Gait kinematics and kinetics in patients with chronic ankle instability and healthy controls: A statistical parametric mapping analysis

BACKGROUND

Chronic ankle instability (CAI) is associated with changes in gait biomechanics which may be related to chronic dysfunction. Traditional statistical models may be limited in their ability to assess the complex 3D movement of the lower extremity during gait. Multivariate analysis of the lower extremity kinematics may reveal unique biomechanical differences associated with CAI.

RESEARCH QUESTION

Do patients with CAI differ from healthy controls in their lower extremity biomechanics and GRF when comparing 3D biomechanics?

METHODS

Thirty-nine young, active adults participated in this study. Data was collected using a 3D motion analysis system while patients walked and jogged. Statistical parametric mapping (SPM) was used to explore 3D GRF, kinematics and kinetics of the of the lower extremity of CAI and healthy patients.

RESULTS

During walking, patients with CAI had greater inversion from 68-100% of gait cycle (p < 0.001, mean difference=3.2°). During jogging, patients with CAI had greater inversion from 20-92% (p < 0.001, mean difference=4.6°). Greater plantar flexion moments were found from 65-71% (p = 0.05, mean difference=347.4Nm/kg) and greater eversion moments were found from 95-100% (p = 0.03, mean difference=74.6Nm/kg) in the CAI group. No differences in GRF were found.

SIGNIFICANCE

Greater inversion may present a potentially injurious position. A faulty position of the rearfoot may require greater muscle function in order to correct the position of the joint resulting in greater eversion moments at the ankle. However, this kinetic change does not appear to correct the ankle position.

Predicting ACL Reinjury from Return to Activity Assessments at 6-months Post-Surgery: A Prospective Cohort Study

CONTEXT

Return to activity(RTA) assessments are commonly administered following ACL-Reconstruction(ACLR) to manage post-operative progressions back to activity. To date, there is little knowledge on the clinical utility of these assessments to predict patient outcomes such as secondary ACL injury once returned to activity.

OBJECTIVE

To identify what measures of patient function at 6-months post-ACLR best predict return to activity and second ACL injury at a minimum of 2-years following ACLR.

DESIGN

Prospective-cohort Setting: Laboratory Patients: A total of 234 patients with primary, unilateral ACLR completed functional assessments at approximately 6-months post-ACLR. A total of 192(82%) completed follow-up ≥ 2-years post ACLR.

MAIN OUTCOME MEASURES

Six-month functional assessments consisted of patient reported outcomes, isokinetic knee flexor and extensor strength, and single-leg hopping. The ability to return to activity and secondary ACL injury were collected at a minimum of two-years following ACLR.

RESULTS

In patients who did RTA(n=155), a total of 44(28%) individuals had a subsequent ACL injury; graft n=24(15.5%), contralateral ACL n=20(13%). A greater proportion of females had a secondary injury to the contralateral ACL(15/24, 63%) whereas a greater proportion of males reinjured the ipsilateral ACL graft(15/20, 75%, P=.017) Greater knee extension symmetry at 6-months increased the probability of reinjury(B=.016, P=.048). In patients who RTA before 8-months, every 1% increase in quadriceps strength symmetry at 6-months increased the risk of reinjury by 2.1%(B=.021, P=.05). In patients who RTA after 8-months, every month that RTA was delayed reduced the risk of reinjury by 28.4%(B=-284, P=.042).

CONCLUSIONS

Patients with more symmetric quadriceps strength at 6-months post ACLR were more likely to experience another ACL rupture, especially in those who returned to sport earlier than 8-months after the index surgery. Clinicians should be cognizant that returning high functioning patients to activity earlier than 8-months post-ACLR may place them at an increased risk for reinjury.

A-16 The Clinical Utility of a Novel Dual-Task Assessment for Sport-Related Concussion in Collegiate Athletes

Objective

To compare the clinical utility of a novel dual-task assessment for sport-related concussion (SRC) to other commonly-used clinical measures in collegiate athletes.

