Below are blog posts, posted by permission by students in the class. For many students, this assignment was their first time reading peer-reviewed scientific articles, and their first time trying their hand at science communication. 

| 2016 |

 

2016


 

CRISPR Just Got Crispier

Robert Czokajlo

Genetic Engineering; what is it? Well, most of the General public thinks it's all bad. Sure, we've all seen Frankenfood and Supersize Me. But, like with a crate of apples, one bad one does not spoil the whole bunch. Yes, there is bad genetic engineering; Monsanto’s “Roundup Ready” canola, Factory Farms, and altering the code of an organism for profit are both examples of the "dark side" of genetic engineering. Yet, when you think about it, Genetic Engineering can be found all over our future; and I’m saying “our” in terms of us as a species. Imagine a world where a simple change in a little bit of someone’s genetic code can cure them from Cancer or a Genetic Disease; something we once thought impossible. To put it simply, think about a railroad track. If a section is damaged (let's say the rails themselves have snapped just enough that it poses a risk to passing trains), Engineers will come along, remove that section, and add in a new one that will eliminate that risk. Simple, right? Eh, sort of.

Hold on, let’s backtrack a bit. Why is some genetic engineering bad? To begin, let's talk about Monsanto. They’re a chemical company known for weed killers such as “RoundUp”. Recently, they created and patented a breed of rapeseed (Canola), that contained RoundUp in its genetic code. This ensured that the breed would be resistant to farmers using the herbicide on their crops. However, for the humans consuming such products, it has been determined that RoundUp Ready Canola is pretty unhealthy for human consumption; ouch. A lot of controversy also stems from farmers who were sued for accidentally growing the product patented by Monsanto4, and it is partially from this that, well, quite frankly, people genuinely fear GMO products. Because of this, many also hear about human gene manipulation, and they’re protesting it before the research even begins. However, as stated before, not all GM is bad GM. To start, let’s talk about that brand new tech we know as CRISPR.

So, to start off, what the heck are they? Clustered Regularly Interspaced Short Palindromic Repeats, also known as CRISPRs, are adaptive immunity mechanisms which can be found in bacteria. They are used, along with CRISPR-associated proteins (Cas proteins) to repel foreign DNA and RNA molecules that may be moving about in bacteria. They’re often created from DNA fragments from previous invaders, and use a “Cascade” targeting complex in order to destroy the invader DNA1. They’re pretty much the Norton Antivirus of bacteria; seeking out any foreign DNA that may be floating about in the bacteria and/or within the DNA sequence.

Since CRISPRs are used to remove foreign DNA sequences in Bacteria, it’s entirely possible that we can use them to further expand our knowledge with genetic engineering. Returning to the Railroad analogy, the engineers who install the new segment of track could be these CRISPRS and their associated proteins. In fact, such research is already underway. Most bacteria use a protein known as Cas3 to neutralize foreign DNA. But recently, two scientists- Dr. Jennifer Doudna of U.C Berkeley and Dr. Emmanuelle Charpentier of Sweden’s Umeå University – invented a new Cas protein known as Cas9. This protein, paired with CRISPR tech, forms CRISPR-Cas93 - a technology which allows scientists to manipulate DNA more quickly and accurately, and could be used to eliminate or cure previously incurable diseases. For example, a person is born with severe autism. In the current world, There is nothing the doctors can do to help this- the child will have the disease whether they like it or not. With CRISPR-Cas9, a scientist can simply enter a few codes into a computer, which can then remove precise “chunks” of that persons DNA; replacing them with “healthy” sequences. Once the operation is complete, the patient wakes up completely fine; it would be as if he or she didn’t even have the disease to begin with.

