Crispr – BioQuakes

Pancreatic Ductal Adenocarcinoma (PDAC) is one of the most deadly forms of of Pancreatic Cancer with a less than 10 percent, 5-year survival rate. Unfortunately, it is the most common form of Pancreatic Cancer. However, scientist were given hope to increase the survival rate when a protein was identified as a aid to the development of PDAC. The protein is Arginine Methyltransferase 1 (PRMT1) and it is involved in gene transcription, DNA signaling, and DNA repair.

It is said that research done by Giulio Draetta, M.D., PhD “strongly suggest a role for PRMT1 in PDAC development and illuminate a path toward the development of therapies for patients in desperate need of innovative solutions”. Draetta’s team developed a platform called PILOT, Patient-Based In Vivo Lethality to Optimize Treatment. The PILOT technology allows researchers to systematically identify epigenetic drivers in patient-derived tumors. The research found hat PRMT1 is a epigenetic driver for PDAC. Using CRISPR, the team was able to confirm that when the proteins were removed from DNA, the growth of the cancer cells were significantly impaired. There is hope that this recent development can save many lives and increase the survival rate of Pancreatic Ductal Andeocarcinoma.

https://commons.wikimedia.org/wiki/File:Diagram_showing_stage_T4_cancer_of_the_pancreas_CRUK_267.svg

The Miracle of CRISPR/Cas9 in Gene Editing

By goldgi

https://en.wikipedia.org/wiki/CRISPR#/media/File:Crispr.png

Some scientists say, “you can do anything with CRISPR” and others are absolutely astonished and amazed.

CRISPR can rapidly change any gene in any animal or plant with ease. It can fix genetic diseases, fight viruses, sterilize mosquitos and prepare organs for transplant. The possibilities are endless – and the prospect of designer babies isn’t far off.

Dead Cas9 can fix a single base pair typo in DNA’s genetic instructions. It can convert a C-G into a T-A pair. Also, we can attach fluorescent tags to dead Cas9 so researchers can locate and observe DNA or RNA in a living cell. Dead Cas9 can also block RNA Polymerase from turning on a gene, in CRISPRi. In CRISPRa, a protein that turns on genes is fused to dead Cas9.

CRISPR can be used for anything involving cutting DNA. It guides molecular scissors (Cas9 enzyme) to a target section of DNA & works to disable or repair a gene, or insert something new.

Many scientists have been thinking of improvements for this miracle gene editor. RNA Biologist Gene Yeo compares the original Cas9 to a Swiss army knife with only one application – a knife. He says that by bolting other proteins and chemicals to the blade, they transformed the knife into a multifunctional tools.

CRISPR/Cas9 is special because of its precision. It is much easier to manipulate and use compared to other enzymes that cut DNA. By using “guide RNA” it can home in on any place selected by the researcher by chemically pairing with DNA bases.

While Cas9 does have some problems, scientists definitely see the potential for greatness with a few tweaks. They wanted to ensure permanent single base pair changes, and they increased that from 15 to 75 percent. Liu used a hitchhiking enzyme called cytidine deaminase.

Scientists researched chemical tags on DNA called epigenetic marks. When scientists placed the epigenetic marks on some genes, activity shot up. This provided evidence that the mark boosts gene activity.

Case can also revolutionize RNA biology. The homing ability of CRISPR/Cas9 is what makes this seem possible. It was found that Cas9 could latch on to mRNA.

CRISPR/Cas9 was first found in bacteria as a basic immune system for fighting viruses. It zeroes in on and shreds the viral DNA. Half of bacteria have CRISPR immune systems, using enzymes beyond Cas9.

Overall scientists predict that in the next few years, results will be amazing. The many ways of using CRISPR will continue to multiply and we will see where science takes us.

Source: https://www.sciencenews.org/article/crispr-inspires-new-tricks-edit-genes

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

Using CRISPR to Prevent Chronic Pain & Inflammation

By sejeology

(https://commons.wikimedia.org/wiki/File:Rheumatoid_Arthritis_Hands.jpg)

Researchers at the University of Utah have recently figured out a way to use CRISPR gene-editing techniques to reduce chronic pain and inflammation.

Normally, inflammation around damaged tissue signals various cells to produce molecules that destroy the damaged tissue. However, this can quickly devolve into chronic pain when the tissue destruction does not stop.

The researchers have found a way to use CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) to relieve and prevent chronic pain. Unlike most popular CRISPR techniques, theirs does not involve altering the gene sequences– it instead relies upon epigenetics, and modifying the expression of the genes in the cytokine receptors in inflammatory areas, to prevent cells from producing the molecules that destroy tissue.

The treatment is delivered through a virus, which is injected into the inflammatory site. It is more potentially therapeutic than current treatments for chronic pain, in that it actually prevents tissue destruction and future pain, rather than just relieving present pain. The method is approximately ten years away from being used to treat human patients.

