ICAR, Penn State team makes a tool small enough to edit plant genomes

Context:

• Researchers have developed a plant genome editor consisting of a protein derived from Deinococcus radiodurans bacteria, famous for being able to survive extreme conditions.
• The protein is less than half the size of the proteins CRISPR commonly uses to target specific parts of the DNA.

CRISPR:

• With the help of the CRISPR gene-editing tool, scientists today can precisely edit genomes to introduce desirable genetic traits or remove undesirable ones.
• CRISPR holds the potential to revolutionise agriculture by allowing agricultural scientists to increase crop yields, improve resistance to disease and anomalous weather through gene-editing.
• However, there has been a critical obstacle: A commonly used form of the CRISPR system is too big for plant genomes.
• This system uses one of two proteins, Cas9 or Cas12, to target specific parts of the DNA.
• But they are too bulky for plant cells to accommodate.

Smaller is better:

• Team of researchers from ICAR and Pennsylvania State University reported developing a plant genome editor consisting of a protein called ISDra2TnpB, derived from bacteria called Deinococcus radiodurans.
• ISDra2TnpB is less than half the size of Cas9 and Cas12.
• Currently, since there are not many options available for plant genome editors, the improved TnpB certainly adds value.
• Scientists can utilise the advantage of the size of TnpB in generating edited plants for various traits of interest.

TnpB’s editing chops:

• TnpB is a protein made up of around 400 amino acid units.
• It belongs to a family of transposable elements, or transposons.
• Sometimes called “jumping genes”, transposons are parts of a genome that can move from one location to another.
• In the new system, TnpB hitches a ride on a piece of RNA that guides it to the target DNA sequence.
• Once there the TnpB binds with the sequence and eliminates it.
• The cell that houses this DNA repairs the cut by restoring the “correct” sequence.
• Thus, the genome is modified to replace an undesirable sequence with a desirable one.

Research:

• The researchers behind the new study exploited the genome editing abilities of a TnpB-based system to achieve a 33.58% editing efficiency in an average plant genome on targets that Cas9 or Cas12 couldn’t reach.
• They demonstrated that the genome editor was effective on both types of flowering plants-monocots (like rice, which have one seed leaf) and dicots (like Arabidopsis, a plant related to cabbage and mustard that has two seed leaves).
• TnpB is a protein extracted from D. radiodurans, a prokaryotic bacteria, which has a different codon for lysine than do eukaryotes like plants.
• So the researchers edited the codon bias of TnpB to match that of rice protoplasts to improve the editing efficiency.
• The second thing the researchers tweaked was the regulatory elements.
• When the TnpB and the specific RNA that guides it to the target DNA are transferred from a prokaryote to a eukaryote, researchers also need to include sequences called promoters and terminators that govern and regulate the expression of TnpB.
• They added promoters that are likely to enhance the expression of TnpB and lead to better editing.

A hi-res upgrade:

• The researchers finished with some finishing touches to the TnpB-based gene-editing system.
• They deactivated TnpB and fused it with another protein to create a ‘hybrid’ base editor.
• When accompanied by the guide RNA, this editor could swap out a single nucleotide in the DNA sequence.
• This wasn’t possible with the previous version, with active TnpB, because it tended only to delete DNA sequences and couldn’t swap one sequence for another.
• The new base editor thus opened up exciting possibilities for crop innovation by facilitating the alteration of genes at the level of individual nucleotides.

A future of edited plants:

• The TnpB-based editors can edit the plant genome using both base editing and transcription activation, two widely used techniques in plant synthetic biology.
• Most of the claims were based on data obtained from protoplasts and that the scenario might change when dealing with processes by which an organism absorbs external DNA and integrates it into its genome.
• It also appeared that the efficiency of the base editing system fell short in dicot plants as indicated by the results (0.2-0.46% average editing efficiency) reported using Arabidopsis.

Way forward:

• The plant genome editing community should try this miniature editing system in crop species of their choice to improve various traits of interest.
• It is exciting to see a novel and effective genome editing tool being invented. While more development will be needed.

Conclusion:

• This miniature genome editing tool will help remove anti-nutrient factors from food crops, reduce their susceptibility to pests, and help rice crops become shorter and less prone to damage during cyclones.

Earth whistles when lightning strikes, and there’s a new melody

Context:

• When a lightning bolt cuts through the air it releases its energy as electromagnetic wave. These waves can be heard as whistling noises.

