The traditional roles of the tumor suppressor protein, p53, in transcriptional regulation are mostly defined in cancer or stressed cells and are centered on control of the cell cycle, DNA repair or senescence. In this thesis, data is presented demonstrating that the p53-regulated transcriptome is highly context-dependent as illustrated using the developing kidney as a model system. To this end, we utilized whole genome transcriptome and ChIP-Seq (chromatin immunoprecipitation-high throughput sequencing) analyses in p53+/+ and p53-/- mice to identify p53 regulated pathways in the embryonic kidney. This integrated approach allowed identification of novel genes that are direct p53 targets in the developing nephron. This approach was further refined using RNA-Seq analysis of lineage-tagged FACS-isolated nephron progenitors. We find that the p53-regulated transcriptome in the embryonic kidney is mostly involved in development, morphogenesis, and metabolic pathways. Interestingly, traditional targets of p53, such as DNA repair, cell cycle and apoptosis, accounted for < 5% of differentially expressed genes. The majority of 7,893 p53-binding genomic regions contain consensus p53 binding sites. Unlike a cancer cell line in which 7% of p53 binding sites lie within proximal promoters, 78% of p53 peaks in the developing kidney overlies the promoter. Moreover, 25% of the differentially expressed p53-bound genes belong to nephron progenitors and nascent nephrons, including key transcriptional regulators, components of Fgf, Wnt, Bmp, and Notch pathways, and ciliogenesis genes. RNA-Seq of nephron progenitors from wild-type and mutant p53 mice demonstrated repression of the nephron stem cell marker, Cited1, but not Six2. Moreover, cytoskeleton, cell adhesion, and energy metabolism genes were downregulated in mutant progenitors consistent with the loosely organized cap mesenchyme and disrupted mesenchyme-to-epithelium transition of p53-/- progenitors. In conclusion, our studies demonstrate that p53 genomic occupancy and regulated transcriptome are distinctly different in development and cancer. p53 is a key regulator of transcriptional programs that maintain nephron niche integrity, nephron progenitor cell renewal and differentiation. / acase@tulane.edu

Thesis (Ed.D.)--Boston University / One goal of science education reform is student attainment of scientific literacy. Therefore, it is imperative for science educators to identify its salient elements. A dimension of scientific literacy that warrants careful consideration is scientific thinking and effective ways to foster scientific thinking among students. This study examined the use of mental models as evidence of scientific thinking in the context of two instructional approaches, transmissional and constructivist. Types of mental models, frequency of explanative information, and scores on problem solving transfer questions were measured and compared among subjects in each instructional context. METHODS: Subjects consisted of sophomore biology students enrolled in general biology courses at three public high schools. The Group Assessment of Logical Thinking instrument was used to identify two equivalent groups with anN of 65. Each group was taught the molecular basis of sickle cell anemia and the principles of hemoglobin gel electrophoresis using one of the two instructional approaches at their schools during five instructional periods over the course of one week. Laboratory equipment and materials were provided by Boston University School of Medicine's MobileLab program. Following the instructional periods, each subject was asked to think aloud while responding to four problem solving transfer questions. Each response was audiotaped and videotaped. The interviews were transcribed and coded to identify types of mental models and explanative information. Subjects' answers to the problem solving transfer questions were scored using a rubric. RESULTS: Students taught in a constructivist context tended to use more complete mental models than students taught in a transmissional context. Fifty two percent of constructivist subjects and forty four percent of transmissional subjects demonstrated evidence of relevant mental models. Overall fifty two percent of the subjects expressed naive mental models with respect to content. There was no significant difference in the frequency of explanative information expressed by either group. Both groups scored poorly on the problem solving transfer problems. The average score for the constructivist group was 30% and the average score for the transmissional group was 34%. A significant correlation was found between the frequency of explanative information and scores on the problem-solving transfer questions, r = 0.766. CONCLUSION: The subjects exhibited difficulty in formulating and applying mental models to effectively answer problem solving transfer questions regardless of the context in which the subjects were taught. The results call into question the extent to which students have been taught to use mental models and more generally, the extent to which their prior academic experience has encouraged them to develop an awareness of scientific thinking skills. Implications of the study suggest further consideration of mental modeling in science education reform and the deliberate integration of an awareness of scientific thinking skills in the development of science curricula.

