Crispr-Cas9 – BioQuakes

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Can Sickle Cell Anemia Be Treated by CRISPR/Cas9 Mediated Gene Therapy?

On April 17, 2024

In Student Post

Founded by Dr. Emmanuelle Charpentier and Dr. Jennifer Doudna, CRISPR is a gene-editing tool that has enabled medical breakthroughs and changed biomedical research. The goal of CRISPR is to treat diseases by developing advanced cell therapies designed to target specific genes that cause or progress the course of a disease. Although in the process of clinical trials, CRISPR could potentially be a treatment for sickle cell anemia.

The CRISPR gene-editing system is split into two parts: Cas9 and a guide RNA. Cas9 is an enzyme that unwinds and cuts two strands of DNA in a specific location in the genome so that DNA can be added or removed. Cas9 has a similar function to the helicase enzyme we studied earlier this year; however, unlike helicase, Cas9 unwinds DNA in an ATP-independent manner and uses the binding energy between the guide RNA and target strand to unzip the DNA. The guide RNA (gRNA) guides Cas9 to a target-specific sequence in the DNA where it should bind and where the edit should be made. This target-specific sequence has a similar function to an RNA primer, which guides the DNA polymerase to this binding site to initiate DNA replication.

Sickle cell anemia is a genetic blood disorder that affects hemoglobin. Sickle cell anemia causes the body to produce hemoglobin S, an abnormal form of the molecule that lessens its function. Hemoglobin S has a distorted shape, which causes obstructions, pain, infections, and inhibits circulation. Sickle cell anemia is a monogenic, autosomal recessive trait, which means that sickle cell anemia can be passed down through generations if there is one mutated sickle cell hemoglobin S gene present, even though it is a recessive trait (a recessive trait usually indicates that there needs to be two mutated genes for the trait to be present in offspring). CRISPR is a perfect solution for sickle cell anemia, as CRISPR involves an ex vivo gene-edited cell therapy where, theoretically, hemoglobin stem cells can be extracted from the patient, edited and corrected, and then put back into the body. Scientists are still in the clinical trial phase of using CRISPR to treat sickle cell anemia, but wouldn’t it be amazing if it worked for thousands of people!

I hope you guys found this post as interesting as I did. Feel free to leave a comment and tell me what you think!

CRISPR Gene Editing: The Key to Pharmaceutical Development

On April 17, 2024

In Student Post

An article published in December of 2023 through ScienceNews identifies how the first CRISPR therapy approved in the U.S. will treat sickle cell disease. CRISPR therapy involves the process of changing the nucleotide sequence of a small segment of guide RNA in order to allow accurate targeting of almost any desired genomic locus for the purpose of correcting disease-causing mutations or silencing genes associated with disease onset (source). On December 8 of last year, the U.S. Food and Drug Administration approved gene editing, or CRISPR, therapy for use in patients ages 12 and older. The treatment, named Casgevy, is the worlds first treatment to alter cells using the Nobel Prize-winning molecular scissors. In addition, Lyfgenia, another gene therapy for sickle cell disease was approved on December 8.

Previously, patients relied on drugs such as hydroxyurea or bone marrow transplants which didn’t always work for everyone. Casgevy on the other hand relies on a patients own cells. CRISPR treatment alters the genetic blueprint of bone marrow cells that give rise to blood cells in order to make new healthy cells.

Approximately 100,000 people in the United States, most of them black or Latino, have sickle cell disease. Sickle cell disease is caused by a genetic defect in hemoglobin, the oxygen-carrying protein in red blood cells. While typical blood cell are flexible enough to slip through blood vessels, sickled blood cells are inflexible and often get stuck resulting in restrictions to blood flow and debilitating pain. People with severe forms of the disease may be hospitalized multiple times a year.

Many scientists are excited about this new treatment option. Kerry Morrone, a pediatric hematologist at Albert Einstein College of Medicine in New York City says CRISPR-therapy treatment for sickle cell disease can give patients a “new lease on life” commenting on the fact that people with the disease often miss school, work, or special events due to the excruciating pain.

Several clinical trials have tested the CRISPR based treatment Casgevy on participants. Victoria Gray, the first sickle cell patient to enroll in the trial recounted how the treatment changed her life. Gray had preciously described bouts of pain that felt like being struck by lightning and getting hit by a train at the same time. Now, pain-free, she is able to enjoy time with her family. Furthermore, Jimi Olaghere, another patient in the trial, told a similar tale. He says before treatment “sickle cell disease dominated every facet of my life” and “hospital admissions were so regular that they even had a bed reserved for me.” After the trial, he is pain free and able to present for his children while also doing the things he loves.

Of course with any new discovery, there are challenges. Patients who wish to be treated with Casgevy must first receive chemotherapy to wipe out existing bone marrow cells so the new ones have a chance to thrive. Chemotherapy can raise the risk of blood cancer and cause infertility. It also kills immune cells which puts patients at higher risk of dying from infections. In addition, the therapy may cost up to $2 million per patient, but healthcare costs for sickle cell patients are already high over their lifetime.

An article published the same day goes into more detail on how exactly this new treatment functions. The article states that the treatment also called exa-cel directs CRISPR to a gene, called BCL11A that typically prevents the body from making a form of hemoglobin found only in fetuses. The new therapy allows physicians to remove a person’s own bone marrow stem cells, edit them with exa-cel, destroy the rest of the person’s untreated bone marrow, and then re infuse the edited cells.

A second article published in January of this year goes into detail about the CRISPR system itself and how it can be used to treat many different conditions. The article states that CRISPR gene editing unlocks the ability to precisely target and edit specific genetic mutations that drive the growth and spread of tumors as well as new possibilities for the development of more effective and personalized cancer treatments. CRISPR gene editing is not only useful for the treatment of sickle cell disease, but also useful in the treatment of a much wider scale.

