Thesis advisor: Tim van Opijnen / Thesis advisor: Michelle Meyer / Although bacteria are often studied as planktonic or free-living organisms, they frequently grow in complex surface-attached communities known as biofilms. Biofilms are communities of microorganisms attached to surfaces and embedded in a self-produced extracellular matrix. Biofilms are dynamic structures analogous to human settlements shaped by space and environment. These microbial communities fulfill critical roles in multiple infections in the human body. Streptococcuspneumoniae is a human pathogen that can cause biofilm-associated infections in various tissues and organs. This thesis offers a unique outlook for the study of S. pneumoniae biofilms by combining in vitro, genome-wide, and in vivo experiments to elucidate the complex population dynamics of S. pneumoniae biofilms. Existing methods to cultivate S. pneumoniae biofilms fail to fully capture the complexity of these communities, and most studies are limited to short periods of time. We developed a robust in vitro assay to grow S. pneumoniae biofilms. This assay can be maintained forever rather than days. We then use this robust assay to study their behavior in vivo and monitor disease outcomes. After establishing clear differences in biofilm and dispersal samples, we monitor population dynamics using genome-wide techniques (Tn-seq, RNA-seq and WGS) to provide some insights into this complex mode of growth. This work includes the first global identification of genetic requirements during biofilm establishment in two different S. pneumoniae strains using Tn-Seq. Coupled with our transcriptomic analysis, we found that genes involved in multiple pathways, such as capsule biosynthesis, nucleotide metabolism, and stress response, contributed to biofilm growth. Lastly, we studied the development of antibiotic resistance to three different types of antibiotics under S. pneumoniae biofilm conditions. We revealed common adaptive pathways to achieve biofilm growth and antibiotic resistance (antibiotic target genes), as well as novel routes of adaptation to develop resistance. Our findings add to the growing body of knowledge in the field of bacterial genetics and antimicrobial resistance, paving the way for future research and therapeutic advancement. / Thesis (PhD) — Boston College, 2023. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

Malaria is vectored by the mosquito Anopheles gambiae (Ag) in Sub-Saharan Africa and infects approximately 500 million people annually. The increasing prevalence of pyrethroid-resistant mosquitoes has amplified the need for development of new, selective mosquitocides for use on insecticide-treated nets. We have developed several phenyl-substituted N-methylcarbamates producing a high degree of selectivity for Anopheles gambiae acetylcholinesterase (AgAChE) over human AChE. Molecular models suggest alternate conformations (flexibility) of W84 and W431 (Ag numbering) at the hydrophobic subpocket of the AgAChE active site and poor flexibility within human AChE, allowing for the high selectivity of our novel carbamates. Initial selectivity data was obtained through screening of these insecticides while using ethanol as a solvent. Re-screening of these carbamates in the presence of 0.1% DMSO (v/v) resulted in antagonism of inhibition for AgAChE, thus reducing the AgAChE-selectivity by at least 10-fold. However, the presence of 0.1% DMSO did not antagonize the inhibition of human, Drosophila melanogaster, or Musca domestica AChE. Non-selective carbamates also displayed no solvent-dependent antagonism of inhibition in any species studied, including AgAChE. Molecular models provide an explanation for antagonism of inhibition when DMSO is present. I, and collaborators, propose that W84 and W431 in AgAChE comprise an allosteric pocket that is stabilized by DMSO and is responsible for the solvent-dependent antagonism of inhibition observed with AgAChE. / Master of Science in Life Sciences

<p dir="ltr">Phospholipase C (PLC) enzymes are essential for normal cardiovascular function. These enzymes hydrolyze phosphatidylinositol 4,5-bisphosphate (PIP₂) at the inner leaflet of the plasma membrane, producing diacylglycerol (DAG) and inositol phosphates (IP₃). IP₃ increases intracellular Ca²⁺, a key secondary messenger in cardiovascular activity. Changes in PLC expression and activity, specifically PLCβ3, have been found to play a critical role in cardiac hypertrophy and contractility. Cardiac hypertrophy, especially left ventricular hypertrophy, is a primary cause of ischemic heart disease, the leading cause of mortality worldwide. Despite the importance of these enzymes, a selective inhibitor for studying their function in cells and animal models has not yet been discovered. To address this unmet need, a lentiviral system for expressing human PLCβ3 and its two major activators, the heterotrimeric G protein subunits Ga_q and Gβγ was developed. These constructs were then utilized to establish a high-throughput screening methodology with the aim of identifying a novel allosteric inhibitor of PLCβ3, and ultimately other PLCs.</p>

