BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Crispr (Page 1 of 2)

Crispr is coming soon to hospitals and medical facilities near you

In 2013, researchers demonstrated a type of gene editing ,called Crispr-Cas9, which could be used to edit living human cells. This means that DNA could be altered. It has been tested in labs, but now it is going to be tested on humans.
Crispr Therapeutics applied for permission from European regulators to test a code-named CTX001, in patients suffering from beta-thalassaemia, an inherited blood disease where the body does not produce enough healthy red blood cells. Patients with the most severe form of the illness would die without frequent transfusions.
If the trials are successful, Crispr, Editas and a third company, Intellia Therapeutics, plan to study the technique in humans with a bigger range of diseases including cancer, cystic fibrosis, hemophilia and Duchenne muscular dystrophy.

Since China is more lenient when it comes to human trials, several studies are already happened, but there was no conclusive data.
Katrine Bosley, chief executive of Editas, says the field of gene editing is moving at “lightning speed”, but that the technique will at first be limited to illnesses “where there are not other good options”.

The reason for this is because, as with any new technology, scientists and regulators are not fully aware of the safety risks involved. “We want it to be as safe as it can, but of course there is this newness,” says Ms Bosley.

Although Crispr-Cas9 has not yet been trialled in humans in Europe or the US, it has already benefited medical research greatly by speeding up laboratory work. It used to take scientists several years to create a genetically modified mouse for their experiments, but with Crispr-Cas9 “transgenic” mice can be produced in a few weeks.
Despite the sucesses, the field of gene editing has been hampered by several setbacks. Editas had hoped to start human trials earlier, but was forced to move the date back after it encountered manufacturing delays. Crispr has lost several key executives in recent months, while Cellectis had to suspend its first trial briefly last year after a patient died.

Crispr is in its beginning stages ,and although it is not yet mainstream, it is expected to be completely groundbreaking in the field of medicine.

Closer to Reality: Gene Editing Technology

In August of 2017, scientists in the United States were successful in genetically modifying human embryos, becoming the first to use CRISPR-cas9 to fix a disease causing DNA replication error in early stage human embryos. This latest test was the largest scale to take place and proved that scientists were able to correct a mutation that caused a genetic heart condition called hypertrophic cardiomyopathy.

CRISPR-cas9 is a genome editing tool that is faster and more economical than othe r DNA editing techniques. CRISPR-cas9 consists of two molecules, an enzyme called cas9 cuts strands of DNA so pieces of DNA can be inserted in specific areas. RNA called gRNA or guide RNA guide the cas9 enzyme to the locations where impacted regions will be edited.

(Source: Wikipedia Commons)

 

Further tests following the first large-scale embryo trial will attempt to solidify CRISPR’s track record and bring it closer to clinical trials. During the clinical trials, scientists would use humans- implanting the modified embryos in volunteers and tracking births and progress of the children.

Gene editing has not emerged without controversy. While many argue that this technology can be used to engineer the human race to create genetically enhanced future generations, it cannot be overlooked that CRISPR technology is fundamentally for helping to repair genetic defects before birth. While genetic discrimination and homogeneity are possible risks, the rewards from the eradication of many genetic disorders are too important to dismiss gene editing technology from existing.

 

The Weirder Side of CRISPR

If you’ve been following science news at all, you’ve heard of CRISPR, the gene-editing tool which is rapidly becoming a very hot topic. Since its discovery, CRISPR has been used for some truly extraordinary things. It’s also done some other things, which stray from medical miracles into the realm of the strange.

Alphr.com reports some of the weirder projects using CRISPR. This includes manufacturing super-dogs, as well as the possibility of bringing back the woolly mammoth! This is all being done as you read this through CRISPR CAS-9

Another project mentioned in the article is an effort to create organs in pigs suitable for human transplants. This has become a larger topic of conversation, as there is always an ample need for organs, and if this project comes to fruition, waiting lists for organ transplants could possibly be abolished completely.

To read the other weird projects using CRISPR right now, check out the article.