Method

Participants consisted of 38 collegiate athletes (19 concussed and 19 matched comparisons, 53% male, age = 20.0 ± 1.34 years, height = 178.2 ± 12.12 cm, mass = 83.4 ± 21.89 kg). Participants were administered the dual-task assessment, Balance Error Scoring System (BESS), Standardized Assessment of Concussion (SAC), and tandem gait (TG) test within 48 hours (T1), at 5 days (T2), and when symptom-free (T3) following a diagnosed SRC. The novel dual-task assessment consisted of concurrent administration of the SAC and TG. The ImPACT and Sensory Organization Test (SOT) were administered at T3 in alignment with the university’s concussion management policy. Sensitivity, specificity, and diagnostic accuracy using receiver operator curve analyses were calculated for each measure for T1-T3 using previously established interpretation guidelines.

Results

For sensitivity, a range of values were observed from T1-T3 for the dual-task (88%–37%), BESS (47%–47%), SAC (53%–26%), TG test (53%–11%). Similarly, a range of specificity values were observed for the dual-task (58%–84%), BESS (84%–63%), SAC (79%–84%), and TG test (95%–100%) from T1-T3. At T3, the ImPACT and SOT were observed to have a sensitivity of 32% and 100% and specificity of 16% and 100%, respectively. A range of diagnostic accuracy values were observed from T1-T3 for the dual-task (84%–62%), BESS (59%–50%), SAC (64%–56%), TG test (82%–71%), ImPACT (T3 = 66%), and SOT (T3 = 50%).

Conclusions

The dual-task assessment had comparable or higher diagnostic accuracy as other commonly-used clinical measures of SRC throughout clinical recovery in collegiate athletes.

Chronic ankle instability patients exhibit higher variability in lower extremity joint-coupling variability during drop vertical jumps

Chronic ankle instability (CAI) has been associated with biomechanical alterations during landing tasks. While joint coupling differences have been reported during gait in patients with CAI, there is no known research assessing joint coupling during a drop-vertical jumping (DVJ). Joint coupling variability measure may provide information on the sensorimotor health of these patients. The purpose of this study was to compare lower extremity joint coupling variability during a DVJ between patients with CAI and controls. Twenty-eight young, active individuals (CAI:n = 14, Control:n = 14) participated in the study. A 3D motion capture system was used to collect kinematics during 15 drop-vertical jump trials. A vector coding analysis was used to assess the variability in the following joint couples: knee sagittal-ankle frontal, knee sagittal-ankle sagittal, hip frontal-ankle frontal, and hip frontal-ankle sagittal. The CAI group had higher joint coupling variability in hip frontal-ankle sagittal, knee sagittal-ankle frontal and knee sagittal-ankle sagittal planes both prior to and following ground contact during the drop vertical jumps. These changes indicate potential adaptations to the constraint of CAI and the task of the DVJ. Higher variability may reflect an attempt by the subjects to explore alternate movement strategies or reflect poor sensorimotor control strategies. Clinicians should consider the challenges of DVJ during rehabilitation as they create a unique task constraint.

Supporting family dementia caregivers: testing the efficacy of dementia care management on multifaceted caregivers' burden

OBJECTIVES

Current research suggests that dementia care management (DCM) can decrease burden and associated health impairments of caregivers. The objective of this secondary analysis is to investigate the impact of DCM on multifaceted caregivers' burden dimensions by differentiating between objective and subjective burden.

METHODS

A sample of n = 317 dyads of caregivers and community-dwelling people with dementia (PwD) participated in a general practitioner-based, cluster-randomized intervention trial (Identifier:NCT01401582) with two arms and comprehensive data assessment at baseline and 12-month follow-up. Data provided by the caregiver included an inventory with 88 items in 20 different dimensions.

RESULTS

Caregivers in the intervention 'DCM' group showed decreased caregiver burden, especially in caregivers' objective burden due to caring (i.e. emotional support), caregivers' subjective burden due to behavior change (i.e. cognition, aggression and resistance, depression, late symptoms) and caregivers' subjective burden due to perceived conflicts between needs and responsibilities to care (i.e. financial losses) compared to caregivers in the control 'care as usual' group, which showed significant increased caregiver burden after 12 months.

CONCLUSION

Our findings support evidence for the effectiveness of DCM to lower family dementia caregivers' burden in multifaceted dimensions.

