The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters cell attachment and crosslinking peptides mentioned, the regenerative process of the ECM has not been mimicked yet in 3D synthetic gels. In an attempt to build in this functionality to PEG-based gels, I performed phage display to identify short oligopeptides that bind either collagen or fibronectin to assess them as potential nucleation points for crosslinking elements in order to emulate the in vivo reconstitution process. A phage display is a library of random oligopeptides expressed on a M13 bacteriophage that allows identification of a phenotype and a genotype with a single screening step. This inexpensive strategy could yield a short oligopeptide with high specificity. I identified the conditions under which phage display is compatible with our targets, and I isolated and identified five peptide candidates for fibronectin binding and two for collagen. Future work includes assessing whether these candidates could facilitate the formation of cell-created crosslinking in 3D synthetic hydrogels.

Chlamydia trachomatis is the most common sexually transmitted bacterial disease agent worldwide, and, though frequently asymptomatic, can cause extreme pathology including infertility. Chlamydial species exhibit a unique biphasic developmental cycle. Once attached to a cell surface, infectious elementary bodies (EB) are internalized within an inclusion, the membrane-bound structure in which EB transform to noninfectious, replicable reticulate bodies (RB). After multiple rounds of division, RB condense to form EB, which are released and can infect new host cells. In culture, exposure to stressors, such as beta-lactam antibiotics, induce chlamydiae to reversibly detour from normal development into a noninfectious, viable state termed persistence. Cell culture data suggest that persistent forms are resistant to azithromycin (AZM), a front-line antibiotic, and are able to alter the host transcriptome. Though persistence has been described in culture for over 50 years, whether or not it: i) occurs in vivo; and ii) influences chlamydial pathogenesis, transmission and therapy has remained unresolved. To address these questions, we developed an animal model of persistent chlamydial infection using amoxicillin (AMX) treatment. AMX exposure decreased shedding of infectious chlamydiae in C. muridarum-infected mice without affecting chlamydial viability, demonstrating the presence of persistent chlamydiae. Shedding of infectious EB resumed following AMX cessation. Shedding data and microarray analyses suggested that host immunity might limit chlamydia’s exit from persistence in our model. Thus, we hypothesized that cyclophosphamide (CTX) treatment would increase the magnitude of chlamydial shedding observed after AMX-treatment cessation. CTX treatment increased post-AMX shedding by more than 10-fold compared to AMX-only controls. To determine whether persistent chlamydiae are resistant to antibiotic eradication in vivo, we induced persistence by administering AMX and treated mice with various AZM dosing regimes. Persistently infected mice demonstrated increased treatment failure following AZM therapy compared to productively infected controls. These data suggest that persistent chlamydiae are refractory to treatment in vivo and provide an explanation for the observation that treatment fails in some patients. In addition to creating the first fully characterized, experimentally tractable, in vivo model of chlamydial persistence, these experiments provide evidence that persistent/stressed chlamydial forms may serve as a long-term reservoir of infectious organisms in vivo.

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research. A pilot facility was operated with nine CO2-supplemented raceway ponds, each with a 33-m2 surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed primary-clarified municipal wastewater at either a 2-day or 3-day hydraulic residence time (HRT), and one set fed the clarified effluent of the 3-day pond set. This second pond-in-series was operated with a 3-day HRT. Areal biomass productivity is reported as gross and net, the former based only on biomass in the pond effluents and the latter subtracting the volatile suspended solids in the influent from those in the effluent. An estimate was also made of autotrophic biomass productivity, as differentiated from heterotrophic growth. Over a year, net productivity averaged 83 metric tons per hectare per year (MT/ha-yr) for the 2-day HRT ponds, 52 MT/ha-yr for the 3-day HRT ponds, and 44 MT/ha-yr for the 3-day HRT ponds receiving clarified effluent of the first set of 3-day HRT ponds (i.e., recycled water). The lower net productivity of the pond receiving water recycling was attributed to two factors. First, the relatively high influent suspended solids concentrations were subtracted from the effluent suspended solids concentrations before net productivity was calculated. Second, the recycled water contained less soluble organic matter than the primary-clarified wastewater leading to less heterotrophic biomass production. The accumulation of inhibitory allelochemicals is a possible third cause of lower productivity , but no specific information was collected on allelopathy. Algae were harvested from pond effluent by sedimentation, with harvest efficiency most affected by the extent of natural bioflocculation occurring in the ponds. Some forms of bioflocculation are thought to be mediated by bacteria, which often make-up a substantial fraction of the settled flocs. Pond samples settled in 1-L Imhoff cones averaged/L total suspended solids after 24 hours of settling; but all ponds fell short of meeting an averaged/L total suspended solids after a 2 hour interval which would be ideally achieved for wastewater effluent. No relationship was seen between settling performance and the bacterial content of flocs. Soluble carbonaceous biochemical oxygen demand (scBOD5) removal by the raceway ponds was sufficient to meet wastewater treatment requirements year around. Influent scBOD5 concentrations averaged 83 mg/L, and the effluent averaged 5.1 mg/L and 4.2 mg/L for the 2-day and 3-day HRT pond sets, respectively. The variable with the greatest influence on productivity in all pond sets, and settling performance in the recycled water pond set, was season (i.e., co-correlated variables of solar insolation and pond temperature). Neither productivity nor settling appeared to be related to prominent algae genera or prevalence of grazers. The high net productivity achieved with a growth medium of primary clarifier effluent and the generally high settleability of algal-bacterial flocs indicate a good potential for algae wastewater treatment and biofuel production. However, the settling of algae grown on recycled water needs improvement to achieve the full potential of wastewater-grown algae biofuel production.