Comment below your thoughts on this article, and the uses of CRISPR in general. I, for one, would love to see a mammoth before my own eyes!

CRISPR: The Next Step for Cancer Treatment

CRISPR is a gene editing technique that is currently still being researched and expanded upon, however, upon recent discoveries, one can note the great advantages this technology brings to the table to enhance cancer immunotherapy .  More specifically, according to the Washington University School of Medicine, “these T cell immunotherapies can’t be used if the T cells themselves are cancerous.” However, there is more to this discovery. Let’s backtrack.

What exactly is CRISPR? “CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. Its many potential applications include correcting genetic defects, treating and preventing the spread of diseases and improving crops. However, its promise also raises ethical concerns.” For the sake of this article, we are just focusing on the benefits it has on cancer treatment solely. Also, what exactly are T cells? They are “a type of white blood cell that is of key importance to the immune system and is at the core of adaptive immunity, the system that tailors the body’s immune response to specific pathogens. The T cells are like soldiers who search out and destroy the targeted invaders.” On the other hand, T cells can become cancerous therefore not being able to accomplish their task of destroying invaders.

How does CRISPR enhance cancer immunotherapy? Scientists at the Washington University School of Medicine engineered human T cells that can attack cancerous human T cells. Additionally, they engineered the T cells to eliminate a harmful side effect known as graft-versus-host disease. This was all thanks to CRISPR. But, how exactly did they figure this out? Were there any flaws or bumps in the road?

Well, this type of treatment cannot work if the T cells they use are cancerous. Supercharged T cells can alternatively be used to kill cancerous T cells, but the cells can also kill each other because they resemble each other closely. This is where CRISPR came in, preventing the human T cells and cancerous human T cells from killing each other. Another benefit of this is that the scientists engineered the T cells so any donors T cells can be used without the fear of not matching the person in need of the T cells.

Overall, anything to better the prevention of cancer is a scientific win in most’s book. But, CRISPR is a controversial tool. Some think it should be put to use and some do not. However, will this technology alter other aspects of the human genome besides diseases and deadly occurrences? How will this affect our ethics as a community? Will our genetics continue to increasingly become more altered? Time will only tell.

CRISPR Defends Bacteria, and Helps Scientists Discover New Bacterial Defenses

Although CRISPR is known for being a gene-editing tool, it can be used in other areas, such as a defense mechanisms in bacteria. This discovery “Probably doubles the number of immune systems known in bacteria,” according to a microbiologist at the University of California. Bacteria have to defend themselves against Phages, which take control over bacteria’s genetic machinery and force them to produce viral DNA. Bacteria use CRISPR to defend themselves against Phages because it stores a piece of past invaders DNA so bacteria can recognize and fight of those future viruses.

 

Photo By J LEVIN W (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

the researchers found that nine groups of bacterial genes were defense systems, and one system protected against plasmids. The data revealed a possible shared origin between bacterial defense systems and defense systems in more complex organisms. Some of the genes contained DNA fragments that are also  important parts of the immune system in plants, mammals, and invertebrates. The discovery of more bacterial defense systems poses the question of wether they will also be useful biotechnology tools like CRISPR is.Only 40% of bacteria have CRISPR, so scientists searched for other bacterial defense mechanisms. To do this, they looked at genetic information from 45,000 microbes, flagging genes with unknown functions located near defense genes, because defense-related genes cluster together in the genome. The researchers then used genomic data to synthesize the DNA and  inserted them into Escherichia coli and Bacillus subtilis, which can both be grown and studied in the lab. They then studied how well bacteria defended themselves during phage attacks with various genes detected. If eliminating certain genes deterred the bacteria’s defense, that determined that those specific genes were a defense system.

 

For more information, click here. For more information on CRISPR’s role in bacteria, click here.