Similar to the methods in which CRISPR alters genes, in AP Biology class, we preformed a transformation lab in which we altered bacteria membranes through a heat shock in order to allow the plasmid, pGLO, to pass through the membrane and activate the gene for glow. CRISPR functions similarly to pGLO as they both are able to alter the genes inside of cells or bacteria in order to cure diseases or just make bacteria glow green as it did in AP Biology class.

I hope this article helped simplify the ways in which CRISPR therapy works to treat sickle cell disease and other major diseases as well as explaining how this new discovery opens of many new possibilities in the world of medicine and pharmaceutical development. I look forward to seeing where CRISPR gene editing and therapy goes and how many diseases it will be able to cure in the future. What do you think?

Researchers Discovered a Possible Antidote for the Most Deadly Mushroom

On April 17, 2024

In Student Post

There is a reason why it is not advisable to eat wild mushrooms; Amanita phalloides, nicknamed death cap mushrooms, closely resemble edible mushroom variants—but are deadly if ingested. If a person chances upon one and happens to eat it, regardless of whether it is cooked, there is a high likelihood that they die.

A. phalloides are the most toxic of any mushroom species and are responsible for the majority of fatal mushroom poisonings. Notable victims of death cap mushroom poisoning include Roman Emperor Claudius, Pope Clement VII, and Holy Roman Emperor Charles VI. A. phalloides poisoning has always been difficult to diagnose and even more difficult to treat, as symptoms emerge after a long delay and there has been no known antidote to A. phalloides toxin—that is, until researchers utilized CRISPR-Cas9.

Death cap mushrooms contain the amatoxin alpha-amanitin. The amatoxins are a group of toxins that share the trait of inhibiting the enzyme RNA polymerase II. In our AP Biology class, we discussed DNA polymerases and their vital function in DNA replication. Similarly, RNA polymerases are a vital component of RNA transcription and synthesis. RNA polymerase II synthesizes mRNA, the template for protein synthesis. Upon the inhibition of RNA polymerase II, cell metabolism comes to a halt and apoptosis (cell self-destruction) ensues.

Alpha-amanitin is possibly the most deadly of the amatoxins. The particular human genes that are triggered by alpha-amanitin were previously unknown, but CRISPR recently revealed these genes, one of which produces the protein STT3B. STT3B is a required component of alpha-amanitin toxicity, therefore an inhibitor of STT3B would negate the effects of alpha-amanitin.

Researchers found just that—an inhibitor of STT3B, indocyanine green. Once the effectiveness of indocyanine green was confirmed in vitro, scientists experimented with a mouse model of alpha-amanitine poisoning and found that indocyanine green had a profound effect if given one to four hours after ingestion of the toxin. However, if eight to 12 hours had elapsed before the indocyanine green was introduced, its effectiveness was greatly reduced, possibly because irreversible organ damage had already occurred in the subject. This fact poses concern, as alpha-amanitine poisoning symptoms take at least six hours to occur after A. phalloides ingestion.

While more investigation needs to be undertaken before indocyanine green can be proposed as a treatment for death cap mushroom poisoning, these latest discoveries represent a significant advancement in our understanding of the process. Any thoughts regarding CRISPR or this topic as a whole are encouraged.

CRISPR-Cas9 – The Human Editor

By walkabuffalo

On April 30, 2023

In Student Post

What is CRISPR-Cas9? CRISPR-Cas9 (Clustered, Regularly Interspaced Short Palindromic Repeats) is a powerful technology that allows geneticists to modify or “edit” parts of the target genome by adding or removing whole sections of the DNA sequence. Currently, CRISPR is the most versatile and accurate DNA modification tool globally. This tool allows scientists to fix flaws in most organisms’ DNA and has minimal risk of off-target damage.

CRISPR-Cas9 has two main molecules that carry out the change in DNA, an enzyme called Cas9, and a piece of RNA called guide RNA (gRNA). The Cas9 enzyme locates the target area and can cut the DNA in a specific location in the genome so that small pieces of DNA can either be added or removed. The gRNA is made of a small piece of a lab-designed RNA sequence, roughly 20 bases long, located within the RNA scaffold. To ensure that the Cas9 enzyme cuts at the right point in the genome, the scaffold binds to the DNA, and the lab-designed sequence pilots the Cas9 enzyme to the correct location. The gRNA has RNA bases that match those of the target DNA sequence in the genome. The Cas9 enzyme follows the gRNA to the specific area and makes a precise cut across both strands of the DNA. During this stage, the cell recognizes that the DNA has been damaged and will try to repair itself. Scientists use this DNA repair system to add or remove changes in one or multiple genes. This technology is consistent with our most recent AP Biology Unit, DNA Replication, and Gene Expression/Replication.

In my opinion, CRISPR-Cas9 is an incredible technology as it has so many practical applications. The future of this technology has potential in many diverse fields such as genetic engineering, bioengineering, and molecular biology, among other areas of study.

The technology has been tested on dogs with Duchenne Muscular Dystrophy, a gene mutation adversely affecting muscle proteins. In this case, a CRISPR gene-editing treatment demonstrated promising signs of permanently fixing the genetic mutation responsible for this disease, which in humans, affects approximately 1 in 3,500 male births worldwide. The mutation prevents an organism from producing an appropriate level of functioning dystrophin which causes muscles to be weak and not respond efficiently. Researchers at the University of Texas Southwestern found that gene editing restored the functioning dystrophin levels in the dog’s muscles and heart tissue. The increase in the dystrophin levels would need to be more significant for it to work in humans, but researchers have been making substantial progress in advancing this developing CRISPR-Cas9 technology.

