On expected durations of birth-death processes with applications to branching processes and SIS epidemics

We study continuous-time birth–death type processes, where individuals have independent and identically distributed lifetimes, according to a random variable Q, with E[Q] = 1, and where the birth rate if the population is currently in state (has size) n is α(n). We focus on two important examples, namely α(n) = λn being a branching process, and α(n) = λn(N −n)/N which corresponds to an SIS (susceptible → infective → susceptible) epidemic model in a homogeneously mixing community of fixed size N. The processes are assumed to start with a single individual, i.e. in state 1. Let T , An, C, and S denote the (random) time to extinction, the total time spent in state n, the total number of individuals ever alive, and the sum of the lifetimes of all individuals in the birth–death process, respectively. We give expressions for the expectation of all these quantities and show that these expectations are insensitive to the distribution of Q. We also derive an asymptotic expression for the expected time to extinction of the SIS epidemic, but now starting at the endemic state, which is not independent of the distribution of Q. The results are also applied to the household SIS epidemic, showing that, in contrast to the household SIR (susceptible → infective → recovered) epidemic, its threshold parameter R∗ is insensitive to the distribution of Q

Engineering Bacterial Gene Expression: Applications towards Biofuels and Antibiotic Resistance

Nature is rarely static. Organisms live in diverse and stressful environments that necessitate rapid response strategies for survival. Microorganisms have responded to this by evolving bet-hedging, wherein they exhibit constitutively heterogeneous gene expression to maximize fitness across numerous background. The goal of this thesis is to “hijack” this phenomenon using novel gene expression engineering techniques to alter how bacteria respond to their environments, in order to address pressing societal concerns.This begins with a systematic exploration of how bacterial gene expression naturally responds to antibiotics and biofuels. This reveals promising gene candidates for targeted manipulation, for which a library of CRISPR gene expression perturbation devices is constructed. This library is applied to Escherichia coli during exposure to antibiotics and biofuels, and the impact of CRISPR perturbation on growth and fitness is quantified. Many perturbations show significant non-heritable improvements or detriments on growth, indicating the potential of this approach for biofuel and antibiotic applications. To improve the desired bacterial response, individual perturbations are combined in a multiplexed fashion. A significant trend towards lower fitness as more perturbations are combined emerges, which is supported by a systematic exploration of combinatorial perturbation libraries. This trend is correlated to a diminished adaptive potential, suggesting the applicability of multiplexed perturbations for restricting bacterial evolution. In a similar vein, the ability of gene expression perturbations to synergize with antibiotics is explored to identify novel potentiating therapies. Significant gene-drug synergies are characterized and used to potentiate antibiotic treatment in an infection model. Therapeutic peptide nucleic acid molecules are subsequently designed to re-sensitize clinically isolated multidrug-resistant bacteria to treatment. Finally, this thesis expands our available synthetic biology toolkit for manipulating gene expression by outlining novel CRISPR engineering strategies. Deactivated CRISPR proteins are fused with bacterial initiation factor one, and the potential for these constructs to increase translation rates by promoting 30S subunit binding to the ribosome is explored. The design of a smart antibiotic utilizing a CRISPR-holin RNA-based kill switch is also presented. Collectively, this thesis demonstrates the power that manipulating gene expression has in affecting desired phenotypes in bacteria

Expression and purification of an active cysteine protease of Haemonchus contortus using Caenorhabditis elegans

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The effects of mindfulness-based cognitive therapy on affective memory recall dynamics in depression:A mechanistic model of rumination

Objectives: converging research suggests that mindfulness training exerts its therapeutic effects on depression by reducing rumination. Theoretically, rumination is a multifaceted construct that aggregates multiple neurocognitive aspects of depression, including poor executive control, negative and overgeneral memory bias, and persistence or stickiness of negative mind states. Current measures of rumination, most-often self-reports, do not capture these different aspects of ruminative tendencies, and therefore are limited in providing detailed information about the mechanisms of mindfulness. Methods: we developed new insight into the potential mechanisms of rumination, based on three model-based metrics of free recall dynamics. These three measures reflect the patterns of memory retrieval of valenced information: the probability of first recall (Pstart) which represents initial affective bias, the probability of staying with the same valence category rather than switching, which indicates strength of positive or negative association networks (Pstay), and probability of stopping (Pstop) or ending recall within a given valence, which indicates persistence or stickiness of a mind state. We investigated the effects of Mindfulness-Based Cognitive Therapy (MBCT; N = 29) vs. wait-list control (N = 23) on these recall dynamics in a randomized controlled trial in individuals with recurrent depression. Participants completed a standard laboratory stressor, the Trier Social Stress Test, to induce negative mood and activate ruminative tendencies. Following that, participants completed a free recall task consisting of three word lists. This assessment was conducted both before and after treatment or wait-list. Results: while MBCT participant’s Pstart remained relatively stable, controls showed multiple indications of depression-related deterioration toward more negative and less positive bias. Following the intervention, MBCT participants decreased in their tendency to sustain trains of negative words and increased their tendency to sustain trains of positive words. Conversely, controls showed the opposite tendency: controls stayed in trains of negative words for longer, and stayed in trains of positive words for less time relative to pre-intervention scores. MBCT participants tended to stop recall less often with negative words, which indicates less persistence or stickiness of negatively valenced mental context. Conclusion: MBCT participants showed a decrease in patterns that may perpetuate rumination on all three types of recall dynamics (Pstart, Pstay, and Pstop), compared to controls. MBCT may weaken the strength of self-perpetuating negative associations networks that are responsible for the persistent and “sticky” negative mind states observed in depression, and increase the positive associations that are lacking in depression. This study also offers a novel, objective method of measuring several indices of ruminative tendencies indicative of the underlying mechanisms of rumination

Importance of small fishes and invasive crayfish in otter Lutra lutra diet in an English chalk stream

The diet composition of the European otter Lutra lutra was assessed using spraint analysis in the Hampshire Avon, a lowland chalk stream in Southern England, over an 18 month period. Small cyprinid fishes were the main prey item taken in all seasons, with bullhead Cottus gobio and stone loach Barbatula barbatula also important; there were relatively few larger fishes of interest to fisheries found. There were significant seasonal differences in diet composition by season, with signal crayfish Pacifastacus leniusculus only being prominent prey items in warmer months and amphibians in winter, revealing that non-fish resources were seasonally important dietary components. Reconstructed body lengths of prey revealed the only species present in diet >350 mm was pike Esox lucius. These dietary data thus provide important information for informing conservation conflicts between otters and fishery interest

Using coupled micropillar compression and micro-Laue diffraction to investigate deformation mechanisms in a complex metallic alloy Al13Co4

In this investigation, we have used in-situ micro-Laue diffraction combined with micropillar compression of focused ion beam milled Al13Co4 complex metallic alloy to study the evolution of deformation in Al13Co4. Streaking of the Laue spots showed that the onset of plastic flow occured at stresses as low as 0.8 GPa, although macroscopic yield only becomes apparent at 2 GPa. The measured misorientations, obtained from peak splitting, enabled the geometrically necessary dislocation density to be estimated as 1.1 x 1013 m-2