VictorJuiz/thesis huggingface dataset:
Formulation and Evaluation of Multi-particulate Antibiotic Alternatives for Oral Delivery to Livestock Animals to Target Gut Pathogens

This thesis explored strategies for enhanced oral delivery of antibiotic alternatives to the livestock intestinal tract to target enteric pathogens. The first part dealt with formulating a liquid essential oil (EO) into solidified granules and subsequently enteric coated for intestinal release. Trans-cinnamaldehyde (CIN), a model EO compound with strong antibacterial activity was formulated into granules using a three-component phase-diagram, yielding granules with high loading and stability, and enteric coated by fluid-bed processing. Antibacterial activity of CIN remained intact throughout manufacturing, after addition of 1% eugenol to prevent autoxidation of CIN which lasted for at least 1 year under ambient storage. In animal trials, coated granules delivered CIN in higher concentrations than free oil to the lower intestinal regions where pathogens colonize. The second part explored bacteriophage microencapsulation for oral, bio-control of intestinal Salmonella in chickens. Preliminary studies revealed the phage intestinal distribution and fecal excretion pattern following a single oral dose, and optimized the Ca-alginate-whey protein formulation of microbeads for quicker phage release. Phage lytic activity studies against a target pathogen showed single phages were insufficient at maintaining reduction of STT104NalR, rather phage cocktails were required to maintain reduction in vitro and in animal digesta, which achieved reductions of several log10CFU/g digesta. Two trials were carried out, testing the effectiveness of pathogen reduction by phage cocktails administered to chicks experimentally infected with STDT104NalR. Trial #1 showed that cocktail 1 did not significantly affect the colonization levels even though in vitro activity was good. Trial 2 re-tested CT1 along with an expanded cocktail 2, with larger animal groups. CT1 yielded a similar lack of efficacy, while CT2 achieved significant reductions of STDT104NalR in ileum, ceca, and colon after 7 days, twice-daily administration with feed. This study suggests that phage cocktails microencapsulated for continuous oral administration with feed could reduce intestinal pathogens.

Keywords: animal science
antibiotic resistance
bacteriophage
coating
essential oil
formulation
Advisor: Wu, Xiao Yu
Wang, Qi
Historical Contingencies in the Ecology and Evolution of Species Diversity

Ecologists have long-sought to explain the high diversity of species in biological communities, given that classic theory predicts that diversity is limited by available niche space. In recent years, ecologists have looked towards â historical contingenciesâ , the persistent effects of past ecological and evolutionary processes, as possible mechanisms that maintain diverse communities, either by relaxing the constraints of niche availability or by adding temporal dimensions to speciesâ niches. In this thesis, I use field and greenhouse experiments to explore three ways in which historical contingencies manifest in annual plant communities. First, my work on maternal effects shows that abiotic (ch. 2) and biotic (ch.3) conditions in the maternal generation have diverse effects on offspring phenotypes across an assemblage of species. Because species differences in environmental responses can facilitate coexistence, these studies suggest that maternal effects could act as a form of niche differentiation, and motivate future research to clarify their influences on coexistence outcomes. Second, I performed, to my knowledge, the first experimental decoupling of dispersal limitation and environmental sorting in a natural landscape by manipulating entire seed pools of annual plants (ch. 4). In doing so, I was able to identify the pervasive and scale-specific influences of dispersal limitation that constrain species distributions in plant communities. Lastly, I used competitive trials to identify macroevolutionary divergence in competitive interactions among species (ch. 5), and found evidence that divergence is contingent on historical competitive interactions in ways that are consistent with character displacement. In sum, my dissertation work has expanded our understanding of (i) the number of potential niche dimensions that might allow species to differentiate, (ii) how this differentiation can arise over evolutionary time, and (iii) the interplay of current and historical conditions in the maintenance of species diversity, and the timescales over which they play out.

Keywords: Biodiversity
Community ecology
Competition
Maternal effects
Metacommunities
Plant ecology
Advisor: Gilbert, Benjamin
Understanding the Regulation and Biological Function of the ComRS Competence Signaling System in Streptococcus mutans