CRISPR Gene and what it’s about

On April 23, 2023

In Student Post

The CRISPR gene isn’t something that everyone in the world knows about. So what is it? CRISPR stands for – clustered regularly interspaced short palindromic repeats. This obviously still won’t help to make sense onto what this is. This gene is used in gene editing. Gene editing is used to make new DNA for any organism. According to the article, it helps with adding, removing, or altering genetic material. CRISPR is a new and more efficient way for gene editing. CRISPR has been used in bacteria when fighting against viruses. When the viruses attacks the first time, the bacteria captures the viruses DNA and creates CRISPR arrays which will then remember the virus the second time and fight it off. Researchers then use the CRISPR as RNA to cut off pieces of DNA with the help of the CAS-9 enzyme. Gene editing and the CRISPR gene help with treatment and help prevent diseases to spread in organisms.

According to this article, there are three ways for the CRISPR gene to work. It can disrupt the DNA sequencing. Then it can also delete a fragment of DNA. The last thing it can do is correct/insert. It can add new DNA or it can make edits to the DNA.

According to this article, the CRISPR gene might be able to be used in things beyond the gene editing world. It might be able to help with quick research and findings for things like cancer and other diseases. Feng Zhang is trying to spread this technology across the world so that they can use this new technology to help with things like this.

This also relates to what we are learning in class this year because we are also talking about gene expression and how it works. We learned about transcription and translation. Transcription is the synthesis of RNA with the use of DNA. Then Translation is the synthesis of the protein by the RNA. All of this ties to the gene editing with the CRISPR gene because the CRISPR gene is another wya that the DNA is edited/corrected. It is a much quicker and more efficient way that might be really helpful going forward.

CRISPR corrects genetic diseases in mice!

On March 20, 2022

In Student Post

Researchers at Duke University have shown that a single systemic treatment using CRISPR genome editing can safely correct Duchenne muscular dystrophy (DMD) in mice for over a year. In 2016 the first successful use for CRISPR to treat an animal model of a genetic disease was published by, Charles Gersbach, the Professor of Biomedical Engineering at Duke. The strategy used by Gersbach can potentially be used for human therapy.

Since 2009, Gersbach has been working on finding a genetic treatment for DMD and his lab was one of the firsts to focus on CRISPR, which is a defense system that slices apart the DNA of invading viruses.The goal was to cut out the dystrophy exons around the mutation and then let the body naturally repair the DNA and stitch it back together to create a shortened dystrophy gene. After eight weeks it was observed in the mice used for the experiment that functional dystrophin was restored and muscle strength increased but the long term effects of the treatment had not been explored.

The new goal of Gersbachs study was to figure out these long term effects. To determine this, doctor Christopher Nelson gave both adult and newborn mice with the dystrophy gene a dose of CRISPR. The mice were monitored over the year to see what kind of genetic alterations were made as well as any immune responses. There were no results of toxicity in any of the mice. Although this is a positive result Gersbach and Nelson know that a mouse immune system can function differently than a human immune system which brings further questions of reliability of CRISPR in humans to the table.

In my AP biology class we recently learned about gene expression. CRISPR systems have been engineered to control gene expression in bacteria. CRISPR is used to target precise parts of DNA which could help to correct abnormalities that cause diseases.

Redesigned Cas9 protein provides safer gene editing than ever before!

By chrisynthesis

On March 20, 2022

In Student Post

Gene editing is a group of technologies that give scientists the ability to change an organism’s DNA. These technologies allow genetic material to be added, removed, or altered at particular locations in the genome. Several approaches to genome editing have been developed. A recent one is known as CRISPR-Cas9, which is short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. The CRISPR-Cas9 system has generated a lot of excitement in the scientific community because it is faster, cheaper, more accurate, and more efficient than other existing genome editing methods.

File:CRISPR-Cas9 Editing of the Genome (26453307604).jpg

CRISPR-Cas9 Editing of the Genome

One of the challenges that come using CRISPR-based gene editing within humans is that the molecular machinery may sometimes make edits to the wrong section of a host’s genome. This is problematic because it creates the possibility that an attempt to repair a genetic mutation in one location in the genome could accidentally create a dangerous new mutation in another spot. Scientists at The University of Texas at Austin have redesigned a key component of a widely used CRISPR-based gene-editing tool, called Cas9, to be thousands of times less likely to target the wrong stretch of DNA while remaining just as efficient as the original version, making it potentially much safer.

File:CRISPR CAS9 technology.png

CRISPR CAS9 technology

The CRISPR-Cas9 system works similarly in the lab. Researchers create a small piece of RNA with a short ‘guide’ sequence that binds to a specific target sequence of DNA in a genome. The RNA also binds to the Cas9 enzyme. As in bacteria, the modified RNA is used to recognize the DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location. Although Cas9 is the enzyme that is used most often, other enzymes can also be used. Once the DNA is cut, researchers use the cell’s own DNA repair machinery to add or delete pieces of genetic material, or to make changes to the DNA by replacing an existing segment with a customized DNA sequence.

Other labs have redesigned Cas9 to reduce off-target interactions, but so far, all these versions improve accuracy by sacrificing speed. SuperFi-Cas9, as this new version has been named, is 4,000 times less likely to cut off-target sites but just as fast as naturally occurring Cas9. Scientists say you can think of the different lab-generated versions of Cas9 as different models of self-driving cars. Most models are really safe, but they have a top speed of 10 miles per hour.

In my opinion, setting aside any and all ethical concerns, genome editing is of great interest in the prevention and treatment of human diseases. Currently, most research on genome editing is done to understand diseases using cells and animal models. Scientists are still working to determine whether this approach is safe and effective for use in people. It is being explored in research on a wide variety of diseases, including single-gene disorders such as cystic fibrosis, hemophilia, and sickle cell disease. It also holds promise for the treatment and prevention of more complex diseases, such as cancer, heart disease, mental illness, and human immunodeficiency virus (HIV) infection.

