Computational Prediction of RNA Secondary Structure with Applications to RNA Viruses

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Biochemistry & Biophysics, 2013.RNA is key in gene expression, and is responsible for multiple catalytic and regulatory mechanisms in the cell. An important step toward understanding RNA function is determining its structure. Computational approaches have become integral to this process, particularly those that predict structure based on the thermodynamics of RNA folding. RNA secondary structure, defined as the collection of canonical base pairs, provides significant information about function. Methods for predicting secondary structure of single-stranded molecules have been refined to become both sophisticated and accurate, but prediction of RNA-RNA interactions has remained a computational challenge. The role of intramolecular structure formation and its influence on determining RNA-RNA interactions is significant, but is a difficult problem that is computationally expensive to solve. A novel algorithm for predicting RNA-RNA interactions was developed that utilizes pseudo-free energy minimization. This is an extension to standard free energy minimization that uses the single-stranded partition function calculations to predict the probability that each nucleotide is involved in self-structure. A pseudo-energy penalty is administered to each nucleotide based on its propensity to form self-structure, augmenting the prediction of RNA-RNA interactions. This algorithm provides a statistically significant increase in sensitivity over the best known method for generalized RNA-RNA interaction prediction. The gold standard for structure determination is comparative sequence analysis. In this method, multiple homologous RNA sequences are compared to identify conserved structure. The accuracy of such structure prediction methods is reliant upon an initial primary sequence alignment that is informative and accurate. Pairwise Hidden Markov models (HMMs) are frequently used for RNA sequence alignment. These algorithms are trained to generate a probabilistic alignment for two sequences at a time. Probabilistic pairwise alignment is currently an important first step in building a multiple sequence alignment for use in automated prediction of conserved secondary structure. An HMM that simultaneously aligns three sequences was developed and benchmarked using the Rfam database of multiple sequence alignments. To our knowledge this is the first algorithm to consider three sequences simultaneously, as each sequence added over pairwise significantly increases the computational demand

Early tracheostomy after initiation of venovenous extracorporeal membrane oxygenation is associated with decreased duration of extracorporeal membrane oxygenation support

Timing of tracheostomy placement for patients with respiratory failure requiring venovenous extracorporeal membrane oxygenation support is variable and continues to depend on surgeon preference. We retrospectively reviewed all consecutive adult patients supported with peripheral venovenous extracorporeal membrane oxygenation for acute respiratory distress syndrome at a single institution with the hypothesis that early tracheostomy (within 7 days of extracorporeal membrane oxygenation initiation) decreases the duration of extracorporeal membrane oxygenation support. The primary endpoint was duration of extracorporeal membrane oxygenation support. Secondary endpoints included mortality, overall and intensive care unit length of stay, duration of mechanical ventilation, and time from extracorporeal membrane oxygenation initiation to liberation from ventilator, intensive care unit discharge, and hospital discharge. Overall and extracorporeal membrane oxygenation–associated hospital costs were compared. A total of 50 patients were identified for inclusion (early n = 21; late n = 29). Baseline characteristics including indices of disease severity were similar between groups. Duration of extracorporeal membrane oxygenation support was significantly shorter in the early tracheostomy group (12 vs. 21 days; p = 0.005). Median extracorporeal membrane oxygenation–related costs were significantly decreased in the early tracheostomy group ($3,624 vs.$5,603, p = 0.03). Early tracheostomy placement is associated with decreased time on extracorporeal membrane oxygenation support and reduced extracorporeal membrane oxygenation–related costs in this cohort. Validation in a prospective cohort or a clinical trial is indicated

Early Decompressive Laparotomy for Intra-Abdominal Hypertension following Initiation of Venovenous Extracorporeal Membrane Oxygenation

Patients supported with venovenous extracorporeal membrane oxygenation are at risk for intra-abdominal hypertension and abdominal compartment syndrome. Flow through the return cannula may be compromised in these patients, resulting in inadequate support and end-organ malperfusion. Early decompressive laparotomy can mitigate these complications and potentially improve outcomes. Here we review a series of nine patients undergoing early decompressive laparotomy for abdominal compartment syndrome at a single institution and propose an algorithmic approach to the management of these patients