Cas9: A Clue Into Making Gene Editing Safer

CRISPR is a revolutionary system that edits the DNA of living organisms with ease. The gene-editing technology offers scientists insight into genetic diseases and is widely used in biotech and agriculture, as well as to treat cancer and viral infections. But the CRISPR system and its mechanisms are not yet fully understood. However, researchers at the Ohio State University have reported that they have figured out the mechanism of how the CRISPR system figures out where and when to cut the DNA strands. This is particularly revolutionary as it provides insight into preventing gene-cutting errors.

Cas9 is an enzyme that is used by the system to target and cut out or insert specific genes. In the second of two paper published in the Journal of the American Chemical Society, the team invalidates the widely-held belief that the enzyme cuts DNA evenly. Professor of chemistry and biochemistry Zucai Suo explains that instead of cutting both sides of the DNA double-helix to the same length, Cas9  actually trims each side to uneven lengths. Ohio State doctoral student Austin Raper and his co-authors determined that the two different parts of the “Cas9 molecule communicate with each other to set the location and timing of a cut”. The first part of the molecule sets forth to cut its respective DNA strand and changes shape and signals to the second part to cut its respective second strand.

Crystal Structure of Cas9 Enzyme

Suo says that he hopes their work allows for scientists to minimize and eventually eliminate gene-editing errors. CRISPR rarely target unintended genes, but gene-editing errors can have very serious consequences. For example, if the system accidentally cut a tumor suppressor gene from a person’s DNA, they would be much more likely to develop cancer. As Raper says, it is important to understand CRISPR and the Cas9 enzyme mechanisms in order to allow CRISPR to advance to its full potential.

 

Source: https://news.osu.edu/news/2018/02/28/cas9-2cuts/

Hello, CRISPR and Goodbye, Malaria

Everybody hates mosquitoes. Not only are they annoying pests that bite us during the summertime, but they are also transmitters of the parasite that spreads malaria–Plasmodium.  However, scientists believe that they have found a way to wipe out malaria for future generations. By using CRISPR in order to alter the fibrinogen-related protein 1 (FREP1), Plasmodium can be stopped from spreading amongst human beings.  The alteration stops the plasmodium from reaching the mosquitoes’ salvatory glands, effectively halting transmission into the human bloodstream.

However, although CRISPR is a lot less drastic than simply wiping out the mosquito population, it does come with minor setbacks.  The alteration made to the FREP1 gene causes the fertility of the mosquito as well as the egg-hatching rate to drop.  These effects cause the reproduction rates of the altered mosquitoes to be significantly lower than that of other mosquitoes.  If the modified mosquitoes are not able to reproduce, then the genetic modifications are unlikely to have any real effect on the transmission of malaria since they are not being passed on generationally.

The solution? Alter the female mosquitoes.  Only female mosquitoes transmit malaria, so scientists have realized that altering the genetic code of female mosquitoes might be the way to solve the problem with reproduction.  This way, the mosquitoes are able to maintain the genetic resistance to Plasmodium whilst avoiding the dramatic drop in reproduction.

Even though the alteration of mosquitoes’ genetics is definitely a scientific feat, there are no certainties when it comes to this attempt to stop malaria. Nobody is positive about whether or not CRISPR is the solution, but it is definitely a huge step in the right direction.

A New Addition to Gene Altering Technology

Today, there is new technology that allows genes to be edited. This is called CRISPR. CRISPR can fix genetic defects that lead to disease, improve food nutrition, and even resurrect extinct species. A research team in Japan created a new technology in addition to CRISPR that can change a single DNA base in the human genome. This is called Microhomology-Assisted eXcision or MhAX. The team called this new technique “absolute precision” in their article published in the Nature Communications journal.

MhAX originated when a group of researched wanted to have a better understanding on single nucleotide polymorphisms (SNP), which are single DNA mutations that can contribute to hereditary disease. In order to discover that these SNPS cause disease, researchers need to compare two genetically matched “twin cells.” However, twin cells are difficult to make because twin cells are not completely identical-they have a single different SNP. MhAX gives a new way to make twin cells.

