BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: #CRISPR/Cas9 (Page 1 of 5)

CRISPR Gene editing makes disease resistant rice

Have you ever enjoyed a delicious bowl of rice and thought, “I wish more rice crops didn’t die of disease”? Well, if you’ve ever had that thought, I’ve got some good news for you! Scientists have been using CRISPR gene editing to make rice more resistant to diseases.

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Researchers by identifying a special strain of rice that showed resistance to various pathogens. They then used CRISPR-Cas9, to isolate the specific gene responsible for this resistance which was RESISTANCE TO BLAST1 (RBL1), which plays a crucial role in phospholipid biosynthesis. By tweaking this gene, they were able to enhance the rice plants’ natural defense mechanisms, making them resistant to diseases like rice blast, which is a fungal disease.

This connects with what we learn in AP Biology about genes and how they’re involved in protein synthesis.When a cell makes a protein, it starts with transcription, where the information in DNA, which is made up of genes, is copied onto mRNA. Then, the mRNA goes to the Rough Endoplasmic Reticulum, where it’s read by ribosomes. These ribosomes make the protein according to the instructions in the mRNA. In the case of the RBL1 gene, this means making a phospholipid. After the protein is made, it heads to the Golgi apparatus, where it gets some final changes based on the mRNA’s instructions before going to its final destination.

Wow, I really thought this was really interesting research especially to me personally because I love rice and think CRISPR research is really fascinating. Reading about this research also makes me wonder what are the different applications of CRISPR outside of agriculture?

Could Gene Editing be the Key to Perpetual Virus Resistance?

Influenza viruses have spread rapidly despite the vaccines many of us, humans, get (I, for one, just had the flu despite being vaccinated). Vaccines help our bodies recognize certain pathogens and create baseline antibodies to help neutralize them, but, as I learned in AP Bio class, mutations randomly happen. Not only is this genetic variation the key to natural selection in nature, but also for viruses (though viruses also often use the recombination process). As host organisms work as the viruses’ environment that they are trying to survive and reproduce in, natural selection could choose the viruses with mutations that are not recognized by our immune system from the vaccine and potentially create a new virus strand our vaccine is ineffective against.

Potentially more effective and permanent than vaccines, scientists are now exploring gene editing. A step up from the human interference in artifical selection that we learned in AP Bio, where humans choose to breed organisms with specifc traits to create ideal offspring, gene editing changes the organisms themselves. Typically thought of with genetically modified organisms (GMO) referring to plants and plant-based foods, gene editing can also be done on animals.

Take, for example, genetically-modified chickens that protect against avian influenza infections that have run throughout poultry farms at devastating costs. Since the ANP32A gene in chickens codes for the protein that influenza viruses rely on to successfully hijack cells, scientists edited that gene with CRISPR molecular scissors. As the protein is absolutely essential to the virus hijacking chicken cells, no simple mutations should be enough to override the gene editing; thus, chickens should theoretically be permanently resistant to the virus.

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

In multiple studies done, this permanent resistance was almost the case: every typical chicken got the flu when closely exposed to high levels of it (at least 1000 infectious particles), whereas genetically-modifed chickens very rarely got it. In the first study, ten out of ten typical chickens got it, while just one out of 10 edited chickens got it and also at a lower level. In another experiment with an astounding 1 million infectous particles in two separate incubators, all of the typical chickens got it in both incubators and none of the modified chicken got it in one of the incubators, but five out of ten got it in the other. As it turns out, viruses in the latter incubator adapted to use proteins very similar to the protein the edited gene eliminated. There are two proteins very similar to the eliminated protein in chickens, so, to create full flu resistance in chickens, those two genes would need to be edited as well, researchers confirmed. However, editing those genes may hurt chicken development.

Chickens are everywhere, vital to many people’s diet, and can pass the flu to pigs and even us. If we can make chickens resistant to the flu, it could do us and our world wonders  plus, who knows where we will go from there!? Thus, I believe researchers should focus on figuring out if they can edit those three genes in chickens without hurting their development and how to create resistance with this incredible gene-editing ability if not.

We need to make use of our incredible technologies to limit illnesses and improve society; do you have any thoughts on gene editing or possibly even how we can maximize its potential to practically accomplish this task?

A New Cure: CRISPR Technology’s Role in Curing Sickle Cell Disease

Affecting more than 100,000 people in the US, SCD, or sickle cell disease, is an inherited condition that causes a person’s blood cells to block blood flow to the rest of the body. In extreme cases, this disease can cause strokes, eye problems, and many other severe adverse effects in somebody with the illness. As of now, the leading treatment is medication; however, this medication can come with side effects such as lower white blood cell levels and platelet count. Recently, though, a ScienceNews article highlighted a new cure for Sickle Cell Disease that was approved by the Food and Drug Administration.

Sickle Cell Anemia

In the article, a CRISPR gene-editing technique is used to cure the disease. The treatment alters the gentic blueprint of the bone marrow that makes blood cells in a patients body. This process uses a patients own cells to defeat Sickle Cell disease by having edited cells make fetal hemoglobin. Fetal hemoglobin, unlike normal hemoglobin, cant be turned sickle and therfore wont clog up blood streams. In a study following people who received this treatment, 29 out of 30 didnt report any pain crises for a year. There are still side effects of this treatment such as increased exposure to cancer due to chemotherapy needed in the bone marrow altering and potentially other undiscovered sideffects. However, the treatment is still relatively new and it is yet to be seen if it can be improved on and it also still may be a better alternative than the current treatments of Sickle cell disease.

Being a carrier for the sickle cell gene myself, I find this research very interesting. Sickle Cell disease has an autosomal recessive pattern which means that the way to express Sickle Cell disease is through getting two of the recessive genes from both of your parents. Therfore somebody who is heterozygous for sickle cell has a higher chance of having a child with sickle cell disease if there partner is either a carrier or has sickle cell disease than somebody who homozygous dominant for not having sickle cell disease. With this topic being so closely related to me it is important that scientists continue to discover and improve on their ways of curing sickle cell disease in the upcoming generations. If you know any information about any other emerging cures for sickle cell disease share them in the comments below!

 

Diving into the Sea of Gene Editing

Have you ever wondered why some people travel across the world just to go snorkeling or scuba diving? The answer is simple, Coral. Coral is one of the most beautiful organisms in the ocean. While coral is amazing, its looks are not all that it achieves. Coral is home to 25% of marine species while also feeding close to half a billion humans. Coral has such a huge impact on the world we live in, yet pollution and global warming are slowly taking out tons and tons of beautiful coral from our oceans. Although there are over 6,000 species of coral, we are going to narrow it down to just 1,500 and analyze the “stony corals” ability to build reef architectures.