Paving The Way For Discovery: Gene Editing In Ticks

On March 20, 2022

In Student Post

What is something that reminds you of summer and your childhood? For me, it is ticks. I know it sounds strange, but the constant reminders from my parents to “check for ticks” after long summer walks are ingrained in my memory. Although the practice of checking for ticks is common, we don’t often stop to question why, or take a moment to expand our knowledge as to just how dangerous a summer walk in long grass could be. Ticks, although tiny, are powerful, disease ridden organisms and have the potential to spread diseases to humans such as Lyme’s disease, Babesiosis, Anaplasmosis, Tularemia, etc.

Despite their ability to pass on such a vast variety of pathogens, research on ticks is extremely limited, especially in comparison to similar organisms like mosquitoes. The challenge when it comes to gene editing in ticks is that tick embryos are very difficult to inject due to high pressure in the eggs, a hard outer shell on the egg, and a wax layer outside the embryo created by Gene’s organ. In a recent study published in iScience, researchers developed a tick-embryo injection protocol that aimed to target gene disruption with CRISPR-Cas9 (using both embryo injection and Receptor-Mediated Ovary Transduction of Cargo. In this technique, researchers removed Gene’s organ to prevent the wax coating along with treating the eggs with chemicals such as benzalkonium chloride and sodium chloride to remove the outer shell and relieve the inner pressure. Gulia-Nuss, the co-author of the study and a molecular biologist at the University of Nevada, states: “Another major challenge was understanding the timing of tick embryo development. So little is known about tick embryology that we needed to determine the precise time when to introduce CRISPR-Cas9 to ensure the greatest chance of inducing genetic changes.”

Essentially, the CRISPR-Cas9 system consists of two main molecules that introduce a mutation to the DNA. The first is an enzyme known as Cas9. The function of this enzyme is to cut the strands of DNA at a specific location in order for pieces to be added or removed. As we learned in AP Bio, enzymes are key when it comes to DNA and DNA replication, for they play a variety of roles that allow DNA to replicate the way it does. For example, helicase untwists the double helix at the replication fork, topoisomerase relieves the strain of twisted DNA strands by breaking and rejoining them, and primase synthesizes short RNA strands that act as a primer. Without these enzymes and their very specific purposes, DNA would not be able to replicate. In the case of Cas9, it performs the essential job of cutting DNA in order for gene editing to occur. The second piece of the system is a piece of RNA called guide RNA. The guide RNA binds to a specific sequence in the DNA due to its RNA bases that are complementary to those of the DNA sequence.

Prior to this study, no lab had displayed the possibility for gene editing in ticks, due to the daunting technical difficulties of such a task. This study is proof to embrace the difficulty and the challenges, in life and in science, for often the most difficult of tasks lead to the greatest outcome. In the case of this study, the discovery of ways in which to target the disruption of genes in ticks will pave the way to the uncovering of the molecular biology of tick-pathogen-host interactions, hopefully in the long run creating ways to prevent and control tick-borne diseases, a process that has the potential to save lives.

Researchers at UT Austin tweak cas9 to make CRISPR gene-editing 4,000x less error-prone

By merrillenmeyerflask

On March 16, 2022

In Student Post

A huge stride in ensuring the efficacy of CRISPR genome-editing has been made by researchers at the University of Texas at Austin. The CRISPR gene editing tool is a new genetic engineering technique that can, by using an enzyme called Cas9, correct problematic genomes in a person’s DNA. It finds the genome that its programmed to and cuts it out of the DNA, leaving the organism without that DNA, and inhibiting the organism from spreading that gene to their offspring. There have been studies have shown CRISPR has been effective in editing genomes that may cause disease. In a study where the Cas9 enzyme was injected into the bloodstream of six people with a rare and fatal condition called transthyretin amyloidosis, those who received the higher dose saw a decline around 87% in production of the misshapen protein that causes this condition.

For many diseases, Gene therapy is the “Holy Grail”. For treatment of Sickle-Cell Anemia, CRISPR has been thought of as a definitive cure. In 2017, it was reported that a 13-year-old boy with HbSS disease had been cured with gene therapy. This treatment also allows the carrier of this gene to reproduce without any risk of their offspring being affected by SCD.

However, there are concerns that when performing the genome editing, the wrong segment of DNA could be targeted by scientists and removed, resulting in potentially drastic consequences. Another concern is that editing out certain genes is societally damaging, as it is considered unnatural to be able to edit the genomes of human bei

ngs. Another major safety concern is mosaicism (when some cells carry the edit but others do not); this could result in many different side effects. Due to the many uncertain aspects around the danger of genome-editing, there has been delay in passing legislation approving genome-editing.

In a study published on March 2nd 2022 at the University of Texas at Austin, researchers have found a previously unknown structure in the Cas9 protein that is thought to attribute to these genetic mistakes. When using cryo-electron microscopy to observe the Cas9 protein at work, the researching team noticed a strange finger-like structure that stabilized the off-target gene section to be edited instead of editing the target gene.

The researchers at the University of Texas at Austin were able to tweak the protein, preventing Cas9 from editing the wrong sequence. This change has made the tool 4,000 times less likely to produce unintentional mutations; the team calls the new protein ‘SuperFi-Cas9’.

While other researchers have made similar edits to make the Cas9 protein more accurate in its editing, these often result in slowing down the genome editing process. At UT Austin, the researchers say that SuperFi-Cas9 still is able to make edits at the normal speed.

The researchers plan to test SuperFi-Cas9 further in living cells as opposed to the testing thats been done with DNA in test tubes. Hopefully they’re able to cement the accuracy of SuperFi-Cas9, and that this may accelerate us on our way to implementing CRISPR gene editing in the current medical world. Let us know in the comments below what your thoughts are on CRISPR editing, and if you think we should continue researching it!

