21794 research outputs found
Sort by
The Proteome Of Bacterial Rnp Condensates (br-Bodies) And Role Of 5’ Nucleotide Modifications In Br-Body Assembly And Messenger Rna Decay
No full textThe bacterial cytoplasm has been assumed to be poorly organized due to a lack of membrane-bound organelles. Biomolecular condensates (hereafter referred to as condensates) were recently discovered as an alternative mechanism to organize the cellular cytoplasm. Condensates are non-membrane-bound organelles that are formed through liquid-liquid phase separation by concentrating a specific set of proteins/nucleic acids to compartmentalize cellular biochemistry. While eukaryotic condensates have been broadly identified and characterized, less is known about the organization and functions of bacterial condensates. Eukaryotic condensates play a critical role in organizing the biochemical steps of gene expression including mRNA transcription, processing, and decay. The first and well studied bacterial condensate being BR-bodies that organize mRNA decay. This dissertation aims to apply a systematic method to define the BR-body proteome and understand the mechanisms by which BR-bodies organize mRNA decay. Using a cellular enrichment by differential centrifugation followed by LC-MS proteomics analysis, we identified \u3e100 proteins enriched in BR-bodies including many proteins known to affect mRNA decay. However, one specific type of protein that is important for mRNA degradation is decapping enzymes (RppH and NudC) that were found to be depleted from BR-bodies. Interestingly, by generating rppH and nudC deletion strains, we found that decapping activity is required for robust BR-body formation. By measuring the global mRNA decay rates utilizing Rif-seq, we observed a significant subset of the C. crescentus transcriptome was turned over more slowly in the rppH deletion strain. GO-term analysis found that RppH regulated mRNAs are enriched in amino acid and carbon metabolism genes. Overall, our results suggest that decapping enzymes induce rapid BR-body formation in cells which could help bacteria to rapidly turnover the transcriptome to shut off genes whose expression is no longer required, thereby adapting to ever changing environmental conditions by regulating translation. Molecular mechanisms of bacterial gene expression remain unclear due to the importance of cellular organization for precise gene expression. However, a comprehensive understanding of BR-body condensates catalyzed mRNA-decay could help in designing new antibiotic targets. Therefore, BR-bodies could be attractive targets for developing next-generation antibiotics to fight antibiotic resistance, a global public health threat
A Theoretical Framework For 3+1d Dynamics Of Relativistic Heavy-Ion Collisions
Get PDFThe primary goal is to enhance a theoretical tool for studying 3D dynamics in relativistic heavy-ion collisions. We aim to explore the effects of stochastic fluctuations within these systems as part of the Beam Energy Scan program at the Relativistic Heavy-Ion Collider. Our approach involves constructing 3D initial conditions using minimal model parameters based on Glauber collision geometry, energy, and momentum conservation principles. We validate the model by comparing its predictions on particle rapidity distributions and anisotropic flow coefficients in specific collision scenarios. Model parameters are calibrated by comparing predictions to observed data from central Au+Au collisions. Additionally, we extend our simulations to include Pb+Pb collisions at Super Proton Synchrotron energies. This research advances the development of a theoretical framework focusing on the propagation of two-point correlation functions associated with stochastic fluctuations and their out-of-equilibrium signatures near a Quantum Chromodynamics critical point.In this study, we proceed a comprehensive examination of the polarization observable of hyperons using a systematic event-by-event approach based on (3+1)D relativistic hydrodynamics. We specifically investigate the impact of initial hot spot size and QGP\u27s specific shear viscosity on the polarization observable. Furthermore, we research the influence of the two formulations of the thermal shear tensor on the polarization observables, employing the same hydrodynamic background. Using event-by-event simulations, we generate predictions for the Fourier coefficients of \u27s longitudinal polarization relative to the event planes associated with various orders of anisotropic flow also, for the charged hadrons too.We exhibit a system size scan with Au+Au, Ru+Ru, and O+O collisions at \,GeV to study the system size dependence of polarization observables at the Relativistic Heavy-ion Collider.We developed the two-point function (variance) of thermal and critical fluctuations in relativistic heavy-ion collisions by solving the evolution equation for . We compare the out-of-equilibrium evolution of the fluctuation with different critical models in (1+1)D Bjorken background for three different critical models that are model A, B, and H. We have developed a theoretical framework that can follow the out-equilibrium evolution of the two-point correlation functions in the presence of critical points in full 3D. We calculate and compare the out-of-equilibrium correction to entropy ratio for Au+Au collision 19.6 GeV and 7.7 GeV