Scleractinia (calcium skeleton of stony corals) at Göteborgs Naturhistoriska Museum 9006

Phillip Cleves is a scientist at Carnegie Melon who set out to use cutting-edge CRISPR/Cas9 genome editing tools to reveal a gene that’s critical to stony corals’ ability to build their reef architectures. Cleves highlights the ecological significance of coral reefs, emphasizing their decline due to human-induced factors like carbon pollution. Carbon emissions lead to ocean warming, causing fatal bleaching events, and ocean acidification, hindering reef growth. This acidification is particularly detrimental to stony corals, as it affects their ability to form skeletons made of calcium carbonate. Understanding the genetic basis of coral skeleton formation is a key research area to address this issue.

You may be wondering, what is CRISPR? CRISPR is like a genetic toolbox that scientists can use to edit DNA. Imagine DNA as a big instruction book that tells our bodies how to work. Sometimes, there are mistakes in the instructions, like a typo in a recipe. CRISPR lets scientists find and fix these mistakes. They can cut out the wrong parts of the DNA and put in the right ones, like editing a sentence in a book. This helps researchers study how genes work and could one day help treat diseases by fixing genetic errors. Using CRISPR, Cleves and his team were able to identify a particular gene called SLC4y which is required for young coral to begin building. The protein it encodes is responsible for transporting bicarbonate across cellular membranes. Interestingly, SLC4γ is only present in stony corals, but not in their non-skeleton-forming relatives. Together, these results imply that stony corals used the novel gene, SLC4γ, to evolve skeleton formation.

Finally, in AP Biology, you learn about genetics, the study of how traits are passed down from parents to offspring through DNA. CRISPR technology is like a super-advanced tool that geneticists use to manipulate DNA. It’s kind of like having a magic eraser for genetic mistakes! CRISPR also brings up the potential for gene editing in humans although sometimes it is seen as unethical. What genes would you edit if you had the chance?

 

Cholesterol Chopping with CRISPR: A Gene-ius Solution for Heart Health!

Dive into the microscopic world within us, where groundbreaking gene editing is poised to revolutionize heart health! In a groundbreaking clinical trial by Verve Therapeutics in New Zealand, a volunteer has become the first person to undergo DNA editing aimed at reducing blood cholesterol levels, a key factor in heart disease. This innovative approach uses a version of the CRISPR gene-editing tool to alter a specific part of the DNA within the patient’s liver cells. The goal of this precise genetic tweak is to permanently lower the levels of “bad” LDL cholesterol, which is responsible for the buildup of plaque in arteries, leading to heart disease and potentially heart attacks. In our AP Biology class, we learned that cholesterol is a type of lipid, or fat,  found in the cells of all animals. It’s essential for creating cell membranes, making hormones like estrogen and testosterone, and helping your body produce vitamin D and bile acids that digest fat. While cholesterol is crucial for these biological functions, too much of it, especially in the form of LDL (“bad” cholesterol”), can lead to health problems like heart disease. Cholesterol: friend, foe, or just misunderstood? Let us know down below!

The patient selected for this trial had a genetic predisposition to high cholesterol levels and was already experiencing heart disease. Verve Therapeutics believes that their gene-editing technique could be applied to a broader population to prevent cardiovascular diseases, the leading cause of death globally. The use of CRISPR technology for common conditions like high cholesterol represents a significant shift from its previous applications, which were mostly limited to rare genetic disorders. This approach could benefit millions who struggle to manage their cholesterol levels through conventional methods.

The treatment targets a gene called PCSK9, known to play a crucial role in regulating LDL cholesterol levels. By introducing a minor error in this gene through base editing, a more precise version of CRISPR that doesn’t cut the DNA but instead changes one DNA base into another, Verve aims to switch off PCSK9’s function. This interruption is expected to result in a significant and lasting reduction in LDL cholesterol, potentially preventing the development of heart disease in individuals with familial hypercholesterolemia (FH), a condition causing abnormally high cholesterol from a young age.

Protein PCSK9 PDB 2p4e

The technology behind Verve’s treatment is akin to the mRNA COVID-19 vaccines, utilizing nanoparticles to deliver genetic instructions to cells. This method directs liver cells to produce a base-editing protein that alters the PCSK9 gene, reducing LDL cholesterol levels. Early trials in monkeys have shown promising results, with a 60% reduction in bad cholesterol that has remained effective for over a year, indicating the potential for a permanent solution.

Cholesterol with numbering

However, the application of gene editing for cholesterol management is not without risks. Concerns include the toxicity of nanoparticles and potential side effects similar to those observed in other PCSK9-lowering drugs, such as muscle pain. Unlike traditional medications that can be stopped if adverse effects occur, gene editing is irreversible, presenting a challenge in managing unexpected outcomes.

Despite these challenges, the prospect of a one-time treatment for high cholesterol offers a revolutionary approach to combating heart disease. Verve’s gene therapy is anticipated to be more affordable than current gene therapies, thanks to the scalable manufacturing process similar to that used for COVID-19 vaccines. This advancement could make gene editing a viable and widespread treatment option, not only reducing the global burden of cardiovascular disease but also extending life expectancy by preventing heart attacks, the leading cause of death worldwide. Do you think that this techonolgy will be as promosing as it looks? Let us know down below!

New Advancements in Curing Sickle Cell!

Do you know someone who has sickle cell or has passed away at the hands on sickle cell? Well, new treatments using CRISPR technology are under way. This revolutionary treatment is made to last much longer than previous gene editing treatment, which lasted for up to a year. This treatment is called exa-gel made by Vertex and CRISPR. 

CRISPR-Cas

How Does It Work?

In sickle cell anemia, mutations in a gene HBB causes a change in the hemoglobin’s structure, causing circular red blood cells to twist into a sickled shape. The sickled red blood cells cause extreme pain and fatigue. In severe cases, beta-thalassemia can occur. Beta-thalassemia causes not enough hemoglobin or red blood cells to be produced, leading to low oxygen levels.  The exa-gel technology targets the hemoglobin protein. It directs the Cas9 enzyme to the BCL11A gene and cuts its DNA off, turning it off. It is then able to produce fetal hemoglobin with normal shape. For this to be done, physicians must remove the bone marrow stem cells, edit them with the exa-cel, destroy the untreated bone marrow, and reinfuse treated cells. In AP Biology, we learned how the regulation of gene expression works. A gene that is usually on but can be turned off is a repressible operon. The operon regulates genes with the help of enzymes. The operator site is where repressor proteins can bind to turn off production. It is in between the promoter and structural genes. Usually, RNA polymerase binds to the promoter to begin production. Once that occurs, mRNA is transcribed. Then, tRNA picks up amino acids and the anticodons bind to the codons for the polypeptide chain to form. Finally, proteins will be produced to allow for the desired outcome to occur. However, Cas9 inhibits this process so that these sick blood cells will not be produced and healthy fetal ones will begin production. 