How CRISPR Can Help Individuals Overcome Obesity

On March 16, 2022

In Student Post

Fat, which is made up of cells that have been distended with greasy or oily materials, or triglycerides, is required for the body to function, but it may also be hazardous if consumed in excess. Fat cells are distinct from other cells such that they lack surface receptors and constitute only a small percentage of the cells in fat tissue. While restricting diets can assist those who are obese lose weight, the results are typically solely temporary. If only there were a way to target fat cells specifically… Well, there just might be!

A group of doctors discuss a potential prospective breakthrough utilizing CRISPR-Cas9, a technology that has proven particularly elusive in the study of adipose tissue, in a recent publication published in the Journal of Biological Chemistry. Their study was tested on mice, in order to see how it worked and what it targeted. The gene-editing technology CRISPR-Cas9 changes genes by precisely cutting DNA and then allowing natural DNA repair mechanisms to take charge. This technology has changed the ability of deleting or inserting certain genes of interest into an organism. Cas9, an enzyme that can break DNA strands as well as a piece of RNA that directs the Cas9 enzyme to a specific location in the genome for modification, is encased in a non-harmful virus and supplied to the cells being studied. The equipment has also been used to study the heart, liver, neurons, and skin cells, to name a few. However, brown fat adipose cells have never been studied.

Using CRISPR-Cas9 components, the physicians were eventually able to target brown fat adipose cells. In mature mice, they were able to knock off the UCP1 gene, which specifies brown adipose tissue and allows it to generate heat. They discovered that knockout mice were able to adjust to the absence of the gene and maintain their body temperature under freezing settings, indicating the existence of additional mechanisms involved in temperature regulation. Overall, the CRISPR interference system assisted mice in losing about twenty percent of their body weight, proving that CRISPR can accurately target fat cells.

Genetics can have a significant impact on the quantity of fat cells you are born with. However, the proportion of tendency to becoming overweight differs by individual. For example, in some people, genes account for just 25 percent of the tendency, but in others, the genetic effect might be as high as 70 percent to 80 percent. Obesity is most commonly associated with the FTO gene. This FTO gene is not found in everyone. For example, around 20 percent of white people have a variation of the gene that increases their risk of obesity. The FTO gene is located on chromosome 16, which is one of the 23 pairs of chromosomes in humans. While this chromosome pair represents under 3 percent of the total DNA in cells, if FTO is present, it can affect whether if one is obese or not, depending on the alleles of the gene. CRISPR has the potential to target this gene as well as other genes that affect body weight, such as brown fat adipose cells.

Your health is essential for the rest of your life! A healthy lifestyle can aid in the prevention of chronic diseases and long-term ailments. The alleles on the FTO gene can have an impact on your health and are linked to type 2 diabetes, obesity, and other health concerns.

How Gene-edited Strawberries are Safe and Beneficial to the Consumer

On March 16, 2022

In Student Post

Over one-third of purchased strawberries end up getting thrown in the trash due to bruising, mold, or mushy texture. However, The J.R. Simplot Company and Plant Sciences Inc. hope to change this outcome. The pair of companies plan to modify the DNA of strawberries with the help of CRISPR-Cas9 and sell them on a commercial scale— and don’t worry! Recently published research suggests that it is safer than other alternatives.

These gene modifications aim to extend strawberry shelf life, prolong its growing season, and reduce consumer waste. This essentially means that farmers can efficiently grow more quality fruit for longer portions of the year.

CRISPR-Cas9 is a tool derived from the immune defense system in Streptococcus Pyogenes bacteria and is currently repurposed to edit sections of DNA sequences. CRISPR-Cas9 or the CRISPR/Cas9 system is primarily made up of the Cas9 protein, crRNA, and tracrRNA (or, more simply, guide RNA).

As we have learned in AP Biology, RNA is a single-stranded molecule crucial to the processes of coding, decoding, regulation, and expression of genes. Our initial understanding of RNA holds to be true as the human-engineered guide RNA from the CRISPR/Cas9 system dictates exactly where the protein to cuts in the sequence. After the targeted section is cut, the Cas9 protein removes the particular section of DNA. Then, Host DNA can be placed in the removed portion of the DNA sequence and elicit a desired trait in the gene. For a deeper explanation of how CRISPR-Cas9 functions, I recommend watching Paul Andersen’s YouTube video on the subject.

This is exactly how The J.R. Simplot Company and Plant Sciences Inc. plan to genetically modify the genes within the strawberry.

This technology is far more efficient than the cumbersome process of selective crop breeding. To boot, Plants modified by the CRISPR/Cas9 system were found to be nearly identical to plants bred using traditional methods. The CRISPR/Cas9 system has also been found to have been thousands of times less likely to target the wrong stretch of DNA, making it potentially much safer than alternative methods of gene editing.

In the near future, The Simplot and Plant Sciences Inc. team plan to sell the strawberries after they identify the key genomes that determine shelf life and edit the plants for ideal crops.

Do you think this is exciting news? Would you try a gene-edited strawberry? Why or why not?

Can CRISPR-Cas9 Cause Unwanted Change?

By hydropherick

On March 16, 2022

In Student Post

Dieter Egli, a biologist at Columbia University whose main goal is to better understand the differences in DNA duplication between cell types, how these differences affect genetic stability, and how certain differences affect people’s functional relevance. CRISPR-Cas9, a powerful gene-editing tool, can have serious side effects in human embryonic cells. In some cases, the consequences of these errors can be quite severe, prompting them to discard large chunks of their genetic material.