Platelet Derived Growth Factor Receptor Alpha (pdgfra) Oncogene Dependency In Glioblastoma
No full textGlioblastoma (GBM) is the most aggressive adult type of glioma, a primary brain tumor. Furthermore, pediatric high-grade gliomas (HGG) are the deadliest childhood cancer. A combination of surgery, radiation, and chemotherapy has been used to treat glioma patients. Only one new therapy has been approved for treating glioma patients since 2005 despite only 17% of patients surviving longer than two years. Platelet derived growth factor receptor alpha (PDGFRA) is important for early brain development and both its expression and activity are altered in GBM patients. While PDGFRA inhibitors have been successful in limiting growth pre-clinically, PDGFRA inhibitors have not been effective in adult and pediatric clinical trials. Patient selection and drug toxicity are two of the reasons for the ineffectiveness of PDGFRA inhibitors. In at least 15% of GBM and HGG patients, PDGFRA is altered by increased gene copy number in amplified genomic regions. Our preliminary data demonstrates that PDGFRA amplification provides a growth advantage in patient-derived mouse models. The goal of this project is to (1) determine GBM tumor requirement for PDGFRA, (2) understand how the need for PDGFRA associates with PDGFRA amplification status, and (3) explain the importance of PDGFRA in the response of tumor cells to stressors such as therapy. In the short term, this will identify patients that respond to PDGFRA inhibitors. In showing that PDGFRA is essential for tumor growth, this will encourage drug developers to refocus on developing better PDGFRA inhibitors
Assessment And Prediction Of Groundwater Infiltration And Surface Water Inflow (i/i) Into Urban Sewer Collection Systems, Pilot Study: Detroit, Mi
No full textABSTRACTASSESSMENT AND PREDICTION OF GROUNDWATER INFILTRATION AND SURFACE WATER INFLOW (I/I) INTO URBAN SEWER COLLECTION SYSTEMS, PILOT STUDY: DETROIT, MI by AMIR SHAHIN KAMJOU October 2023 Advisor: Prof. Carol J. Miller Major: Civil and Environmental Engineering Degree: Doctor of Philosophy Combined sewer collection systems are vital components of urban infrastructure designed to collect wastewater, including sanitary sewage and stormwater runoff. Most of these systems face an enduring challenge known as infiltration and inflow (I/I). Infiltration refers to the groundwater entering the sewer system through deteriorated infrastructure, cracks, faulty joints, and leaks. Inflow refers to the stormwater runoff entering the sewer system through various sources such as roof and yard drains, catchments, and access chamber covers. The excessive I/I significantly overwhelm the capacity of sewer systems, leading to numerous issues, including decreased system efficiency, elevated treatment costs, sewage backups, property damage, soil wash-off and sinkholes, public health risks, and combined sewer overflows (CSO). The CSO events are caused by system failure during heavy rainfall events, which leads to the release of untreated sewage into local water bodies, posing significant risks due to the potential contamination by bacteria, chemicals, pathogens, and excess nutrients into recreational areas and the ecosystem. The quantification of I/I leads to efficient remediation strategies that reduce the occurrence rate and severity of I/I-related problems and protect public health and the environment. Additionally, it can contribute to the longevity and efficiency of the sewer infrastructure, reducing maintenance costs and enhancing the system\u27s overall resilience. The high-performance conventional I/I estimation methods consist of synthetic unit hydrograph and Genetic Algorithm (GA) curve fitting optimization. This study aimed to further enhance the accuracy of I/I estimation and prediction by implementing a superior optimization algorithm called Memetic Algorithm (MA), and a new innovative objective function. The MA algorithm improved the precision by preventing premature convergence and enhanced the overall computational cost compared to GA due to its meta-heuristic search techniques. However, the proposed objective function outperformed the MA algorithm, yielding a higher modeling accuracy. Thus, the combination of MA and the proposed objective function performed an outstanding ability to simulate the flow with lower computational cost. The key findings of this study contribute to the overall efficiency, resilience, and sustainability of the city of Detroit\u27s sewer system, leading to optimized system operation, cost reduction, and improved public health protection
