Hello, lovelies!

It is officially post day!! Today's post is centred on that genetic editing technique that has kind of taken over headlines, generated a lot of public engagement on whether we have gone too far or not - CRISPR. To be honest with you, I am amazed at what this technique is able to do.  Then it hit me, that I do not actually know where this technique came from, it just suddenly appeared out of nowhere and took the world by storm. Have no fear after today's post you will have a better understanding of where the hell CRISPR came from. Enjoy. 

Molecular Biologists, Conservationists, Geneticists believe the discovery of CRISPR is the best thing, well - since sliced bread! With this technologies ability to modify wild and domestic populations, produce hypoallergenic eggs and possibly reverse extinction and bring back the woolly mammoth you could understand the excitement. However, there is a dark side to such technological advancements, CRISPR increases the risk of harmful biological agents being engineered. One question remains on the minds of many swept up by the CRISPR mayhem, what on earth is it?

CRISPR stands for clustered, regularly interspaced short palindromic repeats. Francisco Mojica, spotted these repeats when he was looking at the genome of a microbe known as Haloferax mediterranei. He found that there were 14 DNA sequences that repeated themselves and that they read the same forwards as they did backwards. Utterly transfixed by these repeating units he committed himself to learning more about their function and origins. In his lab, Franciso made the discovery that CRISPR was part of a sophisticated immune system found in bacteria.

Single-celled organisms such as Bacteria and Archaea are under constant threat from invading viruses. As it stands Viruses outnumber their victims ten to one leading to large scale losses in bacterial numbers every single day. In the face of such troubling odds, bacterias only choice for a chance at survival was to adapt and evolve defences against these genetic intruders. Bacteria and Archaea have done this very well with a range of weaponry, however, the most sophisticated system evolved belongs to those with the CRISPR-Cas system.

As it turns out, we share a similar immune response to bacteria. The CRISPR-Cas system used by bacteria and Archaea handles invading viruses in a way that mirrors how our immune system produces antibodies. Between each set of palindromic repeats in a bacterial genome, there are 'spacer' sequences. These sequences are inserted by CRISPR-associated proteins (Cas) and contain genetic remnants of viral invaders. Over time CRISPR-associated proteins build a genetic 'library' in the bacteria's genome. This library of past invasions aids the bacterium's fight against a virus that it has encountered before, by teaching Cas proteins to seek and destroy any genetic invaders (Viruses) with DNA matching the 'spacer' sequence.

Our immune system does a very similar method, the main difference being the scale through which it occurs. When our body is under attack by a pathogen, our immune response launches a counterstrike and eliminates the pathogen. After the attack phase of our response immune cells known as B Lymphocytes remain in our system, ready to remind our body how to deal with the pathogen should it invade again.

Bacteria with the CRISPR-Cas immunity must pay attention to what DNA they insert into the ‘spacer’ sequences. There are many similarities in viral DNA and host bacteria DNA,  as such the risk of inserting their own sequences into the ‘spacer’ would lead to suicide via the autoimmune response.  In single-celled Prokaryotes genetic storage is a problem due to limited available space it would prove difficult to store information on every viral invasion experienced.

When 'spacer' sequences were looked at in greater detail it was found that the sequences were from viruses never documented before. This finding shocked the scientific community as it may highlight just how little is known about the diversity of viruses. On the other hand, some argue that these sequences could belong to viruses that are now extinct, or to viruses that have now mutated their sequence so that they remain undetected by CRISPR. Ultimately, CRISPR-Cas system is likely to be more of a hindrance if the latter is true.  Many ‘spacer’ sequences would be a waste of space if they code for viruses that have gone extinct or have changed their sequence.

CRISPR is proving to be extremely popular for our species, but for Prokaryotes not so much. More than 90% of Archaea employ this system, in contrast to a third of bacteria investing in such a system. Issues with memory storage, mean that bacteria in contact with many viruses are likely to suffer more from ‘genetic burdens’ and not reap the rewards of CRISPR.

Molecular Biologists, Conservationists, Geneticists believe the discovery of CRISPR is the best thing, well - since sliced bread! With this technologies ability to modify wild and domestic populations, produce hypoallergenic eggs and possibly reverse extinction and bring back the woolly mammoth you could understand the excitement. However, there is a dark side to such technological advancements, CRISPR increases the risk of harmful biological agents being engineered. One question remains on the minds of many swept up by the CRISPR mayhem, what on earth is it?

CRISPR stands for clustered, regularly interspaced short palindromic repeats. Francisco Mojica, spotted these repeats when he was looking at the genome of a microbe known as Haloferax mediterranei. He found that there were 14 DNA sequences that repeated themselves and that they read the same forwards as they did backwards. Utterly transfixed by these repeating units he committed himself to learning more about their function and origins. In his lab, Franciso made the discovery that CRISPR was part of a sophisticated immune system found in bacteria.

