RNApredator: fast accessibility-based prediction of sRNA targets

Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5′-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.Additional co-authors: Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, and Manja Marz

Safety and feasibility of third-party multipotent adult progenitor cells for immunomodulation therapy after liver transplantation--a phase I study (MISOT-I)

BACKGROUND: Liver transplantation is the definitive treatment for many end-stage liver diseases. However, the life-long immunosuppression needed to prevent graft rejection causes clinically significant side effects. Cellular immunomodulatory therapies may allow the dose of immunosuppressive drugs to be reduced. In the current protocol, we propose to complement immunosuppressive pharmacotherapy with third-party multipotent adult progenitor cells (MAPCs), a culture-selected population of adult adherent stem cells derived from bone marrow that has been shown to display potent immunomodulatory and regenerative properties. In animal models, MAPCs reduce the need for pharmacological immunosuppression after experimental solid organ transplantation and regenerate damaged organs. METHODS: Patients enrolled in this phase I, single-arm, single-center safety and feasibility study (n=3-24) will receive 2 doses of third-party MAPCs after liver transplantation, on days 1 and 3, in addition to a calcineurin-inhibitor-free "bottom-up" immunosuppressive regimen with Basiliximab, mycophenolic acid, and steroids. The study objective is to evaluate the safety and clinical feasibility of MAPC administration in this patient cohort. The primary endpoint of the study is safety, assessed by standardized dose-limiting toxicity events. One secondary endpoint is the time until first biopsy-proven acute rejection, in order to collect first evidence of efficacy. Dose escalation (150, 300, 450, and 600 million MAPCs) will be done according to a 3 + 3 classical escalation design (4 groups of 3-6 patients each). DISCUSSION: If MAPCs are safe for patients undergoing liver transplantation in this study, a phase II/III trial will be conducted to assess their clinical efficacy

Freiburg RNA tools: a central online resource for RNA-focused research and teaching.

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence.

Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of comprehensive characterization in microbes other than Escherichia coli. We have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (Transposon-directed insertion sequencing), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrate a virulence and motility defect of a Salmonella ΔmgrB mutant and reveal an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Our study highlights the power of interpreting available 'omics' datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria

The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis

Careers in context: An international study of career goals as mesostructure between societies’ career-related human potential and proactive career behavior

Careers exist in a societal context that offers both constraints and opportunities for career actors. Whereas most studies focus on proximal individual and/or organisational‐level variables, we provide insights into how career goals and behaviours are understood and embedded in the more distal societal context. More specifically, we operationalise societal context using the career‐related human potential composite and aim to understand if and why career goals and behaviours vary between countries. Drawing on a model of career structuration and using multilevel mediation modelling, we draw on a survey of 17,986 employees from 27 countries, covering nine of GLOBE's 10 cultural clusters, and national statistical data to examine the relationship between societal context (macrostructure building the career‐opportunity structure) and actors' career goals (career mesostructure) and career behaviour (actions). We show that societal context in terms of societies' career‐related human potential composite is negatively associated with the importance given to financial achievements as a specific career mesostructure in a society that is positively related to individuals' proactive career behaviour. Our career mesostructure fully mediates the relationship between societal context and individuals' proactive career behaviour. In this way, we expand career theory's scope beyond occupation‐ and organisation‐related factors

