Variables affecting the stability of multiple cloning sites and hairpin structures in retroviral vectors

Retroviruses are RNA viruses that replicate through a double-stranded DNA intermediate. The viral enzyme reverse transcriptase copies the retroviral genomic RNA into this DNA intermediate through the process of reverse transcription. Many variables can affect the fidelity of reverse transcriptase during reverse transcription, including specific sequences within the retroviral genome. ^ Previous studies have observed that multiple cloning sites (MCS) and sequences predicted to form stable hairpin structures are hotspots for deletion during retroviral replication. The studies described in this dissertation were performed to elucidate the variables that affect the stability of MCS and hairpin structures in retroviral vectors. Two series of retroviral vectors were constructed and characterized in these studies. ^ Spleen necrosis virus-based vectors were constructed containing separate MCS insertions of varying length, orientation, and symmetry. The only MCS that was a hotspot for deletion formed a stable hairpin structure. Upon more detailed study, the MCS previously reported as a hotspot for deletion was found to contain a tandem linker insertion that formed a hairpin structure. Murine leukemia virus-based vectors were constructed containing separate sequence insertions of either inverted repeat symmetry (122IR) that could form a hairpin structure, or little symmetry (122c) that would form a less stable structure. These insertions were made into either the neomycin resistance marker ( neo) or the hygromycin resistance marker (hyg) of the vector. 122c was stable in both neo and hyg, while 122IR was preferentially deleted in neo and was remarkably unstable in hyg. ^ These results suggest that MCS are hotspots for deletion in retroviral vectors if they can form hairpin structures, and that hairpin structures can be highly unstable at certain locations in retroviral vectors. This information may contribute to improved design of retroviral vectors for such uses as human gene therapy, and will contribute to a greater understanding of the basic science of retroviral reverse transcription. ^

Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation.

MicroRNAs (miRNAs) inhibit mRNA expression in general by base pairing to the 3'UTR of target mRNAs and consequently inhibiting translation and/or initiating poly(A) tail deadenylation and mRNA destabilization. Here we examine the mechanism and kinetics of miRNA-mediated deadenylation in mouse Krebs-2 ascites extract. We demonstrate that miRNA-mediated mRNA deadenylation occurs subsequent to initial translational inhibition, indicating a two-step mechanism of miRNA action, which serves to consolidate repression. We show that a let-7 miRNA-loaded RNA-induced silencing complex (miRISC) interacts with the poly(A)-binding protein (PABP) and the CAF1 and CCR4 deadenylases. In addition, we demonstrate that miRNA-mediated deadenylation is dependent upon CAF1 activity and PABP, which serves as a bona fide miRNA coactivator. Importantly, we present evidence that GW182, a core component of the miRISC, directly interacts with PABP via its C-terminal region and that this interaction is required for miRNA-mediated deadenylation.

How Family Stability Affects Children

The following commentary serves as a response to the article, “Family Stability and Childhood Behavioral Outcomes: A Critical Review of the Literature.” The review article provides a good overview into family factors affecting children, but falls short in discussing how modifying family factors could change specific child behavioral outcomes. The next step in this field of research is a unified definition of family stability, a standardized measure of family stability, and discussion of how child behavior affects family stability, and how changes in family stability could affect child behavior.

An empirical examination of relative profitability in the nursing facility industry between ownership form and regionality in the state of Texas

The purpose of this research is to examine the relative profitability of the firm within the nursing facility industry in Texas. An examination is made of the variables expected to affect profitability and of importance to the design and implementation of regulatory policy. To facilitate this inquiry, specific questions addressed are: (1) Do differences in ownership form affect profitability (defined as operating income before fixed costs)? (2) What impact does regional location have on profitability? (3) Do patient case-mix and access to care by Medicaid patients differ between proprietary and non-profit firms and facilities located in urban versus rural regions, and what association exists between these variables and profitability? (4) Are economies of scale present in the nursing home industry? (5) Do nursing facilities operate in a competitive output market characterized by the inability of a single firm to exhibit influence over market price?^ Prior studies have principally employed a cost function to assess efficiency differences between classifications of nursing facilities. The inherent weakness in this approach is that it only considers technical efficiency. Not both technical and price efficiency which are the two components of overall economic efficiency. One firm is more technically efficient compared to another if it is able to produce a given quantity of output at the least possible costs. Price efficiency means that scarce resources are being directed towards their most valued use. Assuming similar prices in both input and output markets, differences in overall economic efficiency between firm classes are assessed through profitability, hence a profit function.^ Using the framework of the profit function, data from 1990 Medicaid Costs Reports for Texas, and the analytic technique of Ordinary Least Squares Regression, the findings of the study indicated (1) similar profitability between nursing facilities organized as for-profit versus non-profit and located in urban versus rural regions, (2) an inverse association between both payor-mix and patient case-mix with profitability, (3) strong evidence for the presence of scale economies, and (4) existence of a competitive market structure. The paper concludes with implications regarding reimbursement methodology and construction moratorium policies in Texas. ^