Single-celled organisms such as Bacteria and Archaea are under constant threat from invading viruses. As it stands Viruses outnumber their victims ten to one leading to large scale losses in bacterial numbers every single day. In the face of such troubling odds, bacterias only choice for a chance at survival was to adapt and evolve defences against these genetic intruders. Bacteria and Archaea have done this very well with a range of weaponry, however, the most sophisticated system evolved belongs to those with the CRISPR-Cas system.

As it turns out, we share a similar immune response to bacteria. The CRISPR-Cas system used by bacteria and Archaea handles invading viruses in a way that mirrors how our immune system produces antibodies. Between each set of palindromic repeats in a bacterial genome, there are 'spacer' sequences. These sequences are inserted by CRISPR-associated proteins (Cas) and contain genetic remnants of viral invaders. Over time CRISPR-associated proteins build a genetic 'library' in the bacteria's genome. This library of past invasions aids the bacterium's fight against a virus that it has encountered before, by teaching Cas proteins to seek and destroy any genetic invaders (Viruses) with DNA matching the 'spacer' sequence (image below).

Image Source

Our immune system does a very similar method, the main difference being the scale through which it occurs. When our body is under attack by a pathogen, our immune response launches a counterstrike and eliminates the pathogen. After the attack phase of our response immune cells known as B Lymphocytes remain in our system, ready to remind our body how to deal with the pathogen should it invade again.

Bacteria with the CRISPR-Cas immunity must pay attention to what DNA they insert into the ‘spacer’ sequences. There are many similarities in viral DNA and host bacteria DNA,  as such the risk of inserting their own sequences into the ‘spacer’ would lead to suicide via the autoimmune response.  In single-celled Prokaryotes genetic storage is a problem due to limited available space it would prove difficult to store information on every viral invasion experienced.

When 'spacer' sequences were looked at in greater detail it was found that the sequences were from viruses never documented before. This finding shocked the scientific community as it may highlight just how little is known about the diversity of viruses. On the other hand, some argue that these sequences could belong to viruses that are now extinct, or to viruses that have now mutated their sequence so that they remain undetected by CRISPR. Ultimately, CRISPR-Cas system is likely to be more of a hindrance if the latter is true.  Many ‘spacer’ sequences would be a waste of space if they code for viruses that have gone extinct or have changed their sequence.

CRISPR is proving to be extremely popular for our species, but for Prokaryotes not so much. More than 90% of Archaea employ this system, in contrast to a third of bacteria investing in such a system. Issues with memory storage, mean that bacteria in contact with many viruses are likely to suffer more from ‘genetic burdens’ and not reap the rewards of CRISPR.

There you have it a brief introduction to CRISPR origins and what it is. Exploiting CRISPR-Cas's ability to insert genes into genomes of organisms make it beneficial for those who to engineer organisms, whether it be activating gene expression or correcting the 'typos' that cause the onset of genetic diseases.

That is all for this week my lovely people, have an awesome weekend!

Science in the City

xoxo

Image sources for header image:

Mammoth Mosquito Chick and the egg

Information gathered from Nature magazine and the Broader Institute.

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Hello, my lovelies!

We are fast approaching the end of the first month of January! How have those new year resolutions been going for you so far? Not great? Don't worry, everybody hits a few bumps in the road. So what you haven't done your morning exercises for a week or perhaps you haven't started learning that new language, what is a week in your entire life. You are allowed a day off, whatever you need to get back into achieving what you know you can achieve. 

'In order to succeed, we must first believe that we can.'  
- Nikos Kazantzakis

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Invasive species are costing the US economy a minimum of $42 billion in damage each year. Infectious diseases transmitted by vectors are responsible for 1 million deaths annually, many being children. Global food productivity is threatened by pests and competing plants developing resistance to insecticides and herbicides. Scientists are now casting their eyes to a possible solution that tips the laws of genetics in favour for a gene engineered by scientists. Such a technique could play a role in the conservation of endangered animals, eliminating diseases transmitted by vectors and reversing resistance to herbicides or insecticides. Gene drives hold the ability to save a species or wipe out populations. Have we gone too far?

What are gene drives?

Gene drives are the next big thing in the wonderful field of Genetics. Essentially with the help of CRISPR Cas9, this genetic engineering method provides a novel way of tackling both environmental and public health issues, but how? Essentially, a gene coding for a particular trait this could be advantageous or disadvantageous (depending on whether you was to ‘save’ or ‘destroy’ a population) is introduced into an organism.

Gene drives are carried out on sexually reproducing organisms, this poses a problem to geneticists. The engineered gene drive trait has a 50/50 chance of being passed onto the offspring. Sadly this is the awkward and inconvenient truth of sexual reproduction, resulting in the engineered gene being expressed in very few individuals - the opposite to what they want to achieve. This challenge was overcome by modifying the chosen gene to act ‘selfishly’, thereby ensuring it is expressed in a larger proportion of offspring. This can be done in one of two ways.