The research teams used an extensive process to make the edits. First, the SNP modification and fluorescent reporter gene is inputed into the cell. This allows for researchers to see which cells are changed. The researchers then created another same DNA sequence, called microhomology, that was stationed on each side of the fluorescent gene. This allowed for sites where CRISPR can enter and trim the DNA. In order to leave only the SNP in, the research team used microhomology-mediated end system (MMEJ), a repair system that can remove the fluorescent gene. This technique, according to the team of researches, is precise and they are hopeful that it will be used to gain a better understanding of disease mechanisms which could potentially lead to gene therapies.

MhAX is very interesting because it is an additional technique to CRISPR that can help alter genes. It is very fascinating to read about the future of genetics and the new technology being created that can changes genes connected to diseases and improve the lives of people. For more information on MhAX, click here and here. Based on this research, how do you think this technology will be used in the future?

 

 

 

The Future of CRISPR

CRISPR is starting to become more and more of a reality as Harvard professor David Liu continues to work on it. Liu was the person who originally developed CRISPR first base editor which allowed for single letter changes in the genetic code. Liu has come up with two new features to CRISPR-Cas9.

The first is called cellular detective or CAMERA(CRISPR-mediated analog multievent recording apparatus systems). What this function does is it finds the genetic problem that is responsible for the disease someone is experiencing. Cas9 will record all the cell data and piece info together, which overall will provide more information about cancer, stem cells, aging, and overall disease.

Photo Source

The second finding is referred to as sharp scissors which is a CRISPR enzyme. Sharp scissors are way more precise and accurate than the old enzyme making is much safer. The scissors depend on specific DNA to find the region where it is supposed to cut or edit. CRISPR is progressing and as more research is being done could be used on humans in the future.

 

New Enzyme Reducing Off-Target DNA Editing

A new enzyme named xCas9 allows researchers to target more sites in the genome than with traditional CRISPR-Cas9 editing, while also reducing off-target effects. The technique was reported earlier this year (February 28) by a biologist David Liu and his colleagues.

CRISPR-Cas9 has become the gene-editing tool of choice in many labs due to the effectiveness and convenience. But CRISPR-Cas9 has limitations like the necessity of targeting a particular sequence called a PAM near the gene to be modified, which limits researchers’ ability to make specific genetic changes.

“Relief from the PAM restriction is quite important,” Albert Jeltsch of the University of Stuttgart in Germany. “Some of these elements are quite small, and then the restriction can be quite relevant.”

Liu and his colleagues used a laboratory technique to evolve an enzyme that could recognize a broader range of PAM sequences, enabling more sites in the genome to be targeted. It just so happens that xCas9 also turned out to be more specific to the targeted sites, with fewer off-target effects. xCas9 will allow gene therapy to have higher success rates.

CRISPR/Cas9: Is it really the cure?

There are many benefits to the CRISPR/Cas9 defense system. But, do the pros outweigh the cons?

CRISPR is a molecule that can be programmed to target a specific sequence in a genome. It guides an enzyme, such as Cas9, to chop the code like scissors. There have been many studies and tests done using the defense. The most important advantages of CRISPR/Cas9 over other genome editing systems are its simplicity and efficiency. Since it can be applied directly in the embryo, CRISPR/Cas9 reduces the time required to change certain genes compared to other systems.

However, many attempts to use this mechanism have failed. Using the mechanism is not as easy as it sounds. A Cas9 repair is not always precise. On ZMEScience, one HIV patient tried the process. But, the HIV cells were only made stronger. Researchers equipped T-cells to hurt the virus with the enzyme Cas9. T cells are a type of lymphocyte that play a central role in cell-mediated immunity. T cells equipped with Cas9 were seen to successfully hurt the HIV genome, and make it unable to properly reproduce. This project led by Chen Liang from McGill University in Montreal, Canada seemed to work fine. But, the team noticed that two weeks later T cells were producing copies of virus particles that had escaped the CRISPR attack. The area around Cas9 only developed more mutations, aka it made the HIV stronger. It is also impossible to direct the Cas9 exactly where one wants it to go. So in essence, it is a risky gamble.