Genome-wide gene-environment interaction in depression: A systematic evaluation of candidate genes: The childhood trauma working-group of PGC-MDD

Gene by environment (GxE) interaction studies have investigated the influence of a number of candidate genes and variants for major depressive disorder (MDD) on the association between childhood trauma and MDD. Most of these studies are hypothesis driven and investigate only a limited number of SNPs in relevant pathways using differing methodological approaches. Here (1) we identified 27 genes and 268 SNPs previously associated with MDD or with GxE interaction in MDD and (2) analyzed their impact on GxE in MDD using a common approach in 3944 subjects of European ancestry from the Psychiatric Genomics Consortium who had completed the Childhood Trauma Questionnaire. (3) We subsequently used the genome-wide SNP data for a genome-wide case-control GxE model and GxE case-only analyses testing for an enrichment of associated SNPs. No genome-wide significant hits and no consistency among the signals of the different analytic approaches could be observed. This is the largest study for systematic GxE interaction analysis in MDD in subjects of European ancestry to date. Most of the known candidate genes/variants could not be supported. Thus, their impact on GxE interaction in MDD may be questionable. Our results underscore the need for larger samples, more extensive assessment of environmental exposures, and greater efforts to investigate new methodological approaches in GxE models for MDD.

Towards a Consistent, Quantitative Evaluation of MicroRNA Evolution

The miRBase currently reports more than 25,000 microRNAs in several hundred genomes that belong to more than 1000 families of homologous sequences. Quantitative investigations of miRNA gene evolution requires the construction of data sets that are consistent in their coverage and include those genomes that are of interest in a given study. Given the size and structure of data, this can be achieved only with the help of a fully automatic pipeline that improves the available seed alignments, extends the set of available sequences by homology search, and reliably identifies true positive homology search results. Here we describe the current progress towards such a system, emphasizing the task of improving and completing the initial seed alignment.

Evolution of Fungal U3 snoRNAs: Structural Variation and Introns

The U3 small nucleolar RNA (snoRNA) is an essential player in the initial steps of ribosomal RNA biogenesis which is ubiquitously present in Eukarya. It is exceptional among the small nucleolar RNAs in its size, the presence of multiple conserved sequence boxes, a highly conserved secondary structure core, its biogenesis as an independent gene transcribed by polymerase III, and its involvement in pre-rRNA cleavage rather than chemical modification. Fungal U3 snoRNAs share many features with their sisters from other eukaryotic kingdoms but differ from them in particular in their 5’ regions, which in fungi has a distinctive consensus structure and often harbours introns. Here we report on a comprehensive homology search and detailed analysis of the evolution of sequence and secondary structure features covering the entire kingdom Fungi.

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification

Background

snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport. To validate the new version and to demonstrate its improved performance, we tested snoReport 2.0 in different organisms.

Results

Results of the training and test phases of boxes H/ACA and C/D snoRNAs, in both versions of snoReport, are discussed. Validation on real data was performed to evaluate the predictions of snoReport 2.0. Our program was applied to a set of previously annotated sequences, some of them experimentally confirmed, of humans, nematodes, drosophilids, platypus, chickens and leishmania. We significantly improved the predictions for vertebrates, since the training phase used information of these organisms, but H/ACA box snoRNAs identification was improved for the other ones.

Conclusion

We presented snoReport 2.0, to predict H/ACA box and C/D box snoRNAs, an efficient method to find true positives and avoid false positives in vertebrate organisms. H/ACA box snoRNA classifier showed an F-score of 93 % (an improvement of 10 % regarding the previous version), while C/D box snoRNA classifier, an F-Score of 94 % (improvement of 14 %). Besides, both classifiers exhibited performance measures above 90 %. These results show that snoReport 2.0 avoid false positives and false negatives, allowing to predict snoRNAs with high quality. In the validation phase, snoReport 2.0 predicted 67.43 % of vertebrate organisms for both classes. For Nematodes and Drosophilids, 69 % and 76.67 %, for H/ACA box snoRNAs were predicted, respectively, showing that snoReport 2.0 is good to identify snoRNAs in vertebrates and also H/ACA box snoRNAs in invertebrates organisms.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1345-6) contains supplementary material, which is available to authorized users.

Phylogenetic distribution of plant snoRNA families

Background

Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention.

Results

In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families.

