Browsing by Subject "Bacteria"

A series of experiments and mathematical models explore the response of the bacteria E. coli to stressors. Experimentally, the effect of L-homocysteine, a non-protein amino acid, is explored, and via math models, the effect of trimethoprim, a common antibiotic, is also explored. Previous work on L-homocysteine labels it a stressor, and this assertion is refined via the presented work. A mathematical model that improves on a previous work published by Kwon et al. (2008) explores the response of E. coli to various supplementations of amino acids when exposed to trimethoprim. New methods of developing antibiotics and therapeutic drug treatments are also explored.

Three-dimensional (3D) tumor models aim to reduce the need for animal models for drug and gene delivery studies. However, many models are not conducive to environmental manipulation and may not be easily adapted for in situ microscopic analysis of transport phenomena. One goal of this study was to develop a 3D tumor model that can mimic 3D cell-cell interactions to mimic native tumor tissues.

To this end, a novel 3D microfluidics-based tumor model was created which allowed the overnight culture of a high density of tumor cells and could be used for small molecule penetration studies. This microfluidic device facilitated the loading of B16.F10 tumor cells in a densely-packed three-dimensional arrangement in a micro-channel which was accessible for nutrient supply via channels on either side through which culture media was continuously infused. Cell volume fraction in the micro-channel was determined via nuclear staining and counting of cells immediately after loading and after a 12-hr culture period. The average volume fraction of cells in this model was 0.32 immediately after loading and 0.26 after 12-hr culture. The values are comparable to cell volume fractions of the in vivo B16.F10 tumor previously measured in our lab. The reduction in cell volume fraction after overnight culture was due to the change in cell morphology to become more elongated after time in culture. Cell-cell adhesions appeared to have formed during culture, resulting in more uniform packing.

Sodium fluorescein dye was used as a drug analog and the extent of penetration of this fluorescent molecule through the cell compartment was assessed through microscopy. The dye was introduced on one side of the cell micro-channel and fluorescence images were captured for generation of concentration profiles in the cell compartment. Results showed that dye penetration through the cell chamber was greatly limited by the presence of the 3D cell culture and a linear concentration profile was achieved across the cell compartment. Also, the concentration of sodium fluorescein in the cell compartment of the 12-hr microfluidic cell culture was appreciably lower than the concentration in the cell compartment when the dye was introduced immediately after loading cells. These results suggest that the proposed tumor model shows significant resistance to dye penetration and could prove to be extremely useful for mimicking tumor tissue resistance to drug penetration via diffusion.

There are many barriers to gene delivery to tumors which highlight the importance of selecting an effective gene carrier system. Some pathogenic bacteria have been investigated as gene delivery vectors because of their innate ability to selectively proliferate in tumor environments. However, pathogenicity concerns arise when trying to achieve therapeutic levels of gene expression. It has been shown that non-pathogenic bacteria such as E. coli can be engineered to invade mammalian cells and participate as gene delivery vehicles. Hence, the second part of this research project involved the use of the newly developed microfluidic 3D tumor model previously described to visualize the transport behavior of invasive (inv+) and non-invasive (inv-) E. coli. The inv+ bacteria harbored a plasmid containing the inv gene encoding the protein invasin that binds to &beta₁ integrin receptors on the surface of mammalian cells resulting in the phagocytosis of invasin-expressing bacteria by normally non-phaogcytotic cells. Two tumor cells lines were used: B16.F10 and EMT6, which have been shown to differ in expression of &beta₁ integrins. The bacteria were also engineered to express mCherry for fluorescent detection.