Unsupervised construction, evaluation and visualisation of RNA family models

RNA-Familien werden in den Computerwissenschaften durch RNA-Familien Modelle, auch bekannt als Covarianz-Modelle repräsentiert. Covarianz-Modelle bilden Struktur und Sequenz der Familie als statistisches Modell ab. Sie machen es möglich weitere, zuvor unbekannte, Vertreter der RNA Familie in genomischen Sequenzen zu identifizieren. Dieser Vorgang ermöglicht es bekanntes Wissen und experimentelle Ergebnisse von einem auf den anderen Organismus zu transferieren und vereinfacht das Design neuer Experimente. In der Vergangenheit wurden RNA-Familien Modelle durch manuelles Sammeln und Verfeinern, oder durch automatische Losungen für einige wenige spezielle RNA Familien konstruiert. Die Publikation ”RNAlien - Unsupervised RNA-family model construction” stellt eine neue Methode zum automatischen Konstruieren solcher Modelle, prinzipiell für jede RNA Sequenz, vor. RNAlien, ausgehend von einer einzelnen Eingabesequenz, sammelt potentielle Familien- mitglieder durch multiple Iteration von Homologiesuche. RNA-Familien Modelle werden automatisch für die gefundenen Sequenzen gebaut. Die Qualitat von RNA-Familien Modellen und ihre Leistungsfähigkeit in der Homologiesuche hängt von verschiedenen Faktoren ab. RNAlien wertet sowohl die Modelle, als auch die alignierten Sequenzen die zum Bau der Modelle verwendet wurden, aus um so viel Information wie möglich zur Verfügung zu stellen. Dies berücksichtigt allerdings nur das neukonstruierte Modell und setzt es nicht in Beziehung zu anderen Modellen. Die folgende Publikation, mit dem Titel ”CMCompare webserver: comparing RNA families via covariance models”, behandelt den Vergleich zwischen Modellen. Dies erlaubt die Identifizierung von Modellen mit schlecher Spezifität und die Untersuchung von Beziehungen zwischen Modellen. Visualisierung dieser Zusammenhänge hilft bei der Identifizierung von Kandidaten für Clans, Gruppen biologisch verknüpfter Familien. Darüberhinaus wird ein Programmpacket, mit dem Namen TaxonomyTools, vorgestellt, welches die Visualsierung und den Vergleich der Taxonomie von gefundenen RNA Familien Mitgliedern ermöglicht. Sequenzen von Familienmitglieder, die von RNAlien wahrend des Konstruktionsprozesses identifiziert wurden, sind ein Ausgangspunkt für die weitere Untersuchung der Familie. UCSC genome browser hubs visualisieren die gefundenen Familienmitglieder in ihrem genomischen Kontext, was Eigenschaften wie zum Beispiel Orthologie sichtbar macht. Methoden um solche Hubs zu bauen wurden als Beitrag mit der Publikation ”ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines” veröffentlicht und werden hier präsentiert.RNA performs important functions in all organisms, for example mediating gene expression. RNAs are often evolutionary conserved over large set of species, giving rise to families of homologous RNA genes. These RNA families exhibit not only sequence similarity, but are often characterized by strong conservation of the RNA structure. Computationally, RNA families are represented by RNA-family models, also known as covariance models. Covariance models capture structure and sequence of the family in a probabilistic model. They enable the prediction of additional, previously unknown, members of the RNA-family from genomic sequences. This allows a knowledge transfer between organisms and helps in designing experiments. Up to now RNA-family models were constructed by manual collection and curation, or automatic solutions for a few specific RNA families. The peer- reviewed publication for ”RNAlien - Unsupervised RNA-family model construction” introduces a novel method to automatically construct such models, in principle for any RNA sequence. RNAlien, starting from a single input se- quence collects potential family member sequences by multiple iterations of homology search. RNA-family models are fully automatically constructed for the found sequences. The quality of RNA-family models and their performance in homology search depends on several factors. RNAlien evaluates both the models as well as the aligned sequences used to build them, to provide as much information about the model as possible. However this takes only the novel model itself into consideration, but does not investigate it in context with other models. The following manuscript, with the title ”CMCompare webserver: comparing RNA families via covariance models”, addresses the comparison between models. This allows to identify models with poor specificity and to explore the relationship between models. Visualisation of family relationships helps in identifying candidates for clans, groups of biologically related families. Moreover the thesis presents a novel tool to visualise and compare the taxonomy of of found RNA-family members, called TaxonomyTools. Family member sequences found by RNAlien during the model construction process are also a useful starting point for investigating families. UCSC genome browser hubs visualise the found family members in their genetic context, showing traits like orthology. Methods to constructs such hubs were contributed to the publication ”ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines” and are also presented in the thesis