Characterization of Microbial Communities Across Disease States and Environmental Conditions in Kemp’s Ridley (Lepidochelys Kempii) and Green Sea Turtles (Chelonia Mydas)

All species of sea turtles are threatened or endangered, with various diseases and conditions affecting populations around the world. Understanding healthy populations as well as populations beset by disease conditions, such as fibropapillomatosis and cold-stunning, could lead to helpful tools in the conservation management and medical treatment needed to protect these species. Microbial communities, or the microbiome, at different body sites of sea turtles likely play important roles in the health of these animals, from aiding in digestion to immune system regulation. Disruption of these communities, either through disease and/or environmental factors, may play a role in disease processes and recovery in sea turtle species. Given the importance of microbial communities in health and disease, my dissertation sought to: 1) characterize the microbiome of two species of sea turtles, Kemp’s ridley and green turtles, from the same habitat in the wild, 2) characterize the microbiome of cold-stunned Kemp’s ridley turtles through rehabilitation, and 3) investigate the respiratory microbiome of Kemp’s ridley turtles in relation to radiographic lung abnormalities and diagnostic tools. To carry out these objectives, I used sequencing of the 16S rRNA gene to identify microbial community composition of various body sites from sea turtles for each experiment. In wild turtles, I identified distinct core microbes from the oral cavity and cloaca of two species of healthy, wild caught sea turtles. In stranded turtles, I characterized the same body sites, oral cavity and cloaca, throughout rehabilitation and found shifts in the microbial community composition throughout hospitalization, including alterations due to antibiotic therapy. I also found that the microbiome did not correlate with disease condition or physiological abnormalities in stranded cold-stunned turtles. Since lung abnormalities are prevalent in cold-stunned turtles, I also examined the respiratory microbiome through tracheal washes and necropsy samples. I found that lungs contained a diverse and variable microbial community and identified limitations of tracheal washes as a diagnostic tool. Taken together, these results contribute to understanding the microbiome of sea turtles across disease states and environmental conditions by identifying the microbial community composition at different body sites, through different methods, and based on different disease conditions

Constraining domain wall dark matter with a network of superconducting gravimeters and LIGO

There is strong astrophysical evidence that dark matter (DM) makes up some 27% of all mass in the universe. Yet, beyond gravitational interactions, little is known about its properties or how it may connect to the Standard Model. Multiple frameworks have been proposed, and precision measurements at low energy have proven useful to help restrict the parameter space for many of these models. One set of models predicts that DM is a scalar field that "clumps" into regions of high local density, rather than being uniformly distributed throughout the galaxy. If this DM field couples to the Standard Model, its interaction with matter can be thought of as changing the effective values of fundamental constants. One generic consequence of time variation of fundamental constants (or their spatial variation as the Earth passes through regions of varying density) is the presence of an anomalous, composition-dependent acceleration. Here we show how this anomalous acceleration can be measured using superconducting accelerometers, and demonstrate that >20 years of archival data from the International Geodynamics and Earth Tide Services (IGETS) network can be utilized to set new bounds on these models. Furthermore, we show how LIGO and other gravitational wave detectors can be used as exquisitely sensitive probes for narrow ranges of the parameter space. While limited to DM models that feature spatial gradients, these two techniques complement the networks of precision measurement devices already in use for direct detection and identification of dark matter

Dynactin-dependent cortical dynein and spherical spindle shape correlate temporally with meiotic spindle rotation in Caenorhabditis elegans.

Oocyte meiotic spindles orient with one pole juxtaposed to the cortex to facilitate extrusion of chromosomes into polar bodies. In Caenorhabditis elegans, these acentriolar spindles initially orient parallel to the cortex and then rotate to the perpendicular orientation. To understand the mechanism of spindle rotation, we characterized events that correlated temporally with rotation, including shortening of the spindle in the pole-to pole axis, which resulted in a nearly spherical spindle at rotation. By analyzing large spindles of polyploid C. elegans and a related nematode species, we found that spindle rotation initiated at a defined spherical shape rather than at a defined spindle length. In addition, dynein accumulated on the cortex just before rotation, and microtubules grew from the spindle with plus ends outward during rotation. Dynactin depletion prevented accumulation of dynein on the cortex and prevented spindle rotation independently of effects on spindle shape. These results support a cortical pulling model in which spindle shape might facilitate rotation because a sphere can rotate without deforming the adjacent elastic cytoplasm. We also present evidence that activation of spindle rotation is promoted by dephosphorylation of the basic domain of p150 dynactin

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Directional gene flow and ecological separation in Yersinia enterocolitica

Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3–5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species

The formation of a nanohybrid shish-kebab (NHSK) structure in melt-processed composites of poly (ethylene terephthalate) (PET) and multi-walled carbon nanotubes (MWCNTs)

The combination of synchrotron Small- and Wide-Angle X-ray scattering (SAXS/WAXS), and thermal analysis was used to follow the evolution of crystalline morphology and crystallization kinetics in a series of melt-processed composites of poly(ethylene terephthalate) (PET) and multiwall carbon nanotubes (MWCNT). The as-extruded PET-MWCNT composites underwent both hot and cold isothermal crystallizations where a final oriented nanohybrid shish-kebab (NHSK) crystalline structure was observed. An oriented NHSK structure was seen to persist even after melting and recrystallization of the composites. From the scattering data, we propose a model whereby the oriented MWCNTs act as heterogeneous nucleation surfaces (shish) and the polymer chains wrap around them and the crystallites (kebabs) grow epitaxially outwards during crystallization. However, depending on crystallization temperature, unoriented crystallites also grow in the polymer matrix, resulting in a combination of a NHSK and lamellar morphology. In contrast, the neat PET homopolymer showed the sporadic nucleation of a classic unoriented lamellar structure under the same isothermal crystallization conditions. These results provide a valuable insight into the distinctive modification of the crystalline morphology of melt-processed polymer-MWCNT composites prior to any secondary processing, having a significant impact on the use of MWCNTs as fillers in the processing and modification of the physical and mechanical properties of engineering polymers

Two- and Three-Phase Flow Through a 90 Degree Bend

Data are presented for two-phase air/water pipeflow and three-phase air/oil/water in a 0.026 m i.d. pipe and elbow bend (R/d = 0.654) for vertical to horizontal flow. The two-phase results were shown to be dependant on the flow regimes present in the system. The elbow bend acted either to smooth the transition from vertical to horizontal flow when the liquid rate was below the bubble rise velocity in the inlet leg (when negative bend pressure losses were achieved), or to generate droplets and increase the bend pressure drop substantially at higher fluid rates.Three-phase data also showed significant but not such dramatic differences, depending on the combined liquid rate being above or below the bubble rise velocity in the inlet leg. Again the variation of pressure drop for the system could be qualitatively explained by the observed flow regimes.For both two-phase and three-phase systems, the observed bend pressure drop could be correlated using a Lockhart-Martinelli approach based on the single-phase flow data for the bend