A suspension of tumor cells and bacteria was loaded into the microfluidic device and cultured for 12 hrs before imaging bacteria distribution throughout the cell culture. Proliferation of inv+ bacteria was generally uniform throughout the cell compartment in the B16.F10 model and bacterial cells were primarily concentrated outside of cells. Bacteria that were internalized did not appear to migrate far from the plasma membrane of the tumor cell. The non-invasive bacteria proliferated to a much greater extent than the invasive form and this proliferation was also generally uniform throughout the cell compartment. Proliferation of both invasive and non-invasive bacteria in the EMT6 model was less uniform than in the B16.F10 model. Overall bacterial concentration appeared to be lower in the EMT6 model. Viability staining after bacterial infection showed that tumor cells in the 3D model were able to maintain viability despite bacterial cell proliferation.

An additional assay was conducted in culture plate wells to determine the effect of chemical factors secreted by tumor cells on bacterial cell proliferation. The results of this assay revealed that tumor cells may be secreting anti-microbial factors that inhibit the proliferation of bacteria and that the binding of invasin-expressing E. coli to tumor cells may further promote the release of these factors.

The results of this study suggest that tumor cell type plays a major role in the distribution and proliferation of bacteria in a 3D environment. The ability to visualize bacterial spread throughout a 3D tumor model will prove to be useful for observing the effect of various genetic modifications on the transport and gene delivery efficiency of E. coli.

Silver nanoparticles (AgNPs) are increasingly being integrated into a wide range of consumer products, such as air filters, washing machines, and textiles, due to their antimicrobial properties [1]. However, despite the beneficial applications of AgNPs into consumer products, it is likely that their use will facilitate the release of AgNPs into wastewater treatment plants, thereby possibly negatively impacting key microorganisms involved in nutrient removal. For this reason, it is important to characterize the effects of AgNPs in natural and engineered systems and to measure the antimicrobial effect of AgNPs on wastewater microorganisms. Polyvinyl alcohol coated AgNPs have already been linked to decreased nitrifying activity [2] and it is important to determine if AgNPs coated with other materials follow similar trends. Furthermore, it is likely that, with repeated exposure to AgNPs microbial communities could evolve and develop resistance to silver. Thus, a long-term effect of silver nanoparticle exposure could be a reduction of the efficacy of such products in a similar fashion to the development of microbial antibiotic resistance [3]. Therefore, it is critical that the impacts of these materials be ascertained in wastewater treatment systems to prevent long-term negative effects.

The objectives of this dissertation were to: 1) characterize the effect of several different AgNPs on the ammonia oxidizing bacterium (AOB) Nitrosomonas europaea and investigate possible mechanisms for toxicity, 2) test the effects of consumer product AgNPs on a wide range of heterotrophic bacteria, 3) evaluate the effects of AgNPs on bench scale wastewater sequencing batch reactors, and lastly 4) assess the impacts on microbial communities that are applied with AgNP spiked wastewater biosolids.

First, Nitrosomonas europaea was was selected because wastewater nitrifying microorganisms carry out the first step in nitrification and are known to be sensitive to a wide range of toxicants [4].The antimicrobial effects of AgNPs on the AOB N. europaea were measured by comparing nitrite production rates in a dose response assay and analyzing cell viability using the LIVE/DEAD® fluorescent staining assay. AgNP toxicity to N. europaea appeared to be largely nanoparticle coating dependent. While PVP coated AgNPs have shown reductions up to 15% in nitrite production at 20 ppm, other AgNPs such as gum arabic (GA) coated showed the same level of inhibition at concentrations of 2 ppm. The first mechanism of inhibition appears to be a post-transcriptional interference of AMO/HAO by either dissolved Ag or ROS, in treatments where membranes are not completely disrupted but nitrite production decreased (2 ppm GA AgNP and 2 ppm PVP AgNP treatments). The disruption of nitrification is dependent on AgNP characteristics, such as zeta potential and coating, which will dictate how fast the AgNP will release Ag+ and ROS production Finally, total membrane loss and release of internal cellular matter occur.

