cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7274/25980379
title: Revealing How the Catheterized Bladder Environment Induces Anti-inflammatory Macrophage Polarization Resulting in Enhancing Bacterial Urinary Tract Infection

description: Despite short-term benefits, urinary catheterization predisposes patients to developing catheter-associated urinary tract infections (CAUTIs). Different from uncomplicated urinary tract infections, CAUTIs display unique clinical manifestations, diverse causative pathogens, and pathologic mechanisms. Catheter-induced tissue damage trigger fibrinogen (Fg) release into the bladder to form fibrin clots for tissue healing. However, Fg/fibrin accumulation within the bladder provided a scaffold for prevalent CAUTI pathogens, uropathogenic Escherichia coli (UPEC) and Enterococcus faecalis, to establish infection. Using a CAUTI mouse model, we observed that significant macrophage recruitment was ineffective at controlling infection. Importantly, our in vitro, ex vivo, and in vivo studies targeting specific coagulation factors unveiled that Fg or fibrin polarize macrophages to either pro- M1 or anti-inflammatory M2, respectively. Thus, we hypothesized that Fg and fibrin differentially polarizes macrophages: where Fg favors M1s to promote bactericidal response, while fibrin induces M2s to dampen antimicrobial activity. To investigate this, bladders of wildtype (WT) and coagulation-transgenic mice, such as mice with deficient soluble Fg (Fg-AEK; no coagulation) and plasminogen (Pg)-deficient mice (fibrin accumulation), were catheterized and infected with UPEC or E. faecalis for 24 hours. In catheterized Fg-AEK mice, we found higher presence of M1s with decreased bacterial burden. In contrast, catheterized Pg-deficient bladders exhibited higher M2s with increased bacterial burden. Thus, Fg promote M1s where it controls infection, while fibrin enhance M2s, suppressing pathogen control. Furthermore, co-injection with GM-CSF and IL-4 in WT mice with fibrin accumulation led to mixed polarization signals that increased presence of hybrid M1/M2 macrophages, which further exacerbated infection and dissemination by suppressing M1 antimicrobial response. Therefore, our studies demonstrated that the catheter-induced fibrin accumulation in the bladder impairs macrophages’ bactericidal response to active infection, thereby contributing to CAUTI pathogenesis. Thus, these findings will advance understanding CAUTI pathogenesis allowing us to develop future intervention strategies for catheterized patients.
DOI: 10.7274/25980379.v1
title: Revealing How the Catheterized Bladder Environment Induces Anti-inflammatory Macrophage Polarization Resulting in Enhancing Bacterial Urinary Tract Infection

description: Despite short-term benefits, urinary catheterization predisposes patients to developing catheter-associated urinary tract infections (CAUTIs). Different from uncomplicated urinary tract infections, CAUTIs display unique clinical manifestations, diverse causative pathogens, and pathologic mechanisms. Catheter-induced tissue damage trigger fibrinogen (Fg) release into the bladder to form fibrin clots for tissue healing. However, Fg/fibrin accumulation within the bladder provided a scaffold for prevalent CAUTI pathogens, uropathogenic Escherichia coli (UPEC) and Enterococcus faecalis, to establish infection. Using a CAUTI mouse model, we observed that significant macrophage recruitment was ineffective at controlling infection. Importantly, our in vitro, ex vivo, and in vivo studies targeting specific coagulation factors unveiled that Fg or fibrin polarize macrophages to either pro- M1 or anti-inflammatory M2, respectively. Thus, we hypothesized that Fg and fibrin differentially polarizes macrophages: where Fg favors M1s to promote bactericidal response, while fibrin induces M2s to dampen antimicrobial activity. To investigate this, bladders of wildtype (WT) and coagulation-transgenic mice, such as mice with deficient soluble Fg (Fg-AEK; no coagulation) and plasminogen (Pg)-deficient mice (fibrin accumulation), were catheterized and infected with UPEC or E. faecalis for 24 hours. In catheterized Fg-AEK mice, we found higher presence of M1s with decreased bacterial burden. In contrast, catheterized Pg-deficient bladders exhibited higher M2s with increased bacterial burden. Thus, Fg promote M1s where it controls infection, while fibrin enhance M2s, suppressing pathogen control. Furthermore, co-injection with GM-CSF and IL-4 in WT mice with fibrin accumulation led to mixed polarization signals that increased presence of hybrid M1/M2 macrophages, which further exacerbated infection and dissemination by suppressing M1 antimicrobial response. Therefore, our studies demonstrated that the catheter-induced fibrin accumulation in the bladder impairs macrophages’ bactericidal response to active infection, thereby contributing to CAUTI pathogenesis. Thus, these findings will advance understanding CAUTI pathogenesis allowing us to develop future intervention strategies for catheterized patients.
DOI: 10.7274/26288707
title: Functional Divergence and Redundant Functions of the Hippo Pathway Effectors YAP and TAZ in Nephrogenesis

