Gene regulation during placenta development: Murine adenosine deaminase as a model to study placenta specific expression

The formation of the placenta is one of the first and most important developmental events that occur in early mammalian embryogenesis. Even given this importance of the placenta, the academic community has largely ignored studying gene regulation during the development and maturation of the placenta. For this reason, an in-depth study of gene regulation in the trophoblast layer of the placenta using murine Adenosine Deaminase (Ada) as a model system has been undertaken. It has been determined that Ada is highly expressed in the placenta and is critical for embryo development. Dr. Kellems' laboratory has previously described a 1.8 kb fragment of the Ada 5 ′ flanking region that is capable of directing trophoblast specific expression in a transgenic model system. Preliminary studies have demonstrated several critical portions of this fragment that are necessary for the correct tissue specific expression in the placenta. My first specific aim was to elucidate the trans factor binding to one of these sequences, the FP3. Through electromobility shift assays (EMSA), the 30 bp FP3 was narrowed to a 5 bp sequence which computer databases predicted bound to Acute Myeloid Leukemia 1 (AML-1). This was confirmed by supershift analysis. The functional importance of this binding was demonstrated by a transgenic approach. A significant difference in expression of the reporter in the placenta was seen when the 5 bp sequence was mutated. This finding is a novel use for the AML-1 transcription factor which is the DNA binding portion of the heterodimer Core Binding Protein (CBP). The 5′ 240 bp region has also been demonstrated to contain functionally significant sequence. Through EMSA assays and computer predictions, the area has been narrowed to two pertinent regions that are predicted to contain GATA binding motifs. ^

DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS

Next-generation sequencing (NGS) technology has become a prominent tool in biological and biomedical research. However, NGS data analysis, such as de novo assembly, mapping and variants detection is far from maturity, and the high sequencing error-rate is one of the major problems. . To minimize the impact of sequencing errors, we developed a highly robust and efficient method, MTM, to correct the errors in NGS reads. We demonstrated the effectiveness of MTM on both single-cell data with highly non-uniform coverage and normal data with uniformly high coverage, reflecting that MTM’s performance does not rely on the coverage of the sequencing reads. MTM was also compared with Hammer and Quake, the best methods for correcting non-uniform and uniform data respectively. For non-uniform data, MTM outperformed both Hammer and Quake. For uniform data, MTM showed better performance than Quake and comparable results to Hammer. By making better error correction with MTM, the quality of downstream analysis, such as mapping and SNP detection, was improved. SNP calling is a major application of NGS technologies. However, the existence of sequencing errors complicates this process, especially for the low coverage (

