AP Biology class blog for discussing current research in Biology

Tag: Crispr (Page 1 of 5)

Ethical and Scientific Limitations of CRISPR Gene Editing

The Third International Summit on Human Genome Editing issued a closing statement a few weeks ago calling for a pause on human genome editing – not permanently as some activists had hoped on ethical grounds, but instead for the near future because the technology is not currently sufficiently advanced as to ensure success. Gene editing involves editing embryos outside the womb and then implanting them to establish pregnancy. In addition to the numerous ethical concerns, such as a pathway to eugenics that the technology might lead to, the summit decided that the risks are simply too great at the present time.

CAS 4qyzThis is because the edits made can result in unintended – and sometimes dangerous – consequences for the embryo that traditional DNA screenings may not pick up on. Gene editing works by unraveling the double helix with helicase (just like in DNA replication), cutting the DNA strand with an enzyme, and then having the cell’s own mechanisms, such as primase and DNA polymerase, combined with the new “blueprint” for DNA,  tell the cell the order the nucleotides are placed in and complete the double helix again to form a complete, but modified, DNA strand. However, sections of DNA can be permanently lost or mistranscribed in the process, resulting in genetic disorders or cell malfunction, including cancers. These are similar to the risks that occur during DNA replication and the general life of the cell, but are significantly more likely to occur. Furthermore, mosaicism, often seen on small levels like calico cats (where different cells receive different activated genes than others), can occur on a massive scale, where some cells receive edits and others don’t, leading to health problems down the road for the embryo, if it survives at all.

As a result, the summit, composed of the world’s leading experts in CRISPR technology and research, decided to enact a pause on human genome editing for now. As the technology advances and is made safer, however, they claim that they will reconsider it. Until then, the use of CRISPR is limited to other organisms, such as plants and lab animals.

Can Gene Editing Prevent Disease in the future?

There is very exciting news in the world of biology right now. For the first time ever, according to the University of California San Francisco‘s chancellor,  Sam Hawgood, CRISPR gene editing will be delivered to a human in an attempt to study how gene editing can help with asthma.

CRISPR-Cas9 Editing of the Genome (26453307604)

CRISPR-Cas 9 was adapted from a naturally occurring genome that allows bacteria to fight off viruses. When a bacteria was infected with a virus, it would use this genome to take pieces of the DNA from the virus and add them to its own DNA to create a pattern known as a ‘CRISPR array.’ The ‘CRISPR array’ allows the bacteria to remember the virus and cut the DNA of the virus apart.

In 2021, Peter Turnbaugh administered CRISPR into mice in order to target a specific gene and edit it out of the mouses gut. It was this work that inspired the scientists at UCSF to experiment with adding the CRISPR to a human microbiome.

Asthma is the perfect place to start because there is a clear microbial target to attack. There is a molecule that is produced by bacteria in the human gut that can trigger asthma in childhood. The scientists goal is to stop the microbes from producing that molecule, rather than remove the microbe altogether, as that microbe plays other beneficial roles in the human body. By taking a small piece of sgRNA, the scientists would be able to attach that to the target sequence in the DNA of the bacteria that produces that molecule, and ultimately stop the bacteria from producing the molecule that causes asthma.

This can be related to the topic of DNA and Genes that I learned about in AP bio. While reading the UCSF article, I couldn’t help but think about DNA replication, and what implications gene editing would have on DNA replication.

As we learned in AP bio, DNA replication is the process by which a cell copies its DNA before cell division, ensuring that each daughter cell receives a complete set of genetic instructions. During replication, the double-stranded DNA molecule is unwound and separated into two strands, each of which serves as a template for the synthesis of a new complementary strand. The result is two identical copies of the original DNA molecule.

If the scientists at UCSF were able to edit the genes to properly stop the microbes from producing the molecule that causes asthma, would that trait now be passed on to the new complementary strands? Would this gene editing get passed on through DNA replication, and even further would it be passed on to gametes? If both parents were to get this gene edited, would their zygotes now also be immune to asthma, and if so it is almost as if this gene editing is affecting natural selection and evolution.

All of this was very interesting to me and it seems that if/when this becomes a regular part of society, it will have major implications on the way our species sees diseases in the future.

From Bacteria to Biotech: The Surprising Similarities in Immune Systems

Bacteria have always been considered harmful and something to be avoided, but according to a recent study by the University of Colorado Boulder, bacteria might just hold the key to unlocking novel approaches to treating various human diseases. The research reveals that bacteria and human cells possess the same core machinery required to switch immune pathways on and off, meaning that studying bacterial processes could provide valuable insights into the human body’s workings. Moreover, researchers found that bacteria use ubiquitin transferases – a cluster of enzymes – to help cGAS (cyclic GMP-AMP synthase) defend the cell from viral attack. Understanding and reprogramming this machine could pave the way for treating various human diseases such as Parkinson’s and autoimmune disorders.

CRISPR, a gene-editing tool, won the Nobel Prize in 2020 for repurposing an obscure system bacteria used to fight off their own viruses. This system’s buzz reignited scientific interest in the role proteins and enzymes play in anti-phage immune response. Aaron Whiteley, senior author and assistant professor in the Department of Biochemistry, said that the potential of this discovery is much bigger than CRISPR. The team discovered two key components, Cap2 and Cap3 (CD-NTase-associated protein 2 and 3), which serve as on and off switches for the cGAS response. Understanding how this machine works and identifying specific components could allow scientists to program the off switch to edit out problem proteins and treat diseases in humans.

