The UA_handle: a versatile submotif in stable RNA architectures†

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/ANnX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures

Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 3′ end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA

Structural Constraints Identified with Covariation Analysis in Ribosomal RNA

Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab’s new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab’s Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair

Comparative Genomic Analysis of Pathogenic and Probiotic Enterococcus faecalis Isolates, and Their Transcriptional Responses to Growth in Human Urine

Urinary tract infection (UTI) is the most common infection caused by enterococci, and Enterococcus faecalis accounts for the majority of enterococcal infections. Although a number of virulence related traits have been established, no comprehensive genomic or transcriptomic studies have been conducted to investigate how to distinguish pathogenic from non-pathogenic E. faecalis in their ability to cause UTI. In order to identify potential genetic traits or gene regulatory features that distinguish pathogenic from non-pathogenic E. faecalis with respect to UTI, we have performed comparative genomic analysis, and investigated growth capacity and transcriptome profiling in human urine in vitro. Six strains of different origins were cultivated and all grew readily in human urine. The three strains chosen for transcriptional analysis showed an overall similar response with respect to energy and nitrogen metabolism, stress mechanism, cell envelope modifications, and trace metal acquisition. Our results suggest that citrate and aspartate are significant for growth of E. faecalis in human urine, and manganese appear to be a limiting factor. The majority of virulence factors were either not differentially regulated or down-regulated. Notably, a significant up-regulation of genes involved in biofilm formation was observed. Strains from different origins have similar capacity to grow in human urine. The overall similar transcriptional responses between the two pathogenic and the probiotic strain suggest that the pathogenic potential of a certain E. faecalis strain may to a great extent be determined by presence of fitness and virulence factors, rather than the level of expression of such traits

Adverse Perinatal Outcomes and Postpartum Multi-Systemic Dysregulation: Adding Vitamin D Deficiency to the Allostatic Load Index.

Background Allostatic load (AL) is an index of multi-system physiological "wear-and-tear," operationalizing emergent chronic disease risk and predicting morbidity and mortality. AL has been proposed as an organizing framework for studying pregnancy outcomes and additional AL biomarkers for the study of maternal health would be valuable. Objectives To test whether adverse perinatal outcomes are associated with postpartum AL and if including vitamin D deficiency (serum 25(OH)D < 20 ng/ml) as an additional marker of postpartum AL increases the association. Methods The Community Child Health Network is a community-based participatory research network that enrolled women at birth and followed them for 2 years measuring ten biomarkers (body mass index, waist: hip ratio, pulse, systolic and diastolic blood pressures, cortisol slope, c-reactive protein, hgbA1c, HDL, and total cholesterol) at 6 and 12 months postpartum. A composite of four adverse perinatal outcomes (low birth weight, preterm birth, preeclampsia, and gestational diabetes) was collected from medical charts in a sample of 164 women from one site and serum 25(OH)D status was measured 24-39 weeks postpartum in this cohort. Results Twenty-nine percent experienced one or more of the four adverse perinatal outcomes. Serum 25(OH)D was significantly inversely correlated with the AL index (Spearman's r = -0.247, p = 0.002). Logistic regression results adjusting for maternal age and race showed that adverse outcome was significantly associated with higher postpartum AL (OR 1.53 for a 1-unit increase in AL, 95% CI 1.24-1.89). Adding 25(OH)D deficiency as an 11th component to the AL index improved the model fit (Delta (-2LogL) = 3.955, p = 0.047), and improved the Akaike information criterion (180.32 vs. 184.27). Conclusion Women with adverse perinatal outcomes have higher postpartum AL and adding vitamin D deficiency to the AL index strengthens this association

Adverse Perinatal Outcomes and Postpartum Multi-Systemic Dysregulation: Adding Vitamin D Deficiency to the Allostatic Load Index.

Background Allostatic load (AL) is an index of multi-system physiological "wear-and-tear," operationalizing emergent chronic disease risk and predicting morbidity and mortality. AL has been proposed as an organizing framework for studying pregnancy outcomes and additional AL biomarkers for the study of maternal health would be valuable. Objectives To test whether adverse perinatal outcomes are associated with postpartum AL and if including vitamin D deficiency (serum 25(OH)D < 20 ng/ml) as an additional marker of postpartum AL increases the association. Methods The Community Child Health Network is a community-based participatory research network that enrolled women at birth and followed them for 2 years measuring ten biomarkers (body mass index, waist: hip ratio, pulse, systolic and diastolic blood pressures, cortisol slope, c-reactive protein, hgbA1c, HDL, and total cholesterol) at 6 and 12 months postpartum. A composite of four adverse perinatal outcomes (low birth weight, preterm birth, preeclampsia, and gestational diabetes) was collected from medical charts in a sample of 164 women from one site and serum 25(OH)D status was measured 24-39 weeks postpartum in this cohort. Results Twenty-nine percent experienced one or more of the four adverse perinatal outcomes. Serum 25(OH)D was significantly inversely correlated with the AL index (Spearman's r = -0.247, p = 0.002). Logistic regression results adjusting for maternal age and race showed that adverse outcome was significantly associated with higher postpartum AL (OR 1.53 for a 1-unit increase in AL, 95% CI 1.24-1.89). Adding 25(OH)D deficiency as an 11th component to the AL index improved the model fit (Delta (-2LogL) = 3.955, p = 0.047), and improved the Akaike information criterion (180.32 vs. 184.27). Conclusion Women with adverse perinatal outcomes have higher postpartum AL and adding vitamin D deficiency to the AL index strengthens this association