What should you buy if you have the cash to spare? Time, apparently, as opposed to things. Buying time makes you happy. This is the link to the actual scientific paper, hence a bit dry, but it’s not hugely technical.
Finally, this week’s featured image shows the FlyPi, a 3D printed fluorescent microscope system based on a Raspberry Pi computer system that has been developed by the Baden lab here at Sussex University. They can be built for less than 100 Euros, compared to the 1000s that even a basic microscope usually costs. Website includes link to the original paper, with full technical detail, and other resources.
Well, it was only a matter of time. All the major news outlets are reporting the breakthrough of a research team that managed to use CRISPR/Cas9 to edit human embryos that carried a mutation which causes cardiac hypertrophy (MYBPC3) – a thickening of the heart muscle that is the leading cause of death in young atheletes. Continue reading →
Well, what will they think of next? A little while ago, I wrote about the possibilities of using DNA as information storage. Researchers have now managed to insert a little movie into the genome of the E.coli bacterium (the workhorse of the genetics world). They used the CRISPR/Cas9 genome editing technique to insert the five frames of a galloping horse. Essentially, the snippets of DNA generated by CRISPR were used to correspond to pixels. Here’s the GIF:
Of course, you need to decode the message written in the nucleotides of the bacterial DNA to reconstruct the image (or movie), so you also have to have the ability to read it and know the code, and it’s incredibly laborious. You can’t just read it off one cell either, nor with one pass – it took several hundred thousand reads for the whole thing.
So why would you bother? Honestly, that’s a little ambiguous at the moment. Their original idea was to actually create a recording system to monitor changes happening in cells, in order, ultimately, to decipher how brain cells take on distinct identities. Instead of using indirect measurements or experimental perturbation to answer these questions, it would essentially get the cells to tell you what was happening to them themselves. They didn’t achieve that, but it’s a step towards it. Like many science advances, it’s an impressive technical feat that for now remains just a curio, but who knows where it may ultimately lead?
Shipman, S. L., et al. Nature (2017). http://dx.doi.org/10.1038/nature23017
Who would like to hear some really good news? Thought so. One of the promises of the molecular biology and genomics revolutions was that gene therapy – replacing defective, disease-causing genes with functioning ones, or otherwise treating these diseases by genetic means – would become a reality. Even, optimistically, something commonplace. Like so many things, however, it has proved more complicated than hoped, and those longed-for treatments elusive. There has never been a therapy of any kind that alters the disease progress of a neurodegenerative disease – until now. Continue reading →
Probably most of us are aware that plants take sunlight and use it to “fix” carbon from carbon dioxide (CO2) in the atmosphere into sugar compounds by the process of photosynthesis. In fact, natural photosynthesis removes about 100 billion tonnes of CO2 from the atmosphere every year. The natural release and absorption of CO2 is balanced – but humans are releasing over 30 billion tonnes per year on top of that, which is increasing the CO2 in the atmosphere and causing global warming; this exceeds the ability of plants to remove it. But what if we could find a way to make carbon fixation more efficient? Now, a team of researchers have done just that. Continue reading →
Firstly, sincere apologies for the reduced frequency of posting. New job, and new term in full swing (not to mention a lot of baby illness), has meant very little spare time. Things will be slow for a while, but I hope to pick up again more in November.
Lifeforms based on biochemistries other than that found on Earth are a small but firm favourite in science fiction, which is interesting given that so many aliens found in science fiction fall into the “Rubber-Forehead alien” trope beloved of Star Trek. Some of these exotic organisms are just microorganisms, which makes it a bit easier – like the infectious agent in Wyndham’s The Andromeda Strain. I would love to create a truly alien world with fully-fledged thinking aliens based on a unique biochemistry…but I have to say to do so properly would require an enormous amount of research and work (which is to say it would take far more time than I feel I will ever possess!)