In order to test the effects of AgNP products available to consumers, simple bacterial toxicity tests were carried out on well-studied heterotrophic bacteria. A model gram-positive and gram-negative bacterium (B. subtilis and E. coli, respectively) was selected to assess any differences in sensitivity that may occur with the exposure to AgNPs. A third model gram-negative bacterium (P. aeruginosa) was chosen for its biofilm forming capabilities. In addition to testing pure nanoparticles, three silver supplements meant for ingestion, were randomly chosen to test with these three bacteria. Growth curve assays and LIVE/DEAD staining indicate that the consumer product AgNPs had the most significant inhibition on growth rates, but not membrane integrity. Overall, P. aeruginosa was most negatively affected by all AgNPs with nearly 100% growth inhibition for all 2 ppm AgNP treatments. TEM imaging also confirmed cell wall separation in P. aeruginosa and internal density differences for E. coli. The effects on B. subtilis, a gram-positive bacterium, were not as severe but toxicity was observed for several AgNPs at concentrations greater than 2 ppm. Citrate AgNPs appeared to have the most impact on membrane integrity, while other mechanisms such as internal thiol binding might have been at work for other AgNPs.

The effects of varying concentrations of pure AgNPs on complex microbial wastewater reactors are currently being tested. Eight bench-scale sequencing batch reactors were set up to follow the typical "fill, react, settle, decant, idle" method with an 8 hour hydraulic retention time and constant aeration. Reactors were fed synthetic wastewater and treatment efficiency is measured by monitoring effluent concentrations of COD, NH4+, and NO3-. The reactors were seeded with 500 mL of activated sludge from a local wastewater treatment plant. After reaching steady state, the reactors were spiked with 0.2 ppm gum arabic and citrate coated AgNPs. Treatment efficiency was monitored and results showed significant spikes and ammonia and COD immediately following the first spike, but the microbial community appeared to adapt for future AgNP spikes. Microbial community analysis (terminal restriction fragment length polymorphism) showed confirmed this hypothesis.

Overall, this dissertation asserts that by examining AgNP coating type, Ag+ dissolution rates and Stern layer surface charge, it may be possible to predict which AgNPs may be more detrimental wastewater treatment, but not all AgNPs will have the same effect. The results obtained herein must be expanded to other types of AgNPs and microorganisms of ecological importance.

Symbioses have shaped our modern world, providing for the air we breathe; for the plant and animal diversity we celebrate; and for the functioning of ecosystems from the tops of mountains to the ocean floor. Here I study symbiosis using fungal bacterial interactions as a model for understanding symbiotic dynamics. In this dissertation I present interpretations of experimental data about fungal bacterial interactions that lend insight into dynamics of symbiotic establishment and consequences of long-term endosymbiosis. More specifically, I examine the interactions of a plant-associated zygomycete, Mortierella elongata, and its interactions with several Betaproteobacteria in the Burkholderiales. I used genome sequencing, comparative genomics, physiological assays, and time-lapse microfluidic videography to ask the following questions; How are bacterial fungal symbioses initiated? How do bacteria and fungi communicate? What resources do these microbes share? Are long-term symbioses essential for one or both partners? What are the impacts of removing long-term endosymbionts for fungal host physiology? What are the effects long-term fungal endosymbiosis on bacterial genome content?

In chapter 1 I present lessons learned from genome sequencing of fungus Mortierella elongata and its primary resident endosymbiont, Mycoavidus cysteinexigens. I tested the hypothesis that genome reduction is a commonality of eukaryotic endosymbionts, and that characteristic genes and pathways are impacted by gene loss and inactivation in endosymbionts. I found that compared to its free-living relatives, M. cysteinexigens has a highly reduced genome and has lost genes coding for the biosynthesis of amino acids and intermediates of glycolysis, among other metabolic pathways. I describe a method for clearing fungi of endosymbionts using antibiotics. I report comparative physiological data for the cleared and uncleared strains and draw conclusions about the nature of their interactions based on the behavior of the fungal host lacking the endosymbiont. I tested the hypothesis that sharing of fungal fatty acids underpins this symbiosis, as suggested by the genome sequences of both microbes. I found that when cleared of endosymbionts, M. elongata grows more rapidly and accumulates fatty acids that are likely used by M. cysteinexigens when present.