 

Sicklecells

The Future

While this new technology seems exciting, there are a lot of uncertainties about it. First of all,  “the participants have only been tracked for a short time and that problems could arise later.” Although we do not know much about the long term effects of the treatment, we do see promising results. 29/30 of participants with sickle cell anemia reported no pain for a year after the treatment. 39/42 of beta-thalassemia no longer needed blood or bone marrow transfusions for a year after it. Sadly, it is expected for the treatment to cost about $2 million per patient. Due to this absurdly high cost, scientists are looking into a technique called haploidentical transplant to treat sickle cell anemia. This technique, which is also used for cancer, involves replacing a patient’s bone marrow with a parent or sibling who shares 50% of their DNA. 88% of patients with this procedure made normal red blood cells 2 years after it. This procedure is promising and much more cost effective; it could be popular in low income countries. Nevertheless, this new technology is extremely exciting and potentially world altering.

Pig Kidneys and CRISPR: A Swine-Tific Breakthrough! 🐖

The groundbreaking transplant occurred at Massachusetts General Hospital, where surgeons successfully implanted a pig kidney into a 62-year-old patient, Richard Slayman. Slayman, who had been on dialysis for seven years due to complications from type 2 diabetes and high blood pressure, faced a challenging prognosis. Traditional human organ transplants presented a daunting wait time, rendering them an impractical solution. However, the advent of genetically engineered pig organs offered a glimmer of hope.

The pig kidney transplant represents the culmination of years of research and development in xenotransplantation. Scientists have meticulously engineered pigs with modifications to mitigate immune rejection in human recipients. Why pig organs? Egenesis wrote, “Pigs have been identified as a good species for xenotransplantation due to their similarity to humans in terms of organ structure and physiology, in addition to the abundance of the species” (eGenesis). Researchers have tailored pig organs to be more compatible with the human immune system by employing advanced gene-editing techniques such as CRISPR. What is CRISPR gene editing, you might ask? Mr. Anderson has a great in-depth explanation, but I will give you a brief overview. There are a number of genes associated with CRISPR called Cas-genes which make Cas proteins , which in general are helicases and nucleases. In AP Bio, we learned that helicases unwind DNA. Nucleases cut the DNA. The system will transcribe and translate proteins and transcribe DNA to make CRISPR RNA (crRNA). This is a way to fight the viral DNA by breaking it apart, so “before the infection starts, the infection has essentially ended” (Bozeman 2:45). Also note that the “spacers” are basically a history of old infection so that we won’t be infected again. Why is this so popular in the science world? Scientists thought that if we hijack the system, they could use it to inactive genes or embed new genes.CRISPR-Cas

EGenesis, a biotechnology company, spearheaded these efforts by implementing 69 genetic edits to enhance compatibility. To ensure the success of the transplant, Slayman underwent comprehensive preoperative preparations, including antibody-based treatments and immune-suppressing drugs. The procedure’s apparent success offers promising prospects for the future of transplantation medicine. Dr. Leonardo Riella of Massachusetts General Hospital expressed optimism that such transplants could revolutionize treatment paradigms, potentially rendering dialysis obsolete.

A Future without Dialysis? Oink-credible!

Mass General Hospital also released an article. They specifically stated, “Additionally, scientists inactivated porcine endogenous retroviruses in the pig donor to eliminate any risk of infection in humans.” (This was not previously mentioned in the first article).CRISPR illustration gif animation 1In AP Bio, we did an entire unit on DNA, gene expression, and gene regulation. To understand what CRISPR is and how it works, you need to know this unit’s steps. CRISPR facilitates the study of gene function by enabling researchers to manipulate gene expression patterns precisely. Scientists can elucidate the mechanisms governing gene expression and regulatory networks by targeting specific regulatory elements within the genome. We discussed gene expression, where CRISPR plays its role by looking into specifics, such as translation and transcription. It involves using a Cas enzyme (such as Cas9) guided by a small RNA molecule (gRNA) to target specific DNA sequences for modification. While CRISPR itself doesn’t directly involve transcription, it can indirectly manipulate gene expression. By targeting particular regions of DNA, CRISPR can disrupt or modify genes, thereby affecting mRNA transcription from those genes. For example, CRISPR could knock out a gene of interest, decreasing or abolishing the corresponding mRNA transcription.

Moreover, the implications extend beyond medical innovation. The breakthrough holds the promise of addressing systemic disparities in organ transplantation. Dr. Winfred Williams highlighted the potential for increased health equity, particularly for ethnic minority patients facing barriers to accessing donor organs. 

The successful pig kidney transplant represents a triumph of scientific endeavor and human perseverance. As we navigate the complexities of organ shortage and healthcare disparities, innovations in xenotransplantation offer hope. By fostering dialogue and collaboration, we can chart a course toward a future where life-saving treatments are accessible.

As we piggyback into the future of medicine, let’s remember that every breakthrough comes with a side of questions. But with CRISPR in one hand and pig kidneys in the other, who knows what’s next? One thing’s for sure: the future’s looking mighty swine-tastic! 🐖✨

What are your thoughts on the ethical implications of xenotransplantation? How do you envision the future of organ transplantation evolving in light of recent advancements? 🧬🧬

**Used Grammarly as a tool***

Dark Side of the CRISPR

CRISPR-Cas9 editing of the genome
In the bright glow of rapid scientific advancement, CRISPR-Cas9 gene-editing techniques stands out as hope for many people, achieving a future where genetic diseases are no longer an issue to consider about. Awarded the Nobel Prize in Chemistry, biochemists Jennifer Doudna and Emmanuelle Charpentier‘s discovery of CRISPR has shocked the world with the potential to “fix” genetic diseases and malfunctions. However, beneath the surface of this fascinating technique is a complex ethical dilemma: the potential to erase diversity when preventing genetic diseases from occurring

The Promise and Danger of CRISPR

CRISPR offers abilities to edit genes with accuracy, having the power to treat or even eliminate diseases that have plagued humanity for thousands of years. However, this powerful technology also brought up an ethical challenge. It is a risky path that cures diseases but might end up eliminating genetic traits that is undesirable by societal standards, which will decrease the diversity of genes. 