Genetic competence provides bacteria with an opportunity to increase genetic diversity by allowing the acquisition of novel traits that can confer virulence or a survival advantage. The oral biofilm, containing a diverse microbiota at close proximity, is an ideal environment for this form of genetic exchange. Several oral streptococci have been demonstrated to engage in DNA uptake from their environment by the process of genetic transformation. In the cariogenic organism, Streptococcus mutans, competence for transformation is regulated by the ComRS peptide signaling system, comprised of the ComR transcriptional regulator and the ComS pre-peptide required to produce the mature ComX-inducting peptide, XIP. XIP in conjunction with ComR activates the ComX alternate sigma factor critical for DNA uptake and recombination. In this study, we examined the molecular pathways and biological functions of the ComRS regulon in S. mutans. We demonstrated a novel role for ComRS in competence-associated self-lysis. Further analysis of the global transcriptome in response to XIP revealed a role for XIP in the regulation of bacteriocin genes, encoding antimicrobial peptides used by bacteria to lyse closely related species. The coordination of competence development and cell lysis may ensure availability of eDNA for DNA uptake by the competent subpopulation. Aside from cell lysis, supplementation with XIP regulated a number of virulence-associated genes, and resulted in a global transcription profile that mimicked that of the starvation-induced stringent response in S. mutans. Others have shown that genetic competence and the stringent response were regulated by the rcrRPQ operon, encoding an RcrR transcriptional regulator and the RcrPQ ABC transporters. Our work further implicated RcrRPQ in the regulation of comS expression and endogenous XIP levels. Together, our work suggests that the ComRS regulon in S. mutans exhibits a biological role beyond competence induction that includes virulence and stress adaptation.

Advisor: Cvitkovitch, Dennis G
Senadheera, Dilani B
Polymer Hydrogels, Aerogels, and Foams as Biomimetics of the Extracellular Matrix

Three-dimensional (3D) scaffolds that recapitulate the mammalian extracellular matrix (ECM) have potential applications as tissue engineering scaffolds and as in vitro cell culture material. This thesis describes the fabrication and characterization of microgels, aerogels, hydrogels, and foams that are biomimetics of the natural ECM. The ability to tune the mechanical property and structure of the resulting scaffolds is of particular importance. In Chapter 3, we explore a microfluidic platform for making biopolymer composite microgels in which the rigidity and structure can be tuned in high-throughput manner. Chapter 4 describes how cellulose nanocrystals can be used to make nanofibrillar hydrogels, in which the rheological properties and pore sizes can be controlled by the addition of inorganic salts. These properties are highly dependent on the size, charge, and concentration of the cations added. Chapter 5 describes the freeze-casting of aldehyde-functionalized cellulose nanocrystals and hydrazide-functionalized poly(oligoethylene glycol methacrylate) into anisotropic composite aerogels and their corresponding hydrogels. The aerogel structure could be tuned from fibrillar to columnar and lamellar by varying the freeze-cast composition. The Youngâ s modulus and swelling of the hydrogels differed parallel and perpendicular to the freeze-cast direction. Chapter 6 describes the freeze-casting of polyurethanes into anisotropic open-cell foams, which have anisotropic mechanical and thermal properties. The thermal conductivity of these foams could also be switched between anisotropic and isotropic modes.

Keywords: Aerogel
Extracellular Matrix
Foam
Hydrogel
Microgel
Polyurethane
Advisor: Kumacheva, Eugenia
Prevalence, Diversity, Impact, and Applications of CRISPR-Cas Inhibitors

One of the most important modes of bacterial evolution is horizontal gene transfer (HGT), a process by which bacteria acquire foreign DNA, often encoding antibiotic resistance or virulence genes, from other strains or species. CRISPR-Cas systems are one of several mechanisms bacteria employ for protection from potentially harmful foreign nucleic acids, including mobile genetic elements (MGEs) like bacteriophages. CRISPR-Cas systems use an RNA-guided nuclease to locate and destroy foreign DNA, and are expected to constitute a major barrier to HGT. However, studies have shown that the presence of a CRISPR-Cas system does not correlate with lower rates of HGT. An explanation for this paradox could lie in widespread MGE-encoded inhibitors of CRISPR-Cas systems. In support of this idea, the Davidson lab previously discovered the first examples of anti-CRISPRs in bacteriophages infecting Pseudomonas aeruginosa. We hypothesized that anti-CRISPRs were likely to exist for each of the sixteen subtypes of CRISPR-Cas systems present in diverse bacterial species. Since the known anti- CRISPR proteins did not share any common features, I used a bioinformatics â guilt by associationâ method to identify new candidate anti-CRISPRs and to predict their likely CRISPR-Cas target types. Here, I present my discovery of twelve novel anti-CRISPR protein families that are widespread in MGEs of Proteobacteria. Each of these families inhibits type I-E, I-F, or II-C CRISPR-Cas systems. I provide structural and mechanistic data supporting the independent evolution of protein families that inhibit CRISPR-Cas function in distinct ways. Anti-CRISPR genes themselves are transferred among MGEs, and many anti-CRISPRs can inhibit a wide range of homologous CRISPR-Cas systems in different species. Anti-CRISPRs likely have a broad ecological impact on CRISPR-Cas systems, not only by inhibiting but also by modulating their function. Overall, anti-CRISPRs not only impact CRISPR-Cas function and HGT among diverse bacterial species, but they also provide important tools for the study and modulation of CRISPR- Cas activity.