CAS 4qyz

This discovery opens new avenues of research as bacteria are easier to genetically manipulate and study than human cells. Whiteley said that the more scientists understand about ubiquitin transferases and how they evolved, the better equipped the scientific community is to target these proteins therapeutically. The study provides clear evidence that the machines in the human body that are important for just maintaining the cell started out in bacteria, doing some really exciting things. The ubiquitin transferases in bacteria are a missing link in our understanding of the evolutionary history of these proteins. Thus, this research shows the importance of studying evolutionary biology, and how it can provide valuable insights into human health.

The study highlights the similarities between bacteria and human cells in terms of their immune response, specifically, describing how cGAS (cyclic GMP-AMP synthase), a protein critical for mounting a downstream defense when the cell senses a viral invader, is present in both bacteria and humans. This similarity suggests that portions of the human immune system may have originated in bacteria, a concept explored in the evolutionary biology unit. In this past unit, we discussed the origins of life, and how all life originated from a simple bacteria cell. This bacteria cell, though many many many repeated cycles of evolution and natural selection allowed for variation within its species and the formation of new species through the processes of speciation.

Glow in the dark proteins???

Recently scientists have discovered Glow in the dark proteins that could help diagnose viral diseases. Scientist rely on a chemical reaction using the luciferase protein, which “catalyze the oxidation of the substrate in a reaction that results in the emission of a photon”, which then causes the glow in the dark effect. The luciferase protien is then put into sensors that show a light when they find their target. Although these sensors are simple and would make point-of-care testing much easier, scientists have “lacked the sensitivity required of a clinical diagnostic test”. The gene editing tool CRISPR could provide this for them but requires many steps. According to MedlinePlus gene editing is a “a group of technologies that give scientists the ability to change an organism’s DNA“. A well known type of gene editing is called CRISPR, it is supposed to be more efficient and accurate than other genome editing methods. Scientist Maarten Merk decided to use CRIPSR related proteins and combine them with a bioluminescence technique whose signal could be detected. During testing scientists discovered that if a specific viral genome that was being tested for was present, the two CRISPR proteins would bind to the specific nucleic acid sequences and come close to each other, this would then cause the luciferase protein to shine a blue light.

AP Bio Connection

Exons are the coding regions of a gene that are translated into functional proteins. These contain the information needed for the synthesis of a specific protein. Introns are the non-coding regions of a gene that do not code for proteins. Introns are transcribed into RNA along with the exons, but they are removed from the final RNA transcript. Gene editing techniques, such as CRISPR-Cas9, rely on specific recognition of DNA sequences by the Cas9 enzyme. To achieve targeted gene editing, the Cas9 enzyme needs to be guided to a specific site in the genome using RNA molecules called guide gRNAs. gRNAs are designed to bind to a specific sequence in the genome, typically located in an exon, which is then split by the Cas9 enzyme.CRISPR logo

Genetic Variation the Savior

In the article “Genetic variation in the SARS-CoV-2 receptor ACE2 among different populations and its implications for COVID-19,” published in Nature Communications, the authors explore the genetic variation in the ACE2 receptor across different populations and its potential impact on COVID-19 susceptibility and severity. The ACE2 receptor is a key entry point for the SARS-CoV-2 virus into human cells. Its expression level and genetic variants may affect the virus’s ability to infect and replicate within the host. Therefore, understanding the genetic variation in ACE2 among different populations can provide insights into the different susceptibilities and severity of COVID-19 seen across the world. The authors analyzed genetic data from various global populations and found that there is significant genetic variation in ACE2 between populations. Specifically, they identified several ACE2 variants that are more prevalent in certain populations, including a “variant that is more common in East Asian populations” and may affect the receptor’s expression level.


The authors also conducted in vitro experiments – medical procedures, tests, and experiments that researchers perform outside of a living organism – to investigate the impact of these ACE2 variants on SARS-CoV-2 infection. They found that some variants, such as the one more prevalent in East Asian populations, led to reduced viral entry and replication, while others did not significantly affect viral infection. These findings suggest that genetic variation in ACE2 may contribute to the different COVID-19 outcomes observed across different populations. For instance, the higher prevalence of the ACE2 variant in East Asian populations may explain why these populations had a lower incidence of severe COVID-19 despite being initially hit hard by the pandemic. Furthermore, the author highlights the importance of considering genetic variation when developing COVID-19 treatments and vaccines. For instance, vaccines that were designed based on the original strain of SARS-CoV-2 may be less effective against strains that have evolved to better utilize ACE2 variants prevalent in certain populations. Overall, the article sheds light on the genetic variation in ACE2 among different populations and its implications for COVID-19 susceptibility and severity. The authors’ findings show the importance of taking genetic diversity into account when studying diseases and developing treatments and vaccines, particularly in the context of a global pandemic. In our recent DNA unit in class genetic variation was one of the topics of discussion, genetic variation is extremely important for the survival of a population as there is an easier chance that the species will be able to adapt and survive in different situations. Without genetic variation, many species can die out and therefore including the topic of genetic variation in viruses like covid-19 is extremely detrimental to the survival of humans when fighting this illness.