Disability studies scholars, especially those who have genetic conditions, express deep concerns over CRISPR’s application. They fear that perhaps one day humanity will use this technology to “edit out” genetic conditions like cystic fibrosis (CF) and syndactyly, not just from the patient, but from the entire human gene pool. Such result raises the question: Who decides what gene is “normal” or what gene is “bad”?

Ethics.jpg
CC BY 2.0, Link

Ethics
For many, genetic conditions are closely related to their identity and life. Considering these conditions just as errors results in overlooking the richness and diversity of human life. Lives like those of Sandy and Rosemarie, authors of “The Dark Side of CRISPR”, who navigate daily life with CF and syndactyly respectively, points out the value of diverse experiences and perspectives, even if they are often considered “undesired”. They remind us that difference is not always a negative thing and that the quest for a “perfect” genetic makeup is flawed.

Humanity is at a crossroad of genetic editing, we must recognize the significance of decisions we make today on the future. CRISPR technology have the potential for unprecedented medical abilities, but it also have ethical questions that require careful consideration. We must balance the benefits of gene editing while also accounting for genetic diversity and the rights of individuals that live unedited lives.

Connections to AP Biology
In our AP biology class, we’ve learned about the mechanics of genetics, exploring how DNA sequences determine traits and how mutations can lead to genetic disorders. CRSPR-Cas9 gene editing technology ties closely with these topics, demonstrating a real-world application of the knowledge we’ve learned. The vast majority of genetic disorders are due to mutations or errors on the DNA, there is a very small chance that mutations or errors might occur, and even if there is one, most of the time it would have no effect. However, occasionally, it is still possible for a critical place of DNA to have a mutation, which can result in various genetic diseases that seemed impossible to prevent. This is where CRISPR comes in to save the day, its ability to precisely edit these genes brings up closer from being able to correct genetic mistakes that lead to diseases, preventing patients from getting an genetic disease.

Lets Discuss!
The ethical implications of CRISPR technology are topics that deserve our attention and thoughts. How do you perceive the balance between the health benefits of CRISPR and the ethical dilemmas it presents? How can we use this technology in a way that respects and preserves the diversity of all human experiences? Please feel free to share your thoughts in the comments below and we can dive further in this topic! For more information, go ScientificAmerican.com for latest research and updates!

 

 

Almost 200 new kinds of CRISPR systems were Revealed by Search Algorithms

Researchers at the McGovern Institute for Brain Research at MIT, the Broad Institute of MIT and Harvard, and the National Center for Biotechnology Information (NCBI) have developed a groundbreaking algorithm to efficiently explore large microbial sequence databases in search of rare CRISPR systems. These systems, found in diverse bact®eria from environments like coal mines, breweries, and Antarctic lakes, could offer new opportunities in biotechnology.

CRISPR, is a revolutionary technology that allows scientists to edit genes with. Originally discovered as a part of the bacterial immune system, CRISPR has been adapted for use in gene editing in a wide range of organisms. The technology works by using a small piece of RNA to guide an enzyme (often Cas9) to a specific location in the genome, where it can make precise cuts in the DNA. These cuts can then be used to disable a gene, repair a faulty gene, or introduce a new gene. CRISPR has many potential applications, including treating genetic disorders, creating genetically modified organisms, and studying gene function.

CRISPR illustration gif animation 1.gif

The algorithm, called Fast Locality-Sensitive Hashing-based clustering (FLSHclust), uses advanced big-data clustering techniques to rapidly sift through massive genomic datasets. It identified 188 new types of rare CRISPR systems, highlighting the remarkable diversity and potential of these systems.

CRISPR systems are part of bacterial defense mechanisms and have been adapted for genome editing and diagnostics. The new algorithm, created by Professor Feng Zhang’s lab, allowed researchers to analyze billions of protein and DNA sequences from public databases in weeks, a task that would have taken months with traditional methods.

The study revealed new variants of Type I CRISPR systems with longer guide RNAs, potentially offering more precise gene-editing tools with fewer off-target effects. Some of these systems could edit DNA in human cells and may be deliverable using existing gene-delivery technologies. Additionally, the researchers discovered Type IV and VII systems with new mechanisms of action that could be used for RNA editing or as molecular recording tools.

The researchers emphasize the importance of expanding sampling diversity to uncover more rare systems, as many of the newly discovered systems were found in unusual bacteria from specific environments.

This research shows the power of advanced algorithms in uncovering the vast functional diversity of CRISPR systems, paving the way for new biotechnological applications. The findings could lead to the development of novel CRISPR-based tools for genome editing, diagnostics, and molecular recording, with potential applications in medicine, agriculture, and environmental science.

In AP Biology, we learned molecular genetics. We learned the structure and function of DNA, gene expression, and genetic variation. CRISPR-Cas9 provides a real-world example of how these concepts are applied in biotechnology. It genetics we are taught that genes can only be passed down from generation to generation and can not be artificially altered. CRISPR technology goes against what we have learned. It teaches us that we can change the genes and DNA of organisms. We can learn about how CRISPR. is used to edit genes in model organisms like  fruit flies to study gene function. We can also use it to study its potential applications in agriculture to create crops with desired traits or in medicine to treat genetic disorders.

When I heard about CRISPR I immediately thought about the ethical concerns regarding the technology. What are the bad things about this technology? What if countries want to create super humans or weapons of mass destruction with CRISPR? This new technology raises many concerns. I definitely feel that this technology needs to be regulated and that only a select few are allowed to use it and experiment with it. What do you think?

A “CRISPR” Way to Test for Melioidosis

Melioidosis is a deadly tropical disease that flies under the radar. Around 150-200 thousand people get it every year, and more than half of people diagnosed die. One of the largest problems of this disease is that it takes several days to diagnose, meaning it takes several days for patients to receive the correct treatments. However, a new test, using CRISPR, could change that.

A new test has been invented that uses CRISPR to detect a genetic target that is specific to Burkholderia pseudomallei, which is the bacteria that causes meliondosis. The new test can detect the gene with almost a 94% sensitivity. It was developed by researchers at the Mahidol-Oxford Tropical Medicine Research Unit, Chiang Mai University, Vidyasirimedhi Institute of Science and Technology in Thailand, and the Wellcome Sanger Institute in the UK. The results of this new CRISPR test mean that thousands of people could be saved annually from meliondosis, with an easy to use rapid test.

