Scientists develop a novel method to suppress malaria parasite’s virulence genes, break the code of its immune evasion

Revealed: how malaria evades the immune response by using long noncoding RNA to express one gene while silencing others Up More »

Long Noncoding RNAs in Cardiovascular Diseases

In recent years, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological More »

Integrating Large-Scale RNA-Seq and CLIP-Seq Datasets Enables Study of lncRNA

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism More »

Community Curated Database For LncRNA

A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community. Scientists have More »

Finding the function of long noncoding RNA

Mouse experiments suggest that a noncoding RNA can be vital for successful pregnancy The proteins that underlie nearly all biological More »

 

PostDoc Position Available – Bioinformatics and Computational Biology

lncRNA

PostDoc (2 years) position in Bioinformatics and Computational Biology

The Department of Science and Technology, University of Sannio, Benevento, Italy (http://www.bioinformatics.unisannio.it)

Applications are invited for postdoctoral researchers (Assegno di ricerca) in Bioinformatics in the area of high throughput sequence analysis. The successful post-doc candidate will work in our group, a multidisciplinary bioinformatics team composed by computer and life sciences researchers. The candidate will have opportunities to be involved in cutting-edge research with a high potential for career development. The main activities will be focused on the development of novel algorithms in the context of long ncRNA discovery and regulation.

MINIMUM REQUIREMENTS:

  • Postgraduate or PhD in bioinformatics, computer science, statistics or related fields
  • Programming skills (at least Perl/Bioperl or R/Bioconductor)
  • Experience with machine learning algorithms
  • Adequate level of English (or Italian)
  • Age less or equal 32

PREFERRED QUALIFICATIONS:

  • Publication record in peer-reviewed journals
  • Experience in bioinformatics
  • Good comprehension of biologically relevant problems and good problem-solving skills

TERMS:

The start date for this position is expected to be in May/June 2015 and its duration is of 2 (two) years.

HOW TO APPLY:

Applicants can send their application letter to:
lcerulo [at] unisannio [dot] it
ceccarelli [at] unisannio [dot] it

including, CV with a list of publications, a brief description of research interests, and the full contact information of two referees. The selected candidates will be included in a short list and contacted for an interview (by Skype video call).

Annocript – a flexible pipeline for the annotation of transcriptomes also able to identify putative long noncoding RNAs

The eukaryotic transcriptome is composed of thousands of coding and long noncoding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in a given transcriptome. Here researchers from the Anton Dohrn – Zoological Station introduce Annocript, a pipeline which combines the annotation of protein coding transcripts with the prediction of putative lncRNAs in whole transcriptomes. It downloads and indexes the needed databases, runs the analysis and produces human readable and standard outputs together with summary statistics of the whole analysis.

Availability – Annocript is distributed under the GNU General Public License (version 3 or later) and is freely available at https://github.com/frankMusacchia/Annocript

Contactremo.sanges@szn.it

  • Musacchia F, Basu S, Petrosino G, Salvemini M, Sanges R. (2015) Annocript: a flexible pipeline for the annotation of transcriptomes also able to identify putative long noncoding RNAs. Bioinformatics [Epub ahead of print]. [abstract]

Featured lncRNA – acal

Changes in cell shape affect many critical cellular and bodily processes, like wound healing and developmental events, and when gone awry, metastatic processes in cancer. Evolutionarily conserved signaling pathways govern regulation of these cellular changes. The Jun-N-terminal kinase pathway regulates cell stretching during wound healing and normal development. An extensively studied developmental process is embryonic dorsal closure in fruit flies, a well-established model for the regulation and manner of this cell shape changes.

Here researchers from the National Autonomous University of Mexico describe and characterize a processed, long non-coding RNA locus, acal, that adds a new layer of complexity to the Jun-N-terminal kinase signaling, acting as a negative regulator of the pathway. acal modulates the expression of two key genes in the pathway: the scaffold protein Cka, and the transcription factor Aop. Together, they enable the proper level of Jun-N-terminal kinase pathway activation to occur to allow cell stretching and closure.

lncRNA

  • Ríos-Barrera LD, Gutiérrez-Pérez I, Domínguez M, Riesgo-Escovar JR (2015) acal is a Long Non-coding RNA in JNK Signaling in Epithelial Shape Changes during Drosophila Dorsal Closure. PLoS Genet 11(2): e1004927.[article]

Scientists develop a novel method to suppress malaria parasite’s virulence genes, break the code of its immune evasion

lab-tech

Revealed: how malaria evades the immune response by using long noncoding RNA to express one gene while silencing others

Up to one million people — mainly pregnant woman and young children — are killed each year  by the Plasmodium falciparum parasite, which causes the most devastating form of human malaria.

Now, researchers at the Hebrew University of Jerusalem have revealed the genetic trickery this deadly parasite deploys to escape attack by the human immune system.

The parasite is known to replicate within the circulating blood of infected individuals and modify the surface of infected red blood cells. Its virulence comes from its impressive ability to hide from the immune system by selectively changing which surface proteins it displays.

Upcoming Conference – Long Noncoding RNAs: From Evolution to Function

lncrna

Scientific Organizers: Leonard Lipovich, Jeannie T. Lee, John L. Rinn and James (Ben) Brown

March 15—20, 2015
Keystone Resort, Keystone, Colorado, USA

Sponsored by Cell Research, Isis Pharmaceuticals, Inc., Regeneron Pharmaceuticals, Inc. and Sarepta Therapeutics

Meeting Summary

It has become clear that metazoan genomes are replete with transcription from non-protein-coding regions, generating many long noncoding RNA (lncRNA) transcripts. Recent progress has enabled genome-wide mapping of lncRNAs and has unraveled unifying themes; lncRNAs function as epigenetic regulators, scaffolds, decoys, and enhancers. While these and other themes have been pursued in several meetings, the field has matured in numerous novel directions; the meeting leverages these to characterize lncRNAs comprehensively across metazoan genomes. The aim is to broaden our horizons with emerging data from humans and model systems, empowered by novel genomic technologies, including RNA-protein interaction mapping (CLIP- and RIP-seq), reverse genetics for lncRNAs not conserved in evolution (RNA sequencing in control and lncRNA-perturbed backgrounds), and proteogenomics to empirically bound the translational output of putative lncRNAomes. These topics have recently amassed diverse insights into RNA biology. The meeting should integrate novel findings, enhance previously proposed models of lncRNA function and generate new testable hypotheses. Synthesis of RNA structure, function, evolution and informatics will foster progress in this rapidly growing field. (read more…)

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