Conclusions

The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3301-2) contains supplementary material, which is available to authorized users.

U6 snRNA intron insertion occurred multiple times during fungi evolution

U6 small nuclear RNAs are part of the splicing machinery. They exhibit several unique features setting them appart from other snRNAs. Reports of introns in structured non-coding RNAs have been very rare. U6 genes, however, were found to be interrupted by an intron in several Schizosaccharomyces species and in 2 Basidiomycota. We conducted a homology search across 147 currently available fungal genome and identified the U6 genes in all but 2 of them. A detailed comparison of their sequences and predicted secondary structures showed that intron insertion events in the U6 snRNA were much more common in the fungal lineage than previously thought. Their positional distribution across the entire mature snRNA strongly suggests a large number of independent events. All the intron sequences reported here show canonical splice site and branch site motifs indicating that they require the splicesomal pathway for their removal.

An updated human snoRNAome

Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing. In order to construct an up-to-date catalog of human snoRNAs we have combined data from various databases, de novo prediction and extensive literature review. In total, we list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes. Utilizing small RNA-seq data from the ENCODE project, our study characterizes the plasticity of snoRNA expression identifying both constitutively as well as cell type specific expressed snoRNAs. Especially, the comparison of malignant to non-malignant tissues and cell types shows a dramatic perturbation of the snoRNA expression profile. Finally, we developed a high-throughput variant of the reverse-transcriptase-based method for identifying 2'-O-methyl modifications in RNAs termed RimSeq. Using the data from this and other high-throughput protocols together with previously reported modification sites and state-of-the-art target prediction methods we re-estimate the snoRNA target RNA interaction network. Our current results assign a reliable modification site to 83% of the canonical snoRNAs, leaving only 76 snoRNA sequences as orphan.

Shank-rearfoot joint coupling in young adults with chronic ankle instability: a cross-correlation analysis

AIM

Chronic ankle instability (CAI) has been associated with changes in gait kinematics which may be associated with the continued instability in this population. Abnormalities in shank-rearfoot joint coupling during gait may be associated with CAI. Cross-correlation analysis provides an estimate of both synchronous and asynchronous coherency between shank and rearfoot motion during gait. The aim of this study was to identify the coupling relationship between transverse plane shank and frontal plane rearfoot motion throughout the entire gait cycle using cross-correlation analysis.

METHODS

Twenty-eight active adults (CAI, N.=15, control, N.=13) participated. Using a 12-camera motion analysis system and an instrumented treadmill, shank rotation and rearfoot inversion/eversion kinematics were collected during walking and jogging. Cross-correlation coefficients with lag times ranging from +15% to -15% were generated from subject means across three strides and compared between the healthy and CAI groups at each speed.

RESULTS

During walking, the CAI group demonstrated stronger cross-correlation coefficients than the control group from lag +10 to +15 (P<0.05). Likewise, during jogging, the CAI group exhibited stronger cross-correlation coefficients than the control group at lags +6 to +15 (P<0.05).

CONCLUSION

The CAI group demonstrated stronger asynchronous coupling relationships between shank rotation and rearfoot inversion-eversion than the control group during both walking and jogging. The more pronounced coupling behavior in the CAI group may indicate less functional variability in shank and rearfoot kinematics during gait due to a more constrained and less adaptable sensorimotor system.

Conservation and losses of non-coding RNAs in avian genomes

Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.

The Expansion of Animal MicroRNA Families Revisited

MicroRNAs are important regulatory small RNAs in many eukaryotes. Due to their small size and simple structure, they are readily innovated de novo. Throughout the evolution of animals, the emergence of novel microRNA families traces key morphological innovations. Here, we use a computational approach based on homology search and parsimony-based presence/absence analysis to draw a comprehensive picture of microRNA evolution in 159 animal species. We confirm previous observations regarding bursts of innovations accompanying the three rounds of genome duplications in vertebrate evolution and in the early evolution of placental mammals. With a much better resolution for the invertebrate lineage compared to large-scale studies, we observe additional bursts of innovation, e.g., in Rhabditoidea. More importantly, we see clear evidence that loss of microRNA families is not an uncommon phenomenon. The Enoplea may serve as a second dramatic example beyond the tunicates. The large-scale analysis presented here also highlights several generic technical issues in the analysis of very large gene families that will require further research.