Dual Mechanisms Contributing To Pyruvate Dehydrogenase Activity Deficiency In A Barth Syndrome Cell Model
Get PDFBarth syndrome (BTHS) is a rare genetic disease that results from mutations in the TAFAZZIN gene, which encodes the cardiolipin (CL) remodeling enzyme tafazzin (Taz). The mechanisms linking perturbation of CL remodeling and the pathological features of BTHS are not understood. We have recently reported that intermediary metabolism is perturbed in BTHS, and activity of the metabolic gatekeeper enzyme pyruvate dehydrogenase (PDH) is deficient in BTHS models. The mechanism whereby PDH is regulated by Taz is unknown, and this knowledge gap represents an obstacle to the development of therapeutics to treat BTHS. Using an established C2C12 myoblast model of BTHS, TAZ-KO, I identified important mechanisms by which CL regulates PDH function. CL regulates PDH activity through activation of PDK4, and this is mediated by hyperactivation of AMPK activity, which facilitates FOXO1 nuclear translocation and subsequent increase in PDK4 expression in TAZ-KO cells. PDK4 upregulation leads to alterations in fuel utilization, consistent with observed metabolic changes in BTHS patients, including disrupted glucose and fatty acid oxidation and increased fatty acid accumulation in the heart and plasma. In addition, CL regulates PDH activity by facilitating PDP1-mediated dephosphorylation of PDH. Of different CL species tested in isolated TAZ-KO mitochondria, only tetralinoleoyl-CL (TLCL) rescues PDH activity. Interestingly, when phosphatase activity is inhibited, the PDH activity was not rescued by CL. Additionally, PDP1 activity in TAZ-KO cells and TLCL interacted with PDP1 in vitro. These findings suggest that PDP1 is required for CL-activation of PDH activity. It is likely that TLCL serves as a scaffold for concurrent binding of PDP1 and PDH, thereby facilitating their interaction. This is supported by the observed dose-dependency of TLCL rescue. PDP1 activity is also likely reduced by the finding that mitochondrial calcium levels are decreased in TAZ-KO cells, as PDP1 activity is dependent on calcium. TAZ-KO cells exhibit decreased mitochondrial calcium levels and supplementation with calcium lactate (CaLac) rescues PDH activity and oxygen consumption rate (OCR). The perturbation in mitochondrial calcium levels is further reflected in changes observed in ER-MT contacts (MAMs), which play an important role in channeling calcium. Components of MAMs, including IP3R, VDAC1, GRP75 and PDK4, are increased in TAZ-KO cells and mouse TAZ-KO heart tissues. Overall, I proposed two mechanisms whereby CL regulates PDH, including regulation of PDK4 via FOXO1-AMPK and interaction with PDP1 or/and modifying mitochondrial calcium levels. These findings provide insight into the regulatory mechanisms of PDH activity by CL, linking CL function to substrate metabolism and mitochondrial calcium regulation coordinating with ER
Optimal Spatial Design Of Groundwater Level Monitoring Networks Using Machine Learning Methods
Get PDFGroundwater plays a crucial role in sustaining ecosystems, providing drinking water, and supporting various industrial activities. As water scarcity becomes an increasingly pressing global issue, accurate groundwater level monitoring is essential for effective resource management and environmental protection. The study introduces a comprehensive methodology that integrates groundwater flow modeling, stochastic simulations, and ML algorithms to design efficient Groundwater Level Monitoring Networks (GLMNs) in regions with limited groundwater observation data. Two primary ML algorithms, K-means clustering and Relevance Vector Machine (RVM), are used to select and position observation wells strategically. The research addresses the challenge of minimizing data uncertainties and determining optimal well locations to maximize data collection while reducing the monitoring expenditure. To assess the effectiveness of the proposed approach, the study employs a real-world scenario in Metro Detroit, an area lacking comprehensive groundwater observation wells. The results demonstrate the utility of ML-based GLMNs in enhancing hydrogeological understanding, improving