Magnetosphere:

• The earth is surrounded by a bubble-shaped magnetic field that shields the planet from radiation from the Sun and other celestial objects. This field is called the earth’s magnetosphere.

Van Allen radiation belts:

• During a solar storm, the Sun shoots out charged particles with more than usual energy through the space around it.
• Without the magnetosphere, these particles could have rendered life as we know it on earth impossible.
• But because the magnetosphere is there, these particles become trapped in it and zip around the earth rather than towards the ground in two large doughnut-shaped radiation belts in the upper atmosphere.
• These are called the Van Allen radiation belts.

Van Allen study:

• The American astrophysicist James Van Allen discovered these belts in 1958 and studied them in detail.
• Van Allen’s work was important for humans to go to the moon, and today we contemplate visiting even more distant parts of space.
• Van Allen found that some parts of the radiation belts were weaker than others and that flying through these parts would be less damaging to spacefaring humans and instruments.

Whistling noises:

• When lightning strikes, electrical energy flows in a path through the atmosphere that we see as a bolt.
• As it cuts through the air, the bolt releases its energy as electromagnetic waves with a range of frequencies.
• The earth’s magnetic field can guide some of these waves up and into a layer of ionised gas above the atmosphere, where they travel along magnetic field lines like a train moving on tracks between the earth’s northern and southern hemispheres.
• The higher the frequency of these waves, the faster they travel.
• The frequencies of these waves are often within the human hearing range (20–20,000 Hz) and can be heard as whistling noises through a receiver.
• When the lower frequency waves among them travel, they can shed some energy via parts of the upper atmosphere, so their sounds have a declining tone.

Latest discovery:

• Scientists from the University of Alaska reported discovering a new type of whistler wave produced by a previously unknown wave generation mechanism.
• They found lightning energy injected into the ionosphere at low latitudes could get reflected like a light from a mirror into the magnetosphere.
• This contradicted previous claims that energy insertion at low latitudes can’t escape the ionosphere.

Conclusion:

• The discovery has significant implications because including this new form of whistlers could double the amount of lightning energy going into the magnetosphere, which in turn means scientists may have to revise their calculations of lightning’s effects on the Van Allen radiation belts.

After all, it’s a question of humans’ doorway to outer space.

Polio

Context:

• WHO investigating suspected new polio strain in Meghalaya

Poliomyelitis (polio):

• It is a highly infectious viral disease that largely affects children under 5 years of age.
• Transmission: The virus is transmitted by person-to-person spread mainly through the faecal-oral route or, less frequently, by a common vehicle (e.g. contaminated water or food) and multiplies in the intestine, from where it can invade the nervous system and cause paralysis.

Wild Poliovirus:

• Of the 3 strains of wild poliovirus (type 1, type 2 and type 3), wild poliovirus type 2 was eradicated in 1999 and wild poliovirus type 3 was eradicated in 2020. 
• As at 2022, endemic wild poliovirus type 1 remains in two countries: Pakistan and Afghanistan.
• Note: WHO declared India polio-free in 2014 after the last case of wild poliovirus was reported in 2011.

Symptoms:

• Up to 90% of those infected experience no or mild symptoms and the disease usually go unrecognized.
• In others, initial symptoms include fever, fatigue, headache, vomiting, stiffness in the neck, and pain in the limbs. These symptoms usually last for 2–10 days and most recovery is complete in almost all cases.
• However, in the remaining proportion of cases the virus causes paralysis, usually of the legs, which is most often permanent.
• Paralysis can occur as rapidly as within a few hours of infection. Of those paralysed, 5-10% dies when their breathing muscles become immobilized.

Treatment:

• There is no cure for polio; it can only be prevented by immunization.
• The polio vaccine, given multiple times, can protect a child for life.
• In 1988, Global Polio Eradication Initiative was launched.
• An estimated 1.5 million childhood deaths have been prevented through the systematic administration of vitamin A during polio immunization activities.

Eradication:

• Endemic transmission of wild poliovirus is continuing to cause cases in border areas of Afghanistan and Pakistan.
• Failure to stop polio in these last remaining areas could result in as many as 2,00,000 new cases every year within 10 years, all over the world.
• That is why it is critical to ensure polio is eradicated completely, once and for all.