Functions and intramolecular interactions of ribosomal RNA in decoding of termination codons

Two regions in the 3$\prime$ domain of 16S rRNA (the RNA of the small ribosomal subunit) have been implicated in decoding of termination codons. Using segment-directed PCR random mutagenesis, I isolated 33 translational suppressor mutations in the 3$\prime$ domain of 16S rRNA. Characterization of the mutations by both genetic and biochemical methods indicated that some of the mutations are defective in UGA-specific peptide chain termination and that others may be defective in peptide chain termination at all termination codons. The studies of the mutations at an internal loop in the non-conserved region of helix 44 also indicated that this structure, in a non-conserved region of 16S rRNA, is involved in both peptide chain termination and assembly of 16S rRNA.^ With a suppressible trpA UAG nonsense mutation, a spontaneously arising translational suppressor mutation was isolated in the rrnB operon cloned into a pBR322-derived plasmid. The mutation caused suppression of UAG at two codon positions in trpA but did not suppress UAA or UGA mutations at the same trpA positions. The specificity of the rRNA suppressor mutation suggests that it may cause a defect in UAG-specific peptide chain termination. The mutation is a single nucleotide deletion (G2484$\Delta$) in helix 89 of 23S rRNA (the large RNA of the large ribosomal subunit). The result indicates a functional interaction between two regions of 23S rRNA. Furthermore, it provides suggestive in vivo evidence for the involvement of the peptidyl-transferase center of 23S rRNA in peptide chain termination. The $\Delta$2484 and A1093/$\Delta$2484 (double) mutations were also observed to alter the decoding specificity of the suppressor tRNA lysT(U70), which has a mutation in its acceptor stem. That result suggests that there is an interaction between the stem-loop region of helix 89 of 23S rRNA and the acceptor stem of tRNA during decoding and that the interaction is important for the decoding specificity of tRNA.^ Using gene manipulation procedures, I have constructed a new expression vector to express and purify the cellular protein factors required for a recently developed, realistic in vitro termination assay. The gene for each protein was cloned into the newly constructed vector in such a way that expression yielded a protein with an N-terminal affinity tag, for specific, rapid purification. The amino terminus was engineered so that, after purification, the unwanted N-terminal tag can be completely removed from the protein by thrombin cleavage, yielding a natural amino acid sequence for each protein. I have cloned the genes for EF-G and all three release factors into this new expression vector and the genes for all the other protein factors into a pCAL-n expression vector. These constructs will allow our laboratory group to quickly and inexpensively purify all the protein factors needed for the new in vitro termination assay. (Abstract shortened by UMI.) ^

Nosocomial infections and their relationship to non-traditional risk factors in a medical intensive care unit

Background. Nosocomial infections are a source of concern for many hospitals in the United States and worldwide. These infections are associated with increased morbidity, mortality and hospital costs. Nosocomial infections occur in ICUs at a rate which is five times greater than those in general wards. Understanding the reasons for the higher rates can ultimately help reduce these infections. The literature has been weak in documenting a direct relationship between nosocomial infections and non-traditional risk factors, such as unit staffing or patient acuity.^ Objective. To examine the relationship, if any, between nosocomial infections and non-traditional risk factors. The potential non-traditional risk factors we studied were the patient acuity (which comprised of the mortality and illness rating of the patient), patient days for patients hospitalized in the ICU, and the patient to nurse ratio.^ Method. We conducted a secondary data analysis on patients hospitalized in the Medical Intensive Care Unit (MICU) of the Memorial Hermann- Texas Medical Center in Houston during the months of March 2008- May 2009. The average monthly values for the patient acuity (mortality and illness Diagnostic Related Group (DRG) scores), patient days for patients hospitalized in the ICU and average patient to nurse ratio were calculated during this time period. Active surveillance of Bloodstream Infections (BSIs), Urinary Tract Infections (UTIs) and Ventilator Associated Pneumonias (VAPs) was performed by Infection Control practitioners, who visited the MICU and performed a personal infection record for each patient. Spearman's rank correlation was performed to determine the relationship between these nosocomial infections and the non-traditional risk factors.^ Results. We found weak negative correlations between BSIs and two measures (illness and mortality DRG). We also found a weak negative correlation between UTI and unit staffing (patient to nurse ratio). The strongest positive correlation was found between illness DRG and mortality DRG, validating our methodology.^ Conclusion. From this analysis, we were able to infer that non-traditional risk factors do not appear to play a significant role in transmission of infection in the units we evaluated.^

Yoga off the mat: How far and to whom do the benefits extend?