Keywords: anti-CRISPR
bacteriophage
CRISPR
horizontal gene transfer
mobile genetic elements
phage-host coevolution
Advisor: Davidson, Alan R
Virtual Endocasts for Ischyromyidae and Sciuridae: Brain Evolution in Rodentia and a Deeper Understanding of the Ancestral Condition for the Brain of Euarchontoglires

The brain of rodents has rarely been studied from the perspective of the fossil record, and little is known of the process of brain evolution in this group. Whatâ s more, rodents are members of Euarchontoglires and could help form a better understanding of the ancestral condition for this group, augmenting what has been learned from primates. This thesis describes the first fossil and extant virtual endocasts for Rodentia. The study of primitive members of Ischyromyidae, Ischyromys typus (Oligocene), Paramys copei and P. delicatus (Eocene), show that exposure of the midbrain is likely to be primitive for rodents, as observed for Primates. Decrease in the proportion of the olfactory bulbs and increase in neocortical surface area may have occurred through time in rodent evolution similar to Primates, but with less intensity in Rodentia. Ischyromyids exhibit variation in EQ through time, with Eocene taxa displaying a higher EQ compared to Oligocene species, demonstrating that the group did not show a simple increase in EQ through time, although an increase in EQ may have occurred in sciurid evolution specifically. Study of the early squirrel Cedromus wilsoni and extant members of Sciuridae reveal that fundamental changes in the organization of the brain occurred in the transition from more primitive ischyromyids to early squirrels, with an increase in neocortex size, the appearance of a sylvian fossa, and a more complex cerebellar structure including an increase in the relative size of the paraflocculi. These changes could potentially be related to the process of becoming arboreal in rodents. Rather than locomotion, diet may have played a more critical role in Primates, since key changes in that Order postdated the origin of arboreality. Ultimately, this thesis provides a better understanding of the process of brain evolution for Euarchontoglires by studying another Order in this group aside from Primates.

Keywords: Endocast
Euarchontoglires
Paleogene
Rodentia
X-Ray computed tomography
Advisor: Silcox, Mary T
Unique Lemur Traits: Proximate and Ultimate Perspectives

Members of the lemur clade are known to exhibit a number of traits that are unusual in the context of living primates. Here, I investigate the basis of three of these traits: sexual size monomorphism, female dominance over males, and rapid rates of growth and attainment of adult body mass. My research focuses on multiple lemur species from the current and historic colony residing at the Duke Lemur Center in Durham, NC. Using long-term morphological data on 18 lemur species, I determine that rapid growth and early attainment of adult body mass do not constrain the development of sexual size dimorphism in lemurs. Next, I conduct behavioural observations and hair hormone analysis on ring-tailed lemurs (Lemur catta), revealing that receiving aggression leads to chronic stress in males and females and that female dominance and high rates female of aggression in females are potentially mediated by sex steroid hormone concentrations. Finally, using growth records and hair hormone analysis in Coquerelâ s sifakas (Propithecus coquereli), I identify a negative relationship between chronic stress and relative body mass in early life, and demonstrate a potential carryover effect of low body mass in early life on relative body mass in adulthood. Uncovering the proximate and ultimate causes of these unique lemur traits can advance our understanding of the factors underlying trait variation in primates and other mammals.

Keywords: Behaviour
Dominance
Evolution
Growth
Hormone
Primate
Advisor: Schillaci, Michael A
Early Volume Change of High Performance Concrete