In chapter 2 I investigate the transcriptional control of fungal-endosymbiont phenotypes. I continued working with the cleared and uncleared strains developed in chapter 1 and quantified transcript abundance in each isolate. I assigned functions to differentially expressed genes by identifying homologues in the fungal genetic model organism Saccharomyces cerevisiae. I layered on transcriptional data to the patterns that emerged from comparative analyses in chapter 1to better understand fungal response to endosymbiosis. I showed that differential expression of conserved genes underpin the increases in growth and altered metabolism in M. elongata when cleared of M. cysteinexigens. I found that endosymbiont presence is associated with toggling of metabolic programs that result in resources more or less bioavailable to M. cysteinexigens based on metabolic capability predicted by genome annotation. I found that genes with homologues in mating pheromone perception pathways are differentially regulated in cleared isolates of M. elongata, and that this aspect of clearing is shared by other isolates of M. elongata when cleared of their bacterial endosymbionts.

In chapter 3 I examine dynamics of pre-symbiotic signaling events between fungi and bacteria using Mortierella elongata and a free-living bacterium, Burkholderia BT03. Using microbial growth assays and a suite of conditioned medias I showed that growth stimulation is mutual for fungi and bacteria, and that signaling leading up to symbiotic phenotypes involves multiple bi-directional signal exchanges. I designed and used a microfluidic platform along with plate based and liquid culture systems to compare fungal growth rates in response to conditioned medias. By extrapolating rates from microbial growth assays including M. elongata, Burkholderia BT03 and related microbes, I inferred directionality, order, conditionality, specificity, and nature of signal exchange leading to microbial growth stimulation in this system.

As a whole this thesis explores how comparative microbial genomics and phenotypic assays can provide mechanistic insight into symbiotic establishment and the effects of long-term symbioses. The results presented here provide novel insights into biotic and abiotic factors dictating symbiotic establishment. Second, they suggest long-term endosymbionts of eukaryotic cells experience convergent gene loss. Lastly they emphasize that long-term endosymbionts strongly impact host metabolism, and that host-microbe metabolic intertwining is a commonality of many symbioses. The use of a systems biology approach to generate comparative genomics data on multiple levels that enable insight into the consequences of fungal bacterial symbioses is a novel contribution for the field.

The emergence of resistance to existing antibiotic drugs necessitates the development of new strategies to treat bacterial infections. Copper (Cu) has been used since ancient times to inhibit bacterial growth and has recently experienced a resurgence in its clinical utility as an antimicrobial coating for surfaces in hospitals. Small molecule chelators that bind Cu have also been shown to have antibacterial activity and are believed to disrupt metal homeostasis within the microbes they kill. Molecules called ionophores shuttle Cu into the cell to poison it. However, the antibacterial modes of action behind Cu and small molecule ionophores are not well understood. In this work, we employ a variety of biological, spectrometric, and proteomic techniques to study how Cu and a small molecule ionophore called pyrithione (PT) kill bacteria. First, we present antibacterial susceptibility assays that demonstrate PT and a β-lactamase-activated prodrug of PT called PcephPT kill bacteria in a Cu-dependent manner. Cu hyperaccumulated in cells that were cotreated with low-micromolar Cu and either PT or PcephPT, demonstrating their activity as metal-shuttling ionophores. Next, proteome-wide protein expression level and stability measurements were used to probe treatment-induced cellular changes after E. coli were exposed to Cu in the absence and presence of PT or PcephPT. The stability-based study identified key protein targets such as the metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase and isocitrate dehydrogenase, whose activities were confirmed to be inhibited by PT-induced copper toxicity in enzymatic assays. Finally, the impact of Cu on the proteome was further investigated in a metal-induced protein precipitation experiment. Unlike other divalent first row transition metals, low millimolar Cu induced complete protein precipitation from E. coli lysate. Protein solubility was restored by addition of Cu chelators, showing that Cu-induced protein precipitation is reversible. We then obtained Cu precipitation curves for over 800 proteins and saw that some were more sensitive while others were more tolerant to precipitation by Cu. Finally, we analyzed the data set to better understand what biophysical characteristics of the proteins may contribute to making them sensitive or tolerant to precipitation by Cu.