description: In this dissertation, I will provide insight into the role of the downstream effectors of the Hippo pathway, Yes-associated protein 1 (YAP), and paralog WW domain- containing transcription regulator 1 (TAZ (wwtr1)) in renal organogenesis and provide the foundation for further research into the molecular mechanisms underlying kidney development and associated pathologies. The kidney, a complex organ crucial for maintaining homeostasis, undergoes intricate developmental processes to form functional nephron units. Understanding the mechanisms behind kidney development is paramount for elucidating the etiology of renal congenital disabilities and acquired diseases. The Hippo pathway is known for its involvement in various cellular functions, including cell fate determination and differentiation, and emerges as a critical player in renal organogenesis. The downstream effectors of the Hippo pathway, YAP, and TAZ (wwtr1), possess highly conserved protein sequences, leading to the assumption of functional redundancy in their roles during pronephros ontogeny. However, through systematic loss of function studies in the zebrafish Danio rerio, we have uncovered the distinct roles of yap and taz(wwtr1) in developing the different nephron segments. Our findings suggest that (i) there is divergence in the functions of yap and taz(wwtr1) during nephrogenesis and that (ii) both yap and taz(wwtr1) are essential for directing proper ontogeny of multiciliated cells within the nephron. These insights shed new light on the intricate roles of Hippo signaling pathways in renal organogenesis and the specialized cell populations in the nephron.
DOI: 10.7274/26288707.v1
title: Functional Divergence and Redundant Functions of the Hippo Pathway Effectors YAP and TAZ in Nephrogenesis

description: In this dissertation, I will provide insight into the role of the downstream effectors of the Hippo pathway, Yes-associated protein 1 (YAP), and paralog WW domain- containing transcription regulator 1 (TAZ (wwtr1)) in renal organogenesis and provide the foundation for further research into the molecular mechanisms underlying kidney development and associated pathologies. The kidney, a complex organ crucial for maintaining homeostasis, undergoes intricate developmental processes to form functional nephron units. Understanding the mechanisms behind kidney development is paramount for elucidating the etiology of renal congenital disabilities and acquired diseases. The Hippo pathway is known for its involvement in various cellular functions, including cell fate determination and differentiation, and emerges as a critical player in renal organogenesis. The downstream effectors of the Hippo pathway, YAP, and TAZ (wwtr1), possess highly conserved protein sequences, leading to the assumption of functional redundancy in their roles during pronephros ontogeny. However, through systematic loss of function studies in the zebrafish Danio rerio, we have uncovered the distinct roles of yap and taz(wwtr1) in developing the different nephron segments. Our findings suggest that (i) there is divergence in the functions of yap and taz(wwtr1) during nephrogenesis and that (ii) both yap and taz(wwtr1) are essential for directing proper ontogeny of multiciliated cells within the nephron. These insights shed new light on the intricate roles of Hippo signaling pathways in renal organogenesis and the specialized cell populations in the nephron.
DOI: 10.7274/26420110
title: Symbiotic Science: Unveiling Host-Microbe Interactions on a Chip

