“now acceptable for publication” :-)

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Ahhh….the best 4 words in scientific research? It’s been a long, arduous trip but finally we shall be adding a few dents to our current knowledge of alternative splicing/splicing factors/temperature and the clock….will keep you posted.

Made me think about the time it takes to publish scientific research, and I came across this commentary article in Nature from 2016.

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I think many of us working at the coal-face of research will recognise a lot of what it says, e.g.

Many….feel trapped in a cycle of submission, rejection, review, re-review and re-re-review that seems to eat up months of their lives, interfere with job, grant and tenure applications and slow down the dissemination of results.”

Also talks about “resetting the clock” – not to do with circadian clocks, but related to the time stamp of submission and resubmission(s).

Is it taking longer to publish? One contributor to the article says that the average time for their group of papers took 9 months…[9 months is good, no?]

Anyway, for the time being lets focus on…”now acceptable for publication” 🙂

 

Splicing based body-temperature thermometer

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This work from the Lab of RNA Biochemistry at the Freie University Berlin shows just how sensitive splicing is to small changes in body temperature.

They looked at alternative splicing (AS) of U2af26 across a physiologically relevant temperature range (35-40oC). [U2af26 is a component of the essential splicing factor U2af (U2 auxiliary factor) where it can substitute for U2af35 in heterodimers with U2af65]

The authors show that U2af26 exon 6/7 skipping showed a very nice linear correlation with the temperature (see their figure below), suggesting that AS is able to react in a thermometer like way to read body temperature changes.

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The paper goes on to show an involvement for SR proteins in temperature-regulated U2af26 AS, primarily via modulation of the phosphorylation state of SRs. The authors speculate that there will be a physiological role for temperature-controlled AS in other phenomena, such as hypothermia and fever.

 

 

Are RNA thermosensors all around us?

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Are RNA thermosensors more common than we thought? Interesting article in the Journal of Experimental Biology speculating whether RNA thermometers (RNATs), well-studied in Prokaryotes, are prevalent in the other Kingdoms of Life.

Changes in the conformation of RNATs (see their Figure 1, above) typically involve melting of short regions of the mRNA, for example hairpin structures, in response to elevated temperature (a ‘zipper’ mechanism) or a shift between alternative conformations of the mRNA that involve larger regions of the molecule (a ‘switch’ mechanism).

The RNAT contains the Shine–Dalgarno (S–D) sequence (AGGAGG) that, when fully exposed, can bind to the small (30S) ribosomal subunit and allow translation to commence. The start codon (AUG) is often located eight nucleotides downstream from the S–D sequence. Thus melting of the ‘thermometer’ allows the S–D sequence and start codon to interact with the 30S subunit, promoting translation of the mRNA.

Interesting read – I wasn’t familiar with the concept of  ‘marginal stability’ – the idea that for RNA secondary and tertiary structures, thermosensor regions must have the right stability – or ‘balancing act’ – to allow temperature-driven changes in shape to take place when (and only when) a signalling function is required.

I particularly liked the section on ‘Differential translation of allelic mRNAs: another way to modulate the proteome?‘ – the concept that natural variants (allozymes) with different thermal optima can provide a species with an opportunity to establish populations with adaptively different thermal optima in regions of its biogeographic range where temperatures differ. Thus a cold-optimised allozyme might be more common in populations living in colder regions of a species’ range, whereas the warm-optimised allozyme would be dominant in warmer regions, and therefore crucially that slight changes in base composition likely alter the thermally sensitive mRNA structures that govern translational ability in a way that ensures differential translation of distinct allelic messages.

The author, George Somero, make an interesting point that we might assume that “changes in temperature often are regarded as having negative influences on macromolecular stability” adding “However, there is also a ‘good’ side to this thermal perturbation: the alteration in conformation of the macromolecule that is caused by a change in temperature can function as a thermosensing mechanism and lead to downstream changes that are adaptive to the cell.”

Exciting times lie ahead for RNA structure and temperature sensing….