Although there are hopes for this technique to be more refined and successful in the future, for now, its uses are limited.

For more information click here.

CRISP New Technology: CRISPR

If you have ever seen GATTACA, and thought ‘Wow! I want to edit my genes!’… you may be in luck! CRISPR technology is a simple tool for editing ones genomes. (CRISPR is just a nickname for “CRISPR-Cas9”. ) A genome is an organism’s complete set of genes, including non-coding nucleic acid sequences. CRISPR technology has many different applications, including altering DNA sequences, modifying gene function, correcting genetic defects, and preventing the spread of diseases. Although all of these functions sound positive, CRISPR technology seems to raise ethical concerns.

 

DNA Pencil: Edit Photo By: mcmurryjulie

CRISPR stands for “clusters of regularly interspaced short palindromic repeats”, and is a specialized region of DNA with two definitive characteristics: the presence of nucleotide repeats and spacers. Nucleotides are the building blocks of DNA, and eventually proteins. CRISPR technology was adapted from the natural defensive mechanisms of bacteria. In order to repel attacks, these organisms use CRISPR derived RNA and various Cas proteins (including Cas 9), to attack foreign viruses, or other unknown bodies. CRISPRs are specialized stretches of DNA. The protein Cas9 is an enzyme that acts like a pair of “molecular scissors” which acts to cut strands of a person’s DNA. This protein usually binds to two RNA molecules: cRNA and another called tracrRNA. These two forms of RNA guide Cas9 to the target site, where it will make it’s “cut”. Cas9 cuts both strands of the DNA double helix, making what is known as a “double strand break”. This is how genes are editing.

Bouncing back to the defensive bacteria organisms that started this all, they attack foreign invaders by chopping up, and therefore destroying, the DNA. This allows for the manipulation of genes. These bacteria also use the spacers as a bank of memories which allows the bacteria to recognize viruses and other invaders.

However, due to these discoveries of how CRISPR technology works in bacteria, CRISPR technology is now going to be used to edit the genes of people to change genomes and possible diseases and phenotypes. This has caused some ethical concerns to arise in regards to CRISPR technology being used for human genome editing. Most of the changed involving genome editing are limited to somatic, or body cells, (not sperm or egg cells). Changes in body cells can’t be passed from generation to generation, but changes in sex cells can be passed onto future generations. Some of the previously mentioned ethical concerns include whether it would be a good idea to use this technology to enhance normal human traits (including height and intelligence). Due to these ethical concerns these genome edits are actually illegal in many countries!

Could CRISPR Cure Duchenne Muscular Dystrophy?

What is Duchenne Muscular Dystrophy?

https://www.flickr.com/photos/150276478@N03/34406844136

Duchenne muscular dystrophy, DMD, is an X-linked recessive disease caused by defects in the gene that makes the dystrophin protein. This particular gene is made of 79 exons, and the defects can occur on any of them. These defects lead to degeneration of skeletal and heart muscle, forcing patients to rely and wheelchairs and respirators. Without a cure, most people with the disease die by the age of 30. So, the question becomes, how can we find a cure?

What is Precision Editing?

http://www.njsta.org/news/crispr-in-the-classroom-by-simon-levien

CRISPR technology has advanced tremendously in the past several years, with each study building off the last. CRISPR technology has the capability to cut out segments of DNA, but with the risk of cutting out too much or the wrong parts. Thus, it is crucial that the cutting be as precise as possible. The CRISPR-Cas9 gene-editing tool, uses an RNA strand to guide the Cas9 enzyme along the DNA strand, skipping over important “healthy” DNA and leading the enzyme to cut a specific portion of DNA.

 How do DMD and Precision Editing Connect?