Fighting Cancer with CRISPR

For many years the treatment of cancer has remained difficult and uncertain. Though there are many treatment methods such as chemotherapy and bone marrow transplants, these methods are never guaranteed to work. However, a teenage girl named Alyssa diagnosed with T-cell acute lymphoblastic leukemia (T-ALL) has been successfully treated with a new experimental treatment. T-ALL is a type of cancer where cancerous T-cells overpopulate healthy T-cells, leaving the patient susceptible to disease. In this form of cancer, T-cells also mistake each other as threats. CRISPR illustration gif animation 1Due to the nature of this cancer, in order for treatment to be effective, T-cells would have to appear foreign to the patient’s immune system. This is made possible through the gene editing system, CRISPR. For Alyssa’s treatment, doctors utilized and altered donated T-cells. Using CRISPR, the donated T-cells were stripped of CD7 protein, a common T-cell protein, and CD52 protein, a protein recognized by cancer treatment.  Additionally, donated T-cells received a receptor that gave them the ability to target cancerous and healthy T-cells by having the ability to recognize CD7. All of these changes were made through a process called base editing with CRISPR. During base editing, individual letters, or bases, in the T-cells’ DNA code were altered. These minor alterations have the ability to change the nature of the cell. Thanks to this new treatment, Alyssa’s cancer is now undetectable.


I found T-ALL cancer and its destructive nature relatable to the way that viruses take over human body cells, however, our adaptive immunity uses antigens to recognize an intruder. T-cells contain specific proteins which make them recognizable to other T-cells, including cancerous ones. T-ALL destroys the body’s own T-cells which is why this specific treatment needed to use altered T-cells that did not contain recognizable proteins. WheT Lymphocyte (16760110354)n the body is infected by a virus, memory T and B cells use antibodies, a little piece of the virus, to remember and recognize the virus if it were to enter the body again. 


CRISPR May Be the Cure!

There are still many disorders and diseases in this world that cannot be cured, and Huntington’s disease (HD) is one of them.

HD is a neurological disorder that causes individuals to lose control of movement, coordination, and cognitive function. HD occurs because of a mutation in the Huntingtin (HTT) gene where a specific codon sequence repeats, creating a long, repetitive sequence that turns into a toxic, expanded protein clump. These clumps form in a part of the brain that regulates movement called the striatum and prevent the neurons in the striatum from functioning properly. As of now, HD still has no cure, but CRISPR gene editing (Clustered Regularly Interspaced Short Palindromic Repeats) might just be the solution.

Dr. Gene Yeo of UC San Diego School of Medicine, along with his team and colleagues from UC Irvine and Johns Hopkins University, researched RNA-targeting CRISPR/Cas13d technology as a way to possibly eliminate HD and its negative effects on the brain. CRISPR gene editing, as its name suggests, enables scientists to “edit” – add, remove, or alter – existing genetic material. The group desired to see if RNA-targeting CRISPR would be able to prevent the creation of the protein clumps that damage the function of the striatum. As we learned in AP Biology, the addition, removal, or substitution of a base of a codon can drastically change the structure and function of a protein. Each codon codes for a specific amino acid, and if multiple codons have changed due to a mutation, it is likely that the protein will fold differently than it is supposed to and will lose its function.

Yeo and his team desired to develop an effective therapy for HD, hoping to stop the formation of toxic protein clumps and alter the course of the disease. However, they did not want to create permanent changes in the human genome as a precaution. The team instead engineered a therapy that alters the RNA that turns into the protein clumps.  They conducted testing on mice and found that RNA-targeting CRISPR therapy reduced toxic protein levels in a mouse with HD, improving motor coordination. In connection with the molecular genetics unit in AP Biology, since the RNA that causes HD is altered, the protein that is translated will change since different amino acids correspond to different codons.

Transcription and Translation

Further testing will be necessary to confirm the benefits of this therapeutic strategy, but CRISPR does look like a promising medical treatment for HD and many other diseases in the future.

Progress in Treating Huntington’s Disease Thanks to CRISPR Technology

Scientists have discovered a new way to treat Huntington’s disease, thanks to CRISPR technology. Their research has reduced symptoms of the disease in the mice that they tested on. 

Huntington’s Disease, which is a neurological disorder, is caused by a genetic mutation in the HTT gene. More specifically, repetitive and damaging sequences in the HTT gene cause Huntington’s disease. It causes progressive loss of movement, coordination, and cognitive functions. 

Researchers have discovered a possible solution to these symptoms: CRISPR technology. 

According to the article, “CRISPR is a genome-editing tool that allows scientists to add, remove or alter genetic material at specific locations in the genome.” One of the risks of CRISPR use is that it can affect off-target genes and molecules, causing unwanted alterations in chromosomes and genes. 


Study author Gene Yeo, PhD, explains how our cells struggle to copy repetitive DNA, which can lead to errors that cause repetitive sequences to increase with each generation. As we learned in class, the process to copy DNA is a complex one where there are many factors at play. DNA is replicated in a semi conservative manner, meaning that the old DNA strands are conserved and combined with the new, complementary strands. There is a replication fork, with a leading and lagging strand, on which DNA is replicated in the 5’-3’ direction. For replication on the leading strand, RNA primase adds RNA, DNA polymerase III adds nucleotides to the open end of the RNA, then a sliding clamp attaches to the DNA polymerase III and slides it along the strand, resulting in the leading strand being synthesized. 

The scientists directly targeted the RNA involved in the DNA replication process to remove toxic protein buildup that is responsible for the mutation in the HTT genes. They were able to complete this process using CRISPR, and without disrupting other important genes. 

After testing on mice, they reported that their research has resulted in improved motor coordination, less striatal degradation and reduced toxic protein levels. These improvements on the mice’s condition lasted for up to 8 months, and had no on other RNA molecules, making scientists optimistic that this treatment could be effective for humans. 

A Potential Cure: We’ve Waited 151 Years For This!

