UMD Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/3

New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.

More information is available at Theses and Dissertations at University of Maryland Libraries.

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    MICROBIAL BIOFILMS ON MICROPLASTICS: A LOOK INTO THE ESTUARINE PLASTISPHERE OF THE CHESAPEAKE BAY
    (2021) Sosa , Ana Paula; Chen, Feng; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Microplastics are plastic particles that are smaller than 5 millimeters and are often found as pollution in our waterways. These polymer particles are globally distributed and are a direct result of human activity. Because of their rigidity and durability, microplastics are an ideal substrate for enhanced microbial growth and biofilm development. While microplastics have been studied in various contexts, only few studies have characterized the microbial communities on different types of plastic particles, but no study has been done in the estuarine water. In this study, we exposed three different types of plastics (polypropylene, polystyrene, and polylactic acid) to the water of Baltimore’s Inner Harbor, along with a non-plastic glass control. We used both in situ and in vitro incubations to understand the development of biofilm communities on microplastics. Microbial communities were analyzed based on the 16S rRNA gene sequences. We found that microbial composition on biofilm is distinct from that in the surrounding water, and different microplastic types have a minor impact on the composition of biofilm communities. The similarity between microbial communities on plastic and non-plastic particles suggests that surface supports rather than material types could be more critical for biofilm formation. Succession of microbial communities on the microplastics and interesting bacterial groups were described. Isolation and microscopic observations were also applied in this study. The presence of phototrophic organisms like filamentous cyanobacteria and Auxenochlorella on microplastic biofilms is interesting, and little is known about their contribution to carbon fixation in the ocean. Biofilms formed on microplastic surfaces could potentially affect the ecosystems via different mechanisms, including local nutrient cycling and the transportation of invasive or harmful species. As plastic production and mismanagement continues to be pervasive in our society, it is paramount that we include biofilm development into the framework of general ecology in order to truly understand the impact of plastic pollution and safeguard our ecosystems.
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    Towards the synthesis of PNAG crosslinkers to identify protein binding partners
    (2019) Mrugalski, Kevin R; Poulin, Myles; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bacterial biofilms are an area of major concern in the medical field due to natural drug resistance. Many pathogenetic species of bacteria that infect humans including Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Vibrio cholera form biofilms and their associated infections are becoming harder to treat. Poly β-(1→6)-N-acetyl-D-glucosamine (PNAG) is a major component of biofilms across multiple species and has been found to play a key role in the early stages of the biofilm life-cycle. However, little information is known about what proteins interact with this important polysaccharide. Our goal is to create small PNAG analogues to covalently capture and identify PNAG binding partners in E. coli, an important model organism. PNAG analogues will contain photoaffinity groups, that when activated, covalently link associated proteins to the probe. Then, using a proteomics-mass spectrometry-based approach, we will identify PNAG binding partners. Here, we describe the efforts and challenges encountered synthesizing the final PNAG probes. New synthetic routes are proposed based on literature precedent that will enable synthesis of the desired compounds.
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    INTEGRATED THRESHOLD-ACTIVATED FEEDBACK MICROSYSTEM FOR REAL-TIME CHARACTERIZATION, SENSING AND TREATMENT OF BACTERIAL BIOFILMS
    (2016) Subramanian, Sowmya; Ghodssi, Reza; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Biofilms are the primary cause of clinical bacterial infections and are impervious to typical amounts of antibiotics, necessitating very high doses for treatment. Therefore, it is highly desirable to develop new alternate methods of treatment that can complement or replace existing approaches using significantly lower doses of antibiotics. Current standards for studying biofilms are based on end-point studies that are invasive and destroy the biofilm during characterization. This dissertation presents the development of a novel real-time sensing and treatment technology to aid in the non-invasive characterization, monitoring and treatment of bacterial biofilms. The technology is demonstrated through the use of a high-throughput bifurcation based microfluidic reactor that enables simulation of flow conditions similar to indwelling medical devices. The integrated microsystem developed in this work incorporates the advantages of previous in vitro platforms while attempting to overcome some of their limitations. Biofilm formation is extremely sensitive to various growth parameters that cause large variability in biofilms between repeated experiments. In this work we investigate the use of microfluidic bifurcations for the reduction in biofilm growth variance. The microfluidic flow cell designed here spatially sections a single biofilm into multiple channels using microfluidic flow bifurcation. Biofilms grown in the bifurcated device were evaluated and verified for reduced biofilm growth variance using standard techniques like confocal microscopy. This uniformity in biofilm growth allows for reliable comparison and evaluation of new treatments with integrated controls on a single device. Biofilm partitioning was demonstrated using the bifurcation device by