description: The study of host-microbe interactions has been an ongoing field of study since the inception of ‘germ theory.’ It involves the investigation of the symbiotic interactions between microorganisms and their hosts, including plants and animals. Some microorganisms are beneficial to their host, providing nutrients, stimulation needed for biological development, protection from disease, and for some organisms, bioluminescent capabilities used to attract prey or avoid predation. Other symbiotic microorganisms have adverse effects on their host, which we refer to as pathogens. As a function of host protection against pathogenic microbes, beneficial microorganisms have developed numerous strategies to disrupt or kill pathogens through their production of antimicrobial peptides. These antimicrobial peptides serve as a template for the development of novel antimicrobial therapeutics, which are needed for combatting the rise of antimicrobial resistance. 
To advance our understanding of symbiotic interactions between hosts and microbes, the application of 3D tissue-on-a-chip technology offers new approaches for investigating of host-microbe interactions. We developed one such system, called an engineered microvessel (EMV) to reveal new insights into the interactions between host endothelial tissues and two pathogens, invasive Group A Streptococcus (GAS) and SARS-CoV-2. In our investigation of GAS, we described the transcriptional response of GAS to fibrin immobilization, as well as the role of virulence factor streptokinase (SK2b) in directing this transcriptional response. We found that during fibrin immobilization, GAS enters a latency state, which is altered in GAS deficient of functional SK2b. We also showed that the temporal dynamics of this response are altered in a biomimetic EMV system, compared to GAS-fibrin immobilization in a dish. In our investigation of SARS-CoV-2, we examined the effects of viral Spike (S)-protein on endothelial cells (ECs). We found that S-protein alters cytokine production of ECs within the EMV, resulting in the release of pro-inflammatory cytokines, such as IL-6. Furthermore, we described the pro-angiogenic activity of S-protein-treated ECs and angiogenic tube formation within the EMV system, detected through live imaging. This work highlights the benefits and limitations of the application of tissue-on-a-chip systems in the study of host-microbial interactions.
DOI: 10.7274/26420110.v1
title: Symbiotic Science: Unveiling Host-Microbe Interactions on a Chip

description: The study of host-microbe interactions has been an ongoing field of study since the inception of ‘germ theory.’ It involves the investigation of the symbiotic interactions between microorganisms and their hosts, including plants and animals. Some microorganisms are beneficial to their host, providing nutrients, stimulation needed for biological development, protection from disease, and for some organisms, bioluminescent capabilities used to attract prey or avoid predation. Other symbiotic microorganisms have adverse effects on their host, which we refer to as pathogens. As a function of host protection against pathogenic microbes, beneficial microorganisms have developed numerous strategies to disrupt or kill pathogens through their production of antimicrobial peptides. These antimicrobial peptides serve as a template for the development of novel antimicrobial therapeutics, which are needed for combatting the rise of antimicrobial resistance. 
To advance our understanding of symbiotic interactions between hosts and microbes, the application of 3D tissue-on-a-chip technology offers new approaches for investigating of host-microbe interactions. We developed one such system, called an engineered microvessel (EMV) to reveal new insights into the interactions between host endothelial tissues and two pathogens, invasive Group A Streptococcus (GAS) and SARS-CoV-2. In our investigation of GAS, we described the transcriptional response of GAS to fibrin immobilization, as well as the role of virulence factor streptokinase (SK2b) in directing this transcriptional response. We found that during fibrin immobilization, GAS enters a latency state, which is altered in GAS deficient of functional SK2b. We also showed that the temporal dynamics of this response are altered in a biomimetic EMV system, compared to GAS-fibrin immobilization in a dish. In our investigation of SARS-CoV-2, we examined the effects of viral Spike (S)-protein on endothelial cells (ECs). We found that S-protein alters cytokine production of ECs within the EMV, resulting in the release of pro-inflammatory cytokines, such as IL-6. Furthermore, we described the pro-angiogenic activity of S-protein-treated ECs and angiogenic tube formation within the EMV system, detected through live imaging. This work highlights the benefits and limitations of the application of tissue-on-a-chip systems in the study of host-microbial interactions.
DOI: 10.7274/27092704
title: Understanding the Role of Innate Immunity, the Microbiome, and Host Factors in Colitis and Intestinal Fibrosis