CRISPR-Cas9 Editing of the Genome (26453307604)


CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats, is a gene editing tool comprised of DNA sequences from prokaryotes, that is becoming more commonly used to treat and potentially cure life-threatening diseases that have previously been viewed as a death sentence; in December of 2022, a study was conducted at the University of California San Diego School of Medicine, where it was discovered that CRISPR technology can be used to target the gene that causes Huntington’s Disease.


First, we must understand what exactly Huntington’s Disease is. Huntington’s Disease, which was discovered in 1872, is a rare neurological disorder characterized by the gradual destruction of nerve cells in the brain. It is caused by a single defective gene, and this mutation is as dangerous and tragic as it is rare; the disease has no cure, and patients typically do not survive beyond 20 years post-diagnosis. 


However, thanks to CRISPR, it is a very real possibility that that will soon change. 


The study that was conducted at U.C. San Diego involved the experimentation of Cas13d – an RNA editing technique – against toxic RNA and protein buildup that is associated with the HTT gene mutation that causes Huntington’s Disease, and the trial was found to be successful in terms of eliminating that buildup. The experiment was conducted on mice, and it was also discovered that only one injection of the Cas13d therapy was necessary to yield results, and the benefits (improved motor function, lessened symptoms) lasted for eight months.


This discovery is especially fascinating as it connects to our AP Biology units in terms of mutations: The most common genetic mutations are insertions, substitutions, and deletions. The mutation that causes Huntington’s Disease, however, fits into neither one of these categories: if anything, the mutation is considered a duplication, as it is characterized by the unwanted repetition of cytosine, adenine, and guanine; these repetitions are what lead to the protein buildup, and damage the HHT gene. 


In previous years leading up to the U.C. San Diego experiment, trials conducted to target the gene that causes Huntington’s Disease have mostly been unsuccessful, but we can hope that this new discovery is a step in the right direction and may provide the key to figuring out how to treat this disorder that has historically been viewed as a death sentence.

CRISPR technology may be the key to treating Huntington’s Disease

Huntington’s disease is a well-known neurological disorder that is characterized by a loss of movement, coordination, and cognitive function. More than 200,000 people live with Huntington’s disease and more than a quarter million Americans are at risk of inheriting the diseases, but there is currently no cure. Scientists have recently been trying to develop a treatment using RNA-targeting CRISPR/Cas13d technology to eliminate toxic RNA that causes Huntington’s disease. CRISPR allows scientists to edit, add, and remove genetic material from specific places in the genome. This tool is based on a immune-defense mechanism from bacteria. Since there is a risk of editing a part of the genome unintentionally, studies have focused more on targeting RNA directly instead.

Huntington’s disease is caused by a mutation in a gene for the protein huntingtin. This mutation, known as a trinucleotide repeat expansion, causes cytosine, adenine, and guanine to be repeated many more times in the gene that normal. As a result, the protein that is produced can form toxic clumps in the part of the brain responsible for movement, which is called the striatum.

In AP Bio, we learned how genes are used to produce proteins that our bodies use. First, the RNA polymerase creates mRNA from transcribing DNA. A guanine nucleotide is added to the 5′ end, a poly-A tail is added to the 3′ end, and the introns are cut out. Then, the mRNA leaves the nucleus and goes to a ribosome for translation. The anticodon on the tRNA matches with the codon on the mRNA, which brings along the corresponding amino acid. The amino acid connects with the next amino acid to create a protein molecule. The additional CAG sequences in the huntingtin gene are transcribed onto the mRNA, which is then used to create a polypeptide. Since it is longer than normal, this protein’s shape will be deformed and will be toxic to the brain.

In neuronal cultures from patients with Huntington’s disease, scientists have used CRISPR to destroy mutant RNA molecules and clear out toxic protein buildup. Other genes were not affected by this treatment. When tested in mice, scientists found that the mice had better motor coordination and less toxic protein levels.CRISPR CAS9 technology

I chose this topic because I am very interested in how scientists can use mechanisms seen in other organisms to help treat human diseases.


The Quest for the Cure: Could Modified CAR T-Cells Using CRISPR Technology Be the Key?

Cancer: difficult to talk about, but even harder to cure. Unfortunately, most, if not all of us have lost loved ones due to cancer, the disease which took the lives of over 600 thousand Americans in 2022. Lymphoma, one of the most common types of cancer, is cancer of the lymphatic system, which is part of the body’s immune system and includes the lymph nodes, bone marrow, thymus gland, and spleen. Although scientists have not yet discovered a cure for it, scientists across the globe have made significant amounts of discoveries which could help treat lymphoma.


One promising treatment option is CAR (chimeric antigen receptor) T- cell therapy, discovered in 2002 by scientists at Memorial Sloan Kettering Cancer Center. As we learned in AP Biology, T-cells are part of the body’s immune system, and some (helper T-cells) recognize antigens while others (T-Killer cells) kill infected or cancerous cells. Helper T-cells recognize fragments of the antigen on the surface of macrophages and signal for the immune system to destroy the infected cell, a task that is often carried out by T-killer cells. When scientists modify T-cells in a lab by inserting a gene for a chimeric antigen receptor (CAR), the T-cells can better identify and bind to cancerous antigen fragments and signal for the body to destroy the cancer cells. After modifying the T-cells, they are inserted back into the patient. 

However, one major problem with this treatment is that the T-cells often get “T-cell exhaustion,” which is when they are effective and efficient at first but quickly become worn-out and ineffective. To combat this problem, Dr. Michel Sadelain altered the T-cells’ genes through the use of CRISPR technology.