INTRODUCTION: Healthcare practices are rapidly evolving, shifting to multidisciplinary initiatives, and prompting a reevaluation of the current structure in the preparation of medical students. The response of medical schools is to adopt newly modeled curricula that use a flipped classroom structure to implement an integrated curriculum encouraging the practice of multidisciplinary inquiry within the basic sciences to develop physicians capable of thoughtful clinical reasoning skills. This pedagogical shift in medical education and the prevailing reaction of medical schools to fundamentally reform curriculum has lead to the emergence of a demand for innovative educational technology capable of effective distribution of pre-class material. OBJECTIVE: Assess student experience of SoftChalk online biochemistry modules as a pre-class learning tool to determine effectiveness in fostering student learning and engagement. In evaluating perceptions on improvement, future modules can be knowledgeably revised to maximize educational gains and elucidate effective/ineffective implementation practices. Data was stratified by previous biochemistry experience to determine if students who have taken the same traditionally instructed graduate biochemistry course (BI751) would have differing thematic opinions of the flipped model’s pre-learning environment. METHODS: Participants were Boston University’s first year medical school students (n=165) class of 2019’ in an integrated curriculum containing basic science modules. After completion of the modules a mixed-methods anonymous survey with a thematic approach to assess experience and improvement of SoftChalk biochemistry modules were emailed, with reminders. The survey contained demographic data, qualitative free response questions, and likert scale assessment questions with no incentive for completion. The data was analyzed independently by researchers to assess common themes and stratified by previous biochemistry experience. RESULTS: Three main themes emerged in assessment of data: SoftChalk as a quality learning tool, lack of integration/consistency, and formatting concerns with an overall positive perception of the pre-learning tool. Respondents commented on quality of SoftChalk as a pre-learning tool; the majority deeming it helpful, interactive, and having beneficial activities. Integration and consistency concerns surfaced in both experience, with commentary on pre-class modules being too dense, and improvement by consolidating information into one resource. The major formatting concern was the ability to maintain module value in paper form. Themes were furthered by the quantitative data with students perceiving SoftChalk as effective, providing a foundation for material in-class, and questions having the correct difficulty. When data was stratified BI751 disagreed that SoftChalk helped students stay on track with course material despite the class on average agreeing. CONCLUSIONS: While SoftChalk is an effective pre-class learning tool, the challenge is in reversing students’ perceptions that basic material should be instructed and that a comprehensive syllabus is necessary. Future SoftChalk modules can enhance success if pre-class modules are condensed, have a stronger transition from pre-class information to in-class activities and maintain consistency among instructor expectations.

In order to provide an improved in vitro model with which to investigate human diseases, such as cancer that may be promoted by toxicant exposure, we have characterized a newly developed cell line derived from the renal proximal tubule epithelial cells (RPTEC) of a healthy human male donor. The RPTEC/TERT1 cell line has been immortalized using the human telomerase reverse transcriptase (hTERT) catalytic subunit and does not exhibit chromosomal abnormalities (Evercyte Laboratories). We have conducted single-compound and binary mixture experiments with the common environmental carcinogens, cadmium (Cd) and benzo[a]pyrene (B[a]P). Cells exhibited cytotoxicity to concentrations of B[a]P and Cd as low as 1 nM and 3 μM, respectively. We examined a panel of eight genes relevant to the toxic responses of these two agents. RPTEC/TERT1 cells exhibit compound-specific gene expression responses to concentrations as low as 1 nM B[a]P and 1 μM Cd. A significant increase in the expression of genes coding for B[a]P metabolizing enzymes (CYP1A1, CYP1B1) occurred in a dose- and time-dependent manner. Activity of these enzymes was verified using the EROD activity assay. Gene expression changes after co-exposure were consistent with changes in gene expression seen after single-compound exposures. We detected BPDE-DNA adducts after exposure to B[a]P which confirms that the RPTEC/TERT1 cell line responds to B[a]P consistently with what is known regarding these cells in a normal, healthy kidney. Under co-exposure, adducts detected were significantly decreased in some groups. A significant increase in the expression of NRF2 antioxidant pathway genes after co-exposure was observed. Additionally, total glutathione levels were significantly increased in cells exposed to Cd alone and co-exposure groups. These results suggest that Cd may antagonize the formation of BPDE-DNA adducts in RPTEC/TERT1 cells under these conditions. Future studies will test mutagenesis under conditions of co-exposure to Cd and B[a]P. Our studies are the first to provide information regarding toxicological responses in this novel cell line that model those of the target tissue. We conclude that these cells can provide a useful tool for future toxicological studies. These studies will help scientists better understand the initiating events that may promote carcinogenesis in normal, healthy human cells. / acase@tulane.edu

