SHERLOCK: Ace Detective

(Aedes aegypti mosquito, known for carrying Dengue fever and the Zika virus, found on Wikepedia and taken from CDC public domain)

      In the event of an outbreak, fast, reliable diagnoses are of the essence. Recently, researchers have applied CRISPR technology to provide for this need, dubbed SHERLOCK (Specific High sensitivity Enzymatic Reporter unLOCKing). This works by applying a target sequence of RNA (for either Zika or dengue) to a Cas13a enzyme. A reporter RNA that gives off a fluorescent light upon cutting is added to the selected sample. When the Cas13a enzyme finds a matching RNA sequence, it cuts it, and then begins to induce collateral damage to nearby RNA. It is during this phase that it inevitably cuts the fluorescent reporter; this then gives off a signal that alerts to the presence of the select virus.
      The sensitivity of this test is a million times greater than current diagnostic tools used for this purpose. It is also incredibly specific, eliminating false positives. In addition to detecting these viruses, it can easily be outfitted to detect other viruses, bacteria, and even cancer DNA. In addition to its efficiency, it is also economical, with durable field tests using glass paper starting at less than a dollar a sheet.
      In lecture, this particular technology was only briefly touched upon. However, it is evident that current and future advances in genetics will be built upon this technology. Included below is an introductory video explaining CRISPR as a whole and the link to the article this post was based on.

Introduction to CRISPR
Article

Monsanto Adopts CRISPR to Make Food Hardier, Better, Faster, Stronger

Monsanto is back at it again, trying to make the agricultural systems that keep us fed as sustainable and productive as possible. On September 23, the Monsanto closed on a licensing deal with the Broad Institute that allows the agricultural giant the legal rights to use CRISPR-cas in their endeavors to make hardier plants. CRISPR is a tool that allows researchers to “snip” and recombine DNA at specific base pairs, therefore allowing an organism to express a different or additional gene. It is more efficient than its traditional counterpart, classical breeding which can take up valuable time and resources, and is often more reliable than the grafting of plants.

Greenhouses from Monsanto's St Louis research location.

So why do we need Monsanto and their CRISPR crops, anyway? Well, the exponential growth of the global population, the slow decrease of farmable land due to sea level rise and living space, all mixed with a heating world, could easily spell disaster for global food production. One of the most promising methods to feeding the population is using genome editing technology such as CRISPR to shuffle, in a way genes that control important factors of the production - pest resistant chemicals/hormones, drought tolerance, high yield, dehiscence, etc.

And while, Monsanto is not the first (and certainly not the last, with the way things are going), the results are surely highly anticipated.

Links:

https://www.newscientist.com/article/2106946-monsanto-cuts-deal-to-use-crispr-to-engineer-food/

http://news.monsanto.com/press-release/corporate/monsanto-announces-global-licensing-agreement-broad-institute-key-genome-edi

Genetic Diversity Helps to Limit Infectious Disease

Newly found research by the University of Exeter have found that genetic diversity has helped reduce the risk of spreading diseases by limiting parasite evolution.

Even though this study is not new, the answer to why this happens was newly founded. Researchers used a virus that infected and killed bacteria. By using this virus, they could study the effects host diversity had on disease spread. The bacteria defended themselves by using a defense system that they have called CRISPR-Cas. CRISPR-Cas captures random DNA fragments from the virus, thus creating a ‘genetic memory’ of some sort. Now because each bacteria will copy different DNA fragments from the virus, this causes a diversity of bacteria to be formed.

In order for the researchers to see if and why diversity limits the spread of disease, they isolated individual bacteria and grew them in monoculture or mixed them together with other bacteria of diverse populations before exposing them to the virus. The virus spread on the monocultures because the virus was eventually able to outgrow and overcome the CRISPR-Cas immunity. The mixed populations were able to overcome the virus and the virus eventually went extinct; this is because the bacteria had a much larger diversity and were able to overcome the virus all together by herd immunity.