The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies

Coilin protein scaffolds Cajal bodies (CBs)-subnuclear compartments enriched in small nuclear RNAs (snRNAs)-and promotes efficient spliceosomal snRNP assembly. The molecular function of coilin, which is intrinsically disordered with no defined motifs, is poorly understood. We use UV crosslinking and immunoprecipitation (iCLIP) to determine whether mammalian coilin binds RNA in vivo and to identify targets. Robust detection of snRNA transcripts correlated with coilin ChIP-seq peaks on snRNA genes, indicating that coilin binding to nascent snRNAs is a site-specific CB nucleator. Surprisingly, several hundred small nucleolar RNAs (snoRNAs) were identified as coilin interactors, including numerous unannotated mouse and human snoRNAs. We show that all classes of snoRNAs concentrate in CBs. Moreover, snoRNAs lacking specific CB retention signals traffic through CBs en route to nucleoli, consistent with the role of CBs in small RNP assembly. Thus, coilin couples snRNA and snoRNA biogenesis, making CBs the cellular hub of small ncRNA metabolism.

Single-leg drop landing motor control strategies following acute ankle sprain injury

No research currently exists investigating the effect of acute injury on single-limb landing strategies. The aim of the current study was to analyze the coordination strategies of participants in the acute phase of lateral ankle sprain (LAS) injury. Thirty-seven participants with acute, first-time LAS and 19 uninjured participants completed a single-leg drop landing task on both limbs. Three-dimensional kinematic (angular displacement) and sagittal plane kinetic (moment-of-force) data were acquired for the joints of the lower extremity from 200 ms pre-initial contact (IC) to 200 ms post-IC. The peak magnitude of the vertical component of the ground reaction force (GRF) was also computed. Injured participants displayed a bilateral increase in hip flexion, with altered transverse plane kinematic profiles at the knee and ankle for both limbs (P < 0.05). This coincided with a reduction in the net-supporting flexor moment of the lower extremity (P < 0.05) and magnitude of the peak vertical GRF for the injured limb (21.82 ± 2.44 N/kg vs 24.09 ± 2.77 N/kg; P = 0.013) in injured participants compared to control participants. These results demonstrate that compensatory movement strategies are utilized by participants with acute LAS to successfully reduce the impact forces of landing.

Computational prediction of microRNA genes

The computational identification of novel microRNA (miRNA) genes is a challenging task in bioinformatics. Massive amounts of data describing unknown functional RNA transcripts have to be analyzed for putative miRNA candidates with automated computational pipelines. Beyond those miRNAs that meet the classical definition, high-throughput sequencing techniques have revealed additional miRNA-like molecules that are derived by alternative biogenesis pathways. Exhaustive bioinformatics analyses on such data involve statistical issues as well as precise sequence and structure inspection not only of the functional mature part but also of the whole precursor sequence of the putative miRNA. Apart from a considerable amount of species-specific miRNAs, the majority of all those genes are conserved at least among closely related organisms. Some miRNAs, however, can be traced back to very early points in the evolution of eukaryotic species. Thus, the investigation of the conservation of newly found miRNA candidates comprises an important step in the computational annotation of miRNAs.Topics covered in this chapter include a review on the obvious problem of miRNA annotation and family definition, recommended pipelines of computational miRNA annotation or detection, and an overview of current computer tools for the prediction of miRNAs and their limitations. The chapter closes discussing how those bioinformatic approaches address the problem of faithful miRNA prediction and correct annotation.

snoStrip: a snoRNA annotation pipeline

MOTIVATION

Although small nucleolar RNAs form an important class of non-coding RNAs, no comprehensive annotation efforts have been undertaken, presumably because the task is complicated by both the large number of distinct small nucleolar RNA families and their relatively rapid pace of sequence evolution.

RESULTS

With snoStrip we present an automatic annotation pipeline developed specifically for comparative genomics of small nucleolar RNAs. It makes use of sequence conservation, canonical box motifs as well as secondary structure and predicts putative targets.