Sure, it sounds outlandish. But this strange new tech is actually a reality. It’s already been used to prevent HIV infection in human cells4. But, more importantly, it’s actually already in use. A study done in early 2016 involved a group of scientists at U.C Berkeley (Of all places) using the CRISPR-Cas9 system. Heck, they even improved it! Before, in order to manipulate DNA, a microinjection had to occur. According to the scientists involved, however, microinjections “[are] technically demanding, labor-intensive, and costly procedure[s] with poor embryo viability2” Therefore, this group actually developed a new way to insert the Cas9 system. By using electroporation (using electricity to briefly open up the pores in cells and introduce DNA/chromosomes), the tech was inserted in a much more efficient and less-costing manner. This new method, CRISPR-EZ, allowed for more efficient manipulation and much higher embryo viability. In the railroad analogy, CRISPR-EZ would be like installing electric doors over the tunnels that only opened when a train came near.

While we previously discussed the ideas behind how this tech could be used for good, CRISPR-Cas9’s own creators warn of another major use for this tech. This tech could be used to create “designer babies”; babies that are altered genetically to perfectly match the parents’ preferences2. For example, let’s say you’re using this technology. If you have a patient who wants their kid to have red hair and icy blue eyes, you would alter a few things in the embryo’s genome, and presto change-o! They’ll have a kid with red hair and icy blue eyes. The same goes for anyone who wants to alter the gender of their child before they’re born. They would just have to go to their doctor, go through a minute operation, and boom! You wanted a boy but you’re getting a girl? Just kidding, you’ll have a boy now.

However, before you go out and protest the rise of this new tech, just know that Designer Babies are far from being a reality; as are the tools to do such a thing. Remember, CRISPRs were discovered recently, and CRISPR-Cas9 was only discovered in September 2015. In order for something to become the norm, it needs to be researched and scrutinized for many years. Think about computers. Your laptop or your big PC tower trace their humble roots to a room-sized machine from the 1940’s that easily had 1/100th the computing power that you have now.  The same can be said for our humble CRISPR technology. We just discovered it; therefore, for it to become an everyday object, it’ll take another half-century, maybe more, before it happens. To conclude, CRISPR tech is a brand new technology set to turn our knowledge of DNA on its head. This tech might even reach its peak in your lifetime, if enough work is done researching and experimenting with it. But, for now, all we know is that our knowledge about CRISPR just got a lot clearer and… how should I say this…. CRISPier than before.

References

  1. Bei Gong, et al., Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3PNAS 2014 111 (46) 16359-16364; published ahead of print November 3, 2014,doi:10.1073/pnas.1410806111
  2. Chen, Sean, et al., Highly Efficient Mouse Genome Editing by CRISPR Ribonucleoprotein Electroporation of Zygotes, 3 May 2016, Division of Cellular and Developmental Biology, MCB Department, University of California at Berkeley (accessed 28 Nov. 2016)
  3. Doudna, J. (2015, September). We can now edit our DNA, but let's do it wisely. Retrieved December 09, 2016, from https://www.ted.com/talks/jennifer_doudna_we_can_now_edit_our_dna_but_le...
  4. Roundup Ready Crops. (n.d.). Retrieved December 10, 2016, from http://web.mit.edu/demoscience/Monsanto/players.html
  5. Zhang, S. (2015). Everything You Need to Know About CRISPR, the New Tool that Edits DNA. Retrieved December 10, 2016, from http://gizmodo.com/everything-you-need-to-know-about-crispr-the-new-tool...

