Facebook, mySpace, Twitter, and RNA-based metabolic sensors: Remnants of ancient control machinery or ever-present control mechanism?

Social media and riboswitches? They might be more related than you think…. Today, Ruben talks about the ancient origins of riboswitches and poses interesting questions about their future.

If you were a teenager in the early 2000s, you probably used mySpace as your first social media. You might have even posted Emo-inspired pictures and used glittery GIFs. However, unfortunately for mySpace, Facebook was created in 2004 and soon after it started to rapidly overtake mySpace´s users, until 2008 when Facebook became the most used social platform worldwide. Other social media such as Twitter also remain active because it is specialized in a different type of social interaction: less about personal social connections and more about staying informed by following topics, conversations and people. These differences allowed Twitter to conserve their niche on an ever-growing sea of social media options.

This analogy came to my mind while reading about different sensing molecules. In order to survive and reproduce, organism have evolved mechanisms to sense and translate environmental signals as efficiently as possible. It is generally recognized that many of these mechanisms are protein-based molecules, which regulate gene expression in response to a chemical signal (e.g. transcription factors).

Although these protein-based sensing mechanisms explained the regulation of certain biological processes, they are not the only mechanism in action.This is often seen in the lack of correlation between transcriptome and proteome data. Insights into unknown interactions of RNA with metabolites led to the discovery of RNA sensing molecules able to control their own activity, so called: Riboswitches (Templeton et al., 2004).

Continue reading Facebook, mySpace, Twitter, and RNA-based metabolic sensors: Remnants of ancient control machinery or ever-present control mechanism?

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CRISPS/CAS9

It’s appearing all over the place : CRISPR/Cas9. The method has boomed since its 2012 breakthrough moment. Adam Mol walks us through this technology.

Currently, more and more discussions are appearing about CRISPR/Cas9. This technology can be used to edit the genome of almost any organism and the most controversial seems to be editing the genes of human embryos. How does this system works? CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) sequences and CRISPR-associated (Cas) genes were found in a wide variety of bacteria and archaea. The enzyme Cas9 is a DNA endonucleas
e found in many bacteria, where it functions as part of a defense system against invading DNA molecules, e.g. from viruses. The CRISPR/Cas9 system allows for specific genome disruption and replacement in a flexible and simple system, resulting in high specificity and low cell toxicity (Harrison et al., 2014; Peng et al., 2015).

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Fig. 1 CRISPR/Cas9 in action (from Pennisi, 2013; modified)

The CRISPR/Cas9 genome editing system requires the co-expression of a Cas9 protein with a guide RNA. The crRNA and tracrRNA can be fused together to create a chimeric, single-guide RNA (sgRNA). Cas9 has two active sites that each cleave one strand of a double-stranded DNA molecule. The enzyme is guided to the target DNA by an sgRNA that contains a sequence that matches the sequence to be cleaved, which is demarcated by PAM (protospacer-adjacent motif) sequence. (There also exists a RNA-targeting CRISPR/Cas9 complex, called RCas9, that can edit RNA! by J. Doudna; O’Connell et al., 2014).

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Fig. 2 Schematic of the RNA-guided Cas9 nuclease (from Ran et al., 2013)

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Defining Life

What is Life? Why should we care about defining it? As biologists, our research tends to focus on the details, not the bigger picture. Today, Josi Buerger steps back and looks at how the basic concept of “Life” affects topics from conservation to astrobiology.

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The Life Sciences, though young in comparison to other disciplines, have made incredible progress in explaining the tangible world around us. Yet even at the most fundamental level, biological processes remain a mystery. Basic questions remain unanswered: Why did living systems evolve on this planet? Could it have taken radically different forms? Why do organisms display such complexity and diversity?

The fact that we can ask and discuss these questions surely indicates that defining life is unnecessary – we all know what it means and know it when we see it. Our efforts should be aimed at understanding biological processes, not quibbling over a definition…

There are two main concerns why scientists should care about definitions: Firstly, even if we do not fully understand biological processes, there are scenarios where we need to be able to identify and label them. Space exploration comes to mind, or the deep ocean. Secondly, arguing about definitions may not be traditional examples of the “Scientific Method”, but there are concrete examples where definitions affects experimental design: in early evolutionary biology, dentifying life forms from interacting organic material is vital. Or consider the construction of “minimal genomes”: does a self-replicating plasmid suffice as a minimal organism, or does it require a more complex cellular set-up?

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