Science & Technology

The Science Dispatches (24/06/18). Some ‘Junk DNA’ may have role in embryo-development. Laser bursts give more efficient electricity generation.

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The science dispatches for the third week of June, including a newly discovered role for the junk DNA ‘jumping gene’ in embryo development and the unification of theory and experiment concerning the generation of electricity in nano-technology.

Researchers discover a possible role for ‘jumping gene’ in early embryo development

New research indicates that some junk DNA may be vital in moving past the two-cell embryo stage of development

Scientists have long been aware that almost 99% of our genome may effectively serve little purpose, with only 1% accounting for the encoding of proteins. Many of these non-coding regions have been discovered to fulfil important regulatory purposes with other sections considered ‘junk’ accumulated through millions of years of evolutionary history. Over half of this ‘junk’ is made up of transposable elements or transposons, genetic material that replicates itself and inserts copies at various places in the genome, much like a virus. Junk DNA is known to be made up of hundreds of thousands of these replications.

The most common of these sections is known as the ‘LINE1’ transposon, which accounts for roughly 17% of our DNA. This transposon, referred to as a ‘jumping gene’ has previously been held to be little more than a genetic parasite which, much like other transposons, could be responsible for various diseases and afflictions such as the mutations that lead to cancers. Now research published in the journal Cell indicates that the LINE1 transposon may actually have a vital purpose after all.

The LINE1 transposon replicates itself and inserts copies through the genome

The study, led by UC San Francisco scientists, found that early stage mice embryos and stem cells expressed high levels of LINE1 RNA. This led the researchers to believe that the transposon may actually play an important role in embryo development, in particular in helping the embryo pass from the two cell stage of development by turning on genes necessary for the embryo to further develop.

To test this idea, researcher Michelle Perchade, PhD, set about eliminating LINE1 RNA from mouse embryonic stem cells. The result of this was to change the pattern of gene expression changing it to something more likely to be seen in a two-cell arrangement found just after fertilisation. The effect of removing the LINE1 transposon from fertilised eggs was even more dramatic. The team found that in this case, the absence of LINE1 transposons resulted in the embryo being unable to progress past the two-cell stage.

Expanding on these experiments that team discover that rather than simply replicating itself and inserting the copies about the genome, the LINE1 transposon remains enclosed in the nucleus. Here it joins with proteins to form a complex which helps ‘switch off’ the genetic programming that dominates the two-cell stage of development, thus allowing the embryo to move to a new stage of development.

Perchade now hopes that as a result of this pain-staking five-year study, other scientists will follow suit and sit up and take notice of so-called ‘jumping genes’. She may have a long way to go, though. Other scientists have expressed scepticism regarding the findings. Geneticist Haig Kazazian of Johns Hopkins University School of Medicine in Baltimore, Maryland, points out that there are over 500,000 scattered through the genome, many of which are inside genes. He believes that the process of removing LINE1 also resulted in some of these genes being ‘turned off’. Therefore the halt in development may be a result of the failure of these genes rather than the removal of LINE1.

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Generation of electricity by laser burst on the nanoscale more efficient than traditional methods

University of Rochester illustration / Michael Osadciw

Back in 2007, the US Department of Energy issued a challenge to the nation’s physicists. Could they manipulate matter on the nanoscale and understand how matter behaves far beyond equilibrium. In response to this, using glass thread thousands of times finer than a human hair between two metals and a laser burst less than a billionth of second long, physicists have been to generate a burst of electric current across a makeshift circuit, referred to as a nanoscale junction (or nanojunction), faster than any other method of generating electricity. And all without an applied voltage. The direction and magnitude of this current can be changed by simply changing the phase of the applied laser. The remarkable thing about this phenomena is the fact that the glass is transformed by the laser pulse, acting more like a metal.

What the experiment demonstrates is the control of matter by using lasers. Now a group of physicists led by Ignacio Franco, assistant professor of chemistry and physics at the University of Rochester, who initially predicted that pulses of lasers could generate super-fast electricity back in a 2007 paper, believe that this experiment may represent a new phase in our ability of control matter.

The difficulty in performing the experiment practically has been building nanojunctions so small they would demonstrate such effects. Researchers also struggled to measure the effects of the experiment before the laser pulses destroyed the glass (or in some cases carbon) threads. In 2013 researchers at the Planck Institute were able to build a nanojunction and demonstrate the effect and move it beyond theory. Even then the exact mechanics and cause of the effect remained shrouded in mystery.

To solve this mystery, Franco and his team ran a four-year stimulation of the experiment involving millions of hours of computing power. These simulations, the paper states, prove that the phenomena are driven by the ‘Stark effect’ as theorized by Franco in a 2007 paper.

The Stark effect is the splitting of atomic spectral lines by the application of an electric field, similar to the Zeeman effect in all but the fact that the splitting is not symmetrical.

Discussing his work, published this month in Nature Communications, Franco states “This marks a new frontier in the control of electrons using lasers. You will not build a car out of this, but you will be able to generate currents faster than ever before,” Franco says. “You will be able to develop electronic circuits a few billionths of a meter long that operate in a millionth of a billionth of a second timescale. But, more importantly, this is a wonderful example of how differently matter can behave when driven far from equilibrium. The lasers shake the nanojunction so hard that it completely changes its properties. This implies that we can use light to tune the behaviour of matter.”

The successful replication of experimental results in computer simulations represents the uniting of theoretical and experimental physics and the findings themselves may well have profound implications for future advances in computation.

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