Animal bacterial symbioses are pervasive and underlie the success of many groups. Here, I study ecological and evolutionary factors that shape interactions between a host and gut associates. In this dissertation, I interrogate interactions between the carpenter ant (Camponotus) and its associated gut microbiota to ask the following questions: What are the resident microbiota of the Camponotine gastrointestinal tract? How does persistent gut association affect rates of molecular evolution in gut symbionts? How are gut microbiota transmitted between social hosts? How does gut community composition and structure vary across host development? What evolutionary factors facilitate adaptation to the gut? How do the genomes of gut associates respond to selective pressures associated with persistent gut habitation? I use a combination of next generation sequencing, anaerobic isolate culturing, computational modeling, and comparative genomics to illustrate evolutionary consequences of persistent host association on the genomes of gut associates. In chapter one, I characterize the gut community of C. chromaiodes and describe two novel lineages in the Acetobacteraceae (AAB). I demonstrate rapid evolutionary rates, deleterious evolution at 16S rRNA, and deep divergence of a monophyletic clade of ant associated AAB. In chapter two, I design a novel molecular tool to prevent amplification of nontarget DNA in 16S based community screens. I then use this tool to characterize the gut microbiota of C. chromaiodes across several developmental stages and incipient colonies. I argue that highly similar bacterial profiles between a colony queen and offspring are indicative of reliable vertical transmission of gut bacteria. In chapter three, I isolate and culture two strains of AAB gut associates from C. chromaiodes, as well as an associate in the Lactobacillaceae, and perform whole genome sequencing. I use comparative genomic analyses to delineate patterns of genomic erosion and rampant horizontal gene transfer on AAB gut isolates that lead to genomes with mosaic metabolic pathways.

Taken together, this dissertation establishes a new model system for assessing evolutionary consequences of symbioses with gut bacteria. These results provide novel insights into the repercussions of bacterial adaptation to a host gut tract. They establish a foundation to interrogate questions unique to persistent extracellular gut symbionts. Finally, they delineate distinct forces shaping the functional capacity of symbiont genomes: gene loss through reductive evolution and gene acquisition via horizontal transfer from diverse community members.

Chlamydia trachomatis is the obligate intracellular pathogen responsible for the most common bacterial sexually transmitted infection worldwide. While our front-line antibiotics have been historically successful in combatting chlamydial infections, emerging issues including treatment failure and chlamydial persistence necessitate the development of new therapeutic approaches. In this work, an enzyme-focused approach was devised to explore two of the intricate survival strategies of C. trachomatis: virulence and energy metabolism. We sought to employ biochemistry, enzymology, and chemical biology tools to interrogate enzyme functions and inform the design of new antichlamydial agents. To these ends, our efforts focused on characterization of the virulence-associated effector protein chlamydial protease-like activity factor (CPAF) and the futalosine pathway for menaquinone biosynthesis. Mechanistic analyses of CPAF zymogen maturation and peptide hydrolysis were performed that collectively classified CPAF as a serine protease with a catalytic tetrad. Analogs of the natural product salinosporamide A were subsequently explored as CPAF inhibitors. The futalosine pathway was discovered to be a source of novel antichlamydial targets through traditional and chemical genetics analyses in a HeLa cell model of chlamydial infection. The foundation was also established for studying a specific pathway enzyme, CT263, in a continuous coupled enzyme assay. Collectively, this dissertation has progressed our knowledge of several enzymes involved in critical processes for chlamydial pathogenicity and viability. The insights gained on a mechanistic level and in the context of chlamydial infection have laid the groundwork for pursuing virulence and energy metabolism enzymes as antichlamydial targets and for developing inhibitors of their activity, which are much-needed resources to combat this extremely prevalent sexually transmitted infection.