In severe chloride/sulfate exposure conditions, there is need to provide more durable concrete, but this usually requires use of concretes with high cementitious binder contents that increase the risk of cracking due to thermal, autogenous, and drying shrinkage. Cracking is counter-productive to obtaining durability in the field. High performance concrete (HPC) can be durable in aggressive environments due to its superior mechanical, resistance to fluid transport, and durability characteristics. However, HPC mixtures typically have high binder contents (cement, pozzolanic minerals), and low w/cm, and therefore undergo high heat of hydration as well as autogenous shrinkage, resulting in rapid volume changes. The increased risk of autogenous deformation in high performance concrete can increase the risk of the cracking and durability of reinforced concrete structures such as bridge decks. For example, in Ontario the MTO had issues with in-creased incidence of transverse cracking in bridge decks when 50 MPa HPC was used relative to traditional 35 MPa concretes. A review of their construction records indicated that this problem was often related to concretes that set quickly and rapidly developed high temperature rise due to heat of hydration. The effects of ground granulated blast-furnace slag (GGBFS) and silica fume (SF) on the durability of HPC were investigated. In this study, HPC mixtures at 0.33 w/c were made with three sources of blended cements containing 8% SF mixed with 25, 35 and 50% GGBFS replacements by mass of cement. The compressive strength, drying shrinkage, and transport properties were measured. The test results have shown that increased fineness of the silica fume blended cement enhances the resistance to fluid transport and mechanical properties, but results in increased drying shrinkage, leading to increased cracking potential. A comprehensive study was conducted to understand (a) the interrelation between different mechanisms of volume change (thermal deformation, autogenous shrinkage, drying shrinkage) under different standard and non-standard conditions and (b) the role of different shrinkage mitigation methods (e.g. by either increasing GGBFS content to overcome early-age free and re-strained thermal deformation as well as autogenous shrinkage, or by reducing the cement binder content).

Keywords: Autogenous strain
Concrete
Heat of hydration
High Performance Concrete
Shrinkage
Thermal strain
Advisor: Hooton, R.D.
Social Interaction in Zebrafish: Effects of Social Isolation on Behaviour, Neurochemistry, and Stress

Characterization and detailed analysis of social behaviour are necessary to further establish zebrafish as a model for developmental disorders such as Autism Spectrum Disorders and Fetal Alcohol Syndrome Disorder. Social isolation has been used as a tool to study regulation of social behaviour in various species before. The purpose of this thesis was to investigate how social isolation (during development or in adulthood) affects subsequent social and non-social behaviours. I also examined neurotransmitter systems associated with social interaction, namely dopamine and serotonin, and stress hormone cortisol, as isolated fish responded to novelty or to social stimuli. I found that life-long developmental isolation increased locomotor activity, and altered responses to social stimuli and dopaminergic metabolite levels. On the other hand, locomotor activity and social responses of socially raised zebrafish remained unchanged after chronic isolation in adulthood, but a reduction in serotonin metabolite levels was found in response to novelty and social interaction. Behavioural and physiological responses of fish isolated in adulthood were also affected by social stimulus type and prior social hierarchy status. Both developmental and chronic adult isolation reduced anxiety-related behaviour, and cortisol levels indicated that long-term social isolation is not stressful in zebrafish. Findings from zebrafish experiments are discussed in light of isolation literature in other social animals. These analyses help establish translationally relevant zebrafish research as a tool to simplify, explore, and understand behaviour and disorders involving social abnormalities in social vertebrates.

Keywords: Anxiety
Isolation
Monoamine
Social Behaviour
Stress
Zebrafish
Advisor: Gerlai, Robert
Team-based electronic communication in the care of patients with complex conditions

Background: The management of patients with complex care needs often involves specialized care from multiple providers in different settings. Care coordination is often inadequate, leading to poor continuity of care. Digital health tools can connect patients and their team of providers to facilitate communication across institutions, disciplines and health events. This dissertation examines digital health tools for patient-provider team-based communication, their feasibility in practice and role in improving continuity of care. Methods: Three studies were conducted. The first study was a scoping review of web-based tools for text-based communication between patients and providers, including those for team-based communication. The second study was a cluster randomized controlled feasibility trial evaluating the feasibility of implementation and preliminary effectiveness of a web-based tool for asynchronous, patient-provider team-based communication on continuity of care relative to usual care. Finally, a qualitative descriptive study was conducted with participants from the trial to understand their perceptions on the value of the tool. Results: The first study identified tools for a variety of chronic conditions, the majority of which targeted diabetes, chronic respiratory diseases and mental illness for purposes of providing symptom updates or to facilitate lifestyle/behavior change. Few tools were found specifically for team-based communication. In the second study, it was shown that implementation of a tool for patient-centered, team-based communication was feasible. Numerically-higher continuity of care scores were observed in the intervention arm relative to the control arm. In the third study, participants felt that web-based communication tools provided more opportunity to seek clarification between appointments. Patients, however, viewed such communication as supplemental to clinical appointments, highlighting traditional face-to-face interaction with their providers as an integral aspect of the therapeutic relationship. Conclusions: Patient-provider team-based communication tools are promising. It is suggested that patient-centered and team-specific implementation approaches are needed to optimize uptake of tools for team-based communication in the complex care population. Further study is needed to establish the effectiveness of improving continuity of care.

Advisor: Grunfeld, Eva