At least 15 million American adults have participated in yoga at least once in their lifetime (Saper, Eisenberg, Davis, Culpepper, & Phillips, 2004). The field of yoga research is relatively new in the United States, and the majority of studies have concentrated on yoga's effect on measures of physiology (cardiovascular disease, diabetes, obesity) or psychological measures of stress and anxiety. This review attempted to identify studies that had been conducted measuring a different set of outcome measures, specifically violence, trauma, eating, and other behavioral disorders. In 9 of 10 studies reviewed, researchers observed statistically significant effects of yoga interventions. Effects were most evident within multifaceted studies that combined intensive yoga practice with group discussion and training. Only one group (Mitchell, Mazzeo, Rausch, & Cooke, 2007) failed to observe any significant differences between yoga practice groups and control groups. Effects were seen in both sexes, although a majority of the studies were aimed specifically at women. All studies were limited by small sample size and lack of follow-up data. Future research should seek to increase sample size, to diversify recruitment to allow for the randomization of treatment and control groups, and to allow for long-term follow-up.^

Implementing and evaluating a Web -based close call reporting system at an urban hospital

Medical errors and close calls are pervasive in health care. It is hypothesized that the causes of close calls are the same as for medical errors; therefore learning about close calls can help prevent errors and increase patient safety. Yet despite efforts to encourage close call reporting, close calls as well as medical errors are under-reported in health care. The purpose of this dissertation was to implement and evaluate a web-based anonymous close call reporting system in three units at an urban hospital. ^ The study participants were physicians, nurses and medical technicians (N = 187) who care for patients in the Medical Intermediate Care Unit, the Surgical Intermediate Care Unit, and the Coronary Catheterization Laboratory in the hospital. We provided educational information to the participants on how to use the system and e-mailed and delivered paper reminders to report to the participants throughout the 19-month project. We surveyed the participants at the beginning and at the end of the study to assess their attitudes and beliefs regarding incident reporting. We found that the majority of the health care providers in our study are supportive of incident reporting in general but in practice very few had actually reported an error or a close call, semi-structured interview 20 weeks after we made the close call reporting system available. The purpose of the interviews was to further assess the participants' attitudes regarding incident reporting and the reporting system. Our findings suggest that the health care providers are supportive of medical error reporting in general, but are not convinced of the benefit of reporting close calls. Barriers to close call reporting cited include lack of time, heavy workloads, preferring to take care of close calls "on the spot", and not seeing the benefits of close call reporting. Consequently only two = close calls were reported via the system by two separate caregivers during the project. ^ The findings suggest that future efforts to increase close call reporting must address barriers to reporting, especially the belief among care givers that it is not worth taking time from their already busy schedules to report close calls. ^

Prevalence and risk factors of methicillin-resistant Staphylococcus aureus in critically-ill hospitalized patients in a tertiary care center in Houston, Texas: An active surveillance pilot project

Objective. The objective of this study is to determine the prevalence of MRSA colonization in adult patients admitted to intensive care units at an urban tertiary care hospital in Houston, Texas and to evaluate the risk factors associated with colonization during a three month active-screening pilot project. Design. This study used secondary data from a small cross-sectional pilot project. Methods. All patients admitted to the seven specialty ICUs were screened for MRSA by nasal culture. Results were obtained utilizing the BD GeneOhm™ IDI-MRSA assay in vitro diagnostic test, for rapid MRSA detection. Statistical analysis was performed using the STATA 10, Epi Info, and JavaStat. Results . 1283/1531 (83.4%) adult ICU admissions were screened for nasal MRSA colonization. Of those screened, demographic and risk factor data was available for 1260/1283 (98.2%). Unresolved results were obtained for 73 patients. Therefore, a total of 1187/1531 (77.5%) of all ICU admissions during the three month study period are described in this analysis. Risk factors associated with colonization included the following: hospitalization within the last six months (odds ratio 2.48 [95% CI, 1.70-3.63], p=0.000), hospitalization within the last 12 months, (odds ratio 2.27 [95% CI, 1.57-3.80], p=0.000), and having diabetes mellitus (odds ratio 1.63 [95% CI, 1.14-2.32], p=0.007). Conclusion. Based on the literature, the prevalence of MRSA for this population is typical of other prevalence studies conducted in the United States and coincides with the continual increasing trend of MRSA colonization. Significant risk factors were similar to those found in previous studies. Overall, the active surveillance screening pilot project has provided valuable information on a population not widely addressed. These findings can aid in future interventions for the education, control, prevention, and treatment of MRSA. ^

A study of nurses' perceptions of and participation in the resolution of treatment dilemmas for critically ill newborns

This study was an exploratory investigation of variables which are associated with neonatal intensive care nurses' perceptions of and participation in life-sustaining treatment decisions for critically ill newborns. The primary purpose of the research was to examine the extent to which assessment of infants' physical and mental prognoses, parents' preferences regarding treatment, and legal consequences of non-treatment influence nurses' recommendations about life-saving treatment decisions for handicapped newborns. Secondly, the research explored the extent and nature of nurses' reported participation in the resolution of treatment dilemmas for these critically ill newborns. The framework of the study draws upon the work of Crane (1977), Blum (1980), and Pearlman (1982) who have explored the sociological context of decision-making with critical care patients.^ Participants in the study were a volunteer sample of eighty-three registered nurses who were currently working in neonatal intensive care units in five large urban hospitals in Texas. Data were collected through the use of intensive interviews and case study questionnaires. Results from the study indicate that physical and mental prognoses as well as parent preferences and concerns about legal liability are related to nurses' treatment recommendations, but their levels of significance vary according to the type of handicapping condition and whether the treatment questions are posed in terms of initiating aggressive therapy or withdrawing aggressive therapy.^ The majority of nurses reported that the extent of their participation in formal decision-making regarding handicapped newborns was fairly minimal although they provide much of the definitive data used to make decisions by physicians and parents. There was substantial evidence that nurse respondents perceive their primary role as advocates for critically ill newborns, and believe that their involvement in the resolution of treatment dilemmas should be increased. ^