MECHANISM-BASED STRATEGIES TO ENHANCE THE ACTIONS OF A

Heat shock protein 90 (HSP90) is an abundant molecular chaperone that regulates the functional stability of client oncoproteins, such as STAT3, Raf-1 and Akt, which play a role in the survival of malignant cells. The chaperone function of HSP90 is driven by the binding and hydrolysis of ATP. The geldanamycin analog, 17-AAG, binds to the ATP pocket of HSP90 leading to the degradation of client proteins. However, treatment with 17-AAG results in the elevation of the levels of antiapoptotic proteins HSP70 and HSP27, which may lead to cell death resistance. The increase in HSP70 and HSP27 protein levels is due to the activation of the transcription factor HSF-1 binding to the promoter region of HSP70 and HSP27 genes. HSF-1 binding subsequently promotes HSP70 and HSP27 gene expression. Based on this, I hypothesized that inhibition of transcription/translation of HSP or client proteins would enhance 17-AAG-mediated cytotoxicity. Multiple myeloma (MM) cell lines MM.1S, RPMI-8226, and U266 were used as a model. To test this hypothesis, two different strategies were used. For the first approach, a transcription inhibitor was combined with 17-AAG. The established transcription inhibitor Actinomycin D (Act D), used in the clinic, intercalates into DNA and blocks RNA elongation. Stress inducible (HSP90á, HSP70 and HSP27) and constitutive (HSP90â and HSC70) mRNA and protein levels were measured using real time RT-PCR and immunoblot assays. Treatment with 0.5 µM 17-AAG for 8 hours resulted in the induction of all HSP transcript and protein levels in the MM cell lines. This induction of HSP mRNA levels was diminished by 0.05 µg/mL Act D for 12 hours in the combination treatment, except for HSP70. At the protein level, Act D abrogated the 17-AAG-mediated induction of all HSP expression levels, including HSP70. Cytotoxic evaluation (Annexin V/7-AAD assay) of Act D in combination with 17-AAG suggested additive or more than additive interactions. For the second strategy, an agent that affected bioenergy production in addition to targeting transcription and translation was used. Since ATP is necessary for the proper folding and maturation of client proteins by HSP90, ATP depletion should lead to a decrease in client protein levels. The transcription and translation inhibitor 8-Chloro-Adenosine (8-Cl-Ado), currently in clinical trials, is metabolized into its cytotoxic form 8-Cl-ATP causing a parallel decrease of the cellular ATP pool. Treatment with 0.5 µM 17-AAG for 8 hours resulted in the induction of all HSP transcript and protein levels in the three MM cell lines evaluated. In the combination treatment, 10 µM 8-Cl-Ado for 20 hours did not abrogate the induction of HSP mRNA or protein levels. Since cellular bioenergy is necessary for the stabilization of oncoproteins by HSP90, immunoblot assays analyzing for expression levels of client proteins such as STAT3, Raf-1, and Akt were performed. Immunoblot assays detecting for the phosphorylation status of the translation repressor 4E-BP1, whose activity is modulated by upstream kinases sensitive to changes in ATP levels, were also performed. The hypophosphorylated state of 4E-BP1 leads to translation repression. Data indicated that treatment with 17-AAG alone resulted in a minor (<10%) change in STAT3, Raf-1, and Akt protein levels, while no change was observed for 4E-BP1. The combination treatment resulted in more than 50% decrease of the client protein levels and hypophosphorylation of 4E-BP1 in all MM cell lines. Treatment with 8-Cl-Ado alone resulted in less than 30% decrease in client protein levels as well as a decrease in 4E-BP1 phosphorylation. Cytotoxic evaluation of 8-Cl-Ado in combination with 17-AAG resulted in more than additive cytotoxicity when drugs were combined in a sequential manner. In summary, these data suggest that the mechanism-based combination of agents that target transcription, translation, or decrease cellular bioenergy with 17-AAG results in increase cytotoxicity when compared to the single agents. Such combination strategies may be applied in the clinic since these drugs are established chemotherapeutic agents or currently in clinical trials.

Factors influencing participation in individuals with disability: A secondary data analysis

Individuals with disabilities face numerous barriers to participation due to biological and physical characteristics of the disability as well as social and environmental factors. Participation can be impacted on all levels from societal, to activities of daily living, exercise, education, and interpersonal relationships. This study evaluated the impact of pain, mood, depression, quality of life and fatigue on participation for individuals with mobility impairments. This cross sectional study derives from self-report data collected from a wheelchair using sample. Bivariate correlational and multivariate analysis were employed to examine the relationship between pain, quality of life, positive and negative mood, fatigue, and depression with participation while controlling for relevant socio-demographic variables (sex, age, time with disability, race, and education). Results from the 122 respondents with mobility impairments demonstrated that after controlling for socio-demographic characteristics in the full model, 20% of the variance in participation scores were accounted for by pain, quality of life, positive and negative mood, and depression. Notably, quality of life emerged as being the single variable that was significantly related to participation in the full model. Contrary to other studies, pain did not appear to significantly impact participation outcomes for wheelchair users in this sample. Participation is an emerging area of interest among rehabilitation and disability researchers, and results of this study provide compelling evidence that several psychosocial factors are related to participation. This area of inquiry warrants further study, as many of the psychosocial variables identified in this study (mood, depression, quality of life) may be amenable to intervention, which may also positively influence participation.^

Physician adoption of a practice guideline: Effect on the cost of medical care for adult patients with diabetes

In the demanding environment of healthcare reform, reduction of unwanted physician practice variation is promoted, often through evidence-based guidelines. Guidelines represent innovations that direct change(s) in physician practice; however, compliance has been disappointing. Numerous studies have analyzed guideline development and dissemination, while few have evaluated the consequences of guideline adoption. The primary purpose of this study was to explore and analyze the relationship between physician adoption of the glycated hemoglobin test guideline for management of adult patients with diabetes, and the cost of medical care. The study also examined six personal and organizational characteristics of physicians and their association with innovativeness, or adoption of the guideline. ^ Cost was represented by approved charges from a managed care claims database. Total cost, and diabetes and related complications cost, first were compared for all patients of adopter physicians with those of non-adopter physicians. Then, data were analyzed controlling for disease severity based on insulin dependency, and for high cost cases. There was no statistically significant difference in any of eight cost categories analyzed. This study represented a twelve-month period, and did not reflect cost associated with future complications known to result from inadequate management of glycemia. Guideline compliance did not increase annual cost, which, combined with the future benefit of glycemic control, lends support to the cost effectiveness of the guideline in the long term. Physician adoption of the guideline was recommended to reduce the future personal and economic burden of this chronic disease. ^ Only half of physicians studied had adopted the glycated hemoglobin test guideline for at least 75% of their diabetic patients. No statistically significant relationship was found between any physician characteristic and guideline adoption. Instead, it was likely that the innovation-decision process and guideline dissemination methods were most influential. ^ A multidisciplinary, multi-faceted approach, including interventions for each stage of the innovation-decision process, was proposed to diffuse practice guidelines more effectively. Further, it was recommended that Organized Delivery Systems expand existing administrative databases to include clinical information, decision support systems, and reminder mechanisms, to promote and support physician compliance with this and other evidence-based guidelines. ^