During embryo development, one trait is chosen from either the maternal chromosome or the paternal chromosome and that is the one that is expressed e.g. brown eyes from your dad. This is avoided by the engineered trait copying itself onto both chromosomes so either way, you get the same outcome! Or, molecular biologists can ensure that the competing trait proves deleterious and results in lower viability for those inheriting it. Either way, the end product is the desirable gene increasing in frequency and spreading through the population like wildfire.

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There are two forms of gene drives seeking to achieve different outcomes: Modification and Suppression. Modification gene drives aim to ‘save’ populations by spreading desirable traits through a population. Typical gene targets for Modifying gene drives include ‘blocking pathogen development’ or ’increasing survivability’. Suppression gene drives aim to reduce/eliminate populations as such the genes targeted often provide no fitness benefit to the chosen organism including ‘reduced life spans’ and deliberately introducing a bias to ‘sex ratios’.

Potential role in Conservation:

Gene drives provide the opportunity to spread advantageous traits such as resistance to a species-specific disease. This is where engineering trumps mother nature, as the gene for disease resistance spread through the population at a faster rate compared to the long hauled process of natural selection.  

Globally, populations of amphibians are declining at an accelerated rate due to Batrachochytrium dendrobatidis otherwise known as the chytrid fungus.  How the chytrid fungus causes such high mortality remains a bit of mystery, however, it has been shown that it can disrupt an amphibian's skin. Many amphibians breathe through their skin, as such, any disruption in the epidermal layer can cause the amphibian to suffocate. Implementation of a modified gene drive may avoid future localised extinctions.

Alternatively, gene drives could aid the fight against invasive species. Invasive species have adverse effects in the areas ecology as well as the economy, this has lead people to take drastic action to mitigate against further losses.  A gene rendering a species vulnerable to a species-specific molecule (a poison or a disease) could aid in kerbing an invasive species populating growth. Such approaches are increasing in popularity due to their minimal ecological impact.

The Potential role of gene drives in disease management:

Vectors are organisms that are capable of transmitting a disease or parasite from one animal or plant to another. Common vector-borne diseases include Malaria, Chikungunya, Chagas Disease, Plague and the Zika Virus. The Anopheles genus of mosquito is perhaps one of the most famous vectors, responsible for the transmission of Malaria, Dengue Fever and Zika virus.

There have been small successes in the production of genetically engineered dengue-resistant mosquitoes, however, these mosquitoes were later found to be resistant to one subtype of dengue fever. Nonetheless, tests remain promising.   Scientists are focusing their efforts on the Anopheles that is responsible for transmitting Malaria. Malaria claims the lives of 650,000 people each year, so the need for a solution is high.

Geneticists begin by looking for a target of which to base the gene drive on, in the case of combating infectious diseases the aim is to reduce the transmission rates. Two genes instantly drew attention including the AKT transgene found in the midgut of the mosquito and the single chain antibody located in the salivary glands. The reason why these genes are receiving all the attention becomes clear when looking at the life cycle of Plasmodium (the microorganism responsible for the onset of Malaria), the image below shows the life cycle.

Image Source

The midgut of the Anopheles mosquito provides the optimal conditions for the Plasmodium gamete to become an oocyst. Once the oocyst has been formed it bursts, releasing loads of sporozoites that migrate from the midgut straight to the salivary glands so that they are successfully passed on with the Mosquito's next blood meal. The aforementioned genes play a vital role in providing an opportunity to block pathogen development or block the Mosquitoes ability to become a vector.

Limitations of gene drives:

Firstly, gene drives require the genetically engineered organisms to have many generations in order to spread through the population. Therefore, the time lapse between release and successful spread through a population depends on multiple factors of the vectors biology such as the time needed for each generation, the impact of the gene drive on individual fitness and their mating system dynamics.

When manufacturing a harmful trait to be used for a gene drive, it must be made deadly but not too deadly… Anything too deadly will result in the engineered organism dying well before they manage to pass on the trait to their offspring.

Evolution is working against you...  Gene drives work on the basis of introducing harmful traits and ensuring that they spread through a population like a wildfire. However, evolution by natural selection works on the basis of favouring individuals with advantageous traits and dooming the individuals with deleterious ones. Therefore, it is very likely that through the duration of the gene drive natural selection will lead to one organism acquiring resistance to the harmful trait and thus will be favoured, making the efforts of the gene drive obsolete.

Overall, this is an exciting field of genetics whether it be for agriculture, conservation, or for health purposes. With the development of CRISPR Cas9, it is plausible that further research into Gene Drives may well lead to them becoming a viable option in future. Is this a step too far? Or a natural progression to a solution for a long-standing problem?

Science in the City

xoxo

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