Who is the “New Kid on the Block?”

By oxergin

CRISPR/ Cas 9 is newest technology, that is exciting many scientists. CRISPR stands for clustered, regularly interspaced, short, palindromic repeats. This system is a a bacterial defense mechanism thats is RNA based. Its goal is to eliminate and identify DNA which is foreign that would normally invade the bacteriophages and the plasmids. The Cas endonuclease has the role of cleaving at specific locations of the DNA, by being guided by RNA. Now that we have a general idea what this system is lets find out how it can be beneficial!

We understand that CRISPR, at the DNA cleavage site, has the ability to introduce mutations or genetically engineered DNA.

https://commons.wikimedia.org/wiki/File:DNA_Overview2.png

Here are some examples of how CRISPR can be used in the future:

Treat disease in humans
Eliminate Malaria
Give humans other animals’ organs
Create new medications
Genetically modify humans

As the list above only refers to some of the many possibilities CRISPR can have, we can see that this new technology can help humans is many ways. It is evident why CRISPR is referred to as “the new kid on the block.” Hopefully this new system will be able to accomplish the things listed above and many more!

https://www.jax.org/news-and-insights/jax-blog/2014/march/pros-and-cons-of-znfs-talens-and-crispr-cas

Here are some other interesting sites about CRISPR to learn more!

http://www.popularmechanics.com/science/a19067/11-crazy-things-we-can-do-with-crispr-cas9/

http://www.sciencealert.com/this-video-explains-perfectly-why-crispr-really-will-change-humanity-forever

Anti-CRISPR Proteins: What are they and can they be beneficial?

By dnaitza

NIH Image Gallery Image Link

Understanding CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

For many bacteria, one line of defense against viral infection is the RNA guided “immune system” known as CRISPR-Cas. This particular complex is unique because of its ability to recognize viral DNA and trigger its destruction. Scientists have used CRISPR to degrade sections of viral RNA and use the CRISPR systems to remove unwanted genes from an organism. CRISPR proteins have also been studied with the hope of eliminating serious disease and illnesses. However, this CRISPR system does not always work do to anti-CRSPR proteins that inhibit the complex from working properly.

Research

According to an article on ScienceDaily, researchers have finally discovered how these anti-CRISPR proteins work! Research done by biologist Gabriel C. Lander from the Scripps Research Institute, discovered that anti-CRISPR proteins work by inhibiting CRISPR’s ability to identify and attack viral genomes. Just like there are different CRISPR systems, there are multiple anti-CRISPR proteins as well. One in particular mimics DNA to throw the CRISPR-guided detection machine off its course. Scientists have been able to further discover certain aspects of CRISPR and anti-CRISPR systems by using a high-resolution imaging technique called cryo-electron microscopy. They have discovered that the CRISPR surveillance complex analyzes a virus’s genetic material to see where it should attack by having proteins within the complex wrap around the CRISPR RNA, exposing specific sections of bacterial RNA. These sections of RNA then scan viral DNA, looking for genetic sequences they recognize. Lander describes these proteins as being very clever because they “have evolved to target a crucial piece of the CRISPR machinery. If bacteria were to mutate this machinery to avoid viral attacks, the CRISPR system would cease to function.” Therefore, CRISPR systems cannot avoid anti-CRISPR proteins without completely chancing the mechanism used to recognize DNA. Another type anti-CRISPR protein works a bit differently. Based on its location and negative charge, this anti-CRISPR protein acts as a DNA mimic, fooling CRISPR into binding this immobilizing protein, rather than an invading viral DNA.

Can Anti-CRISPR Proteins be beneficial?

Researchers are saying that the understanding of how these anti-CRISPR proteins work are extremely important! According to an article on GEN, the discovery and understanding of anti-CRISPR proteins actually allows researchers to have greater control over gene-edits. In this article, Dr. Sontheimer, a professor in the RNA The RNA Therapeutics Institute at UMass Medical School, expressed how “CRISPR/Cas 9 is a good thing because it introduces specific chromosome breaks that can be exploited to create genome edits, but because chromosome breakage can be hazardous, it is possible to have too much of a good thing, or to have it go on for too long.” Anti-CRISPR proteins can be beneficial and work as an off switch for CRISPR, therefore advancing gene editing!

More CRISPR Improvements

By jdna

On May 1, 2016

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.

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/

A Cure to HIV is Near, But Not Here Yet

By fineflagellum

On May 1, 2016

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

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

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:

Crispr-Cas9: Coming to a Theater Near You

By marsupialniche

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.

(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

By mosmosisjones

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

By benadryl

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

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.

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

By linbicdendrite

Structure of a Nucleosome

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.

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

By agman

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?

By biospearb