AVAILABILITY AND IMPLEMENTATION

The snoStrip web service and the download version is available at http://snostrip.bioinf.uni-leipzig.de/

Matching of Soulmates: coevolution of snoRNAs and their targets

Ribosomal and small nuclear RNAs (snRNAs) comprise numerous modified nucleotides. The modification patterns are retained during evolution, making it even possible to project them from yeast onto human. The stringent conservation of modification sites and the slow evolution of rRNAs and snRNAs contradicts the rapid evolution of small nucleolar RNA (snoRNA) sequences. To explain this discrepancy, we investigated the coevolution of snoRNAs and their targeted sites throughout vertebrates. To measure and evaluate the conservation of RNA-RNA interactions, we defined the interaction conservation index (ICI). It combines the quality of individual interaction with the scope of its conservation in a set of species and serves as an efficient measure to evaluate the conservation of the interaction of snoRNA and target. We show that functions of homologous snoRNAs are evolutionarily stable, thus, members of the same snoRNA family guide equivalent modifications. The conservation of snoRNA sequences is high at target binding regions while the remaining sequence varies significantly. In addition to elucidating principles of correlated evolution, we were able, with the help of the ICI measure, to assign functions to previously orphan snoRNAs and to associate snoRNAs as partners to known chemical modifications unassigned to a given snoRNA. Furthermore, we used predictions of snoRNA functions in conjunction with sequence conservation to identify distant homologies. Because of the high overall entropy of snoRNA sequences, such relationships are hard to detect by means of sequence homology search methods alone.

Genomic and morphological evidence converge to resolve the enigma of Strepsiptera

The phylogeny of insects, one of the most spectacular radiations of life on earth, has received considerable attention. However, the evolutionary roots of one intriguing group of insects, the twisted-wing parasites (Strepsiptera), remain unclear despite centuries of study and debate. Strepsiptera exhibit exceptional larval developmental features, consistent with a predicted step from direct (hemimetabolous) larval development to complete metamorphosis that could have set the stage for the spectacular radiation of metamorphic (holometabolous) insects. Here we report the sequencing of a Strepsiptera genome and show that the analysis of sequence-based genomic data (comprising more than 18 million nucleotides from nearly 4,500 genes obtained from a total of 13 insect genomes), along with genomic metacharacters, clarifies the phylogenetic origin of Strepsiptera and sheds light on the evolution of holometabolous insect development. Our results provide overwhelming support for Strepsiptera as the closest living relatives of beetles (Coleoptera). They demonstrate that the larval developmental features of Strepsiptera, reminiscent of those of hemimetabolous insects, are the result of convergence. Our analyses solve the long-standing enigma of the evolutionary roots of Strepsiptera and reveal that the holometabolous mode of insect development is more malleable than previously thought.

Evolution of the let-7 microRNA family

The increase of bodyplan complexity in early bilaterian evolution is correlates with the advent and diversification of microRNAs. These small RNAs guide animal development by regulating temporal transitions in gene expression involved in cell fate choices and transitions between pluripotency and differentiation. One of the two known microRNAs whose origins date back before the bilaterian ancestor is mir-100. In Bilateria, it appears stably associated in polycistronic transcripts with let-7 and mir-125, two key regulators of development. In vertebrates, these three microRNA families have expanded to form a complex system of developmental regulators. In this contribution, we disentangle the evolutionary history of the let-7 locus, which was restructured independently in nematodes, platyhelminths, and deuterostomes. The foundation of a second let-7 locus in the common ancestor of vertebrates and urochordates predates the vertebrate-specific genome duplications, which then caused a rapid expansion of the let-7 family.

RNAsnoop: efficient target prediction for H/ACA snoRNAs

MOTIVATION

Small nucleolar RNAs are an abundant class of non-coding RNAs that guide chemical modifications of rRNAs, snRNAs and some mRNAs. In the case of many 'orphan' snoRNAs, the targeted nucleotides remain unknown, however. The box H/ACA subclass determines uridine residues that are to be converted into pseudouridines via specific complementary binding in a well-defined secondary structure configuration that is outside the scope of common RNA (co-)folding algorithms.

RESULTS

RNAsnoop implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant. Complemented by an support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H/ACA snoRNA target sites. We apply RNAsnoop to identify the snoRNAs that are responsible for several of the remaining 'orphan' pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H/ACA snoRNAs in Drosophila.

