Random versus Deterministic Descent in RNA Energy Landscape Analysis.

Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time-critical component of such methods is steepest, or gradient, descent in attraction basins of local minima. We analyse the speed-up achievable by randomised descent in attraction basins in the context of large sample sets where the size has an order of magnitude in the region of ~10(6). While the gain for each individual sample might be marginal, the overall run-time improvement can be significant. Moreover, for the two nongradient methods we analysed for partial energy landscapes induced by ten different RNA sequences, we obtained that the number of observed local minima is on average larger by 7.3% and 3.5%, respectively. The run-time improvement is approximately 16.6% and 6.8% on average over the ten partial energy landscapes. For the large sample size we selected for descent procedures, the coverage of local minima is very high up to energy values of the region where the samples were randomly selected from the partial energy landscapes; that is, the difference to the total set of local minima is mainly due to the upper area of the energy landscapes.

A new heuristic method for approximating the number of local minima in partial RNA energy landscapes.

The analysis of energy landscapes plays an important role in mathematical modelling, simulation and optimisation. Among the main features of interest are the number and distribution of local minima within the energy landscape. Granier and Kallel proposed in 2002 a new sampling procedure for estimating the number of local minima. In the present paper, we focus on improved heuristic implementations of the general framework devised by Granier and Kallel with regard to run-time behaviour and accuracy of predictions. The new heuristic method is demonstrated for the case of partial energy landscapes induced by RNA secondary structures. While the computation of minimum free energy RNA secondary structures has been studied for a long time, the analysis of folding landscapes has gained momentum over the past years in the context of co-transcriptional folding and deeper insights into cell processes. The new approach has been applied to ten RNA instances of length between 99 nt and 504 nt and their respective partial energy landscapes defined by secondary structures within an energy offset ΔE above the minimum free energy conformation. The number of local minima within the partial energy landscapes ranges from 1440 to 3441. Our heuristic method produces for the best approximations on average a deviation below 3.0% from the true number of local minima.

Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs.

MOTIVATION: We study microRNA (miRNA) bindings to metastable RNA secondary structures close to minimum free energy conformations in the context of single nucleotide polymorphisms (SNPs) and messenger RNA (mRNA) concentration levels, i.e. whether features of miRNA bindings to metastable conformations could provide additional information supporting the differences in expression levels of the two sequences defined by a SNP. In our study, the instances [mRNA/3'UTR; SNP; miRNA] were selected based on strong expression level analyses, SNP locations within binding regions and the computationally feasible identification of metastable conformations. RESULTS: We identified 14 basic cases [mRNA; SNP; miRNA] of 3' UTR-lengths ranging from 124 up to 1078 nt reported in recent literature, and we analyzed the number, structure and miRNA binding to metastable conformations within an energy offset above mfe conformations. For each of the 14 instances, the miRNA binding characteristics are determined by the corresponding STarMir output. Among the different parameters we introduced and analyzed, we found that three of them, related to the average depth and average opening energy of metastable conformations, may provide supporting information for a stronger separation between miRNA bindings to the two alleles defined by a given SNP. AVAILABILITY AND IMPLEMENTATION: At http://kks.inf.kcl.ac.uk/MSbind.html the MSbind tool is available for calculating features of metastable conformations determined by putative miRNA binding sites.

Acute vision loss: a fuzzy presentation of sarcoidosis.

BACKGROUND: Acute vision loss is a devastating problem for patients and a challenging diagnostic dilemma for Emergency Physicians. This chief complaint is one in which we must be adept at quickly evaluating and initiating either care or referral. OBJECTIVES: This case reviews the approach to acute vision loss and shows the importance of expanding the differential in atypical and complex presentations. CASE REPORT: A 31-year-old, previously healthy, white woman presented to the Emergency Department (ED) with 1 day of painless right eye vision loss. Ocular ultrasound and slit-lamp examination were unremarkable. Fundoscopic examination revealed retinal hemorrhages and papillitis. Her chest X-ray study was significant for bilateral hilar adenopathy, and subsequent lymph node biopsy confirmed the diagnosis of sarcoidosis. CONCLUSIONS: Although sarcoidosis is more common in African Americans, it must be considered in all patients in the appropriate clinical context. Sarcoidosis is an important diagnosis to include on the differential of many chief complaints that present to the ED, including acute vision loss and dyspnea.

Repeated ethanol exposure during late gestation alters the maturation and innate immune status of the ovine fetal lung.

Little is known about the effects of fetal ethanol exposure on lung development. Our aim was to determine the effects of repeated ethanol exposure during late gestation on fetal lung growth, maturation, and inflammatory status. Pregnant ewes were chronically catheterized at 91 days of gestational age (DGA; term approximately 147 days). From 95-133 DGA, ewes were given a 1-h daily infusion of either 0.75 g ethanol/kg (n = 9) or saline (n = 8), with tissue collection at 134 DGA. Fetal lungs were examined for changes in tissue growth, structure, maturation, inflammation, and oxidative stress. Between treatment groups, there were no differences in lung weight, DNA and protein contents, percent proliferating and apoptotic cells, tissue and air-space fractions, alveolar number and mean linear intercept, septal thickness, type-II cell number and elastin content. Ethanol exposure caused a 75% increase in pulmonary collagen I alpha1 mRNA levels (P < 0.05) and a significant increase in collagen deposition. Surfactant protein (SP)-A and SP-B mRNA levels were approximately one third of control levels following ethanol exposure (P < 0.05). The mRNA levels of the proinflammatory cytokines interleukin (IL)-1beta and IL-8 were also lower (P < 0.05) in ethanol-exposed fetuses compared with controls. Pulmonary malondialdehyde levels tended to be increased (P = 0.07) in ethanol-exposed fetuses. Daily exposure of the fetus to ethanol during the last third of gestation alters extracellular matrix deposition and surfactant protein gene expression, which could increase the risk of respiratory distress syndrome after birth. Changes to the innate immune status of the fetus could increase the susceptibility of the neonatal lungs to infection.

Serotonin syndrome in a patient taking Lexapro and Flexeril: a case report.

The serotonin syndrome is a rare toxicological emergency increasingly seen in emergency practice, secondary to increased use of proserotinergic drugs. In this case report, the condition is described in a patient taking the selective serotonin reuptake inhibitor Lexapro and the muscle-relaxant Flexeril. Based on this case, Cyclobenzaprine should be considered on the growing list of medications that can precipitate the serotonin syndrome. With the increasing prevalence of proserotinergic polypharmacy, this uncommon toxidrome should be considered by the alert emergency medicine physician.

Spinal cord arteriovenous malformation in a toddler presenting with altered mental status and fever.

Central nervous system arteriovenous malformations (AVMs) are a rare cause of subarachnoid hemorrhage and neurologic deficits. About 90% of these lesions are supratentorial, with a smaller percentage occurring in the posterior fossa and an even smaller number found throughout the spine. Although spinal AVMs are uncommon, these disorders represent a treatable cause of significant morbidity in a young age group. We report a case of a T11-T12 spinal AVM in a 14-month-old girl presenting with low-grade fever and lethargy who was found to have subarachnoid hemorrhage on evaluation and describe a reasonable stepwise approach to these patients in the emergency department utilizing computed tomography, lumbar puncture, magnetic resonance imaging, and angiography.