RNAtips aqua

Here’s an interesting tool I came across recently. It’s called RNAtips (RNA (temperature-induced perturbation of structure). It’s a web based tool that aims to tell you regions of RNA that are likely to undergo structural alterations due to temperature change. Here’s the citation:

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The input for RNAtips is either one or two RNA sequences of the same length (in FASTA format). You then specify two temperatures to define the temperature range for which the RNA structural perturbation should be calculated (the default range is 32–39oC).

One of the types of output plots is at the top of this post, where the density of the most temperature-sensitive positions over the whole RNA sequence together with localization of clusters (red blocks) and localisation of nucleotide substitutions (if any) are plotted.

How does it do this? RNAtips deciphers those nucleotides within the RNA sequence, which change the most in their probability to form Watson–Crick bonds in response to a given temperature change. One of the first steps appears to be the calculation of probabilities of nucleotides being paired in a double-stranded conformation  by using the RNAfold tool of the ViennaRNA package. The calculations performed are derived from those described in paper in RNA Biology in 2012. The web server output plots clusters of these temperature-sensitive positions within a sequence, therefore representing the most temperature-sensitive structural regions of that RNA.

This is a very interesting tool and it is useful to make interesting hypotheses relating to your RNA of interest. For example, how do the temperature sensitive regions of an RNA relate to possible alternative splice sites or predicted RNA binding site regions, or to particular secondary structure folds or sequence polymorphisms.

I wonder to what extent the temperature range selected when inputing the sequence data on the web-form influences things. The range 32-39oC is not really applicable to (most) plants. Does this mean the inferences made on RNA structure are ‘wrong’. It would be nice, also if the sequence plots (e.g. picture at the top of post) could be overlaid with multiple plots in order to compare multiple sequences.

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Feeling Fly

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This fly paper caught my eye. It examines how Drosophila monitors daily temperature changes via network of circadian clock regulated neurons. It seems the fly continually integrates temperature informations in order to coordinate sleep and activity patterns.

The work shows that nodes within the circadian network are sensitive to brief changes in temperature, and show that particular neurons are inhibited by heating and excited by cooling. It seems also that light and temperature are processed in distinct ways in the clock neutron network.

Interested to see the use of a fluorescent protein tool called CaMPARI that photo-converts from green to red in proportion to Ca2+ levels –  could this be used in plant work? Would require both light (photo-activation) and temperature manipulation…

The kinetics of temperature response was monitored by measuring intracellular Ca2+ concentrations using a calcium sensor called GCaMP6m and showed that particular neurons showed increases in intracellular calcium during cooling and decreases during heating.

The authors state that their findings reveal that the circadian network transduces brief and transient temperature changes and prolonged increases in temperature in distinct ways.

Thermoreceptors are found in structures in the antennae, called the aristae. Each arista contains both cold-sensitive and heat-sensitive cells. From their figure (below), they found that the responses to cooling and heating were attenuated when the aristae was removed.

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This work is interesting to use since we are trying to understand how plants respond to everyday changes in temperature – both short-term (daily fluctuations) and long term (seasonal) changes in temperature.