groundwater modeling accuracy, and managing installation budgets. The modeling performance is evaluated by using statistical error metrics to measure predictive accuracy and validate the modeling, comparing model predictions with real-observed groundwater levels. The research highlights that the groundwater models containing proposed GLMNs more accurately represent aquifer behaviors by minimizing errors, contributing to better-informed decision-making. Furthermore, the study evaluates the efficiency gains in terms of the calibration time required for model development. ML-based network design expedites the calibration process, enabling more efficient modeling and management of groundwater resources
The Mechanisms Of Trail Resistance In Triple-Negative Breast Cancer
No full textTriple-negative breast cancer (TNBC) is an aggressive form of breast cancer that lacks targeted therapies. Previous studies have shown that TNBC cells are highly sensitive to tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), making it a promising agent for treating TNBC. However, the development of TRAIL resistance limits its further clinical development, and the underlying mechanisms are not fully understood. In this study, we report the role of PD-L1 and inflammation in TRAIL resistance. Specifically, we found that TRAIL treatment increases PD-L1 expression in TRAIL-sensitive cells and that basal PD-L1 expression is increased in acquired TRAIL-resistant cells. Mechanistically, we found that increased PD-L1 expression was accompanied by increased ERK activation. Using both genetic and pharmacological approaches, we showed that knockdown of ERK by siRNA or inhibition of ERK activation by the MEK inhibitor U0126 decreased PD-L1 expression and increased TRAIL-induced cell death. Furthermore, we found that knockout or knockdown of PD-L1 enhances TRAIL-induced apoptosis, suggesting that PD-L1-mediated TRAIL resistance is independent of its ability to evade immune suppression. These findings suggest that the mechanisms of TRAIL resistance extend beyond intrinsic and extrinsic apoptosis pathways. Because TRAIL-resistant cells were not eliminated after PD-L1 knockdown and knockout, we speculate that there are other TRAIL resistance mechanisms in these TNBC cells. To better understand the mechanism of TRAIL resistance, we performed RNA sequencing and gene expression analysis in TRAIL-sensitive and TRAIL-resistant MDA231 and SUM159 cells. This approach led us to identify several differentially expressed genes (DEGs) and pathways in MDA231-R and SUM159-R cells when compared to their TRAIL-sensitive counterparts. We showed that a number of DEGs and pathways were associated with immune response and inflammation in MDA231-R and SUM159-R cells. Among these pathways, we found that cytokine-cytokine receptor interaction and TNF signaling were the most affected. Because TRAIL is a TNF superfamily cytokine, we wanted to know if it played a noncanonical role in inducing inflammation and whether this was caused by pro-inflammatory cytokines IL-6 and IL-1α in TRAIL-resistant cells. Using western blot analysis, we showed that basal levels of IL-6 and IL-1α were increased in MDA231-R and SUM159-R cells. Furthermore, we found that knockdown of IL-6 and IL-1α enhances TRAIL-induced apoptosis, suggesting that inflammation plays a role in TRAIL resistance in TNBC. In summary, this dissertation has identified two new noncanonical mechanisms by which PD-L1, IL-6, and IL-1α promote TRAIL resistance in TNBC cells, which could be targeted for TNBC therapy
Understanding The Experiences Of Black Students Supported By A Black Mentor While Attending A Predominantly White Institution
No full textAmerica’s higher education system was not created with consideration to supporting Black students. Now, centuries later, the majority of Black students choose to attend predominantly White institutions (PWIs) and enroll at comparable rates to their White peers. However, Black students do not graduate at the same rate as White students, with only 40% completing their degree within six years compared to 64% of White students completing their degree in the same timespan (National Center for Education Statistics, 2019). Black students continue to report PWI campuses as being hostile, toxic environments that can negatively impact their psychological well-being and learning experiences (Harvey, Harvey, & King, 2004; Beasley, Chapman-Hilliard, & McClain, 2016; Cabrera, Watson, & Franklin, 2016; Means & Pyne, 2017). Many PWIs have worked to implement diversity initiatives focused on supporting underrepresented minority populations, including Black students (Patton, Sanchez, Mac, & Stewart, 2019). However, many institutions