CRISPR (clustered regularly interspaced short palindromic repeats) technology is a cutting-edge method of genome editing which physically cuts and/or replaces nucleotides in DNA.  

CRISPR-Cas9 editing of the genome

As we learned in AP Biology, DNA, the genetic “code” in every living thing, is composed of two strands, in the shape of a double helix, which are made of a phosphate and deoxyribose sugar “backbone,” and bases which attach to each sugar. There are four bases: A (adenine), T (thymine), G (guanine), and C (cytosine). A base, sugar, and phosphate together form what is called a nucleotide, and these are what CRISPR replaces or deletes.

DNA codes for all characteristics of a living organism, so when it is altered, the genetic makeup and traits change. This is an essential fact when considering CRISPR technology, since it can alter the base sequence within DNA, causing potentially life-saving gene alterations. Dr. Sadelain used this technology to insert a gene in T-cells which makes them more resilient and less prone to T-cell exhaustion. Dr. Park of Memorial Sloan Kettering recently proved Dr. Sadelain’s discovery to be effective in a clinical trial which used Sadelain’s method to use CRISPR to insert CARs and a molecule called 1XX into T-cells which were then injected into patients with lymphoma.  The alterations Sadelain made were intended to create T- cells that work efficiently for longer periods of time and therefore will be more effective in destroying lymphoma cells. The results of the trial were very promising since it was very successful, safe, and used a relatively small amount of modified T-cells, meaning that the treatment could be accessible to more people if it is approved.  Do you think this treatment method will be a success?

As confirmed through this trial, the capabilities of CRISPR and CAR T-cell therapy are evolving to a mind-blowing extent and are providing safer and more effective treatments for cancer and other diseases every year. Although a universal cure for cancer has not yet been discovered, the discoveries of this study could alter the future of lymphoma treatment and save the lives of thousands.

Overcoming a Critical Limitation of CRISPR

Recent research demonstrates that CRISPR Spherical Nucleic Acids (SNAs) can be delivered across the cell membrane and into the nucleus, all while retaining bioactivity and capability of gene editing. Gene editing is technology which allows a scientist to change an organism’s DNA. 

The work displayed in this article builds on a 25-year study to uncover the properties of SNAs and the factors that distinguish them from the blueprint of life. SNAs are structures typically composed of spherical nanoparticles covered with DNA or RNA, giving them chemical and physical properties different from those forms of nucleic acids found in nature. 

Core-filled and Core-less Spherical Nucleic Acids 01

A variety of SNAs exist, with cores and shells of different chemical compositions and sizes. SNAs are also now being evaluated as potent therapeutics in human clinical trials, such as trials for brain cancer and skin cancer. 

According to nanotechnology pioneer Chad A. Mirkin, “these novel nanostructures provide a path for researchers to broaden the scope of CRISPR utility by dramatically expanding the types of cells and tissues that the CRISPR machinery can be delivered to.” “We already know SNAs provide privileged access to the skin, the brain, the eyes, the immune system, the GI track, heart and lungs. When this type of access is coupled to one of the most important innovations in biomedical science in the last quarter-century, good things will follow.”

Mirkin’s team used Cas9 (protein required for gene editing) as the core of the structure, and attached DNA strands to the surface to form a new type of SNA. These SNAs were also preloaded with RNA capable of performing gene editing and fused with peptides to control their ability to navigate compartmental barriers of the cell, making it the most efficient. In AP Biology, we learned that peptides are molecules containing two or more amino acids. Peptides that contain several amino acids are called polypeptides or proteins. These SNAs effectively enter cells without the use of transfection agents, and display high gene editing efficiency between 32% and 47% across several human and mouse cell lines. 

If You Give A Mouse…Sight!

In a recent study published in the Journal Of Experimental Medicine, researchers in China successfully used CRISPR Gene-Editing technology to restore sight to mice with retinitis pigmentosa.

That’s a lot of vocabulary all at once, so let’s establish some definitions first and foremost.  According to the National Eye Institute, retinitis pigmentosa is a “genetic disease that people [and animals] are born with…that [affects] the retina (the light-sensitive layer of tissue in the back of the eye)”. As for CRISPR Gene-Editing technology, YG Topics defines it as, “a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence”.

Most inherent forms of blindness and loss-of-vision stem from genetic mutations, and thus retinitis pigmentosa is one of many forms of genetically caused blindness.  However, through CRISPR technology, the researchers in the study successfully edited the DNA of mice who had the mutation to eliminate retinitis pigmentosa and give them the ability to see.  The results of the study are very promising, as not only does retinitis pigmentosa affect mice, but human beings.  Thus, there is evidence that CRISPR could be used to cure blindness among everyday people.  Kai Yao, a professor from the Wuhan University of Science and Technology who contributed to the study said, “The ability to edit the genome of neural retinal cells, particularly unhealthy or dying photoreceptors, would provide much more convincing evidence for the potential applications of these genome-editing tools in treating diseases such as retinitis pigmentosa”.

In AP Biology, we discussed how DNA factors into the traits of a living being.  DNA is made up of 3 base codons that form up to 20 different amino acids.  These amino acids code for specific proteins.  Through a process of DNA transcription and translation, the DNA uses various forms of RNA to code for proteins, which help tell the cell what to do.  Thus, the way the cell acts is largely determined by its DNA.  Essentially, DNA codes certain traits through various amino acid sequences.  Mutations and alternations to amino acid sequences cause different traits, such as red hair, blue eyes, or blindness.