AVAILABILITY

The C source code of RNAsnoop is freely available at http://www.tbi.univie.ac.at/ -htafer/RNAsnoop

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

BACKGROUND

Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available.

RESULTS

A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs.

CONCLUSION

The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.

Accurate and efficient reconstruction of deep phylogenies from structured RNAs

Ribosomal RNA (rRNA) genes are probably the most frequently used data source in phylogenetic reconstruction. Individual columns of rRNA alignments are not independent as a consequence of their highly conserved secondary structures. Unless explicitly taken into account, these correlation can distort the phylogenetic signal and/or lead to gross overestimates of tree stability. Maximum likelihood and Bayesian approaches are of course amenable to using RNA-specific substitution models that treat conserved base pairs appropriately, but require accurate secondary structure models as input. So far, however, no accurate and easy-to-use tool has been available for computing structure-aware alignments and consensus structures that can deal with the large rRNAs. The RNAsalsa approach is designed to fill this gap. Capitalizing on the improved accuracy of pairwise consensus structures and informed by a priori knowledge of group-specific structural constraints, the tool provides both alignments and consensus structures that are of sufficient accuracy for routine phylogenetic analysis based on RNA-specific substitution models. The power of the approach is demonstrated using two rRNA data sets: a mitochondrial rRNA set of 26 Mammalia, and a collection of 28S nuclear rRNAs representative of the five major echinoderm groups.

Evidence for human microRNA-offset RNAs in small RNA sequencing data

MicroRNA-offset-RNAs (moRNAs) were recently detected as highly abundant class of small RNAs in a basal chordate. Using short read sequencing data, we show here that moRNAs are also produced from human microRNA precursors, albeit at quite low expression levels. The expression levels of moRNAs are unrelated to those of the associated microRNAs. Surprisingly, microRNA precursors that also show moRNAs are typically evolutionarily old, comprising more than half of the microRNA families that were present in early Bilateria, while evidence for moRNAs was found only for a relative small fraction of microRNA families of recent origin.

Non-coding RNA annotation of the genome of Trichoplax adhaerens

A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences

Genome-wide multiple sequence alignments (MSAs) are a necessary prerequisite for an increasingly diverse collection of comparative genomic approaches. Here we present a versatile method that generates high-quality MSAs for non-protein-coding sequences. The NcDNAlign pipeline combines pairwise BLAST alignments to create initial MSAs, which are then locally improved and trimmed. The program is optimized for speed and hence is particulary well-suited to pilot studies. We demonstrate the practical use of NcDNAlign in three case studies: the search for ncRNAs in gammaproteobacteria and the analysis of conserved noncoding DNA in nematodes and teleost fish, in the latter case focusing on the fate of duplicated ultra-conserved regions. Compared to the currently widely used genome-wide alignment program TBA, our program results in a 20- to 30-fold reduction of CPU time necessary to generate gammaproteobacterial alignments. A showcase application of bacterial ncRNA prediction based on alignments of both algorithms results in similar sensitivity, false discovery rates, and up to 100 putatively novel ncRNA structures. Similar findings hold for our application of NcDNAlign to the identification of ultra-conserved regions in nematodes and teleosts. Both approaches yield conserved sequences of unknown function, result in novel evolutionary insights into conservation patterns among these genomes, and manifest the benefits of an efficient and reliable genome-wide alignment package. The software is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/NcDNAlign/.

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5′- or 3′-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus.

Factors associated with anterior cruciate ligament injury: history in female athletes

AIM

Little is known about the association of lower extremity structural malalignments, flexibility patterns, generalized laxity, postural control, previous ankle sprain history and the increased risk of anterior cruciate ligament (ACL) injuries in females. We hypothesized that females with a history of ACL injury would be more likely to have a history of prior ankle sprain and different structural alignments than females without a history of ACL injury.

METHODS

It is a case control study: 33 young adult females with a history of an ACL injury and 33 controls with no history of knee injury provided their knee and ankle injury history and had 16 lower extremity measures taken.

