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Tebubio's blog - Acting and reacting in life sciences and biotechnologies
  • Home
  • Research areas
    • ADME-Tox
    • Biomarkers
    • Cell Biology and Signalling
    • Cell Sourcing – Cell Culture Technologies
    • Drug Discovery
    • Gene Expression – Molecular Biology
    • Stem Cells
    • Supplying Discovery Tools
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  • Meet the authors
News

AACR2017 Poster download – Modulation of CAF expressed podoplanin activity in TME

18/04/2017 by Sara Pierre No Comments

This year again, we were pleased to attend the Annual meeting of the AACR (American Association for Cancer Research), which took place in Washington DC, USA at the beginning of April.

Nadia Normand Ph.D. (Business Development Manager, tebu-bio), presented a poster with results from collaborative work between the Centre for Molecular Biophysics of the CNRS (Orléans, France), tebu-bio Laboratories (Le Perray en Yvelines, France), Anaxomics Biotech (Barcelona, Spain) and the Institute of Immunology and Experimental Therapy (Wroclaw, Poland).

miRNome analyses reveal that activity of CAF expressed podoplanin in the tumor microenvironment is modulated by exosome miRNAs involved in the PTEN-PI3K-AKT-mTOR signaling
This poster “miRNome analyses reveal that activity of CAF expressed podoplanin in the tumor microenvironment is modulated by exosome miRNAs involved in the PTEN-PI3K-AKT-mTOR signaling” is now available for downloading – get your copy here.

News

miRNA modulates immune response to Mycobacterium

18/02/2016 by Ana Arraztio No Comments
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Source: Kumar M. et al. (DOI: http://dx.doi.org/10.1016/j.chom.2015.01.007).

The outcome of the interaction between Mycobacterium tuberculosis (Mtb) and a macrophage depends on the interplay between host defense and bacterial immune subversion mechanisms. MicroRNAs (miRNAs) critically regulate several host defense pathways, but their role in the Mtb-macrophage interplay remains unclear.

Recently, Kumar et al. performed a miRNA profiling, and investigated the downregulation of miR-let-7f in a manner dependent on the Mtb secreted effector ESAT-6.

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Biomarkers

The hunt for predictive biomarkers

20/10/2015 by Ana Arraztio No Comments

stock-photo-34045768-young-women-operating-the-control-panel

Searching for predictive biomarkers lies in the heart of the concept of Personalised Medicine. Leaving aside some ethical aspects such as whether you want to know (or having other people knowing) your genetic disposition and/or the impact that your life style / environment will have in your future health (not to mention that these tools are still only accessible to a small percentage of the world’s population), we mention here some points that should be addressed if you want to start a study to find new predictive biomarkers.

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Gene Expression - Molecular Biology

Small RNAs have diverse 5′ end structures

16/09/2015 by Mark Livingstone No Comments

Piero Carninci’s group at RIKEN published an article last year demonstrating that small RNAs can possess a large variety of 5′ cap structures including a 2,7 dimethylguanosine modification and found multiple cap structures (mGpppC, 7mGpppG, GpppG, GpppA, and 7mGpppA) in small RNA pools.

journal.pone.0102895.g004

Source: DOI: 10.1371/journal.pone.0102895

This adds a further level of complication to small RNA sequencing library prep, as such protocols generally allow for sequencing only of RNAs with a 5′ monophosphate. In general, mature, functional microRNAs are thought to carry a simple 5′ monophosphate, and ligation kits such as the CleanTag™ Ligation Kit for Small RNA Library Preparation that use T4 RNA Ligase to fix oligonucleotides to the 5′ end of RNA will effectively oligocap this 5′-monophosphated RNA population. Carninci’s group used a variety of approaches including decapping with tobacco acid pyrophosphatase, CAGE, and immunoprecipitation with 2,2,7-trimethylguanosine to perform their study, but this isn’t the first time we have heard about cap structures on small RNAs.

Source: "MiRNA-biogenesis" by Narayanese at English Wikipedia. Licensed under CC BY-SA 3.0 via Commons - https://commons.wikimedia.org/wiki/File:MiRNA-biogenesis.jpg#/media/File:MiRNA-biogenesis.jpg

Image Source: “MiRNA-biogenesis” by Narayanese, Wikipedia. 

 

We have known for quite some time that small RNAs can possess 5′ structures. The now discontinued ScriptMiner™ small-RNA–seq library prep kit from Epicentre® (an Illumina Company), for example, included protocols for removal of 5′ cap structures with Epicentre’s tobacco acid pyrophosphatase to allow capture of small 5′-capped and 5′-triphosphorylated RNAs in addition to 5′-monophosphate RNAs. Due to the discontinuation of tobacco acid pyrophosphatase, tebu-bio’s Decapping Pyrophosphohydrolase or CellScript’s Cap-Clip™ Acid Pyrophosphatase is now recommended to convert RNAs with diverse 5′ structures to 5′-monophosphate RNA for oligo-capping.

While next generation sequencing is quickly replacing array-based genomics/transcriptomics technologies, library prep for miRNA sequencing remains relatively complex. Due to the complexity of adapter-dimers and 5′ cap structures, array-based genome-wide miRNA expression analysis remains the first choice for many researchers.

The cap structures present on small RNAs appear to be either added during transcription or may be the result of a yet-to-be characterized mechanism for capping of RNA degradation products. An excellent resource for learning more about RNA 5′ structures is the Modomics website, which allows users to visualize various cap structures and gives the identify of the enzymes responsible for the modifications.

Source: http://modomics.genesilico.pl/pathways/pppN/

Source: http://modomics.genesilico.pl/pathways/pppN/

 

Here are some of tebu-bio’s top products and services for isolating and studying small RNAs:

  • RNAzol® RT RNA Isolation Reagent – the most effective reagent for isolation of total RNA and small RNA from samples of various origins
  • MasterPure™ RNA Purification Kits – for isolation of total RNA without columns and without dangerous solvents
  • CleanTag™ Ligation Kit for Small RNA Library Prep –  includes chemically modified adapters that greatly reduce adapter dimers
  • iSWAB™ RNA – collection kit for RNA from buccal swabs or blood drops stabilizes donor samples at room temperature
  • miRNA solutions – qPCR primers, 3’UTR target clones, precursor miRNA expression clones, miRNA inhibitors
  • tebu-bio’s 3D-Gene® miRNA profiling platform – a full service array-based miRNA profiling service
  • custom synthetic miRNAs and 2’-O-methylated oligonucleotides – tebu-bio can provide the most complex chemically-modified oligonucleotides
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