The disease is caused by Burkholderia pseudomallei, which is found in water and soil of sub tropical and tropical regions. It enters the body through cuts on the skin, ingestion, or inhalation. One of the reasons it’s difficult to diagnose is that the symptoms range from pneumonia to those of a chronic infection. This, paired with the fact its more common in rural areas, causes this disease to be under reported.

Currently, melioidosis is diagnosed in patients after bacterial samples are cultured, which takes three to four days. But, in Thailand, 40% of patients die after just a couple days while waiting for the tests to come back. Currently, there is no vaccine for this disease, but it can be treated with an antibiotic such as carbapenem. However, due to the range of the symptoms, many other and or wrong antibiotics are prescribed, which wastes time and money.

To develop a new test, researchers identified a genetic target specific to B. pseudomallei by analyzing over 3,000 B. pseudomalleigenomes. Their new test called CRISPR-BP34, ruptures bacterial cells and using a recombinase polymerase amplification reaction to amplify the bacterial target DNA for increased sensitivity. In addition to this, a CRISPR reaction is used to provide specifics. The researchers collected samples from about 100 people with the disease and 200 without, in order to test the legitimacy of the test. The new test got results in just four hours and enhanced the sensitivity from about 66% to almost 94%.

This relates to our study of the immune system in AP Biology. As we’ve learned in Biology, first macrophages and neutrophils are the first responders, and they attempt to engulf and destroy the disease. The helper T-cells try and coordinate the response while killer T-cells are attempting to destroy the disease. And cytokines signal molecules to come help defeat the disease. While these attempts by our body is unsuccessful more often than not, it still displays the immune system response learned in AP Biology.

This new test will help save thousands of lives by making diagnoses faster, which will allow the correct treatment to be given in hours, instead of days. This is truly a groundbreaking invention.

Where else do you think CRISPR can be used?

Had you ever heard of Melioidosis before?

Why do you think there is such a large range of symptoms for Melioidosis?Melioidosis world map distribution

CRISPR and Sickle Cell Disease

A blood smear of someone with sickle cell disease under a microscope

Scientists are starting to use genetic editing tools to edit out genetic diseases, starting with sickle cell disease.

Sickle cell disease is a non-dominant genetic disease that is the result of the red blood cells becoming well, sickle shaped. These cells then die early, and catch on things in veins, resulting in clots.

In addition, the cells aren’t able to properly deliver their cargo to cells- oxygen. The recipients then also promptly die early, resulting in a multitude of complications, many of which are potentially fatal.

CRISPR (short for “clustered regularly interspaced short palindromic repeats”) technology utilizes Cas9 proteins, guided with a sliver of RNA, and it will comb through the DNA and clip the matching strands off, in which it will either be forced to mutate, or function correctly (should it be a mutation that we are seeking to eliminate). 

In this case, CRISPR is being used to alter the genes that cause this disorder (that without morality, natural selection would have done its work in weeding it out) as a replacement for the support (i.e. blood transfusions) . 

Before the actual editing process, the patient’s stem cells are collected and the patient undergoes high dose chemotherapy to clear the existing bone marrow so that the edited cells can take prevalence

Casgevy, the name of one of the gene editing drugs, does exactly that. Blood is drawn, the blood is treated, then the now edited blood is reinserted into the patients bone marrow. It is currently approved for people 12 and over, but that is likely a base number and one’s doctor would properly evaluate for.

29 of 44 treated patients had achieved 12 consecutive months within the span of 24 months without SCD complications, and all 44 treated patients had successfully accepted the mutated stem. 

Common side effects included low platelet and white blood cell levels, mouth sores, headaches, itching, febrile neutropenia, vomiting, abdominal pain, and musculoskeletal pain.

How many other genetic diseases can CRISPR edit out?

Breaking the Chains of Sickle Cell: A New Dawn with Gene Therapy

The U.S. Food and Drug Administration has made a significant advancement in the treatment of sickle cell disease (SCD) by approving two new cell-based gene therapies, Casgevy and Lyfgenia, for patients aged 12 and older. Sickle cell disease is a genetic blood disorder that affects about 100,000 people in the U.S., predominantly African Americans, and is characterized by a mutation in the hemoglobin protein. This mutation leads to red blood cells adopting a crescent shape, which can obstruct blood flow and oxygen delivery, causing severe pain, organ damage, and potentially life-threatening complications.

The mutation in the hemoglobin protein that characterizes sickle cell disease (SCD) alters the structure and function of hemoglobin, which is crucial for transporting oxygen in the blood.  Hemoglobin is made up of four protein subunits, and in SCD, a mutation occurs in the gene that codes for the beta-globin subunit. This mutation leads to the production of an abnormal form of beta-globin known as hemoglobin S (HbS). In normal RBC (red blood cells), hemoglobin (a protein) has a particular shape. We learned in AP biology that proteins need a specific shape to carry out their function. In people with sickle cell anemia, that protein is mutated doesn’t have the correct shape, and cannot carry out its function.  The reason it doesn’t have the right shape is that the mutated hemoglobin sequence is modified at a single amino acid.

Under certain conditions, such as low oxygen levels, dehydration, or acidosis, HbS molecules tend to stick together, forming long, rigid chains within the red blood cells. These chains distort the shape of the red blood cells from their normal, flexible disc shape to a rigid, crescent or “sickle” shape. Unlike normal red blood cells that can easily move through the bloodstream, these sickled cells are stiff and sticky. Its interesting how such a small change can have such a significant effect in our body!

The crescent-shaped cells can get trapped in small blood vessels, blocking the flow of blood. This blockage prevents the delivery of oxygen to nearby tissues, which can cause pain and damage to tissues and organs. Furthermore, the sickled cells are more prone to breaking apart, leading to hemolysis (the destruction of red blood cells), which can cause anemia (a shortage of red blood cells) and other complications. The recurring blockage of blood vessels and the chronic shortage of red blood cells and oxygen supply lead to the severe symptoms and complications associated with sickle cell disease, including acute pain crises, increased risk of infections, and organ damage.

Casgevy stands out as the first therapy of its kind to employ CRISPR/Cas9, a groundbreaking genome editing technology, to modify patients’ hematopoietic stem cells. This process aims to increase the production of fetal hemoglobin in patients, which helps prevent the sickling of red blood cells. On the other hand, Lyfgenia uses a lentiviral vector to genetically modify blood stem cells to produce a variant of hemoglobin that reduces the risk of cells sickling. Both therapies involve modifying the patient’s own blood stem cells and reintroducing them through a one-time infusion, following a high-dose chemotherapy process to prepare the bone marrow for the new cells.

