhanced green fluorescent protein (EGFP). These cells were used to monitor the Stx-induced inhibition of protein synthesis by monitoring the loss of EGFP fluorescence from cells. We screened a panel of 13 plant compounds, and indentified grape seed extract and grape pomace extract as inhibitors of Stx activity. Grape seed extract and grape pomace extract were also shown to block the toxic activities of ETA and ricin, providing the basis for a future high-throughput screen for multi-toxin inhibitors.

Single polymer passage through geometrically confined regions is ubiquitous in biology. Recent technological advances have made the direct study of its dynamics possible. We studied the capture of DNA molecules by the electroosmotic flow of a nanopore induced by its surface charge under an applied electric field. We showed theoretically that the DNA molecules underwent coil-stretch transitions at a critical radius around the nanopore and the transition assisted the polymer passage through the pore. To understand how a polymer worms through a narrow channel, we investigated the translocation dynamics of a Gaussian chain between two compartments connected with a cylindrical channel. The number of segments inside the channel changed throughout the translocation process according to the overall free energy of the chain. We found a change in the entropic driving force near the end of the process due to the partitioning of the chain end into the channel rather than the initial compartment. We also developed a theory to account for the electrophoretic mobility of DNA molecules passing through periodic confined regions. We showed that the decrease in the translocation time with the molecular weight was due to the propensity of hairpin entries into the confined regions. To further explore the dynamics of polymer translocation through nanopores, we performed experimental studies of sodium polystyrene sulfonate translocation through α-hemolysin protein nanopores. By changing the polymer-pore interaction using different pH conditions, we identified the physical origins of the three most common event types. We showed that increasing the polymer-pore attraction increased the probability of successful translocation. Motivated by understanding the dynamics of a polymer in a crowded environment, we investigated the dynamics of a chain inside a one dimensional array of periodic cavities. In our theory, the chain occupied different number of cavities according to its confinement free energy which consisted of entropic and excluded volume parts. By assuming that the chain moved cooperatively, the diffusion constant exhibited Rouse dynamics. Finally, we performed computer simulations of a chain inside a spherical cavity. We found that the confinement effect was best described by the hard sphere chain model. We further studied the escape dynamics of the chain out of the cavity through a small hole. The equilibrium condition of the chain during the escape was discussed.

This thesis investigates DNA dynamics and translocation through nanopores using Brownian dynamics (BD) simulations, offering insights into sequencing technologies, DNA marker detection, and accurate barcoding utilizing solid-state nanopore platforms. First, we in silico study the intricate process of capture and translocation in a single nanopore. Our simulation reveals a high probability of hairpin loop formation during the capture process. However, attaching a charged tag to one end of DNA improves multi-scan rates and enhances unidirectional translocations. We use modulating voltage biases to multi-scan a lambda-phage dsDNA with oligonucleotide flap markers (tags) through a single and double nanopore system. Our study shows that the bulkier tags introduce velocity variations along the chain length that lead to potential inaccuracies in genetic distance (barcode) estimations. We introduce an interpolation scheme that incorporates both the tag velocities and the average velocity of the chain to improve barcode precision. Subsequently, we include bead and side-chain tags to explain asymmetric dwell time distributions as observed in double nanopore experiments. Our findings indicate that local charge interactions between tags and the nanopore's electric field introduce dwell time asymmetries that can be used for discriminating tags based on their net charges. Finally, we obtain the current blockades of the molecular motifs attached to a dsDNA using electrokinetic Brownian dynamics (EKBD) simulation. Our simulation demonstrates that divalent salt reduces the translocation speed, facilitating precise measurement of the motif's dwell time. Finally, we formulate a volumetric ansatz to construct current blockade diagrams from the ordinary BD simulation in a computationally efficient way and show that using simple scale factors, these volumetric blockades can be mapped accurately to the ionic current blockades obtained from more expensive EKBD simulation. Our studies present comprehensive explorations of DNA translocation and barcoding methods in solid-state nanopores, demonstrating their utility in nanopore sequencing and nanobiotechnology

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No description available.

The Laysan teal, an endangered species, is restricted to a single population on Laysan Island, a remote atoll of the Hawaiian archipelago. Little is known of the Laysan teal's ecology, therefore, I examined food habits, habitat use, and population dynamics. These aspects of its ecology are fundamental to the species management and conservation. I described diel and nocturnal habitat use, home range, and foraging with radio telemetry in 1998-2000. Most individuals showed strong site fidelity during the tracking period, but habitat selection varied between individuals. Mean home range size was 9.78 ha (SE 2.6) using the fixed kernel estimator (95% kernel; 15 birds with >25 locations). Foraging was strongly influenced by time of day: birds spent only 4% of their time foraging in the day, but spent 45% of their time foraging at night. Time activity budgets from the island's four habitat zones indicated that the coastal zone was rarely used for foraging. The birds foraged 42% of the time they spent in the terrestrial zone at night, but foraged only 4-6% of the time they spent there during other times. Fecal analysis and behavioral observations revealed that the Laysan teal is not a 100% macro-insectivore as previously reported, but consumed seeds, succulent leaves, and algae, in addition to adult diptera, diptera larvae and pupae, ants, seeds, lepidoptera, coleoptera, and Artemia. I concluded that this species exhibits high plasiticity in foraging behavior. Laysan teal appear to opportunistically select abundant, high energy prey for the breeding season, due to constrained resources on Laysan Island. I also studied the parameters influencing the Laysan teal's population dynamics. Adult survival is high, but duckling survival on Laysan is low, and is a primary demographic parameter limiting population growth. Estimates indicate the population density was high (between 546-827) from 1991 until August 1993, prior to a population crash that occurred between September and December 1993. The most current population estimate (Sept-Nov 2001) is 444 (SE 181) adults. Additional populations (translocation), along with control of non-native mammalian predators, are needed to reduce extinction risks to the Laysan teal. / Ph. D.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

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