Burkholderia pseudomallei (Bp) is a major public health concern in the endemic regions of southeast Asia and northern Australia, yet the organism has a worldwide distribution and cases are likely under-reported. In northeast Thailand the mortality rate associated with Bp infection is over 40%. The inherent resistance of Bp to multiple antibiotics impairs treatment, and relapse is seen in more than 25% of survivors. Beyond its public health significance, Bp is considered a potential biological warfare agent by the U.S. DHHS and was recently listed as a Tier 1 select agent. Despite enhanced research and vaccine efforts, traditional vaccine strategies employing attenuated bacterial strains, recombinant proteins, or purified polysaccharides have failed to elicit complete protection against aerosol challenge with Bp. We have previously shown that immunization with outer membrane vesicles (OMVs) derived from Bp can protect mice from lethal melioidosis. In this work we characterize the interactions of OMVs with antigen presenting cells in order to elucidate innate immune responses to the OMV vaccine. Vaccine-mediated antibody responses and protective efficacy were characterized in BALB/c mice. We also tested the safety and immunogenicity of the OMV vaccine in non-human primates (NHP). We show that Bp OMVs interact with dendritic cells and macrophages and are internalized by these antigen presenting cells (APCs).Internalization is dependent on actin polymerization and cholesterol present in APC membranes. OMVs also upregulate MHC class I and II on APCs, as well as promote the production of pro-inflammatory cytokines in a TLR2/4 dependent manner. Immunization of mice with Bp OMVs by the s.c. and i.m. routes induced the production of OMV-specific IgM and IgG and significantly protected mice against aerosol challenge. Addition of alum and MPL did not significantly change the antibody profiles of immunized mice and did not significantly enhance vaccine mediated protection. OMVs were well tolerated in a large animal NHP model. There were no adverse clinical reactions, and NHPs mounted significantly increased levels of OMV-specific IgG and OMV specific CD4+ T cell responses. These results suggest that Bp OMVs can stimulate innate and adaptive immune responses and may represent a safe and efficacious vaccine against melioidosis / acase@tulane.edu

Mycobacterium tuberculosis (Mtb) is the causative agent of the disease tuberculosis (TB). While approximately one third of the world’s population is infected with this pathogen, only a small minority of these individuals has active TB infection, where these individuals are able to transmit the pathogen to others. In previous microarrays performed in our lab from lung tissue of non-human primates (NHPs), it was noted that animals undergoing the activation of TB showed greatly increased expression of lymphocyte activation gene 3 (LAG-3). This protein performs immunomodulatory roles, which include: increased function of regulatory T cells, decreased function of Th1 effector T cells, and decreased monocyte differentiation. When studied in rhesus macaques infected with Mtb, RNA expression and protein levels of LAG-3 in lung tissue of active TB animals was found to be greatly increased when compared to lung from animals with latent TB. Interestingly enough, there was a bimodal distribution of LAG-3 expression in animals undergoing reactivation of the disease; the animals with greater levels of LAG-3 were the fast reactivators. LAG-3 expression in the lung tissue of animals with Mtb infections was mainly isolated to the outer periphery of the Mtb induced lung granuloma, where predictably, LAG-3 was expressed by lymphocyte populations of immune cells; mainly NK cells and various populations of T cells. To gain a greater understanding of the function of LAG-3, we created a co-culture system where CD4 T cells derived from blood and lung of Mtb infected NHPs were supplemented to Mtb infected differentiated monocytes. With this co-culture model, we utilized short interfering RNA (siRNA) to silence LAG-3. We observed a decreased bacterial burden, as well as decreased frequencies of IL-10 and IFN-γ producing CD4 T cells. This illustrates that the silencing of LAG-3 in CD4 T cells resulted in increased bacterial clearance, not due to up-regulation of IFN-γ. We believe that the bacterial reduction may be due to increased T cell proliferation, along with production of another proinflammatory cytokines. In the near future, we will utilize cytokine assays and microarrays to better understand the mechanism of action through which increased bacterial killing is occurring. / acase@tulane.edu