Crispr

These therapies represent a major leap forward in treating sickle cell disease, addressing a significant unmet medical need for more effective and targeted treatments. The FDA’s approval of Casgevy and Lyfgenia is based on the promising results of clinical trials, which demonstrated a substantial reduction in the occurrence of vaso-occlusive crises, a common and painful complication of SCD, among treated patients.

The approval of these therapies also underscores the potential of gene therapy to transform the treatment landscape for rare and severe diseases. By directly addressing the genetic underpinnings of diseases like SCD, gene therapies offer a more precise and potentially long-lasting treatment option compared to conventional approaches. The FDA’s support for such innovative treatments reflects its commitment to advancing the public health by facilitating the development of new and effective therapies.

However, it’s important to note that these therapies come with risks and side effects, such as low blood cell counts, mouth sores, and the potential for hematologic malignancies, particularly with Lyfgenia, which carries a black box warning for this risk. Patients receiving these treatments will be monitored in long-term studies to assess their safety and effectiveness further. Despite these challenges, the approval of Casgevy and Lyfgenia marks a hopeful milestone for individuals with sickle cell disease, offering new avenues for treatment and the promise of improved quality of life. If you were diagnosed with Sickle cell disease, would you try this no-treatment when available? Do the positives outweigh the negatives? Let us know!

Gene Editing Used to Eliminate Invasive Rodent Species’ on Islands

Species of Invasive House Mice have been not just a nuisance, but potentially dangerous and damaging on islands for hundreds of years. These house mice can be dangerous, as they have the potential to spread diseases by getting into food stores or biting humans, to cause asthma or allergy flare ups, and to bring unwanted insects such as fleas, ticks, or  lice into a home. Scientists have been looking for a way to remove these invasive pests from homes throughout time, and to no avail. Now, they have found a new way to eliminate entire populations of these pests at a time in a mere 25 years. 

Mouse white background

With the emergence of DNA editing technology, scientists have found  a way to edit the mice’ DNA so that a certain chunk of the edited DNA is inherited way more often than the average trait. This lab-created trait is called a gene drive, which had in the past been used to successfully reduce many pesky populations of insects before, but had not been proven effective in mammals. To fix this issue, scientists decided that they most discover more about the haplotypes, which are “naturally occurring group(s) of genes that gets passed on as a unit during replication” within house mice. They discovered that the t-haplotype within house mice get passed on to offspring 95% of the time, instead of the usual percentage of 50%. The editing of this t-haplotype was found to be very favorable. This haplotype evolved naturally within these house mice, meaning that will continue to be present in the wild, and there is no projection of resistance to this haploytpe being found anytime soon. Another reason why the editing of this gene sequence is favorable is that it is only present in the invasive species of house mice, meaning that it will not effect other noninvasive species

 

Now the only question is, how will scientists change this haplotype? Well, as CRISPR technology is emerging and evolving, it has been found as the obvious tool to use to edit this gene. Molecular Biologists have used CRISPR to edit the mice’ DNA to add the CRISPR tool into the t-haplotype. There are two affects of this change, when male mice with a heterozygous genotype of the edited gene mate, the CRISPR genes inserted will cause any baby female mice created to be infertile. The other effect of this genetic change is that males with the homozygous genotype of the edited gene will be sterile.

CRISPR logo

Now you might be asking, “has this format gene editing to eliminate the population of the invasive house mice actually been proven effective in any way?” Well, the answer to that is complicated, as scientists have not yet properly tried it out on any island populations. They have used computer simulations to test their hypothesis, finding that in the simulation that after adding 256 mice with the altered gene into the population, the island population of this mouse would go extinct within 25 years. Scientists have still only tested the changing of the t-haplotype within these mice in labs, and have not yet tested the use of CRISPR to effectively damage genes needed for fertility in the house mice. More testing must be done to effectively ensure that this method of eliminating the species is effective, and so we might have to wait some years to begin the overall mission. Overall, scientists are hoping to find a way to eliminate populations of invasive species such as the house mouse in timelines smaller than 25 years,  and many are looking to the future of CRISPR technology as the true way to achieve this goal.

CRISPR gene editing: The Benefits and the risks

CRISPR gene editing is a precise technique that uses the Cas9 enzyme and gRNA to modify DNA sequences in an organism’s genome. This method is inspired by a natural bacterial mechanism that protects against viruses. It can change existing genes, introduce new genetic material, and revolutionize fields such as industry, agriculture, and medicine.

CRISPR gene editing was first invented in 1987 by Ishino Etal. Scientists first hypothesized that prokaryotic cells use this method as part of their adaptive immune systems. However, this method was not elucidated until 2007. This gene-editing technique uses RNA molecules to direct the Cas9 enzyme to the precise location where the DNA strands are being cut, thus allowing genetic materials to be modified or added. To be more specific, this system relies on the enzyme’s ability to cleave DNA double helix strands at a particular location, allowing scientists to modify the DNA sequence. This technique is especially beneficial to the medicinal fields due to its specificity; it can potentially treat genetic diseases such as cystic fibrosis, Alzheimer’s, Huntington’s, Parkinson’s, or cancer by modifying the immune cells and directing them to target and kill cancer cells.

CRISPR-Cas9 Editing of the Genome (26453307604)

Despite the benefits, CRISPR also contains some serious risks. A specific protein called p53, also known as the “guardian of the genome,” helps to detect any damage in the DNA and thus; heads the cells to stop diving to prevent any mistakes. The CRISPR technique might trigger a p53 response, in which edited cells can be “tagged” as damaged and eliminated, thus reducing the efficiency of the gene editing process. However, recent research also indicates that CRISPR can lead to cell toxicity and genome instability. In addition, CRISPR may disrupt normal cell functioning, which leads to cells being unable to detect any DNA damage or extra cell division, thus increasing the risk of further mutations.

Nonetheless, CRISPR still goes deep down into our biology field as it contains molecular biology, where it goes deep down into the cells and modifies DNA sequence. However, changing an organism’s DNA sequence using CRISPR gene-editing technology could have unintended consequences such as off-target effects, incomplete editing, and unknown long-term effects such as cancer or DNA mutation if the matching went wrong.

In First, Scientists Use CRISPR for Personalized Cancer Treatment

Behold, have researchers found a groundbreaking method to fight tumors? Could genome-edited immune cells finally provide a way to defeat cancer?

In a recent clinical trial, immune cells were modified by CRISPR gene editing to recognize mutated proteins specific to tumors. When released into the body, the cells could target and kill the specific tumor cells. This cancer research utilized gene editing and T-cell engineering.