Dr. Olsen is Co-Director of the Wellstone Muscular Dystrophy Cooperative Research Center, a lab in which a team has been working to apply precision editing to DMD. The method uses one single cut of DNA along strategic points and is less intrusive than other methods. Scientists have developed guide RNAs with the purpose of finding mutation “hotspots” along the dystrophin gene. The RNA strand guides the Cas9 enzyme to 12 regions where most DMD mutations have been found. According to the article, “the new strategy can potentially correct a majority of the 3,000 types of mutations that cause DMD.” Wow! In a recent study using this method, these RNAs helped rescue cardiac function to near-normal levels in human heart muscle tissue.

Why is it Important?  

The new study demonstrates eliminating abnormal splice sites in human DNA can correct a wide range of mutation. In the case of DMD, the splice sites that were removed using CRISPR technology instruct the genetic machinery to build abnormal dystrophin molecules. Once these sites are removed, an improved dystrophin protein was observed. Even more fascinating, correcting only half of the damaged cells restored cardiac function to a healthy level. Does this sound fascinating? If you answered yes, click here to learn more!

What Does the Future Hold?

The strategy of single-cut editing may be useful for treating other single-gene diseases. News of such prospects has generated a great deal of hope for patients. Much more research is needed before CRISPRCas9 can be used on human patients. Labs and researchers around the world are working to perfect this method so that it can get federal government approval and move to the next stage – human trials. As research progresses, it will be faced with backlash from some who believe DNA should not be altered and that the technique is too risky and support from those who believe this new technique could save lives. Which side do you fall on?

CRISPR/Cas9 System undoing genetic disease? Maybe!

A recent study released from the Whitehead Institute for Biomedical Research discuss the pioneering way scientists are using CRISPR technology to help boys born with Fragile X syndrome.

Fragile X syndrome is a rare condition affecting 1 out of 3600 boys born. Symptoms of this genetic condition are delayed development, often impulsive actions and intellectual difficulties. There is no cure. The disease is caused by DNA methylation, which is caused by the random addition of a methyl (CH3) group to the DNA strand. CRISPR technology has made it possible for this methylation to be removed – essentially, the CRISPR/Cas9 system removes the extra CH3 group.

Source: https://commons.wikimedia.org/wiki/File:DNA_methylation.svg

The mutation occurs in the FMR1 gene on the X chromosome, as the name suggests. The methylation prevents the expression of the FMR1 gene, and the CRISPR/Cas9 system removes the added CH3 group, allowing the gene to be expressed. The FMR1 gene is crucial in brain and cognitive development, so the CRISPR technology allows for this gene to function – virtually rescuing the person from the disease.

Due to the successful application of CRISPR technology to Fragile X syndrome and the FMR1 gene, this rare disease is better understood by scientists. This same technology, which removes the added CH3 group, thus removing the methylation, is hypothesized to be useful in lessening or eliminating symptoms from diseases such as muscular dystrophy.

What is CRISPR-Cas9?

CRISPR-Cas9 is a new(ish) technology that is used for knocking out human genes in cell lines for the purpose of seeing what these genes do. CRISPR-Cas9 has a “protein scissor”, the cas-9 protein, and a location that shows the cas9 where to bind to. The “location” is actually a strand of RNA that is complementary to a specific strand of DNA. This RNA strand is like glue in that it binds to the DNA and allows the Cas9 to cut the DNA. This process or the CRISPR-Cas9 technology is like an endless cycle of cutting and repairing DNA until the repair enzyme can no longer repair the DNA or makes a mistake. This technology can make the process of cutting and disabling genes five times faster. It allows scientists to edit parts of a genome by altering, removing, or adding certain sections of DNA. While this technology can be very useful in trying to understand what genes do it does have a downside, “these approaches are costly and time-consuming to engineer, limiting their widespread use, particularly for large scale, high-throughput studies.” The picture below shows what this process looks like on a very basic scale. Hopefully this technology will eventually allow us to fully understand what every gene does.

 

Epigenetics Fight Against Pancreatic Cancer

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

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.

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

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

(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?”

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:

  1. Treat disease in humans
  2. Eliminate Malaria
  3. Give humans other animals’ organs
  4. Create new medications
  5. 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?

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!

 

 

 

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