 Image result for genetic engineeringGenetic Engineering Utilization

            Genetic engineering, is the “applied techniques of genetics and biotechnology used to cut up and join together genetic material, especially DNA,” as defined by Merriam Webster. In laymen’s terms, genetic engineering is the taking of a specific characteristic from one organism, and placing that characteristic into another organism. A good way to think about genetic engineering would be using paint samples; think of one characteristic as the color red, then think of a different characteristic as the color blue, and when you mix those two colors you will get purple. The color purple represents what is possible with genetic engineering, because without the combination, or the manipulation of the two original colors then the third color would’ve never been possible. Genetic engineering has been present throughout many different disciplines, but the two major disciplines that it is used most frequently is in agriculture and in medicine. With agriculture, genetic engineering is referred to genetic modification. Despite the negative news around GMO’s in foods, there is no evidence that shows that GMO’s are harmful in anyway, in fact, GMO’s are nothing more than the cross-breeding of two different organisms, nothing is added to them to make them harmful, and nothing is added to them to make them unsafe.  Most of the time the characteristics added are to preserve the fruit and help it to withstand stimuli from the environment it is. This type of thinking is also highlighted in the studies produced in the article Chloroplast genomes: diversity, evolution, and applications in genetic engineering (2016). They made arguments that the applications of genetic engineering in plants, specifically the chloroplasts within the plants. Which is helping to advance safer and more efficient ways to genetically modify plants and make them better for the general population. Also, GMO’s from an agriculture background help to yield more crops and help them to stay for longer periods than those without any genetic modification. In the medical field, genetic engineering is most commonly used in orthopedic studies. In the medical field, it’s used primarily for the regeneration of bones and cartilage, they use it by taking the genetic code of bones and cartilage and try to replicate the same material. This would be used for people with arthritis or general chronic bone injuries or inflammations; which, would either be the replacing or the connecting of new made material and the original material in the body.

            Now that we have a better understanding of what genetic engineering is and what it can be used for, I think we can dive right into a study about how genetic engineering can be helpful to the masses in the medical field, by describing a peer-reviewed article about the usage of genetic engineering. In this article from 2010, titled “Animals Models for Cartilage Regeneration and Repair,” it highlights the usage of genetic engineering to rebuild cartilage within animals. Which could later be translated to the rebuilding of cartilage within humans. The major premise of this study would be the determination of size within the animal model and that was the major issue that the researchers experienced. They experienced this because animals generally have smaller and more fragile or denser bones than what humans have so, they first had to gather information about the bone densities of the animal models they would be using, and then interpreting how the cartilage would need to be changed or engineered to the needs of the animals. Once they were able to determine the most appropriate animal model that would closely represent the human model, without it having to be a human in the trial runs. The initial animals that they used for this study would be mice and rats, but they wanted to be able to transfer the information from mice and rats to larger animals, such as canines and mini-pigs, to mimic the sizes found in humans, at least to a closer extent than the mice and rats. We can see similar research highlighted in the study “Generation of human muscle fibers and satellite-like cells from human pluripotent stem cells in vitro.” This study showed the way genetic engineering could be used for muscle regeneration, in chronic muscle diseases. But where muscle fibers are more individualistic it takes more time and more energy to regenerate those types of internal human structures. Eventually both methods will be able to be used in e fuller scale, and to a productivity level that suits the needs of the medical professionals using them.

            Overall, genetic engineering is an interesting, complex field that needs to be further explored to unlock the fullest potentials that it could wield. This potential could be within many different disciplines, used throughout all of science, used for a plethora of incredibly useful advancements, in any practice. Genetic engineering could be key to curing diseases that are chronic, diseases that make life difficult for all those involved, and diseases that make people go into disability. Not only does genetic hold the potentials to help people with the diseases that they can contract, but it could also help them to help people with major injuries and help them get back to a life that is injury free. Where most can see the effects of genetic engineering in agriculture, I feel that the most important advances in genetic engineering are being made in the medical fields, advancing our knowledge in what we can do for humanity, to where nobody will have to live with a disabling injury or chronic disease.

References:

Constance R. Chu, Michal Szczodry, and Stephen Bruno. Tissue Engineering Part B: Reviews. February 2010, 16(1): 105-115. doi:10.1089/ten.teb.2009.0452.

Xing, D., Chen, J., Yang, J. et al. Curr Mol Bio Rep (2016) 2: 90. doi:10.1007/s40610-016-0038-2

Chal, Jérome, Ziad Al Tanoury, Marie Hestin, et. al. "Generation of Human Muscle Fibers and Satellite-like Cells from Human Pluripotent Stem Cells in Vitro." Nature Protocols 11.10 (2016): 1833-850. Web.