The trial involved 16 individuals who suffered from solid tumors (including breast and colon cancer). The results were published in Nature by Heidi Ledford and then presented on November 10, 2022 in Boston, Massachusetts at The Society for Immunotherapy of Cancer conference. The findings were later released in Scientific American.

According to Antoni Ribas, a co-author of the study and a cancer researcher and physician at the University of California, Los Angeles, ” It is probably the most complicated therapy ever attempted in the clinic.” He describes the process as “trying to make an army out of a participant’s own T cells.”

To begin the study, Ribas and his colleagues ran DNA sequencing on each patient’s blood sample and tumor biopsies. The goal was to identify unique mutations of the timer, but not present in the blood. Ribas notes that these mutations differ across different types of cancer, with only a few being shared. Then using algorithms, Ribas’s team predicted which mutations were the most likely to initiate a response from the T cells(a type of white blood cell that functions to notice and destroy irregular cells); however, immune systems rarely destroy cancerous tumors. With that being said, the team used CRISPR gene editing to insert designated t-cell receptors that recognized the tumor. Patients were given medication to reduce normal immune cells before the researchers infused the engineered cell.

Joseph Fraietta, who specializes in designing T-cell cancer therapies at the University of Pennsylvania in Philadelphia, describes the process as “tremendously complicated”, for some cases could take more than a year to complete in certain cases.

Each individual in the study received T cells engineered to target up to three sites, and after some time, the concentration of the engineered T cells was higher than the average T cells in the bloodstream near the tumors. A month after the treatment, five participants’ tumors had not progressed, and only 2 showed evidence of T-cell activity.

While the treatment’s effectiveness was limited, Ribas notes that a small dose of T cells was used at first and stronger doses would be proven more effective. Fraietta feels “The technology will get better and better.”

Although engineered T cells, also known as CAR T cells, were approved to treat certain blood and lymphatic cancers, CAR T cells only target proteins that are present on the surface of tumor cells, and According to Fraietta, no surface proteins have been discovered in solid tumors. Additionally, tumor cells may suppress immune responses by releasing immune-suppressing chemical signals and consuming local nutrient supplies to promote their rapid growth.

Researchers are hopeful to engineer T cells to not only recognize cancer mutations but also to become more active in the vicinity of the tumor. Potential techniques include ” removing the receptors that respond to immunosuppressive signals, or by tweaking their metabolism so that they can more easily find an energy source in the tumor environment,” as Heidi Ledford, writes in her article. With advances in CRISPR technology, researchers anticipate revolutionary ways of engineering immune cells in the next ten years.

In AP Biology this year, we learn about the Immune system. This topic is specifically related to the adaptive, or pathogen-specific, Immune response. T Lymphocytes, or T cells for short, are a part of the cell-mediated immune response where T-cells can identify, and kill infected or cancerous cells, while also preventing reinfecting.

The Blood Brain Barrier Can’t Block This!

University of Wisconsin-Madison Professor, Shaoqin “Sarah” Gong is ready to take on finding cures for brain disease such as Alzheimer’s and Parkinson’s disease. Gong and her colleagues strive to enable a “noninvasive, safe and efficient delivery of CRISPR genome editors” that can be used as forms of therapy for these diseases. According to MedlinePlus, there are many forms of brain disease, some caused by tumor, injury, genetics; however, Gong’s research focuses on degenerative nerve diseases. Degenerative nerve diseases can affect balance, movement, talking, breathing and heart function. The reason cures for degenerative nerve disease are difficult to create is because of the blood brain barrier. According to the American Society for MicroBiology, the blood brain barrier is a feature of the brain and central nervous system blocking the entrance of “microorganisms, such as bacteria, fungi, viruses or parasites, that may be circulating in the bloodstream”. Unfortunately, the barrier block is a very selective site that won’t let vaccines and therapies through. Fortunately, Gong’s nano-capsules with CRISPR’s genome editors point toward brain disease therapy and a cure.

 

Alzheimer's disease brain comparison

Gong’s study proposes dissolvable nano sized capsules that can carry CRISPR genome editing tools into organs. According to CRISPR Therapeutics, CRISPR technology meaning Clustered Regularly Interspaced Short Palindromic Repeats is an “efficient and versatile gene-editing technology we can harness to modify, delete or correct precise regions of our DNA”. CRISPR edits genes by “precisely cutting DNA and then letting natural DNA repair processes take over.” CRISPR targets mutated segments of DNA that can produce abnormal protein causing diseases such as degenerative nerve disease.  CRISPR works with the help of a guide RNA and Cas9. Together the complex can recognize and bind to a site next to a specific target sequence of DNA that would lead to the production of an abnormal protein. CAS9 can cut the DNA and remove a segment. As a result natural DNA pathways occur and RNA polymerase will return to rebuild and correct the mutated segment. 

via GIPHY

Consequently with the addition of glucose and amino acids the nano-capsules containing CRISPR Technology can pass through the blood brain barrier to conduct gene editing to target the gene for the amyloid precursor protein that is associated with Alzheimer’s. The topic of gene editing coincides with the Gene Expression portion of the AP Biology curriculum. In the topic of gene expressions 2 processes are emphasized: transcription (the process of making an RNA copy of DNA) and translation ( the process of making proteins using genetic information from RNA). In the CRISPR technology the editing of genes closely relates to the process of transcription. Transcription mistakes can be made which can lead to mutations, these mutations can potentially cause nonsense, missense or deletions of nucleotides ultimately producing wrong codons that would code for incorrect/abnormal proteins. However, the CRISPR technology would be able to correct these mutations in the DNA, replacing the incorrect nucleotides to correct ones and preventing the production of abnormal proteins. Fortunately, Gong’s unique nano-capsules have successfully been tested on mice, giving scientists hope that treatments and therapy for these brain diseases are coming soon and can help many.

The End Of Malaria

Introduction

Attention everyone, what if we told you that there is a way to potentially wipe out the bad mosquito species that causes malaria? Scientists have developed a genetic weapon, a self replicating bit of DNA called a gene drive, that interferes with the mosquitoes ability to reproduce. This can be revolutionary and save millions of children’s lives in the future.

What is malaria

Malaria is a deadly disease killing about 643,000 people every year. It is transmitted by a parasite -mosquito bites. The symptoms of malaria include fever, chills, and other flu-like symptoms.