The classic is probably the “silicon based lifeform”, perhaps most recognisably in the Horta, the, er, rock beast thing that Spock communed with in Star Trek (after they’d finished zapping it, anyway)
The X-files went one further and had a silicon-based fungus that sent you slightly bonkers (of course). Our life is, famously, “carbon-based” – this is actually referring to the vast majority of organic compounds that are built around carbon and its remarkable talent for bonding with other elements. Silicon, a similar element, is often argued as an alternative, but there are problems with this: silicon is a much larger atom, and it doesn’t form bonds with other elements nearly so readily as carbon does. Moreover, carbon is far more abundant in the galaxy. In fact, on our planet, silicon is the more abundant element, but life arose from carbon anyway.
As an interesting aside, a thermophilic bacterium that lives in hot springs has been found to have a fundamental metabolic enzyme, cytochrome c, that can incorporate silicon into organic molecules, really as an accidental byproduct. Researchers have recently artificially selected this enzyme so that is several thousand times more efficient at this process; not that useful, at the moment, but very interesting nonetheless (and yes, they thought of the Horta too!).
Now researchers are trying to make an organism with a modified genetic code. The genetic code is how the information in DNA is converted into a protein. Three nucleotide bases of a DNA (that sequence of A,T,G and C you’ve all seen) codes (via a “messenger” RNA intermediate) for one amino acid, the building block of a protein. A few encode “start” and “stop” signals for the synthetic machinery. There are about 20 commonly used amino acids in living organims (on this planet), although the code allows for more – there are 64 of these “codons” in fact, and some of them are redundant; that is, they can code for more than one amino acid (you will notice from the table below that it is the last base in the triplet that tends to vary). This reduces the possibility of a mutation in the DNA sequence actually causing a potentially damaging change in the protein.
What these researchers have now done is eliminate 7 of the redundant codons in the bacterium E.coli, to leave 57, reasoning that since they were redundant this was unlikely to do the cell any harm. This may sound a little underwhelming, but it is no mean technical feat: they would have to remove every instance of these codons (all 62,214 of them) in the nearly 4 million bases of DNA in the bacterium. Removing them piecemeal would have taken too long, so they essentially re-sequenced the entire genome from scratch.
Figure 2A: Codons AGA, AGG, AGC, AGU, UUA, UUG, and UAG were computationally replaced by synonymous alternatives (center). Other codons (e.g.,UGC) remain unchanged. Color-coded histograms represent the abundance of the seven forbidden codons in each segment.
Why bother? Like a lot of speculative science, it’s a little hard to tell how useful it will be, but there are a lot of potential uses. E.coli is used to synthesise a lot of proteins useful to us, like a little bioreactor, and this could render it immune to infection by viruses that depend on the codons it no longer uses. Additionally, these seven removed codons could now be used to code for a new synthetic amino acid not normally found in nature, potentially opening up a world of novel proteins. (Oh, and yes, they did build in a failsafe). This is still a work in progress; the genome hasn’t been completely assembled yet, but it’s an interesting and conceptually radical idea. It’s not a non-carbon based biochemistry, to be sure, but, if it were taken a few steps further, it could mean we could create an entirely synthetic organism with an entirely different genetic code to our own. And that’s pretty science fiction, if you ask me.
Ostrov et al, 2016: Design, synthesis and testing toward a 57-codon genome, Science Vol. 353, Issue 6301, pp. 819-822 DOI: 10.1126/science.aaf3639
(Edit note: I somehow disappeared this whilst correcting an image, so if it’s still problematic, drop me a note!)
One of the major medical advances of the last century was that of organ transplantation: replacing diseased organs with healthy ones from donors (usually the recently dead, but there are exceptions: you can donate one kidney, or parts of your liver, for example). It is a process that has become ever more successful, with improvements in surgery and drugs that suppress the immune system, preventing it from destroying the donated organ. However, this has created a demand for donor organs that is not being met: about 100,000 people worldwide are waiting for donor organs, and many thousands die before they receive one. Continue reading →