fail to identify the specific, unique issues faced by Black students before implementing these programs (Brooks, Jones, & Burt, 2013), which has led to achieving minimal progress and change (Newkirk, 2019).Higher education institutions have increasingly implemented mentorship programs as the leading initiative to positively impact the experiences of Black students attending PWIs (Johnson, 2013). However, many mentorship programs do not consider the impact of racial matching when establishing the mentee-mentor pairings, which has been shown to influence personal and academic success metrics for Black students. The purpose of this study was to understand the experiences of Black students who are supported by a Black mentor while attending a predominantly White institution, including the impact made to the students’ mentorship experience when the mentor and mentee have the same racial identity. This research was conducted as a phenomenological study, collecting individual interviews from 12 participants. All participants are Black and are/were students at a 4-year PWI in the Midwest. They were all members of a learning community that paired them with a Black mentor to support them during their attendance at the institution. The findings of this study show that pairing a Black student with a Black mentor can yield a positive experience on the student’s experience at a PWI and can also positively impact personal and academic success metrics for the students
i Was Taught To Treat Everyone The Same : An Examination Of Color-Conscious Conversations In White Households And The Moderating Effects Of White Guilt
No full textWhite parent racial identity development and parent racial attitudes are influential on the ways in which White parents are discussing race with their children (Zucker & Patterson, 2018; Perry, Skinner, & Abaied, 2019; Pahlke, Patterson & Hughes, 2020). Furthermore, the development of positive healthy White identity, defined by Helms (1995) as movement through abandoning racism and defining a nonracist White identity, makes it more likely that parents will discuss the pervasiveness of racism with their children (Zucker & Patterson, 2018). Emotion-based factors, like White guilt, likely influence the ways in which White parents socialize their children and teach them to understand the impact of race and racism in society, but research has not directly illustrated this relationship ((Helms, 1995; Spanierman et al., 2012). Sample participants (N=70) included primary caregivers of children between the ages of 5 and 12. All participants identified themselves and their children as White. Using the adapted Parent Racial Socialization Measure (Pahlke et al., 2012; Pahlke et al. 2020; Hughes & Chen, 1997), participants in this sample were less likely to use ethnic-racial socialization messages related to Group difference, Racemute, and Preparation for Bias and were more likely to use messages related to Discrimination, History of Other Groups, and Egalitarianism. In accordance with White racial identity development theory (Helms, 1995), average participant scores fell within the last three statuses of White identity development (i.e., characterized by movement toward development of nonracist identity: Pseudo-Independence (34.81, SD=3.36), Immersion/Emersion (30.37, SD=5.71), and Autonomy (35.90, SD=3.96). All three moderation analyses, which used Immersion/Emersion racial identity as the predictor variable and White guilt as the moderator, were all found to be significant (i.e., Discrimination as dependent variable (β = -.266, p = .019); Egalitarianism as dependent variable (β = -.277, p = .016); History of Other Groups as dependent variable (β = -.310, p = .020). Specifically, there was a positive relationship between Discrimination and History of Other Groups racial socialization messages and White racial identity that becomes weaker as White guilt increases. Alternatively, there was a negative relationship between Egalitarian styles of messaging and White racial identity that becomes stronger as White guilt increases. Meaning, participants who identified in the Immersion/Emersion status, and therefore demonstrated willingness to confront one’s own biases and become more active in combating racism and oppression, might utilize strategies that align with color-conscious socialization. However, White guilt, and varying levels of White guilt, might also inhibit parents with this identity status from speaking with their children in color-conscious ways. The complexity of this finding is further discussed. Overall, this research adds to current literature by exploring the emotion-based mechanisms influencing White parent socialization strategies with their children