BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Crispr

More CRISPR Improvements

Crispr-Cas9 is a genome editing tool that is creating a whole lot of buzz in the science world. It is the newest faster, cheaper and more accurate way of editing DNA.  Crispr- Cas9 also has a wide range of potential applications. It is a unique technology that enables geneticists and medical researchers to edit parts of the genome by cutting out, replacing or adding parts to the DNA sequence.  The CRISPR-Cas9 system consists of two key molecules that introduce a mutation into the DNA. The first Molecule is an enzyme called Cas9. Cas9 acts as a pair of scissors that can cut the two strands of DNA at a specific location in the genome so that bits of DNA can be added or removed.  The second is a piece of RNA called guide RNA or gRNA. This consists of a small piece of pre-designed RNA sequence located within a longer RNA scaffold. The scaffold part binds to DNA and the pre-designed sequence guides Cas9 to the right part of the genome. This makes sure that the Cas9 enzyme cuts at the right point in the genome.Screen Shot 2016-04-10 at 4.50.55 PM

CRISPR-Cas9 is efficient compared to previous gene-editing techniques, but there’s still plenty of room for improvement. CRISPR is less efficient when employing the cellular process of homology-directed DNA repair, or HDR, as opposed to nonhomologous end joining.  Jacob Corn, the scientific director of the Innovative Genomics Initiative at the University of California, Berkeley, and his colleagues have come up with a way to improve the success rate of homology-directed repair following CRISPR-Cas9. “We have found that Cas9-mediated HDR frequencies can be increased by rationally designing the orientation, polarity and length of the donor ssDNA to match the properties of the Cas9-DNA complex,” the researchers wrote in their paper, “We also found that these donor designs, when paired with tiled catalytically inactive dCas9 molecules, can stimulate HDR to approximately 1%, almost 50-fold greater than donor alone.”

“Our data indicate that Cas9 breaks could be different at a molecular level from breaks generated by other targeted nucleases, such as TALENS and zinc-finger nucleases, which suggests that strategies like the ones we are using can give you more efficient repair of Cas9 breaks,” coauthor Christopher Richardson, a postdoc in Corn’s lab, said in a statement.

Original Article:

http://www.the-scientist.com/?articles.view/articleNo/45159/title/More-CRISPR-Improvements/

Other Addtional Helpful Links:

http://www.yourgenome.org/facts/what-is-crispr-cas9

 

A Cure to HIV is Near, But Not Here Yet

The study of genetics, specifically gene editing, has taken monumental leaps over the past few years. One of the biggest achievements of late is the discovery and further research into CRISPR/Cas9. Being able to use CRISPR/Cas9 to edit the genome sequences of living cells far has been the efficient tool geneticists have dreamed of. However, a recent study proved that CRISPR/Cas9 is not yet able to work as the perfect antiviral mechanism.

Image courtesy of AJC ajcann.wordpress.com, https://flic.kr/p/c9ktfQ

Image courtesy of AJC ajcann.wordpress.com, https://flic.kr/p/c9ktfQ

Scientists from McGill University, the University of Montreal, the Chinese Academy of Medical Sciences and Peking Union Medical College did a study where CRISPR/Cas9 was inserted to the replicative process of the HIV invested cell. After HIV enters a cell it’s RNA is converted to DNA which attaches to a cell’s pre-existing strand of DNA. This is when CRISPR/Cas9 is used, it breaks up these two DNA strands. The study found that many of the targeted viruses were killed, however the others viruses developed mutations on even just one nucleotide that made them more resistant and impossible for Cas9 to identify. In conclusion, scientists realize they may need to target more than one region of the DNA at once to effectively kill viruses like HIV.

This topic is very interesting to me because it reflects how we are on the cusp of some incredible biological achievements. I am particularly interested in this study because the effect of HIV/AIDs has devastated not only our country, but also the world, and this study seems like an important step in finding the cure that could save millions of lives. CRISPR/Cas9 seems to offer amazing possibilities, and this is one specific area that grabbed my attention. Do you think a solution to currently incurable diseases is near? Why/Why not? Let me know in the comments below.