Malaria knocks you flat, keep covered, use your repellent (4647891178)

How it works 

Gene drives work starts with taking one transgenic organism into the lab so it can be modified. It then can be engineered for release into wild populations to spread an altered allele. Two types of drives are possible: modification drives spread an advantageous gene, while suppression drives spread a gene that reduces the population. As the gene spreads this ultimately allows for the death of mosquitoes to spread exponentially. This topic also relates to what we learned in the AP Biology units on genetics and DNA. The connection to genetics is evident in the ability to control breeding of species, such as mosquitoes, using the knowledge of Punnett squares and the principles of dominant and recessive traits. However, the most significant connection between genetics and mosquito control lies in the ability to manipulate and alter DNA.

CRISPR illustration gif animation 1

Future

Gene drives can potentially save millions of lives by reducing mosquito populations and preventing the spread of malaria. The technology is being tested in Africa, where malaria is most prevalent. Soon it will hopefully be around the entire world and save millions of lives all together. 

 

 

CRISPR Tool PASTEs in New Genes

Researchers at Massachusetts Institute of Technology developed a revolutionary new gene editing tool. The tool is called PASTE, and it is a new CRISPR-Cas9 based genome editing tool. It combines traditional CRISPR and integrases, enzymes that can insert or remove DNA sequences, to cut out certain DNA segments and “paste” in other DNA segments. This new method removes the necessity for double-stranded DNA breaks, which can lead to mutations in the DNA sequence. CRISPR logo

PASTE combines CRISPR-Cas9 nickase, which cuts out a singular DNA strand, with serine integrase, an enzyme that can insert a lot of DNA, and reverse transcriptase, an enzyme that allows PASTE to add a single strand of DNA each time while preventing double-stranded DNA breaks. PASTE produces less indels than CRISPR-Cas9 alone. Indels(insertions or deletions are genetic mutations that often occur when a gene is edited. They can alter the function of genes, thus affecting the organism’s overall health or specific traits (New Atlas).

Additionally, PASTE researchers believe that PASTE could possibly treat genetic diseases by replacing “bad” genes with “good” genes. This is because PASTE is great at “pasting” genes into various parts of an organism’s genome. PASTE researchers tested PASTE against homology-independent targeted insertion and homology-directed repair, discovering that paste had higher insertion effectiveness than homology-independent target insertion, but lower insertion effectiveness than homology-directed repair. PASTE, however, produced less “inaccuracies” than homology-directed repair. These inaccuracies occur when the tool inserts DNA into the wrong part of an organism’s genome, effectively risking unwanted effects (Genome Web).

While PASTE is still in its infancy, it is already revolutionizing the gene editing industry. It not only reduces the risk of undesired mutations, but also increases the efficiency of gene insertion. It is pioneering treatment of genetic diseases. 

AP Bio Side Note 🙂

This technology relates to AP Bio because of its use of introns and exons. PASTE can remove or replace introns and exons, depending on what causes the genetic mutation. This is interesting because although introns are noncoding sequences of DNA, mutations in them can still cause negative effects in people. Additionally, while more intuitive, it is also revolutionary that technology is able to replace exons. I am excited to see what the future for Crispr tools holds. Please leave a comment if you found this post interesting!

No need to buy fragrances, we can just create them: a new way of creating everyday items from scratch.

Gene modification.

In a rapidly developing industry, genome editing technology has been growing to a point where “food, drugs, cosmetics, and biofuels” can be synthesized by microbes. Eric Rhodes investigates this phenomenon through the use of CRISPR/Cas9 gene editing technology. Emmanuelle Charpentier and Jennifer Doudna’s findings reveal how scientists can target specific segments in genes and then inactivate, delete, insert, and alter to however the scientist pleases.

At a closer look at what CRISPR technology is, Rhodes, elaborates and shows that multiple genes can be edited. It can be altered to produce any of the approximately 30 biosynthetic gene clusters to produce any natural product. Some popular compounds that are produced include carotenoids, citric acid, 1,3-propanediol, phenylethanol, and squalene. This can make great strides by making common commodities more accessible to the average human. Whether it is pigments (cartenoids), flavoring agents (citric acid), cosmetics (phenylethanol), or components in vaccines (squalene), the opportunities are endless.

We had recently done a bio lab on E.coli and through independent research, we found E.coli’s importance to our digestive system. CRISPR technology too can be used in the engineering of enzymes similar which have seen massive practicality in the modern world. In biology class we learned about epigenetics and how gene expressions can be more pronounced or repressed. In the case of CRISPR technology, CRISPRa involves fusing a catalytically inactive Cas9 (dCas9) protein to a transcriptional activation domain, which can attach transcriptional things to a specific promoter and enhance gene expression.

Perhaps a more pressing matter that this CRISPR technology can target is finding greener alternatives in our world. Rhodes claims that “CRISPR can also be used to modify microbes to grow at lower temperatures” this way high demand species that are endangered will have less pressure of being threatened. This could pose a creative way of solving some endangered species problems by simply providing a cleaner alternative.

The growing potential of genome editing technology, specifically CRISPR/Cas9, to produce a range of useful products from common commodities to components in vaccines, presents endless opportunities for the future of industrial biotechnology, and may help address issues related to endangered species.

CAST is in the past, it’s time for HELIX

CRISPR stands for clustered regularly interspaced short palindromic repeats.’ The term references a series of repetitive patterns in the DNA of bacteria discovered in the 90s. 20 years later, Jennifer Doudna and Emmanuelle Charpentier discovered that CRISPR-Cas9 could be used to cut any desired DNA sequence by just providing it with the right template, meaning it could be used as a gene-editing tool. To add a desired DNA sequence, one needs an upgraded version of CRISPR editing called CAST, CRISPR-associated transposases. Unfortunately,  CASTs suboptimally insert more DNA sequences than wanted and have a relatively high rate of unwanted off-target integration at unintended sites in the genome. This leads to mutations, the three being, silent mutations, missense mutations, and nonsense mutations. A silent mutation is an insertion or deletion of a nucleotide that doesn’t change the amino acid sequence. A missense mutation is an insertion or deletion of a nucleotide that changes one or more of the amino acids. Lastly, a nonsense mutation leads to an early stop signal.

4.2. The CRISPR Cas 9 system II

Luckily, new research published in Nature Biotechnology tells the reader that an improved CAST system called HELIX now exists. Helix stands for Homing Endonuclease-assisted Large-sequence Integrating CAST-compleX. This mouthful dramatically increased the efficiency of correct DNA insertions, reducing insertions at unwanted off-target sites. HELIX has over a 46% increase in on-target integration compared to that of the CAST system. This discovery is one of many that will continue to help us understand the complexity of our genes.

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