Dr. Stineke van Houte recalls: "Viruses could spread on monocultures but when the individual bacteria were mixed together, the virus went extinct very rapidly. This revealed a strong monoculture effect in our experimental system."

I think this article was very interesting in proving that different variations of bacteria can overcome a virus when they are mixed together. This shows that diversity is good when it comes to bacteria but it could also become harmful if they are harmful bacteria. The mixture of bacteria were able to survive because they were able to increase the immunity of the population as a whole.

A Cure using Crispr?

For those who don't know, the Crispr-Cas9 gene, it is a gene that aids flesh-eating bacteria to fight off "invasive viruses." The Crispr gene stores fragments of virus DNA in serial compartments. The "thing that [makes] Crispr-Cas9 tantalizing was its ability to direct its protein, Cas9, to precisely snip out a piece of DNA at any point within the genome and then neatly stitch the ends back together" (NY Times).

Among experimenting the gene, researchers observed that the gene depends on two different types of RNA: "a guide, which targeted the Cas9 protein to a particular location, and a tracer, which enabled the protein to cut the DNA" (NY Times). Researchers Jennifer Doudna and Martin Jinek composed multiple possible models of the RNA molecules, until they came along to a two-in-one type model, "combining them into a single tool." This tool, combined the two molecules of RNA; therefore, combining their two system, "[allowing] researchers to target and excise any gene they wanted — or even edit out a single base pair within a gene. (When researchers want to add a gene, they can use Crispr to stitch it between the two cut ends.) Some researchers have compared Crispr to a word processor, capable of effortlessly editing a gene down to the level of a single letter" (NY Times). Thus, the Crispr-Cas9 gene being utilized to help patients with infected bacteria, by using the gene to cut and strip the bacteria of it's protective immune system.

This article really sparked my attention since we had recently learned about restriction enzymes, and how interesting it was to see that a gene, along with it's protein, could act in a similar behavior. I hope that this new found technology can really help those suffering of invasive viruses.

New Gene-Editing Technique Makes Strides Towards HIV Resistance

According to the Centers for Disease Control (CDC), 1,155,792 people in the United States have been diagnosed with acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV). HIV targets T-cells via the CCR5 gene receptor which serves as a channel for the virus into cells. The virus then replicates inside the T-cells, eventually killing the host cells. This destruction of T-cells ultimately results in a highly susceptible immune system.While countless research projects aspire to develop a cure for the devastating virus, an approved cure has yet to be determined. However, hopes for finding a cure remain as vast strides towards a cure have been accomplished by some promising research.

Using a new gene-editing technique, researchers for the Harvard Stem Cell Institute (HSCI) at Massachusetts General (MGH) and Boston Children's (BCH) hospitals have created an effective technique for blocking HIV from invading and destroying its subject's immune system. The researchers effectively and precisely used CRISPR-Cas gene-editing technology to edit clinically relevant genes out of human hematopoietic stem cells and T-cells. The team was able to remove the CCR5 gene receptor out of of hematopoietic stem cells and demonstrate that these cells could differentiate into functional blood cells without the CCR5 gene. This outcome suggests that gene-edited stem cells could be delivered into HIV patients by bone marrow transplantation. The procedure would result in an HIV-resistant immune system. Dr. David Scadden, co-director of HSCI, stated that the new work is "a tremendous first step in editing out what makes human cells vulnerable to HIV."

The team identified areas of caution regarding the future of the new gene-editing therapy such as unexpected complications with the new therapy and the potential difficulty involved in treating people in the areas where HIV is most prevalent.The team also believes the new therapy will be ready for human safety trials within 5 years. The new therapy will undergo animal trials, and once they are completed, the team will apply for phase I human trials.

The more I read about the advances in gene-editing techniques, the more I am humbled at how far medical technology has come in such a short time period. I am excited to follow the development of this therapy through its trials. Advances such as this will encourage hope globally regarding the devastating virus.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
 Article: http://news.harvard.edu/gazette/story/2014/11/a-promising-strategy-against-hiv/
Related Article: http://www.nejm.org/doi/pdf/10.1056/NEJMoa0802905