Sources:

https://www.sciencedaily.com/releases/2016/04/160407132307.htm

 

Crispr-Cas9: Coming to a Theater Near You

This sequel to GATTACA is to be released shortly, and this time, they’re transcending the movie screen and bringing the experience to reality!

Crispr-Cas9 is a fairly recent DNA-editing technique that has been developed, and allows for extremely easy and precise gene editing, a development said to be at least on par with PCR for bio engineering. In many ways, this is great. Now biologists won’t have to spend the time nor undergo the difficulty of creating variant DNA through old methods, meaning that all these cool genetic breakthroughs should be happening at an unprecedented pace! The problem is, it may be going too fast for humans to wrap their head around.

Similar to the ethical questions raised by the film GATTACA, countries and scientists are debating what regulations should be put on this new and powerful tool. With Crispr-Cas9, the possibility to genetically modify humans becomes a very real option to consider. Scientists could remove DNA sequences which lead to defects and diseases such as albinism and Huntington’s Disease. Or anything else, really.

(The miracle protein)

The main point of Crispr-Cas9 is not necessarily the ability it gives to scientists to easily modify DNA, but the increased rate at which we can understand what specific sequences of DNA do by altering them. Not only are we more able to modify DNA, we are now able to figure it out at breakneck speed.

 

Where it gets complex is, as always, how humans deal with it. Some people, such as Mark Leach, whose daughter has down-syndrome, believes that children with disabilities not only are still able to live rich lives, but also teach others to be more compassionate. Although debating if I would choose to let my child have down-syndrome or not for that reason seems like an absurd consideration, and most likely a coping mechanism, the point still stands that some people are uneasy with fixing genetic-related problems because “they wouldn’t be the same person.” (That’s the point!)

People are really afraid of change, aren’t they?

 

However, for those on the more lethal/completely disabling part of the genetic spectrum, the answer is more than clear.  Charles Sabine, the brother of the renown British lawyer John Sabine, who both have Huntington’s Disease at varying stages, says “If there was a room somewhere where someone said, ‘Look, you can go in there and have your DNA changed,’ I would be there breaking the door down.” Similarly, Matt Wilsey, a parent of a child with a terminal genetic illness, is awestruck at the ridiculousness of the situation: “As a parent with an incredibly sick child, what are we supposed to do — sit by on the sidelines while my child dies?” The oddity of the situation is, we have the capability to start figuring out how to solve these genetic issues with a very effective and efficient technique, it’s just that humans are riding the brakes, trying to slow down the almost inexorable progress of the freight train that is Crispr-Cas9. The irony is that many are afraid with tampering with the “sanctity” of human embryos. I would agree, except that humans defile it all the time. Birth defects, genetic diseases, miscarriages, etc. Of course, this is not intentional, but the parents have the largest hand in these outcomes, as they provide all the material,genetic and otherwise, to create the embryo, fetus, and eventually child. We are already making horrible mistakes with human embryo’s that cripple or kill the resulting child through the natural birth process. Personally, I would go off of this to say we should at least learn from this, so we could eventually progress far enough to prevent these things from ever happening, but I only ask all of the readers to keep this in mind: Nature (very badly) screws up too.

File:Crispr.png

(The process Cas9 facilitates)

I’m not saying that we should be careless with this new and potentially dangerous or aberrant-spawning technology, but I think it’s time that humans come to terms with the fact that their world, and their lives, are entering a new era of existence. For millennia, structured humans have lived in a world where the outside world is the only thing we can manipulate, but now the very structure and formation of ourselves as well. I understand that such a change from a thousands-year-running viewpoint can be hard to make. We’ve never had to think about these things before as a species, because it wasn’t understood and out of our reach. It is daunting. It is terrifying. Only because it is unknown. But how are we to learn, to benefit, from this great potential, if we are too afraid to explore it? I understand that like any form of potential, it can go either way, but this is a great new time of possibilities that simply won’t go away, but reemerge constantly.