Wireless Local Area Networks (WLAN) have proliferated in the last 5 years. The IEEE 802.11b products have become commonplace both in the residential and business places for untethered Internet access. However the end user experience has often been less satisfactory than what the technology can offer. The degradation in the performance of the system is mainly attributed to the poor network design. The current network design is primarily RF centric. There are two factors that need to be in the incorporated in the design. Firstly a clear understanding of the traffic sources in the network such as the peak load of the system is necessary. Secondly the design should account for the limitations of the indoor propagation such as interference and multipath. The goal of this thesis is to develop a simulator which will predict the performance (throughput) of an end user. The throughput is predicted for a given topology and traffic source. The simulator is built on object oriented design. To validate the simulator a measurement campaign was conducted. The campaign was conducted in two different channel conditions, office space and open hall. The channel measurements were also performed at these locations to understand the multipath. Comparative studies indicate that the choice of the rate adaptation algorithm hugely influences the predicted throughput. The simulator results match very well with the measurement results for the open space scenario. For the office space scenario the simulator varied by roughly 20% from the measurement results. This was due to existence of multipath leading to Inter Symbol Interference. / Master of Science

In each individual cell, there are many signaling pathways that may interact or cross talk with each other. Especially, some can sense the same signal and go through different pathways but eventually converge at some points. Therefore repetitive signal stimulations may result in intricate cell responses, among which the priming effect has been extensively studied in monocytes and macrophages as it plays an unambiguously crucial role in immunological protection against pathogen infection. Priming basically describes the phenomena that host cells can launch a dramatically enhanced response to the second higher dose of stimulus if cells have been previously treated with a lower dose of identical stimulus. It was reported to be associated with many human immune diseases (such as rheumatoid arthritis and hepatitis) that are attracting more and more researches on the priming effect. It is undoubtable that many genes are involved in this complicated biological process. Microarray is one of the standard techniques that are applied to do the transcriptome profiling of cells under repetitive stimuli and reveal gene regulatory networks. Therefore a well-established pipeline to analyze microarray data is of special help to investigate the underlying mechanism of priming effect. In this research, we aimed to design a strategy that can be used to interpret microarray data and to propose gene candidates that potentially participate in priming effect. To confirm our analysis results, we used a detailed mathematical model to further demonstrate the mechanism of a specific case of priming effect in a computational perspective. / Master of Science

Due to the increasing resistance demonstrated by insects to conventional insecticides, the need for compounds with novel modes of action is becoming more urgent. Also, the discovery and production of new insecticides is vital as regulations and restrictions on conventional insecticides become increasingly stringent (Casida and Quistad 1998). Research in this area requires screening of many candidate compounds which is costly and time-consuming. The goal of this research was to produce in vitro insect neurons from Sf21 insect ovarian cell lines, which could lead to new high throughput screening methods and a way to mass produce insect material for basic research. This study used a culture of Sf21 cells and a mixture of differentiation agents to produce viable neuron-like cells. In the presence of the molting hormone 20-hydroxyecdysone (20-HE), or insulin, in the growth medium, Sf21 cells began to express neuronal morphology, or the production of elongated, axon-like processes within 2-3 days. Maximal differentiation occurred when in the presence of 42 μM 20-HE or 10 μM insulin. Effects were maximal on day 2 for 20-E and day 3 for insulin. Insulin was more potent at day 2 for inducing differentiation (EC₅₀ = 247 nM) than 20-HE (EC₅₀ = 13 μM). In combination, 20-HE and insulin produced apparent synergistic effects on differentiation. Caffeine, a central nervous system (CNS) stimulant, inhibited induction of elongated processes by 20-HE and/or insulin. Caffeine was a potent inhibitor of 42 μM 20-HE, with an IC50 of 9 nM, and the inhibition was incomplete, resulting in about one quarter of the differentiated cells remaining, even at high concentrations (up to 1 mM). The ability to induce a neural phenotype simplifies studies with of insect cells, compared to either the use of primary nervous tissue or genetic engineering techniques. The presence of ion channels or receptors in the differentiated cells remains to be determined. If they are present, high throughput screening for new insecticides will be accelerated and made more economical by the utility of this method. / Master of Science

Thesis (Ph.D.)--Indiana University, 2009. / Title from screen (viewed on February 2, 2010). Department of Biochemistry and Molecular Biology, Indiana University-Purdue University Indianapolis (IUPUI). Advisor(s): Mark R. Kelley, Millie M. Georgiadis, John J. Turchi, Martin L. Smith. Includes vitae. Includes bibliographical references (leaves 114-133).