Predictors of weight stability in women and men: The aerobic center longitudinal study, 1987--1995

It is estimated that more than half the U.S. adult population is overweight or obese as classified by a body mass index of 25.0–29.9 or ≥30 kg/m 2, respectively. Since the current treatment approaches for long-term maintenance of weight loss are lacking, the National Institutes of Health state that an effective approach may be to focus on weight gain prevention. There is a limited body of literature describing how adults maintain a stable weight as they age. It is hypothesized that weight stability is the result of a balance between energy consumption and energy expenditure as influenced by diet, lifestyle, behavior, genetics and environment. The purpose of this research was to examine the dietary intake and behaviors, lifestyle habits, and risk factors for weight change that predict weight stability in a cohort of 2101 men and 389 women aged 20 to 8 7 years in the Aerobic Center Longitudinal Study regardless of body weight at baseline. At baseline, participants completed a maximal exercise treadmill test to determine cardiorespiratory fitness, a medical history questionnaire, which included self-reported measures of weight, dietary behaviors, lifestyle habits, and risk factors for weight change, a three-day diet record, and a mail-back version of the medical history questionnaire in 1990 or 1995. All analyses were performed separately for men and women. Results from multivariate regression analyses indicated that the strongest predictor of follow-up weight for men and women was previous weight, accounting for 87.0% and 81.9% of the variance, respectively. Age, length of follow-up and eating habits were also significant predictors of follow-up weight in men, though these variables only explained 3% of the variance. For women, length of follow-up and currently being on a diet were significantly associated with follow-up weight but these variables explained only an additional 2% of the variance. Understanding the factors that influence weight change has tremendous public health importance for developing effective methods to prevent weight gain. Since current weight was the strongest predictor of previous weight, preventing initial weight gain by maintaining a stable weight may be the most effective method to combat the increasing prevalence of overweight and obesity. ^

Intervening to reach adolescents and affect health

Background. Assessing the health status of adolescents is challenging for health care providers. Personal disclosure has been associated with improved health outcomes. Story-centered care was examined as an intervention for promoting adolescent disclosure during an urgent care visit. ^ Objectives. This study explored: (1) the effectiveness of story-centered care for promoting adolescent disclosure; (2) health-associated words used by adolescents to describe pressing concerns after an urgent care visit when they had standard care (SC) or story-centered care (SCC) conducted by a Nurse Practitioner (NP). ^ Methods. Subjects were randomly assigned to SC or SCC. In SC, adolescent presenting concerns were identified and treated. In SCC, presenting concerns were treated and NP-adolescent dialogue, facilitated through a screening tool, queried matters of importance to adolescent life. After the visit, adolescents wrote about pressing concerns for 15 minutes. Written words were analyzed with Linguistic Inquiry and Word Count, a software program for analyzing narrative. Ratios were calculated for the number of words (adolescent: NP) used during the urgent care visit. Analysis of variance (ANOVA) was used to evaluate gender-intervention differences in health-associated words. ^ Results. One hundred and six adolescents [Hispanic (65%), White (35%)] completed the study. Fifty-five were female; the average age was 17 (sd = 2.1) years. ^ Adolescents in the story intervention used more words (adolescent: NP, 1:1.3) than those in standard intervention (adolescent: NP, 1:2.7) in proportion to the number of words used by the NP during the urgent care visit. There were gender-intervention differences (p < .01) in positive emotion words and past-tense words in writings about pressing concerns. Males who received the story intervention used more positive emotion and less past-tense words than adolescent males with standard care. Females used more social words (p < .01) in their writings regardless of intervention group. ^ Conclusion. SCC enhanced adolescent disclosure during an urgent care visit. Adolescents will talk to health care providers during episodic visits and males may benefit more than girls may from this approach. Evidence suggests there is value in attending to both presenting and pressing concerns of adolescents. ^