I think it’s time we gathered the courage to face it.

Should We Use It: Crispr-Cas 9 Edition

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https://www.youtube.com/watch?v=7C20s4eAGtU

Arguably the greatest thing to happen to genetics since the Human Genome Project, Crispr-Cas 9 has been getting a lot of attention.  The Los Angeles Times wrote an article approximately 4 months ago discussing the ins and outs of the new gene editing breakthrough.  The concept of editing genes is nothing new for scientists.  They’ve been doing it since the 1970s.  So many people are asking “What makes Crispr so special?”  The answer is convenience.  Crispr-Cas 9, although still filled with flaws, is the easiest gene editing tool to use out there right now.  Scientists from UC Irvine and UC San Diego have used it on mosquitoes to fight malaria and scientists have begun to use it on human embryos as well.  Crispr is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats which is a relatively complicated way of saying “gene editing tool.”  What Crispr does is it can target certain parts of a strand of DNA and “delete” them from the strand.  In reality they aren’t being “deleted” but “turned off” so RNA doesn’t code it and begin to manufacture proteins for it.  But the real question is why certain people are against gene editing.  Everyone’s seen the movie GATTACA where gene editing is not only commonplace, but discriminatory.  However in today’s world, the fear is much more strongly rooted than a fear of “geneticism” (genetic rascism).  Using Crispr on viable human embryos to edit genes may have undesired effects.  The turning off/on of one gene could result in the unintentional turning on/off of another.  Also, many scientists believe that a parent making decisions for an unborn child can be unethical and unfair if the child did not want those changes to be made.  And who knows, maybe in the future with the continuous use of Crispr and the development of more complex gene editing tools, “geneticism” could be a reality.

Other articles pertaining to Crispr are linked here and here for more information on the subject.

Biomedical Engineers paving the way for Immunology

For many years Biomedical Engineers have been attempting to find ways to make precise, efficient, and deliberate changes to the genetic material of living cells. Developments in this field can, not only help to eradicate many genetic diseases but it can also ensure what many scientists call “adaptive immunity”. With their newfound CRISPR – Cas9 technology, they may have found a solution to the problem that has been giving them so much grief

hela-cells-544318_960_720

Adaptive Immunity occurs when a foreign body is recognized specifically for what it is and how it can harm the body. The other form of immune response is the innate response, in which there is a foreign body identified and the immune system sends any type of immune-response cell to general area to kill it. However, in adaptive immunity the body can individually recognize the problem and send exactly what needs to be sent, a much more efficient process.

Moreover, scientists hope that a cell’s ability to perform adaptive immunity will help contribute to eliminating harmful genetic mutations. Researchers hypothesize that, with this newfound technology, cells will be able to identify and respond to invading genetic material from a bacteriophage or invader of any sort. (quite possibly eradicating HIV and all other viruses from the Earth).

The science behind this new genetic-police force is as confusing as it is difficult to say… CRISPR…Cas9… what does any of that even mean?

CRISPR stands for Clustered Regulatory Interspaced Short Palindromic Repeats

Cas9 comes from the name of the protein-9 nuclease that scientists first found in Strep (Streptococcus Pyogenes) cells back in 2007 which help the bacteria participate in adaptive immunity.

koli-bacteria-123081_960_720

All in all, its some pretty crazy and extremely complex stuff.

If you do so please, I suggest doing some of your own research on this topic if you have any questions. The opportunities afforded by this breakthrough are endless.

ORIGINAL Article: https://www.neb.com/tools-and-resources/feature-articles/crispr-cas9-and-targeted-genome-editing-a-new-era-in-molecular-biology

CRISPR Inhibited by Nucleosomes

CRISPR/Cas9 is currently being researched as a method to alter genes by editing or silencing them. This enzyme is derived from bacteria and archaea that use it to protect themselves from viruses. Researchers are currently finding more practical applications for this discovery. However, it has been recently been found that nucleosomes may play a large effect on CRISPR.