Receptores nucleares controlam a transcrição em células eucarióticas quando ativados por ligantes e, além do sítio de interação com ligantes, há outros sítios alternativos em sua superfície que podem ser alvo de compostos capazes de interferir com as interações proteína-proteína desativando o RN. A ativação do Receptor X de Pregnano (RXP) e do Receptor Constitutivo de Androstano (RCA) resulta na indução do metabolismo e efluxo de fármacos. Portanto, RXP/RCA sao responsáveis por causar reações adversas ou falhar terapias. Uma abordagem combinando a triagem experimental à nível cellular, em uma biblioteca de fármacos, e validação com ensaios in vitro e in silico, conseguimos identificar três novos antagonistas de RXP e cinco novos contra RCA, cada um com um perfil único de interação. / Nuclear receptors can control transcription in eukaryotic cells in a ligand-dependent manner and, besides the ligand-binding pocket there is evidence of the existence of alternative ligand-binding sites on the surface, which can be addressed by small organic molecules that disrupt specific protein-protein interactions and thereby may antagonise NR function. Activation of pregnane X receptor (PXR) and constitutive androstane receptor (CAR) results in the induction of first-pass metabolism and drug efflux. Hereby PXR/CAR may cause adverse drug reactions or therapeutic failure of drugs. Therefore, PXR and/or CAR antagonists can minimise adverse effects or improve therapeutic efficiencies. Combination of cellular high-throughput screen identified CAR and PXR potent antagonists in a library of approved and investigational drugs. Further validated by cellular and in vitro assays, as well as molecular docking, suggesting additional or exclusive binding outside the classical ligand binding pocket. In conclusion, we here have identified three approved drugs as novel potent PXR antagonists and five potential CAR inverse agonists with differential receptor interaction profiles.

The interferon (IFN) response is a crucial component of cellular innate immunity, vital for controlling virus infections. Dysregulation of the IFN response however can lead to serious medical conditions including autoimmune disorders. Modulators of IFN induction and signalling could be used to treat these diseases and as tools to further understand the IFN response and viral infections. We have developed cell-based assays to identify modulators of IFN induction and signalling, based on A549 cell lines where a GFP gene is under the control of the IFN-β promoter (A549/pr(IFN-β).GFP) and the ISRE containing MxA promoter (A549/pr(ISRE).GFP) respectively. The assays were optimized, miniaturized and validated as suitable for HTS by achieving Z' Factor scores >0.6. A diversity screen of 15,667 compounds using the IFN induction reporter assay identified 2 hit compounds (StA-IFN-1 and StA-IFN-4) that were validated as specifically inhibiting IFNβ induction. Characterisation of these molecules demonstrated that StA-IFN-4 potently acts at, or upstream, of IRF3 phosphorylation. We successfully expanded this HTS platform to target viral interferon antagonists acting upon IFN-signalling. An additional assay was developed where the A549/pr(ISRE).GFP.RBV-P reporter cell line constitutively expresses the Rabies virus phosphoprotein. A compound inhibiting viral protein function will restore GFP expression. The assay was successfully optimized for HTS and used in an in-house screen. We further expanded this assay by placing the expression of RBV-P under the control of an inducible promoter. This demonstrates a convenient approach for assay development and potentiates the targeting of a variety of viral IFN antagonists for the identification of compounds with the potential to develop a novel class of antiviral drugs.

This work is focused on the issue of wireless networks according to the IEEE 802.11 standard. The main subject of research is the Rate Adaptation Algorithms (RAA). The work also contains a description of simulation environments NS-3 and OMNeT in terms of adaptation algorithms. At the end of the work there is a summary of wireless network simulations in NS-3 and OMNeT environments and their comparison with the actual measurement of network parameters.