Many HIV-positive (HIV+) males on Highly Active Anti-Retroviral Therapy (HAART) experience metabolic abnormalities, including Non-Alcoholic Fatty Liver Disease (NAFLD) and lipodystrophy. The intestinal microbiota and short chain fatty acids (SCFA), participate in bidirectional communication with their host. Dysbiosis in HIV+ males on HAART demonstrate a Prevotella-rich enterotype shaped by multiple factors including, medications, adiposity, diet, intestinal permeability, and lifestyle; our objective was to investigate these factors. 19 HIV+ and 21 HIV- males were enrolled. BMI and hip-to-waist ratio (H:W) were obtained, and FibroScan for liver health. Intestinal permeability markers Claudin-21, flagellin, and intestinal fatty acid binding protein (IFABP) in serum via enzyme-linked immunoassay (ELISA). Stool was collected for 16s rRNA sequencing, SCFAs (gas chromatography), and proximate analyses (PA). PA analyses: Bomb calorimetry (kcal), soxhlet for lipids, kjeldhal for protein, and fiber. Dietary intake by food frequency questionnaires (FFQ). HIV+ males had significantly higher H:W and hepatic steatosis (pPrevotella and Lachnospiraceae compared to HIV- males. Additionally, HIV+ males had significantly higher central obesity and hepatic steatosis. In a retrospective analysis, all HIV+ men were men that have sex with men (MSM). These findings support differences in intestinal microbiome and SCFAs, and measures of altered lipid metabolism between HIV+ and HIV- males. These findings lay the framework for investigations into intestinal microbiome, SCFAs and metabolism in HIV+ MSM.

Eutypa dieback, one of several grapevine trunk diseases (GTDs), is of serious concern to the grape industry globally. This disease is caused by the fungus Eutypa lata but it is often seen in consortia growth with Phaeoacremonium minimum and Phaeomoniella chlamydospora. It is vital to understand the mechanisms for how this disease functions to develop control measures to combat it. Brown rot fungi are able to use a complex of low molecular weight (LMW) metabolites to induce a Fenton reaction to deconstruct woody tissue. These metabolites are part of a chelator mediated Fenton (CMF) chemistry that produces reactive oxygen species that are capable of depolymerizing wood polymers. We propose that a mechanism similar to CMF chemistry may be occurring in grapevine trunk disease pathogens. This thesis investigates how LMW metabolites produced by the fungi contribute to the disease and decay progression in GTDs. Research on Mite control in the laboratory with abamectin was also investigated, as research in this area was required when mites infested our fungal cultures and suitable laboratory controls were not available. Research on the GTD fungi was initiated by first examining whether metabolites produced by the three fungi can function in a manner to promote reactions like the CMF system. We separated and identified specific metabolites that potentially could contribute to CMF chemistry. We found that all three GTD fungi were able to produced LMW metabolites that promoted CMF chemistry, and we hypothesized that this mechanism contributes to processes leading to tissue necrosis in grapevine trunk wood. To explore the development of effective control measures based on this newly discovered mechanism for pathogenesis, we also explored the use of antioxidant/chelator compounds, BHA and BHT, in the control of the consortia fungi. Biocontrol organisms, Bacillus subtilis and Trichoderma atroviride, that produce antioxidants were also tested as biocontrols against the fungi involved in Eutypa Dieback disease. We found that BHA was highly effective in inhibiting fungal growth for all three fungi at concentrations higher than 0.5mM, and both B. subtilis and T. atroviride proved to be effective biocontrol agents in inhibiting E. lata, P. minimum, and P. chlamydospora.

Food borne illnesses continues to be a public health challenge in the United States (U.S.); an estimated 9.4 million incident cases occurred in 2011. In view of this challenge we conducted two food safety studies; 1) related to product formulation (hummus spoilage challenge study) and 2) evaluating the microbial safety of domestic kitchen surfaces in Residential Child Care Institutions (RCCI pilot study). Hummus is of Mediterranean origin but is currently eaten globally. This challenge study evaluates a variety of industrial hummus formulations (four in total, differing in pH and/or addition of a preservative (natamycin). Two batches were setup: batch 1; aseptically inoculated hummus with 100 CFU/g fungal isolates and batch 2; uninoculated hummus. Samples of both hummus batches were stored at both 20oC (10 days accelerated testing) and 4oC (84 days recommended temperature testing). Inoculated samples were analyzed for fungus, whiles both fungi and bacteria (standard plate count (SPC) and Lactococci) counts were done for uninoculated samples. Results indicate that accelerated testing inaccurately predicts fungal growth at 4oC in hummus, also fungal growth inhibition requires a pH ≤ 4.0 ± 0.2 and refrigeration. Limited studies have specifically evaluated the prevalence of pathogenic bacteria in domestic kitchens in the U.S, for this reason we assessed the microbial safety of 6 RCCI locations in MA. Fifteen key food contact surfaces and dish washing sponges, if available at each RCCI facility were assessed for SPC, yeast and molds, total coliform and E. coli, Listeria sp and Salmonella sp. Microbiological assessments were conducted preceding and after a hazard analysis and critical control point (HACCP) food safety training and implementation at each location. Microbial growth varied by surface for each type of microorganism, wet surfaces had higher most probable number (MPN) counts. Compared to dry surfaces, wet surfaces had significantly higher mean total coliform counts. For both E. coli and total coliform, microbial load differed significantly by surfaces sampled (P = 0.0323 and 0.014) respectively. The surface and training interaction effect was highly significant for only E. coli (P = 0.0089). Training overall had no significant effect on reducing the microbial load on kitchen surfaces.