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Improved Gateway

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Trying to re-learn the language of GATEWAY cloning. ‘BP reactions’, ‘LR cloning’, ‘attB sites’, ‘entry clones’, ‘destination vectors’, ‘binary vectors’…I could go on. Thinking of trying a series of ‘Improved Gateway Binary Vectors (ImpGWBs)‘ to make plants express our genes of interest (GOIs) fused to markers. These are described in this paper:

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As for the choice of marker, there is a dizzying choice, so as well as trying to get to grips with GATEWAY, there is the question of what best to use as marker. I’ve had disappointing results fusing our GOIs to green fluorescent protein (GFP) in the past, so maybe time to try something else. As you can see, there is no shortage of choice:

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How long is a piece of stri…promoter?

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Trying to work out how long to make the upstream promoter region for some plasmid constructs. I’ve been using the SnapGene tool to visually stitch together DNA sequences.

How long is the promoter for a particular plant gene? 500, 1000, 2000 bp? or is it defined by particular features in the promoter? I guess for some genes the upstream region barges into other gene loci.

I tried out this web-tool, plantpromoterdb.

Seems quite useful. It displays some features of the promoter that might be considered when deciding the promoter chunk length e.g. it will show the predicted transcriptional start site, and other cis– features.

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Seems, though, that most studies take a nominal 1000 to 2000bp upstream of the translational start codon (ATG). Think it’s good to know some of the promoter ‘landscape’ though. Here’s the reference for plantpromoterdb:

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We are Stu-Dents

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Always amuses me the infographic from Matt Might called ‘The illustrated guide to a Ph.D,’ (click here for the full infographic page). Very useful for new Ph.D. candidates, but it I guess it’s just as valid for anyone working at the coal-face of scientific research. We are all just trying to make small dents at the boundary of scientific knowledge – ‘suppose that makes us all eternal stu-dents!

 

Friday read

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Science is a pretty earnest endeavour, sometimes it’s healthy to poke fun at it. The Independent Standard is a serious sounding web-site, but it’s effectively along the lines of the ‘Daily Mash‘ or ‘The Poke‘ for the Sciences.

I would recommend visiting this site if you want to cut-free from the Science wheel for a while. They are all spoof stories but sometimes the parody is so deep that it actually makes you think about the process of Science.

Some good examples are:

Human Tears Are The Best Thing For Precipitating DNA…..worth thinking about the next time a DNA/RNA prep comes around

An ‘Eppendorf For Life’ Scheme Launched…we have shopping bags for life…what about Eppendorfs for life..

and Leeds Scientist Refuses To Do Southern Blot….reporting regional variations in attitudes to molecular biology techniques

 

Collecting Cobras 2

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As a follow-up to the earlier ‘Counting Cobras‘ post, Hugh pointed out this recent opinion article from The EMBO Journal written by Alain Prochiantz.

The author recommends playing the science ‘game’ – for example by trying to publish in the so-called high ranking journals even if they do not necessarily reflect novelty and importance, because this is important for obtaining grant funding. Interestingly the idea of developing side projects appealed to me – the concept of planting seeds that, although would probably not get published in stellar journals or even accepted by peers short-term (see “You should stop science”, “you are making a fool of yourself”), but nonetheless with time might grow and branch out into research with high impact.

Other notable comments were the idea that “…there never really is a golden age [in science research]” and ” …it was not better yesterday but [..] it will be better tomorrow, provided that we never forget to defend the “Value of science”.

and finally…”Science remains a game, a game that must be taken very seriously, but nevertheless enjoyed”.

I suppose it’s trying to keep that balance – to play the game enjoyably!?

Collecting Cobras

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Interesting article last week – “performance-driven culture is ruining scientific research‘ – in the Guardian that has led to much discussion amongst the post-docs. All about the impact factor (IF) metrics – an arbitrary measure of how high (…or low) a journal is ranked. The article argues that a fixation on IFs, together with the Research Excellence Framework (REF) excise, detrimentally affects the diversity of Science research. The article starts off with an interesting anecdote about collecting cobra snakes during British rule in India…

Interesting also to see the range of comments after the article, ranging from – Science should be no different from other areas of work where performance led metrics are used  – to there needs to be a change in culture, would Darwin’s or Einstein’s ideas have emerged in a performance led scientific culture? Oh, and someone else noted the cheesy stock photo (above) as a common sight in all labs!