Thus, successfully altering the DNA of mice has huge implications for the human race.  CRISPR could potentially be used to edit the DNA of humans, and thus help limit and prevent certain genetic conditions.  Many diseases are based on genetic mutations, and if CRISPR Gene Editing technology is proven successful, we could potentially eliminate genetic diseases in a few decades.  While “much work still needs to be done to establish both the safety and efficacy” of CRISPR technology, some groundbreaking scientific treatments could be coming sooner than you think (Neuroscience News).

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The “Most Complicated” Cancer Treatment EVER

There are many approaches to treating cancer, ranging from invasive surgeries to extremely damaging radiation and chemotherapy.  The teeny-tiniest clinical trial ever began at UCLA in yet another attempt to find another way to eradicate cancer.  With only 16 participants, this trial combined two areas of research: gene editing and T-cell engineering.   The reason for the miniscule sample size is the intensely customized nature of the treatment.  Each patient’s tumor had completely unique mutations, so each patient needed equally unique T-cell engineering through gene editing.  

One reason cancer is so hard to treat is because they have adapted to be resistant to the body’s own immune response.  The patients that have cancers, especially ones in the later stages, have lost the battle against their cancer with their own immune system, so a new super-immune system must now be built.  This army of new T-cells (white blood cells, which identify and kill bad cells, seen below) will need “training” for its difficult battle ahead.  First, however, the researchers must determine how to train these cells so they will actually be successful.  They used algorithms to find identifiable mutations in the tumor, something that the T-cell can seek out to differentiate the cancerous cells from the normal cells.  Healthy Human T Cell

After testing to make sure that the T-cells can actually identify these mutations, T-cell receptors are designed specifically to their tumor.  Then, each patient’s blood is taken so that the DNA code for the new receptors can be inserted using CRISPR,  a genome editing technology at the cutting edge of genetic medical research.  The DNA code is transcribed to mRNA, which is then used in the ribosome to build polypeptides, in this case, the receptor proteins for the T-cells.  In order to ensure that these new T-cells (with the special receptors) are received, the patients had to take medication that suppressed the number of immune cells, so that the ones they are given can take hold.  

One month into treatment, 5 of the patients’ tumors stopped growing, and only 2 of the participants had associated side effects.  Although only 5 patients had the desired results, Dr. Ribas, one of the researchers, says that they “need to hit it stronger the next time” because they were limited to a small dosage of T-cells to start in order to establish safety.  Additionally, the technology will only get better and better as the research progresses and the T-cells can have more and more mutation targets to look for in a tumor.  

CRISPR: how one tool can change an entire generation (of invasive mice).

In recent years, technology has heavily impacted scientists abilities to change the world. CRISPR is a recently discovered gene editing tool that is revolutionizing the way scientists are treating patients and curing diseases. Recent research has also found that CRISPR can be used to help mice infestations in certain parts of the world (random, but cool)!

CRISPR logoMice infestations are a problem in many islands, and CRISPR is here to help. Scientist believe they had found a way to make an entire mice population extinct (in a few decades) by using gene editing via CRISPR. In order to understand exactly how scientists plan on doing this, it is important to understand what a “haplotype” is. A haplotype is a set of genes that are inherited by the next generation together. The “regular house mouse” has what’s called a “t-haplotype,” and it’s passed down roughly 95% of the time (a lot compared to the normal 50%). The study states that male house mice with two t-haplotype copies become infertile, and females with two t-haplotype copies will become sterile as well. As we know from AP-Biology, when an organism has two copies of some gene, it is known as homozygous- meaning it has two of the same alleles of some gene. In this case the phenotype that makes the mouse homozygous would be the altered t-haplotypes. If a mouse has two of these altered t-haplotype genes, it becomes sterile and cannot reproduce.

Mouse white background

CRISPR plays a crucial role here – by using gene editing through CRISPR technology, scientists are able to edit the t-haplotype of the M. musculus house mouse so that next time a male M. musculus mates with a female, the offspring will become infertile. That’s right, CRIPSR can be used to completely alter and wipe an an entire M. musculus population over the course of a few years. By using computer technology, scientists predict that by adding just 256 “altered” mice to a certain island population of mice, an island of 200,000 mice can be fully wiped out within about 25 years.

Researchers in laboratoryScientists are hopeful, optimistic, and invested in CRISPR technology. The “25 years later” prediction is a long time to wait, and scientists hope that sometime in the future, CRISPR will be able to work faster, allowing problems to be solved more quickly and more efficiently. I think that this study is an important part of CRISPR potential, and it makes me very curious to see what CRISPR has in store for the future, and what other kinds of animal related issues it can help solve.

New CRISPR Technique can Potentially be a Treatment for Leukemia

An article published on December 11, 2022 on newscientist, shares fascinating information on a 13 year old patient with leukemia, having no detectable cancer cells after being the first person to receive a new type of CRISPR treatment, to attack cancer.  

The 13-year-old leukemia patient, Alyssa, has had many treatments that have been unsuccessful in helping her condition. Leukemia is caused by immune cells in the bone marrow dividing and growing rapidly. This relates to what we learned about in Biology class in how cancer cells become cancerous by cells dividing uncontrollably. It is also related to how cancer is caused by changes to the DNA (mutations) that alter important genes and change the behavior of them. Leukemia is also caused by the mutations in DNA.