Acid-base disturbances have serious clinical consequences and are particularly critical in patients whose cardiopulmonary function is compromised. Cellular transport of NH3 and NH4+ has important physiological significance in the regulation of acid-base balance. In the kidney, production and excretion of NH3/NH4+ is critical for net acid excretion. Recently, two non-erythroid glycoproteins (Rhbg and Rhcg) belonging to the Rh family were suggested to be involved in NH3/NH4+ transport. Thus far, the functional properties of these membrane proteins as transport mechanisms are not resolved. In this study, we expressed Rh proteins in Xenopus oocytes and demonstrated that they transport both NH4+ and NH3. As such, the Rh transporters are unique in being able to transport both the ionic and the neutral gaseous components of ammonia. Previous studies have shown that DIDS, a stilbene derivative known to inhibit anion exchangers, was shown to inhibit CO2 transport by AQP1. This led us to hypothesize that DIDS might also inhibit transport of other gases such as NH3 by Rh proteins. We therefore conducted the present study to test the effects of DIDS on NH4+ and NH3 transport by Rh glycoproteins. To do so we used ion-selective microelectrodes and two-electrode voltage clamp to measure changes in surface pH (pHs) and whole cell currents (I) induced by NH3/NH4+ and methyl ammonium (MA/MA+) with or without DIDS. All experiments were conducted in Xenopus oocytes expressing Rhbg. Rhbg was expressed by injecting the oocytes with cRNA of the cloned genes. Control oocytes were injected with H2O. Our results indicate that in oocytes expressing Rhbg, exposure to 5mM NH4Cl (NH3/NH4+) caused a decrease in surface pH (pHs) and an inward current. The decrease in pHs is caused by NH3 influx whereas the inward current is due to electrogenic NH4+ influx. In the presence of DIDS, exposure to 5mM NH4Cl caused a significantly smaller decrease in pHs and current. The %inhibition of pHs and ΔI were 33% and 49%, respectively (P<0.05). Similarly, exposing oocytes expressing Rhbg to 5mM MA/MA+ (a substitute to NH3/NH4+) caused a decrease in pHs and an inward current. In the presence of DIDS, the MA/MA+ induced changes in pHs and current were also inhibited (37% and 63%, respectively; P<0.05). DIDS had no effect on NH3/NH4+ transport in H2O-injected oocytes (not expressing Rhbg). In summary, our data support the following conclusions: 1) RhAG and Rhbg transport both the ionic NH4+ and the neutral NH3 species. 2) Transport of NH4+ is electrogenic. 3) RhAG and Rhbg expression both enhance MA transport, an electroneutral component. 4) Like Rhbg, RhAG also transports MA+, an electrogenic component. The charged MA+ seems to be a direct substrate for RhAG whose transport likely resembles that of NH4 +. 5) Rhcg is likely to be a predominantly NH3 transporter. 6) RhAG and Rhbg are unlikely to be NH4 +/H+ exchangers. Regarding the effect of DIDS, our data also indicate that 1) DIDS partially inhibits the transport of NH3 and MA by Rhbg without affecting endogenous NH3 and MA transport. 2) DIDS also inhibits the electrogenic transport of NH4 + and MA+ by Rhbg. 3) DIDS is the only inhibitor shown to block both gas (NH3) and ionic (NH4 +) transport by Rhbg. / acase@tulane.edu

Rupture of atherosclerotic plaque can cause acute life-threatening events such as myocardial infarction and ischemic stroke; therefore, there is much interest in developing therapies aimed at increasing plaque stability. More stable lesions are characterized as having high collagen content and containing a large number of vascular smooth muscle cells (SMCs) of contractile/differentiated phenotype. In our previous studies using an apolipoprotein E-deficient (Apoe-/-) mouse model of atherosclerosis, we found that insulin-like growth factor-1 (IGF-1)-infusion not only reduced total plaque burden, but also increased collagen expression and the number of alpha-smooth muscle actin (αSMA)-positive cells in plaque. In this study, we identify cellular mechanisms responsible for these observations. We found that in human aortic smooth muscle cells (HASMCs) grown in culture, IGF-1 post-transcriptionally upregulated expression of the procollagen type I alpha-1 subunit (pro-α1(I)) as well as contractile proteins, αSMA and smooth muscle 22-alpha (SM22α), via a PI3K-dependent but Erk1/2- and mTOR-independent signaling mechanism. Furthermore, experiments using an inhibitor of collagen synthesis or a blocking antibody against the alpha2beta1-integrin (α2β1) suggested that interaction with collagen type I promotes HASMC contractile phenotype. To elucidate mechanisms underlying IGF-1 upregulation of collagen synthesis we investigated the effect of IGF-1 on the mRNA-binding protein, la ribonucleoprotein domain family member 6 (LARP6), which had been shown to bind a conserved stem-loop secondary motif in the 5’UTR of COL1a1 and COL1a2 mRNA. IGF-1 rapidly increased LARP6 expression in HASMCs leading to increased COL1a1 and COL1a2 mRNA bound LARP6 and increased synthesis of collagen type I. Mutation of the 5’stem-loop of Col1a1 mRNA (that inhibited binding by LARP6) or overexpression of a 5’stem-loop RNA molecular decoy (that sequesters LARP6) both prevented the ability of IGF-1 to increase pro-α1(I) synthesis as well as mature α1(I) expression in cultured medium. Furthermore, IGF-1-infusion in Apoe-/- mice increased LARP6 and pro-α1(I) expression in aortic lysates, and SMC-specific IGF-1-overexpression in transgenic mice robustly increased collagen fibrillogenesis in atherosclerotic plaque. In conclusion, this work identifies LARP6 as a critical mediator by which IGF-1 augments synthesis of collagen type I in vascular smooth muscle, and uncovers key mechanisms whereby IGF-1 promotes atherosclerotic plaque stability. / acase@tulane.edu