Exploring a model of skillful engagement in nursing practice

Prominent challenges facing nurse leaders are the growing shortage of nurses and the increasingly complex care required by acutely ill patients. In organizations that shortage is exacerbated by turnover and intent to leave. Unsatisfactory working conditions are cited by nurses when they leave their current jobs. Disengagement from the job leads to plateaued performance, decreased organizational commitment, and increased turnover. Solutions to these challenges include methods both to retain and to increase the effectiveness of each nurse. ^ The specific aim of this study was to examine the relationships among organizational structures thought to foster the clinical development of the nurse, with indicators of the development of clinical expertise, resulting in outcomes of positive job attitudes and effectiveness. Causal loop modeling is incorporated as a systems tool to examine developmental cycles both for an organization and for an individual nurse to look beyond singular events and investigate deeper patterns that emerge over time. ^ The setting is an academic specialty-care institution, and the sample in this cross-sectional study consists of paired data from 225 RNs and their nurse managers. Two panels of survey instruments were created based on the model's theoretical variables, one completed by RNs and the other by their Nurse Managers. The RN survey panel examined the variables of structural empowerment, magnet essentials, knowledge as identified by the Benner developmental stage, psychological empowerment, job stage, engagement, intent to leave, job satisfaction and the early recognition of patient complications. The nurse manager survey panel examined the Benner developmental stage, job stage, and overall level of nursing performance. ^ Four regression models were created based on the outcome variables. Each model identified significant organizational and individual characteristics that predicted higher job satisfaction, decreased intent to leave, more effectiveness as measured by early recognition and acting upon subtle patient complications, and better job performance. ^ Implications for improving job attitudes and effectiveness focus on ways that nursing leaders can foster a more empowering and healthy work environment. ^

A practice-based culminating experience: Writing a HRSA grant application with Texas Organ Sharing Alliance for public education efforts to increase solid organ donation

In November 2010, nearly 110,000 people in the United States were waiting for organs for transplantation. Despite the fact that the organ donor registration rate has doubled in the last year, Texas has the lowest registration rate in the nation. Due to the need for improved registration rates in Texas, this practice-based culminating experience was to write an application for federal funding for the central Texas organ procurement organization, Texas Organ Sharing Alliance. The culminating experience has two levels of significance for public health – (1) to engage in an activity to promote organ donation registration, and (2) to provide professional experience in grant writing. ^ The process began with a literature review. The review was to identify successful intervention activities in motivating organ donation registration that could be used in intervention design for the grant application. Conclusions derived from the literature review included (1) the need to specifically encourage family discussions, (2) religious and community leaders can be leveraged to facilitate organ donation conversations in families, (3) communication content must be culturally sensitive and (4) ethnic disparities in transplantation must be acknowledged and discussed.^ Post the literature review; the experience followed a five step process of developing the grant application. The steps included securing permission to proceed, assembling a project team, creation of a project plan and timeline, writing each element of the grant application including the design of proposed intervention activities, and completion of the federal grant application. ^ After the grant application was written, an evaluation of the grant writing process was conducted. Opportunities for improvement were identified. The first opportunity was the need for better timeline management to allow for review of the application by an independent party, iterative development of the budget proposal, and development of collaborative partnerships. Another improvement opportunity was the management of conflict regarding the design of the intervention that stemmed from marketing versus evidence-based approaches. The most important improvement opportunity was the need to develop a more exhaustive evaluation plan.^ Eight supplementary files are attached to appendices: Feasibility Discussion in Appendix 1, Grant Guidance and Workshop Notes in Appendix 2, Presentation to Texas Organ Sharing Alliance in Appendix 3, Team Recruitment Presentation in Appendix 5, Grant Project Narrative in Appendix 7, Federal Application Form in Appendix 8, and Budget Workbook with Budget Narrative in Appendix 9.^