CRISPR-Cas9 is an innovative technology that allows researchers to edit parts of genes by removing, adding, or changing sections of the DNA sequence. It is a faster, cheaper, and more accurate DNA editing technique than others such as genome editing. These techniques enable researchers to investigate the function of the gene. Researchers can use these systems to permanently modify genes in living cells and organisms, and in the future, they may be able to correct mutations at specific locations in the genetic code to treat genetic causes of disease such as blindness

DNA Repair-colourfriendly

Adapted to be accessible to those with red-green colorblindness, this image depicts DNA repair after a CRISPR-Cas9 double-strand break.

CRISPR-Cas9 embryos and other kinds of human cells have already demonstrated that editing chromosomes can cause unwanted effects. This can be in relation to the unpredictability of the repair due to the fact of different cells react differently to gene editing. Another possibility for the CRISPR-Cas9 treatment not working efficiently is a change made to sperm, eggs, or embryos that can be passed down to future generations, raising the stakes for any mistakes made along the way. An example of this would be CRISPR-Cas9 genome editing on early-stage human embryos with a mutation in the gene called eyes shut homolog, which causes hereditary blindness.

CRISPR–Cas9 efficiently edits the genome in a variety of cell types and whole organisms, repairing genetic mutations, removing pathogenic DNA sequences, and turning genes on or off in Gene Regulation, where the appropriate gene is expressed to help an organism respond to its environment.

CRISPR Gene Editing: The Future of Food?

By biosyntaysis

On March 16, 2022

In Student Post

Biology class has taught me a lot about genes and DNA – I know genes code for certain traits, DNA is the code that makes up genes, and that genes are found on chromosomes. I could even tell two parents, with enough information, the probabilities of different eye colors in their children! However, even with all this information, when I first heard “gene editing technology,” I thought, “parents editing what their children will look like,” and while this may be encapsulated in the CRISPR gene editing technology, it is far from its purpose! So, if you’re like me when I first started my CRISPR research, you have a lot to learn! Let’s dive right in!

Firstly, what is CRISPR Gene Editing? It is a genetic engineering technique that “edits genes by precisely cutting DNA and then letting natural DNA repair processes to take over” (http://www.crisprtx.com/gene-editing/crispr-cas9). Depending on the cut of DNA, three different genetic edits can occur: if a single cut in the DNA is made, a gene can be inactivated; if two separate DNA sites are cut, the middle part of DNA will be deleted, and the separate cuts will join together; and if the same two separate pieces of DNA are cut, but a DNA template is added, the middle part of DNA that would have been deleted can either be corrected or completely replaced. This technology allows for endless possibilities of advancements, from reducing toxic protein to fighting cancer, due to the countless ways it can be applied. Check out this link for some other incredible ways to apply CRISPR technology!

In this blog post however, we will focus on my favorite topic, food! Just a few months ago, the first CRISPR gene-edited food went on the market! In Japan, Sicilian Rouge tomatoes are now being sold after the Tokyo-based company, Sanatech Seed, edited them to contain an increased amount of y-aminobutyric acid (GABA). “GABA is an amino acid and neurotransmitter that blocks impulses between nerve cells in the brain” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). It supposedly (there is scarce scientific evidence of its role as a health supplement) lowers blood pressure and promotes relaxation. In the past, bioengineers have used CRISPR technology to “develop non-browning mushrooms, drought-tolerant soybeans and a host of other creative traits in plants,” but this is the first time the creation is being sold to consumers on the market (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/)!

So, how did Sanatech Seed do it? They took the gene editing approach of disabling a gene with the first method described above, making a single cut in the DNA. By doing so, Sanatech’s researchers inactivated the gene that “encodes calmodulin-binding domain (CaMBD)” in order to increase the “activity of the enzyme glutamic acid decarboxylase, which catalyzes the decarboxylation of glutamate to GABA, thus raising levels of the molecule” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). These may seem like big words, but we know from biology that enzymes speed up reactions and decarboxylation is the removal of carbon dioxide from organic acids so you are already familiar with most of the vocabulary! Essentially, bioengineers made a single cut in DNA inside of the GABA shunt (a metabolic pathway) using CRISPR technology. They were therefore able to disable the gene that encodes the protein CaMBD, and by disabling this gene a certain enzyme (glutamic acid decarboxylase) that helps create GABA from glutamate, was stimulated. Thus, more activity of the enzyme that catalyzes the reaction of glutamate to GABA means more GABA! If you are still a little confused, check out this article to read more about how glutamate becomes GABA which will help you better understand this whole process – I know it can be hard to grasp!

After reading all of this research, I am sure you are wondering if you will soon see more CRISPR-edited food come onto the market! The answer is, it depends on where you are asking from! Bioengineered crops are already hard to sell – many countries have regulations against such food and restrictions about what traits can actually be altered in food. Currently, there are some nutritionally enhanced food on the market like soybeans and canola, and many genetically modified organisms (GMOs), but no other genome-edited ones! The US, Brazil, Argentina, and Australia have “repeatedly ruled that genome-edited crops fall outside of its purview” and “Europe has essentially banned genome-edited foods” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). However, if you are in Japan, where the tomatoes are currently being sold, expect to see many more genome edited foods! I know I am now hoping to take a trip to Japan soon!

Thank you so much for reading! If you have any questions, please ask them below!

New anti-CRISPR Proteins Serving as Impediments to this Miraculous System.

On March 17, 2019

In Student Post

CRISPR-Cas9 systems are bacterial immune systems that specifically target genomic sequences that in turn can enable the bacterium to fight off infecting phages. CRISPR stands for “clusters of regularly interspaced short palindromic repeats” and was first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco. Cas9 is a protein enzyme that is capable of cutting strands of DNA, associated with the specialized stretches of CRISPR DNA.

Diagram of the CRISPR prokaryotic antiviral defense mechanism.