Lyme disease is the most commonly reported vector-borne disease in the United States. The causative agent of Lyme disease, can alter gene expression to enable survival in a diverse set of conditions, including the tick midgut and the mammalian host. External environmental changes can trigger gene expression in B. burgdorferi, and the data demonstrate that B. burgdorferi can similarly alter gene expression as a stress-response when it is treated with the antibiotic doxycycine. After treatment with the minimum bactericidal concentration (MBC) of doxycycline, a subpopulation can alter its phenotype to survive antibiotic treatment, and to host adapt and successfully infect a mammalian host. Furthermore, our data demonstrate that if a population is treated with the MBC of doxycycline, a subpopulation may alter its phenotype to adopt a state of dormancy until the removal of the antibiotic, whereupon the subpopulation can regrow. We demonstrate that the chance of regrowth occurring increases as a population reaches stationary phase, and present a mathematical model for predicting the probability of a persister subpopulation within a larger population, and ascertain the quantity of a persister subpopulation. To determine which genes are expressed as stress-response genes, RNA Sequencing analysis, or RNASeq, was performed on treated, untreated, and treated and regrown B. burgdorferi samples. The results suggest several genes were significantly different in the treated group, compared to the untreated group, and in the untreated and regrown group compared to the untreated group, including a 50S ribosomal stress-response protein, coded from BB_0786. The appendices discuss the theory and methods that were used in RNA Sequencing (RNASeq) analysis, and provide an overview of the database that was created for the B. burgdorferi transcriptome. Additional studies may demonstrate further how persister subpopulations form, and which genes can trigger a persister state in B. burgdorferi. / acase@tulane.edu

Regulatory T cells (Tregs) suppress effector immune responses and have been implicated in promoting chronic viral infections. Their role during influenza infection and vaccination, however, is still unclear. Influenza is a major public health concern, claiming over 49,000 lives annually in the U.S. alone. Vaccination is the best approach for preventing disease but frequent mutations of immunogenic epitopes requires a new vaccine to be formulated and administered annually. This poses a challenge for vaccine manufacturing and may strain patient compliance. A universal influenza vaccine, which targets the highly conserved extracellular domain of the influenza matrix protein 2 (M2e), may circumvent this problem by generating cross-protective immunity. In this study, we tested the efficacy of the M2e universal vaccine in the ferret, and determined whether vaccination induces a Treg response after influenza infection. We found that vaccination promotes the development of M2e specific IgM and IgG antibodies after boosting. Upon challenge with A/Memphis H1N1, vaccinated ferrets exhibited a lower body temperature and reduced virus titer compared to non-vaccinated animals. Together these findings suggest that the M2e vaccine protects ferrets against influenza infection. In order to determine whether Tregs increase after vaccination in ferrets, we had to first clone and characterize genes involved with Treg phenotype and function including CD25, Foxp3, and IL-10. The reciprocal nature between Tregs and Th17 cells and their involvement during influenza infection prompted us to also clone ferret IL-17F. Using these sequences, we designed a qRT-PCR array to measure the expression of Foxp3, IL-10, and IL-17F in ferret tissue. We also identified cross-reactive antibodies against ferret CD8, CD25, and Foxp3 for use in FACS, western blot, and ICC. Using these tools, we found that vaccination significantly increased the expression of Foxp3 in the spleen. An increased percentage of Foxp3+ lymphocytes was detected in both the PBMCs and splenocytes of immunized animals. In contrast, IL-10 and IL-17F expression decreased significantly in both immunized and non-immunized ferrets compared with naïve animals. These studies suggest that the M2e influenza vaccine induces a regulatory T cell response in ferrets and protects against influenza infection. / acase@tulane.edu