Normal and cancer cells structure

The most common treatments for leukemia are known as killing all bone marrow cells with chemotherapy and then replacing it with a transplant. If this treatment is unsuccessful, an approach known as CAR-T therapy is used. This involves adding a gene to a type of immune cell known as a T cell that causes it to destroy cancerous cells. This also relates back to how in biology class we learned about the functions of T- cells being vital because they protect us from infection. The modified cells are called CAR-T cells. Alyssa’s leukemia was caused by T cells so if they used this technique to modify CAR-T cells to attack other T cells, it would lead to these cells killing each other. Wasseem Quasim at the University College London Great Ormond Street Institute of Child Health, has discovered many drawbacks with this treatment. Due to the many problems conventional gene editing can cause, Qasim and his team used a modified form of the CRISPR gene-editing protein, and Alyssa is the first person ever to be treated with. Alyssa received a dose of immune cells from a donor that had been altered to attack the cancer, and tests revealed 28 days later she had no signs of cancer cells. CRISPR is technology that can be used to edit genes. It finds specific DNA inside a cell and then changes that piece of DNA. It has also been discovered that CRISPR can be an effective tool for cancer  treatment. This new approach to CRISPR treatments could be hugely beneficial  to cancer patients and Many other treatments involving CRISPR base editing are being developed.  





Analyzing Viruses in One Step Using LUNAS

In this article from the American Chemical Society, Maarten Merkx and his colleagues research how to use and combine CRISPR-related proteins with a bioluminescence technique whose signal could be detected with a digital camera. This new technique can diagnose illnesses faster while being much more efficient and practical. Bioluminescence is a chemical reaction involving the luciferase protein that causes the luminescent, glow-in-the-dark effect. The luciferase protein has been incorporated into sensors that emit an easily observed light when they find their target, but they lack the incredibly high sensitivity required of a clinical diagnostic test.

Mareel - Bioluminescence in Norra Grundsund harbor 2

CRISPR, a gene-editing technique, has the ability to increase sensitivity, but it requires many steps and additional specialized equipment. With the new technique, called LUNAS (luminescent nucleic acid sensor), two CRISPR/Cas9 proteins specific for different neighboring parts of a viral genome each have a distinct fragment of luciferase attached to them. If a specific viral genome that the researchers were testing for was present, the two CRISPR/Cas9 proteins would bind to the targeted nucleic acid sequences and come close to each other, allowing the complete luciferase protein to form and shine blue light in the presence of a chemical substrate. RPA-LUNAS successfully detected SARS-CoV-2 RNA within 20 minutes, even at concentrations as low as 200 copies per microliter.

This is similar to the process of gene regulation that uses an inducible operon as we learned in class. An inducible operon is a type of negative regulation that turns on when it interacts with an inducer. It is usually off which means there is an active repressor that binds to the operator to block the RNA polymerase from transcribing the DNA. When there is the inducer, such as the virus, the inducer inactivates the repressor by binding to the allosteric site which allows the RNA polymerase, such as the CRISPR/Cas9 proteins, to transcribe and eventually produce the protein, such as the luciferase protein.

As we are recovering from the devastating COVID-19 Pandemic, how can new medical advancements and technology help us prepare for future outbreaks?

The Fluorescent Frontier: Glow in the Dark Proteins in Disease Research

We all know that although science is improving rapidly on a global scale, diagnostic tests for diseases remain sensitive and require complicated techniques. One evident example is the tests for COVID-19. This complexity can range from their preparation to an interpretation of their results. However, recent research from the American Chemical Society has developed a method that is able to analyze viral or infected nucleic acids in less than 30 minutes and in just one step. This is all due to “glow in the dark” proteins.

Bioluminescence is a scientific phenomenon that powers many animals: a firefly’s flash, an anglerfish’s glowing head, and even phytoplankton’s blue color.  Here a chemical reaction occurs, involving the luciferase protein. This protein essentially causes the “glow in the dark” effect. The protein is incorporated into sensors which emit a light when a target is located. Although the simplicity of these sensors is idyllic for clinical diagnostic testing, they still lack the sensitivity

One solution to this problem is presented by a particular gene editing technique: CRISPR. The Broad Institute defines CRISPR as; Clustered Regularly Interspaced Short Palindromic Repeats. It is essentially an efficient and customizable alternative to other existing genome editing tools. With this new technique, Maarten Merkx and his coworkers wished to use CRISPR-connected proteins while combining them with a bioluminescence form whose glow could be seen by humans, through a digital camera for example.

CRISPR CAS9 technology

To ensure that there was an ample amount of DNA or RNA to analyze, they used a technique known as Recombinase Polymerase Amplification, or RPA. This is a simple method which works continuously at a temperature of 100 F. With this  two CRISPR proteins specific for different parts of a viral genome each have a different fragment of luciferase attached. In other words, the new treatment known as LUNAS (Luminescent Nucleic Acid Sensor), takes two CRISPR proteins for different parts of a viral genome and has a distinct fragment of luciferase added to each.

Moreover, if one specific viral genome that the researchers were testing was present, the two CRISPR proteins would bind to the targeted nucleic acid sequence. This would allow them to come together and promote the full luciferase protein to form and glow. Additionally, to account for the luciferase being depleted, the researchers used a control reaction which turned green. In the event of a positive viral detection the color would change from green to blue. To prove the validity of this method, the researchers tested LUNAS on clinical samples of nasal swabs testing COVID-19. The method successfully detected the virus in less than 20 minutes, even at low concentrations. With this, the LUNAS method holds great potential in detecting other viruses in a concise and efficient manner.