Recently, a blockage to the systems was found by researchers which are essentially anti-CRISPR proteins. Before, research on these proteins had only showed that they can be used to reduce errors in certain genome editing. But now, according to Ruben Vazquez Uribe, Postdoc at the Novo Nordisk Foundation Center for Biosustainability (DTU), “We used a different approach that focused on anti-CRISPR functional activity rather than DNA sequence similarity. This approach enabled us to find anti-CRISPRs in bacteria that can’t necessarily be cultured or infected with phages. And the results are really exciting.” These genes were able to be discovered by DNA from four human faecal samples, two soil samples, one cow faecal sample and one pig faecal sample into a bacterial sample. In doing so, cells with anti-CRISPR genes would become resistant to an antibiotic while those without it would simply die. Further studies found 11 DNA fragments that stood against Cas9 and through this, researchers were ultimately able to identify 4 new anti-CRIPRS that “are present in bacteria found in multiple environments, for instance in bacteria living in insects’ gut, seawater and food,” with each having different traits and properties. “Today, most researchers using CRISPR-Cas9 have difficulties controlling the system and off-target activity. Therefore, anti-CRISPR systems are very important, because you want to be able to turn your system on and off to test the activity. Therefore, these new proteins could become very useful,” says Morten Sommer, Scientific Director and Professor at the Novo Nordisk Foundation Center for Biosustainability (DTU). Only time will tell what new, cool, and exciting discoveries will be made concerning this groundbreaking system! What else have you guys heard? Comment below!

Successful Progeria Treatment in Mice Also Bodes Well For Humans

On March 12, 2019

In Student Post

A successful CRISPR-Cas9 treatment of Progeria in mice may be the beginning of anti-aging in humans.

When Juan Carlos Izpisua Belmonte set out to study “the molecular drivers of aging,” he could not have picked a more appropriate disorder than Progeria. Progeria is an accelerated aging disorder “caused by a mutation in the LMNA gene.” In both mice and humans, progeria induces many symptoms of aging, such as “DNA damage, cardiac dysfunction and dramatically shortened life span,” early in life. Molecularly, Progeria “shifts the production of lamin A,” a protein, ” to progerin,” a toxic form of lamin A that builds up with age.

In order to “to diminish the toxicity from the mutation of the LMNA gene that leads to accumulation of progerin inside the cell,” the Belmonte-led group used CRISPR-Cas9 to disrupt both lamin A and progerin. To do so, RNA first guides Cas9 to a spot on the DNA. Then, it makes a cut that “renders lamin A and progerin nonfunctional.”

As a result, the treated mice enjoyed a 25% longer life span and were stronger and more active. The successful treatment bodes well not only for mice, but for humans. In the future, “efforts will focus on making the therapy more effective” and compatible for humans.

CRISPR/Cas9: Controlling Genetic Inheritance in Mammals

By karlylinnaeus

On March 12, 2019

In Student Post

Often the subject of debate, CRISPR/Cas 9 has come to the forefront of the scientific community as its development bridges the worlds of Sci-Fi and reality. Yet while CRISPR/Cas9 has been successfully used in altering the genetic inheritance of insects, applying the same technology to mammals has proven to be significantly more complex. With the recent development of active genetics technology in mice by UC San Diego researchers, a huge stride has been made for the much contested future of gene technology.

Releasing their findings in January, the team led by Assistant Professor Kimberly Cooper engineered a copycat DNA element into the Tyrosinase gene controlling fur color. The copycat DNA results in mice that would have been black appearing white. Over two years they determined the copycat element could be copied from one chromosome to another, repairing breaks targeted by CRISPR. Ultimately, the genotype was converted from heterozygous to homozygous.

Following the success of her lab’s single gene experiment, Cooper hopes to use the technology to control the inheritance of multiple genes and traits in mice. Her experiment, the first active genetic success in mammals, has biologists hopeful for future development of gene drive technologies to balance biodiversity and mitigate the adverse effect of invasive species.

Fighting the mosquito disease problems with… mosquitos?

On October 10, 2018

In Student Post

Since the discovery of CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), gene editing has become a highly debated topic. One of the reasons backing the use of CRISPR-cas9 is to prevent diseases. These diseases include mosquito-borne diseases such as zika, dengue fever, and malaria. Malaria in particular kills around 3,000 children every year. Various groups of scientists have worked on genetically modifying mosquitos to stop the spread of malaria by making female offspring sterile and unable to bite, making male offspring sterile, or making mosquitos resistant to carrying diseases. A point of concern was if the modified gene would stay relative and would carry from generations. In order to make offspring, genes from both parents must be used, resulting in the offspring carrying the modified gene only half the time. In particular cases, mutations would occur in the altered DNA, which nullified the genetic changes. This has been solved by developing a gene drive, which makes the desired gene dominant and occur in the offspring almost 100% of time. This entails almost the entire mosquito population could have this modified gene in as little as 11 generations.

Image by Author

Recently, the government of Burkina Faso, a small land-locked nation in west Africa, has approved for scientists to release mosquitos that are genetically modified anytime this year or next year. The particular group of mosquitos to be released first is a group of sterile males, which would die rather quickly. Scientists want to test the impact of releasing a genetically modified eukaryotic organism in the Africa. It is the first step in “Target Malaria” project to rid the region of malaria once and for all.

One of the major challenges in gaining allowance to release the genetically modified species was the approval of the residences, who lack words in the local language to describe genetics or gene editing. Lea Pare, who leads a team of scientists modifying mosquitos, is working with linguists to answer questions the locals may have and tp help develop vocabulary to describe this complex scientific process.

What do you think about gene editing to possibly save millions?

Read the original article here.

View a video explaining how scientists can use genetic engineering to fight disease here.

A Treat for the Muscles!