Mechanical properties have a decisive role in the fundamental functions of biological systems, including migration of cells, cell apoptosis, and proliferation of cells and bacteria. This is also true for cancer metastasis and morphogenetic processes during embryonic development. It isn’t easy, however, to study biological systems due to their complex behavior, such as their activity and nonlinear material properties. Note that while the individual mechanical properties of specific biological systems, such as biopolymers, have been well established, the collective behavior of these elements has a different response, as the comparative studies of the mechanical properties of single cancer cells and cancerous tissue demonstrate. Thus, numerous experimental instruments have been developed over the years to investigate biological systems’ mechanical properties, individually or collectively. These experimental techniques can evaluate mechanical properties at multiple scales. Theycan target individual biological entities, like single cells, or assess the collective mechanical properties of more complex biological systems, such as tissues or organoids. The resolution of these studies ranges from single-cell analyses to those concerning embryonic morphogenesis. Simulating biological systems’ individual or collective behavior using a discretized approach (i.e., Molecular Dynamics) or a continuum approach (i.e., Finite Element) is an adjunct to experimental studies. This thesis explores the collective behavior observed in individual cells and embryonic tissue. This exploration was carried out through the development of experimental protocols and the application of continuum mechanics models. In the initial two chapters of this thesis, we delve into the fundamental mechanical concepts essential for understanding the mechanical properties of cells and tissues. We also discuss prior studies that employed shell mechanics to model cellular and embryonic deformations. In the third chapter, we detail our collaborative work with Dr. Samaneh Rezvani focuses on the role of the actin cortex in the deformation of individual suspended spherical cells. For this purpose, we utilized double-trap optical tweezers in conjunction with a viscoelastic pressurized-thick-shell model. Using our simulation approach, we determined the mechanical properties of the actin cortex from the experimental results. The elastic shear modulus of the actin cortex ranged between 4.5 kPa and 7.5 kPa. In modeling the steady deformation of single cells with the shell model, we observed that cell volume remains conserved during deformation. Instead of reducing volume, cells extend the actin cortex to accommodate the increased surface area. We also introduced a multilayer viscoelastic shell model to examine the time-dependent mechanical behaviors of cells, focusing on hysteresis due to dissipative processes. Our model incorporated a fluid core within a viscoelastic shell, offering a more thorough understanding of cell mechanics. Our findings indicate that the damping response in cells is predominantly influenced by the viscosity of the cytosol rather than that of the actin cortex. The fourth chapter describes the modeling of experiments conducted by Dr. Renata Garces on gram-negative E. coli bacteria uniaxially compressed between parallel plates. We used Finite Element Modeling (FEM) to examine the collective mechanical behavior of the peptidoglycan layer (PG) in the bacterial cell wall, modeled as a thin, pressurized rod-shaped shell. Finally, in chapter five, we investigated, in collaboration with Dr. Chonglin Guan, the cells’ collective behavior in epithelial tissue during dorsal closure (DC) in developing Drosophila melanogaster embryos (DME). Utilizing glass microprobes, we deformed various tissue types, specifically amnioserosa (AS) and lateral epidermis (LE), and subsequently recorded their responses to assess the impact of tissue mechanical properties on embryonic development. We simulated a viscoelastic flat shell, replicating the geometry of individual embryos, using the Finite Element Method (FEM) to model tissue deformations. Through this methodology, we quantified the mechanical characteristics of amnioserosa and lateral epidermis, encompassing both their viscosity and elasticity. Our analyses determined the elasticity of AS to be approximately (110 to 180 kPa) and its viscosity to be (0.86 to 1.05 Pa.s). Additionally, we executed step-function experiments to ascertain tissue mechanical properties and evaluate tissue relaxation time. Our findings are in line with our previous results obtained from hysteresis studies.