description: Inflammatory Bowel Disease (IBD) affects millions of Americans and is steadily increasing in incidence globally every year. IBD is typically broken down into Crohn’s Disease (CD) and Ulcerative Colitis (UC), with an approximately even distribution of diagnoses. This disease is categorized by an uncontrolled, pathogenic inflammation in the gastrointestinal tract and is thought to be caused by a combination of genetic and environmental factors. There is currently no cure to IBD, but historically, treatments have been developed by targeting immune mechanisms. This thesis examines several models of IBD to contribute a better understanding of the interaction between the innate immune system, the gut microbiome, and host factors in the pathogenesis of IBD.
The role of the innate immune system in IBD is poorly understood as it is typically overshadowed by the adaptive immune system. Suppression of T cells is commonly the target of IBD therapies, while the innate immune system remains understudied. This thesis examines a mouse model of colitis that is exclusively driven by the innate immune system through the knockout of RAG1 and transgenic expression of TNF Alpha Induced Protein 3 (TNFAIP3) under a villin promoter so that it is constitutively active in the epithelial cells of the GI tract. Through this model, this thesis demonstrates that the innate immune system can respond to a disrupted gut microbiome which leads to intestinal inflammation. This model was then expanded upon to uncover the role of innate lymphoid cells (ILCs) by knocking out retinoid orphan receptor gamma t (ROR?t) and it was shown that ROR?t is dispensable for the development of this colitis.
The gut microbiome is the community of bacteria, archaea, fungi, and viruses that colonize the digestive tract. The composition of the gut microbiome is important for the maintenance of a variety of health functions including obvious functions nutrient acquisition and digestion, but increasing evidence shows that the gut microbiome may also influence the susceptibility to mental health conditions such as anxiety and depression, as well as diseases like Parkinson’s, Alzheimer’s, and IBD. This thesis demonstrates that the gut microbiome in fact drives the innate model of colitis developed and studied in this thesis.
Host factors are an extremely important means for both how the human body interacts with itself as well as with external factors such as infections, tissue damage, and the gut microbiome. Host factors can influence homeostasis not only of our own cellular functions, but of the populations of microbes that colonize our guts. This thesis investigates the role of the host factor Gastrokine-1 (Gkn1) on both the microbiome and additional host proteins to protect against the induction of colitis. The work presented in this thesis is aimed at advancing our understanding of the GI tract and the molecular mechanisms that trigger IBD.
DOI: 10.7274/27092704.v1
title: Understanding the Role of Innate Immunity, the Microbiome, and Host Factors in Colitis and Intestinal Fibrosis