File:Nucleosome 1KX5 colour coded.png

Structure of a Nucleosome

At UC Berkeley, researchers have been studying the interaction of these prokaryotic enzymes with eukaryotic cells. They have found that nucleosomes may inhibit CRISPR/Cas9. Because bacteria likely do not use this enzyme to explore eukaryotic chromatin structures, their enzymes are not adapted to these types of structures. This is seen by many of the researchers’ experiments where stretches of DNA with low concentrations of nucleosomes had higher activity of CRISPR while others stretches with high concentrations of nucleosomes had lower activity. Scientists have also added chromatin remodeling enzymes while using CRISPR and found higher activity.

This has a few implications on the usage of the enzyme. While gene editing may be less influenced because only one cut is needed to introduce a sequence, scientists should take nucleosome concentration into account in gene silencing and epigenetic editing. CRISPR/Cas9 is an amazing discovery for genetics but we still have much to learn about how it works and how we can use it.

Original Article

HIV > CRISPR-Cas 9

https://commons.wikimedia.org/wiki/Category:HIV#/media/File:HIV-infected_H9_T_Cell_(6813314147).jpg

HIV Infecting a Cell

CRISPR-Cas 9 is an extremely advanced gene editing tool. This tool has efficiently created ways to make precise and targeted changes to the genome of living cells. However, in a study in the journal Cell Reports, scientists from the McGill University AIDS Center in Canada discovered drawbacks in using CRISPR to treat HIV. Instead of simply removing the virus from affected cells, the process of using CRISPR can also strengthen the infection by causing it to replicate at a much faster rate.

HIV has always been a popular disease to conduct research on. Scientists are constantly attempting to come up with ways to kill HIV. Several cures to HIV have been developed such as various as antiretroviral drugs, however, these medicines stop being effective after the patient has ceased to take them. As scientists have started to utilize gene editing tools to remove HIV they have been noticing the huge drawback. They realize that while the gene alteration allows the virus to be killed off in some cases, the resulting scar tissue can lead to the infection becoming stronger! Kamel Khalili, a scientist at Temple University, pointed out that the key to eliminating HIV could lie in attacking the virus at different sites using CRISPR.

Link to Original Study

Link to Original Article 

Link to Original Photo

CRISPR: Is Science Going Too Far?

CRISPR is a some-what new genetic tool in the field of science to edit human embryos. Using CRISPR, scientists can edit the genes of organisms more precisely than ever before. It uses RNA and an enzyme that slices up invading virusesF. One use of this new technology is to fix mutations that cause genetic diseases.

Crispr

https://en.wikipedia.org/wiki/CRISPR

Ethical concerns arose in April of 2015 when Chinese research used CRISPR to edit nonviable human embryos. In addition, some fear that the use of CRISPR to give the embryo traits not found in their genetic code can lead to a obsessive gene culture like the one found in Gattaca. This ethical debates caused scientists to meet at an international summit hosted by the United States National Academies of Sciences and Medicines, where the scientists discussed the ethical concerns of CRISPR but agreed to continue researching it cautiously.

In addition, some argue that using CRISPR for gene editing defeats the sacredness of the human genome and is unnatural. To this point, Sarah Chan from the EuroStemCell argues, “There is nothing sacred or sacrosanct about the genome as such. The human genome – the genome of humanity as a whole, and the unique individual genome we each possess – is merely the product of our evolutionary history to date”. From this point of view, the genome is merely a record of one’s history, but to some religious groups it is a symbol of life which should not be tainted with.

So readers, what do you think? Should we use this tool to help cure treatable diseases, or does this new technology cross the line between scientific mechanisms and morality? What type of genes should this new tool be allowed to edit?

 

Other sources

https://www.sciencenews.org/article/year-review-breakthrough-gene-editor-sparks-ethics-debate

http://www.sciencemag.org/news/2016/04/crispr-debate-fueled-publication-second-human-embryo-editing-paper

http://www.wired.com/2015/12/stop-dancing-around-real-ethical-problem-crispr/

http://www.eurostemcell.org/commentanalysis/ethics-changing-genes-embryo

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