The welfare state determinants of health: Implications of regimes and pathways

Background. Population health within and between nations is heavily influenced by political determinants, yet these determinants have received significantly less attention than socioeconomic factors in public health. It has been hypothesized that the welfare state, as a political variable, may play a particularly prominent role in affecting both health indicators and health disparities in developed countries. The research, however, provides conflicting evidence regarding the health impact of particular regimes over others and the mechanisms through which the welfare state can most significantly affect health.^ Objective. To perform a systematic review of the literature as a means of exploring what the current research indicates regarding the benefits or detriments of particular regimes styles and the pathways through which the welfare state can impact heath indicators and health disparities within developed countries.^ Methods. A thorough search of the EBSCO, Pubmed, Medline, Web of Science, and Scopus electronic databases was conducted and resulted in the identification of 15 studies that evaluated the association between welfare state regime and population health outcomes, and/or pathways through with the welfare state influences health. ^ Results. Social democratic countries tended to perform best when infant mortality rate (IMR) was the primary outcome of interest, whereas liberal countries performed strongly in relation to self perceived health. The results were mixed regarding welfare state effectiveness in mitigating health inequities, with Christian democratic countries performing as well as social democratic countries. In relation to welfare state pathways, public health spending and medical coverage were associated with positive health indicators. Redistributive impact of the welfare state was also consistently associated with better health outcomes while social security expenditures were not.^ Discussion/Conclusions. Studies consistently discovered a significant relationship between the welfare state and population health and/or health disparities, lending support to the hypothesis that the welfare state is, indeed, an important non-medical determinant of health. However, it is still fairly unclear which welfare state regime may be most protective for health, as results varied according to the measured health indicator. The research regarding welfare state pathways is particularly undeveloped, and does not provide much insight into the importance of in-kind service provision or cash transfers, or targeted or universal approaches to the welfare state. Suggestions to direct future research are provided.^

Stability and potential application of spliced nuclear pre -mRNA introns

A major portion of this thesis work was dedicated to study the nature and significance of spliced introns. The initial work was focused on studying the IVS1$\sb{\rm C\beta 1}$ intron from a T-cell receptor (TCR)-$\beta$ gene. Compared to an intron lariat control from adenovirus pre-mRNA that was spliced in vitro, IVS1$\sb{\rm C\beta 1}$ was debranched less efficiently by HeLa S100 extracts, although IVS1$\sb{\rm C\beta 1}$ also used the consensus branchpoint in vivo. Subcellular-fractionation analysis showed that most IVS1$\sb{\rm C\beta 1}$ lariats cofractionated with pre-mRNA in the nucleus, consistent with the possibility that intron degradation releases splicing factors which will be available for further rounds of splicing. The half-life of IVS1$\sb{\rm C\beta 1}$ from the endogenous TCR-$\beta$ gene was measured using the general transcription inhibitor actinomycin D to be about $\sim$15 min, which was similar to that of unstable mRNAs such as c-myc mRNA.^ The general transcription inhibitor DRB was also used for intron stability analysis. Unexpectedly, DRB decreased intron and pre-mRNA levels only initially, it later increased the levels of intron-containing RNAs. Inhibition of transcription initiation appeared to be the major early effect (the reduction phase); whereas enhanced premature transcription termination was dominant later (the induction phase).^ Having established the procedures for studying in vivo spliced introns, this approach was applied to study the mechanism of nonsense-mediated downregulation (NMD), a phenomena in which premature termination codons (PTCs) decrease the levels of mRNAs. In this study, the novel intron-oriented approach was applied to study the mechanism of NMD. The levels of spliced introns immediately upstream and downstream of a PTC-bearing exon in a TCR-$\beta$ gene were identified and analyzed along with their pre-mRNA. Although PTC reduced the mRNA levels by 4 to 9 fold, the steady-state levels of spliced introns and the pre-mRNA-to-intron ratios were not significantly altered, indicating that the PTC did not significantly inhibit TCR-$\beta$ RNA splicing. Consistent with this conclusion, the half-lives of the PTC$\sp+$ and PTC$\sp-$ pre-mRNA were similar. The protein synthesis inhibitor cyclohexmide (CHX) upregulated the levels of the PTC$\sp+$ mRNA over 10 fold without affecting the levels of the spliced introns, suggesting that the reversal effect of CHX was through stabilization, not production. These results indicated that inhibition of splicing could not be the major mechanism for the NMD pathway of the TCR-$\beta$ gene, instead, suggesting that mRNA destabilization may be more important. (Abstract shortened by UMI.) ^