description: Inflammatory Bowel Disease (IBD) affects millions of Americans and is steadily increasing in incidence globally every year. IBD is typically broken down into Crohn’s Disease (CD) and Ulcerative Colitis (UC), with an approximately even distribution of diagnoses. This disease is categorized by an uncontrolled, pathogenic inflammation in the gastrointestinal tract and is thought to be caused by a combination of genetic and environmental factors. There is currently no cure to IBD, but historically, treatments have been developed by targeting immune mechanisms. This thesis examines several models of IBD to contribute a better understanding of the interaction between the innate immune system, the gut microbiome, and host factors in the pathogenesis of IBD.
The role of the innate immune system in IBD is poorly understood as it is typically overshadowed by the adaptive immune system. Suppression of T cells is commonly the target of IBD therapies, while the innate immune system remains understudied. This thesis examines a mouse model of colitis that is exclusively driven by the innate immune system through the knockout of RAG1 and transgenic expression of TNF Alpha Induced Protein 3 (TNFAIP3) under a villin promoter so that it is constitutively active in the epithelial cells of the GI tract. Through this model, this thesis demonstrates that the innate immune system can respond to a disrupted gut microbiome which leads to intestinal inflammation. This model was then expanded upon to uncover the role of innate lymphoid cells (ILCs) by knocking out retinoid orphan receptor gamma t (ROR?t) and it was shown that ROR?t is dispensable for the development of this colitis.
The gut microbiome is the community of bacteria, archaea, fungi, and viruses that colonize the digestive tract. The composition of the gut microbiome is important for the maintenance of a variety of health functions including obvious functions nutrient acquisition and digestion, but increasing evidence shows that the gut microbiome may also influence the susceptibility to mental health conditions such as anxiety and depression, as well as diseases like Parkinson’s, Alzheimer’s, and IBD. This thesis demonstrates that the gut microbiome in fact drives the innate model of colitis developed and studied in this thesis.
Host factors are an extremely important means for both how the human body interacts with itself as well as with external factors such as infections, tissue damage, and the gut microbiome. Host factors can influence homeostasis not only of our own cellular functions, but of the populations of microbes that colonize our guts. This thesis investigates the role of the host factor Gastrokine-1 (Gkn1) on both the microbiome and additional host proteins to protect against the induction of colitis. The work presented in this thesis is aimed at advancing our understanding of the GI tract and the molecular mechanisms that trigger IBD.
DOI: 10.7274/27299802
title: Elucidating the Protein Composition and Biogenesis Mechanisms of Tumor Microvesicles

description: Motivated by their established roles in cancer progression and clinical promise, we explore tumor microvesicle (TMV) biology through the investigation of their molecular constituents and the underlying mechanisms dictating biogenesis. Utilizing a proximity ligase assay, we have developed a novel approach to characterizing TMV protein cargos. These studies enhance our overall understanding of the molecular “signature” of TMVs, which will act as a library to gain insight into all areas of their biology. Among the proteins identified, we confirm and characterize the annexin A1- S100A11 tethering complex in the biogenesis of TMVs. We demonstrate these structures form membrane contact sites between ER and ARF6-positive endosomes, which facilitate the positioning of these endosomal compartments to the cell surface for MAPK signaling and TMV release. We further determine the formation of this tethering complex is dictated by annexin A1 post-translational modifications. Finally, we provide preliminary evidence to suggest that annexin A1 phosphorylation and cleavage impact not only TMV biogenesis but other key pathways in the endolysosomal system. Overall, this dissertation utilizes novel approaches to studying TMVs and makes significant strides in our understanding of their biology.
DOI: 10.7274/27299802.v1
title: Elucidating the Protein Composition and Biogenesis Mechanisms of Tumor Microvesicles

description: Motivated by their established roles in cancer progression and clinical promise, we explore tumor microvesicle (TMV) biology through the investigation of their molecular constituents and the underlying mechanisms dictating biogenesis. Utilizing a proximity ligase assay, we have developed a novel approach to characterizing TMV protein cargos. These studies enhance our overall understanding of the molecular “signature” of TMVs, which will act as a library to gain insight into all areas of their biology. Among the proteins identified, we confirm and characterize the annexin A1- S100A11 tethering complex in the biogenesis of TMVs. We demonstrate these structures form membrane contact sites between ER and ARF6-positive endosomes, which facilitate the positioning of these endosomal compartments to the cell surface for MAPK signaling and TMV release. We further determine the formation of this tethering complex is dictated by annexin A1 post-translational modifications. Finally, we provide preliminary evidence to suggest that annexin A1 phosphorylation and cleavage impact not only TMV biogenesis but other key pathways in the endolysosomal system. Overall, this dissertation utilizes novel approaches to studying TMVs and makes significant strides in our understanding of their biology.