By frantibiotic

On October 10, 2018

In Student Post

Scientists using CRISPER-Cas9 gene-editing technique have managed to better the lives of four dogs suffering from the most common form of muscular dystrophy, Duchenne.

https://commons.wikimedia.org/wiki/File:Smiling_Dog_Face.jpg

A research team led by U.T Southwestern Medical Center edited muscle cells in young dogs with Duchenne to remove a short, problematic segment of protein-coding DNA that occurs in both canine and human patients. Within about two months, the dogs were producing a greater amount of dystrophin.

To get this gene-editing technology into the dog’s muscles, the research team created viruses to transport the gene-editing machinery. To do so, the scientists had to extract some of the virus’s own DNA in order to fit the gene-editing machines. The viruses were assigned either of two tasks. Some viruses carried Cas9-molecular “scissors” to cut out the DNA sequence that blocks the production of dystrophin in muscle cells. The other viruses carried a guide molecule to help the Cas9 to identify where it should make those cuts.

Using viruses as a means to transport the gene-editing technology is very helpful because viruses are very small, even smaller than bacteria. When a virus enters your body, it invades some of the cells and takes control of the cell’s functions by injecting its genetic materials into the cell.

For now, the research team has already demonstrated that CRISPR can treat Duchenne in human cells in the lab, but this test was the first success with a large mammal. Adding on, for this study, the research team focused on the protein level, not on how this treatment may have affected the dog’s behavior.

To conclude, one question that remains in the air after this demonstration is how long one injection with CRISPR will last in human Duchenne patients versus dogs. The research team is hoping once, but there is still so much to discover!

CRISPR/CAS9: Potential to destroy malaria?

On March 12, 2018

In Student Post

CRISPR. Sounds more like a new brand of potato chip than something potentially revolutionary (Bold new flavor. Bold new crunch. CRISPR.). Nevertheless, this tool used for easy gene editing and slicing is tearing up the science world because it could be the key to combatting disorders and diseases.

Recent research indicates that CRISPR/Cas9 based genome editing tools could aid in the fight against malaria, one of the “big three” diseases that has long affected and continues to affect humans worldwide. How is CRISPR/Cas9 able to do this?

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) originally are how bacteria protect themselves from foreign viruses. CRISPRs contain DNA from viruses that have attacked the bacteria, and so when a similar virus attacks, the bacteria knows that this virus and his DNA are bad. Essentially, CRISPRs allow bacteria to build up immunity. When foreign DNA is detected, the Cas9 enzyme is guided by the CRISPR and is able to cut the desired DNA. Scientists have come up with a way to engineer and manipulate the CRISP/CAS9 system into other organisms (such as mosquitoes) so that we can successfully edit genome sequences and genes to produce desired results. We take advantage by specifying which genes the Cas9 should cut/replace, and then it does just that. Therefore, the CRISPR/Cas9 system allows us new genome editing potential like none before.

Made by Viktoria Anselm.

How does this apply to mosquitoes and malaria? Scientists experimented with genetically modified malaria-transmitting mosquitoes (Anopheles gambiae), altering the fibrinogen-related protein 1 (FREP1) gene on them. This gene essentially codes for a protein that makes mosquitoes a vector for malaria. The scientists used the CRISPR/Cas9 to inactivate this gene.

The results produced mosquitoes with significantly less transmission of malaria to both human and rodent cells. However, these mosquitoes have “reduced fitness”: a significantly lower blood-feeding propensity, egg hatching rate, a retarded larval development, and reduced longevity after a blood meal. Essentially this means that these mosquitoes have a low chance of affecting populations of mosquitoes in the wild without being “pushed” by scientists, where scientists are “forcing DNA to inherit particular sets of genes.” This is called a gene drive. With a strong push for a couple of years, there is potential for worldwide mosquito populations to be significantly changed in 10-15 years.

Photo taken by JJ Harrison

I chose to write about this new research and potential breakthrough because it really means something to me, as I have lived in and visited countries threatened by malaria. I had to take preventative pills every morning, and I would have to sleep in a restrictive mosquito net. All that made me wonder about and feel for a kid in the same country who didn’t have those things and how he or she would manage without those barriers to malaria. Having said that, I really do believe this is a worthwhile option we should explore, and I think it can make a difference for the world.

What do you think? Do you think it is realistic for theses mosquitoes to change the entire mosquito population and effectively help reduce malaria transmission? Will CRISPR/Cas9 work as we hoped? Or is it too good to be true?

Deleting Genes to Stop Malaria

On March 12, 2018

In Student Post

A new discovery has highlighted the positive effects that the revolutionary new gene editing tool, CRISPR-Cas9, can have. Scientists at the Johns Hopkins Bloomberg School of Public Health’s Malaria Research Institute have discovered that the deletion of a single gene from the Anopheles Gambiae mosquito, called the FREP1 gene, yields promising results in the eradication of the malaria disease.

Image result for mosquito gene editing

Gene Editing

The FREP1 gene has been associated with being a malaria “host factor” gene because it helps the parasite live in the gut of the mosquitoes. However, the scientists, using the CRISPR-Cas9 gene editing procedures, have been able to delete the FREP1 gene from the mosquitoes and have seen significant decreases in the spread of malaria. Without the host factor gene, the parasite has difficulty surviving in the mosquito, which decreases the spread of the disease to other organisms.

The deletion of the FREP1 gene had other effects in addition to the resistance of the malaria parasites. In the mosquitoes where the gene was deleted, many showed no signs of sporozoite-stage parasites in their salivary glands, which can spread to humans through mosquito bites. George Dimopoulos, PhD, professor in the Bloomberg School’s Department of Molecular Microbiology and Immunology, commented on the study, saying that “if you could successfully replace ordinary, wild-type mosquitoes with these modified mosquitoes, it’s likely that there would be a significant impact on malaria transmission”.

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