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. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench

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

Bioreducible Liposomes for Gene Delivery: From the Formulation to the Mechanism of Action

BACKGROUND: A promising strategy to create stimuli-responsive gene delivery systems is to exploit the redox gradient between the oxidizing extracellular milieu and the reducing cytoplasm in order to disassemble DNA/cationic lipid complexes (lipoplexes). On these premises, we previously described the synthesis of SS14 redox-sensitive gemini surfactant for gene delivery. Although others have attributed the beneficial effects of intracellular reducing environment to reduced glutathione (GSH), these observations cannot rule out the possible implication of the redox milieu in its whole on transfection efficiency of bioreducible transfectants leaving the determinants of DNA release largely undefined. METHODOLOGY/PRINCIPAL FINDINGS: With the aim of addressing this issue, SS14 was here formulated into binary and ternary 100 nm-extruded liposomes and the effects of the helper lipid composition and of the SS14/helper lipids molar ratio on chemical-physical and structural parameters defining transfection effectiveness were investigated. Among all formulations tested, DOPC/DOPE/SS14 at 25:50:25 molar ratio was the most effective in transfection studies owing to the presence of dioleoyl chains and phosphatidylethanolamine head groups in co-lipids. The increase in SS14 content up to 50% along DOPC/DOPE/SS14 liposome series yielded enhanced transfection, up to 2.7-fold higher than that of the benchmark Lipofectamine 2000, without altering cytotoxicity of the corresponding lipoplexes at charge ratio 5. Secondly, we specifically investigated the redox-dependent mechanisms of gene delivery into cells through tailored protocols of transfection in GSH-depleted and repleted vs. increased oxidative stress conditions. Importantly, GSH specifically induced DNA release in batch and in vitro. CONCLUSIONS/SIGNIFICANCE: The presence of helper lipids carrying unsaturated dioleoyl chains and phosphatidylethanolamine head groups significantly improved transfection efficiencies of DOPC/DOPE/SS14 lipoplexes. Most importantly, this study shows that intracellular GSH levels linearly correlated with transfection efficiency while oxidative stress levels did not, highlighting for the first time the pivotal role of GSH rather than oxidative stress in its whole in transfection of bioreducible vectors

Community-Driven Data Analysis Training for Biology

The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org. We developed an infrastructure that facilitates data analysis training in life sciences. It is an interactive learning platform tuned for current types of data and research problems. Importantly, it provides a means for community-wide content creation and maintenance and, finally, enables trainers and trainees to use the tutorials in a variety of situations, such as those where reliable Internet access is unavailable

Deregolazione ipossia-dipendente del ciclo cellulare nelle cellule tumorali MDA-MB 231. Ruolo delle mitogen-activated protein kinases (MAPKs) e dell\u2019hypoxia-inducible factor-1\u3b1 (HIF-1\u3b1)

E\u2019 noto dalla letteratura che le cellule tumorali sono caratterizzate dalla deregolazione del ciclo cellulare e da ipossia, associata alla overespressione del trasduttore dell\u2019ipossia, HIF-1\u3b1 (hypoxia-inducible factor-1\u3b1). Inoltre, in studi precedenti, \ue8 stata trovata una correlazione tra l\u2019ipossia e il pathway delle mitogenactivated protein kinases (MAPKs) nella regolazione del ciclo cellulare. Per contribuire a questi studi abbiamo voluto verificare la correlazione tra HIF-1\u3b1 e il pathway delle tre MAPKs principali, p38, JNK1/2 ed ERK1/2, nella regolazione del ciclo cellulare in ipossia. A questo scopo abbiamo utilizzato un modello cellulare tumorale (MDA-MB 231), invasivo e sensibile allo stimolo ipossico. Per simulare la condizione d\u2019ipossia, abbiamo utilizzato il CoCl2 che \ue8 in grado di attivare HIF-1\u3b1. In questo modello, abbiamo studiato l\u2019effetto dell\u2019ipossia simulata sull\u2019espressione di HIF-1\u3b1 e delle MAPKs e la relazione tra di loro, mediante Western blotting; successivamente, mediante citofluorimetria, abbiamo analizzato il ruolo di HIF-1\u3b1 e delle MAPKs nella regolazione del ciclo cellulare con l\u2019uso di inibitori specifici delle MAPKs. I risultati ottenuti mostrano che il CoCl2 mima una condizione d\u2019ipossia, attivando l\u2019espressione di HIF-1\u3b1 e che, dopo 16 h, ha un effetto citotossico sulle MDA-MB 231, diminuendo la vitalit\ue0. Abbiamo, quindi, analizzato l\u2019effetto del CoCl2 sul ciclo cellulare. I dati mostrano che ad 1 h d\u2019ipossia si ha un accumulo delle cellule in fase S, mentre a 16 h si ha l\u2019arresto del ciclo in fase S; l\u2019ipossia, inoltre, induce l\u2019aumento dell\u2019espressione degli inibitori del ciclo, p21 e p27 sia ad 1 h che a 16 h di trattamento e una riduzione dell\u2019espressione delle cicline D ed E, pi\uf9 marcata a 16 h. Inoltre, l\u2019analisi dell\u2019espressione delle MAPKs in presenza di CoCl2 indica che l\u2019ipossia modula la loro espressione. L\u2019utilizzo di inibitori specifici delle tre MAPKs mostra che l\u2019inibizione dell\u2019espressione di ERK1/2 e di p38 sono correlate ad una modulazione dell\u2019espressione di HIF-1\u3b1. Infine lo studio del ciclo cellulare in - 2 - condizioni ipossiche, con l\u2019utilizzo degli inibitori specifici delle MAPKs, indica che esse sono coinvolte nella progressione del ciclo sia in senso positivo che in senso negativo. In particolare ERK1/2 e JNK1/2 svolgono un ruolo di promotori nella progressione del ciclo cellulare, mentre p38 ha un ruolo negativo, di inbitore della proliferazione. Le MAPKs agiscono sulle varie fasi del ciclo alterando l\u2019espressione delle cicline D ed E, implicate nella regolazione delle fasi G1/S ed S e sugli inibitori del ciclo, p21 e p27. Concludendo, in condizioni ipossiche, le tre MAPKs, p38, JNK1/2 e ERK1/2, in correlazione con HIF-1\u3b1, contribuiscono in maniera diversa alla regolazione della progressione del ciclo cellulare e quindi al destino della cellula tumorale. Sulla base di questi risultati, le MAPKs possono essere considerate un buon target per le terapie anticancr

Templating the semantic web via RSLT

In this paper we introduce RSLT, a simple transformation language for RDF data. RSLT organises the rendering of RDF statements as transformation templates associated to properties or resource types and producing HTML. A prototype based on AngularJs is presented and we also discuss some implementation details and examples