exposing three of the four channels to various treatments. We studied a novel bacterial biofilm treatment independent of traditional antibiotics using only small molecule inhibitors of bacterial quorum sensing (analogs) in combination with low electric fields. Studies using the bifurcation-based microfluidic flow cell integrated with real-time transduction methods and macro-scale end-point testing of the combination treatment showed a significant decrease in biomass compared to the untreated controls and well-known treatments such as antibiotics. To understand the possible mechanism of action of electric field-based treatments, fundamental treatment efficacy studies focusing on the effect of the energy of the applied electrical signal were performed. It was shown that the total energy and not the type of the applied electrical signal affects the effectiveness of the treatment. The linear dependence of the treatment efficacy on the applied electrical energy was also demonstrated. The integrated bifurcation-based microfluidic platform is the first microsystem that enables biofilm growth with reduced variance, as well as continuous real-time threshold-activated feedback monitoring and treatment using low electric fields. The sensors detect biofilm growth by monitoring the change in impedance across the interdigitated electrodes. Using the measured impedance change and user inputs provided through a convenient and simple graphical interface, a custom-built MATLAB control module intelligently switches the system into and out of treatment mode. Using this self-governing microsystem, in situ biofilm treatment based on the principles of the bioelectric effect was demonstrated by exposing two of the channels of the integrated bifurcation device to low doses of antibiotics.
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    Exopolysaccharide Analysis and EPS Depolymerases as Possible Biofilm Control Strategies
    (2014) Bales, Patrick; Nelson, Daniel; Molecular and Cell Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bacteria form biofilms by adhering to surfaces and secreting high molecular weight macromolecules. When in the biofilm mode of growth, bacteria possess increased resistance to the action of antimicrobials and the immune system. By gaining an increased understanding of the structure of the biofilm extrapolymeric substance (EPS) and investigating ways to break up the EPS matrix, more effective treatment of biofilm-related infections can be achieved. In this thesis, the isolation and characterization of the polysaccharide portion of the EPS of several bacterial species is reported. The identification of 14 possible biofilm-degrading enzymes is described. One of these enzymes, HexNW, is shown to be highly thermostable and effective as a biofilm treatment.
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    AN INTEGRATED MICROSYSTEM FOR BACTERIAL BIOFILM DETECTION AND TREATMENT
    (2014) Kim, Young Wook; Ghodssi, Reza; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bacterial biofilms cause severe infections in clinical fields and contamination problems in environmental facilities. Due to the unique complex structure of biofilms that comprise diverse polysaccharides and bacteria, traditional antibiotic therapies require a thousand times higher concentration compared to non-biofilm associated infections. The early detection of biofilms, before their structures are fully established in a given host/environment, is critical in order to eradicate them effectively. Also, the development of a new innovative biofilm treatment method that can be utilized with a low dose of antibiotic would be extremely important to the medical community. In this dissertation, a biofilm sensor and a new biofilm treatment method were independently developed to detect and treat biofilm communities, respectively. Furthermore, an integrated microsystem was demonstrated as a single platform of the sensor with the treatment method. The sensor was based on the surface acoustic wave (SAW) detection mechanism, which isn extremely sensitive for biofilm monitoring (hundreds of bacterial population detection limit) and consumes very low power (~100 µW). A piezoelectric ZnO layer fabricated by a pulsed laser deposition process was a key material to induce homogeneous acoustic waves. Reliable operation of the sensor was achieved using an Al2O3 film as a passivation layer over the sensor to protect ZnO degradation from the growth media. The sensor successfully demonstrated real-time monitoring of biofilm growth. The new biofilm treatment was developed based on the principles of the bioelectric effect that introduces an electric field along with antibiotics to biofilms, demonstrating significant biofilm inhibition compared to antibiotic treatment alone. Specifically, the new bioelectric effect was implemented with a superpositioned (SP) electric field of both alternating and direct current (AC and DC) and the antibiotic gentamicin (10 µg/mL). With the SP field treatment, significant biofilm reduction was demonstrated in total biomass (~ 71 %) as well as viable bacterial density (~ 400 times respected to the only antibiotic therapy) of the treated biofilms. This method was transferred to a microfluidic system using microfabricated planar electrodes. The microsystem-level implementation of the bioelectric effect also showed enhanced biofilm reduction (~ 140 % total biomass reduction improvement). The integrated system was based on the SAW sensor with the addition of coplanar thin electrodes to apply electric signals for the biofilm treatment. The chip was tested with two bacterial biofilms (Escherichia coli and Pseudomonas aeruginosa) that are clinically relevant strains. In both biofilm experiments, the integrated system demonstrated successful real-time biofilm monitoring and effective biofilm inhibition. This systematic integration of a continuous monitoring method with a novel effective treatment technique is expected to advance the state of the art in the field of managing clinical and environmental biofilms.