RESULTS

The factors most associated with ACL injury history were greater generalized laxity (r(2) change: 0.073), greater genu recurvatum (r(2) change: 0.069), and decreased iliotibial band (ITB) flexibility (r(2) change: 0.069). There was also a significant association between ACL injury history and previous ankle sprain injury history (chi squared=5.27; P=0.02). Those with a history of ACL injury were more likely to have had a prior ipsilateral ankle sprain.

CONCLUSION

Increased generalized laxity, greater genu recurvatum, and decreased ITB flexibility discriminated between females with and without history of ACL injury. A relationship linking previous ankle injury and ACL injury risk was found. Taking a thorough medical history and screening for generalized laxity, genu recurvatum, and a tight ITB in those with a history of LAS, may help identify those at risk for an ACL injury and who may benefit most from preventive measures.

Computational RNomics of drosophilids

Background

Recent experimental and computational studies have provided overwhelming evidence for a plethora of diverse transcripts that are unrelated to protein-coding genes. One subclass consists of those RNAs that require distinctive secondary structure motifs to exert their biological function and hence exhibit distinctive patterns of sequence conservation characteristic for positive selection on RNA secondary structure.

The deep-sequencing of 12 drosophilid species coordinated by the NHGRI provides an ideal data set of comparative computational approaches to determine those genomic loci that code for evolutionarily conserved RNA motifs. This class of loci includes the majority of the known small ncRNAs as well as structured RNA motifs in mRNAs. We report here on a genome-wide survey using RNAz.

Results

We obtain 16 000 high quality predictions among which we recover the majority of the known ncRNAs. Taking a pessimistically estimated false discovery rate of 40% into account, this implies that at least some ten thousand loci in the Drosophila genome show the hallmarks of stabilizing selection action of RNA structure, and hence are most likely functional at the RNA level. A subset of RNAz predictions overlapping with TRF1 and BRF binding sites [Isogai et al., EMBO J. 26: 79–89 (2007)], which are plausible candidates of Pol III transcripts, have been studied in more detail. Among these sequences we identify several "clusters" of ncRNA candidates with striking structural similarities.

Conclusion

The statistical evaluation of the RNAz predictions in comparison with a similar analysis of vertebrate genomes [Washietl et al., Nat. Biotech. 23: 1383–1390 (2005)] shows that qualitatively similar fractions of structured RNAs are found in introns, UTRs, and intergenic regions. The intergenic RNA structures, however, are concentrated much more closely around known protein-coding loci, suggesting that flies have significantly smaller complement of independent structured ncRNAs compared to mammals.

SnoReport: computational identification of snoRNAs with unknown targets

Unlike tRNAs and microRNAs, both classes of snoRNAs, which direct two distinct types of chemical modifications of uracil residues, have proved to be surprisingly difficult to find in genomic sequences. Most computational approaches so far have explicitly used the fact that snoRNAs predominantly target ribosomal RNAs and spliceosomal RNAs. The target is specified by a short stretch of sequence complementarity between the snoRNA and its target. This sequence complementarity to known targets crucially contributes to sensitivity and specificity of snoRNA gene finding algorithms. The discovery of 'orphan' snoRNAs, which either have no known target, or which target ordinary protein-coding mRNAs, however, begs the question whether this class of 'housekeeping' non-coding RNAs is much more widespread and might have a diverse set of regulatory functions. In order to approach this question, we present here a combination of RNA secondary structure prediction and machine learning that is designed to recognize the two major classes of snoRNAs, box C/D and box H/ACA snoRNAs, among ncRNA candidate sequences. The snoReport approach deliberately avoids any usage of target information. We find that the combination of the conserved sequence boxes and secondary structure constraints as a pre-filter with SVM classifiers based on a small set of structural descriptors are sufficient for a reliable identification of snoRNAs. Tests of snoReport on data from several recent experimental surveys show that the approach is feasible; the application to a dataset from a large-scale comparative genomics survey for ncRNAs suggests that there are likely hundreds of previously undescribed 'orphan' snoRNAs still hidden in the human genome.

AVAILABILITY

The snoReport software is implemented in ANSI C. The source code is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/snoReport.

Variations on RNA folding and alignment: lessons from Benasque

Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Structured RNAs in the ENCODE selected regions of the human genome

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic-stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to approximately 2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3'-UTRs. While we estimate a significant false discovery rate of approximately 50%-70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).