To connect to our AP Bio class, we learned about how specific proteins code for specific actions or results in our bodies. At their tertiary and quaternary structures, proteins have a myriad of functions ranging from acting as a receptor to interacting with an enzyme. This parallels with the luciferase’s specific function of creating a glow affect. Additionally we learned about cell communication and how interaction with a receptor would result, or cause a specific occurrence. This connects to luciferase’s binding to its sensor, causing the glow affect. This cell communication also connects to the two CRISPR proteins attaching to a specific nucleid acid sequence. If the nucleid acid holds the viral genome and the luciferase, it would connect and form a glow response – a direct example of intercellular communication. Continually, we learned about DNA manipulation and alteration and how segments can be added in, substituted, or even removed. This occurs in CRISPR gene editing’s nature as a genome editing tool. It exemplifies all these manipulations to both DNA and RNA. We also learned about ideal protein function at a variety of temperatures, pHs, and environmental settings. This idyllic setting in seen in RPA’s function at a continuous 100 F.

To close, I feel that the use of luciferase, or “glow in the dark” proteins fronts an entirely new way of combating diseases and supporting disease identification. It would provide a new way for doctors and scientists to diagnose patients in a time efficient manner. And frankly, the idea of being diagnosed by something “glow in the dark” is entirely lightening and provides some relief to the gravity of the situation. I invite any and all comments regarding this specific method of disease identification or any other relevant discussion points.

Biological Warfare: Bacterial Edition

Ubiquitin cartoon-2-

In February 2023, a study was published announcing that bacteria possess something similar to humans that can activate and deactivate immune pathways, and therefore this “something” could be used to cure diseases; that “something” is called the ubiquitin transferase enzyme

Biological warfare, the use of infectious agents to kill diseases caused by other infectious agents, has been considered as a potential solution in the past. In fact, years prior, a family of DNA sequences now referred to as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) were discovered in bacteria, and it was determined that these sequences were capable of killing other phages and being used to cure infections. 

Our immune pathways, as we learned in our immunity unit in AP Biology, is crucial for our survival as a species. Our immune system consists of innate immunity, involving natural killer cells that serve as our first line of defense against pathogens, and adaptive immunity, involving B cells and T cells that need to be trained to fight these pathogens. Our immune pathways alone, however, cannot rid us of neurodegenerative diseases, and these diseases still unfortunately have no cure.

One may be wondering now, how can the ubiquitin transferase enzyme work to treat diseases like Parkinson’s? How does it help our immune pathways? Well, the answer to that is protein editing. The enzyme contains two proteins, CD-NTase-associated protein 2 and 3 (also known as Cap2 and Cap3); these proteins are what serve as the activation and deactivation for immune pathways: they can direct old, unnecessary, or damaged proteins to be broken down. 

When the potential of CRISPR was discovered, scientists used genome editing to direct the machine so it would kill its targeted diseases. A similar attempt could be made with the ubiquitin transferase enzyme. 

Finding the existence of this in bacteria especially is an amazing discovery, as not only does it propel us in the right direction in terms of potentially curing Parkinson’s or other neurodegenerative disorders, but it connects back to our other lesson in AP Biology that humans and bacteria are not so different after all. We share about a thousand genes!

It is particularly interesting knowing how biological warfare could be used to help us.

The Science of Love

The neurobiology of love is not as simple to figure out as one may think. Throughout time, researchers have studied the prairie vole when looking to discover more about what exactly is going on in our brains when we fall in love. The prairie vole is used because they form monogamous relationships, in which they show empathy for and display actions that we would describe as love. The monogamy of prairie voles was tested and proven nearly 50 years ago, and since then, we have been researching prairie voles to discover the neurobiology of their love.

Prairie vole.gif
When first looking at exactly what happens in a prairie vole’s head when they “fall in love” the hormones oxytocin and vasopressin were found to play a key role in the bonding of prairie voles. These hormones work just as any hormone we have learned about in this AP Biology class does, they are peptides that bind to receptors, resulting in the change of the shape of the receptor, resulting in a change within the cell. This signal caused by oxytocin and vasopressin has been shown have the ability to change a solitary or polygamous prairie vole, into one that forms a monogamous bond with another prairie vole. This is unique to other voles, as the receptors for these hormones in prairie voles are in a separate location to those within other types of voles. This discovery opened up a doorway into understanding how the location and abundance of hormones receptors can affect the bonding of animals or even ourselves. In order to truly understand this though, researchers had to find a way to manipulate the ways that genes encode these receptors.

Vasopressin labeled  Oxytocin

Vasopressin                                               Oxytocin

Although this phenomenon has been well studied in the past,  the invention of CRISPR technology has opened many more doors into studying the ways that these hormone receptors work. Throughout time, it has been accepted that oxytocin in the true hormone that controls the bonds of these prairie voles. But, after a research team used CRISPR to “delete the gene that encodes the oxytocin receptor in prairie vole embryos,” it was found that the genetically modified prairie voles were still able to form bonds as easily as their non-modified brethren. Scientists are now trying to really figure out what the biology of the love of these voles is, as their original hypothesis that oxytocin controls it has been found incorrect. Scientists are now looking to hormones such as vasopressin, to see if that was the missing part of the puzzle they need. This discovery that oxytocin is not the entire basis of the bonding of prairie voles does show that as usual, love is less complex than we may think, and that they must look at the neurobiology of love as having a much bigger scale than before thought of.


Currently, scientists are aiming to look at the activity of genes in the brain to further look to what causes love bonds. Recent studies like this have shown that after the voles have mated, genes important to memory and learning are turned on, and that their brain’s reward structure turns on after a stable amount of time with a bond. These studies have also proven that the voles brains become “activated,” once they have created a bond, as their neural activity “lights up” and their brains “re-wire themselves.”

“How does this relate to us humans?” you may ask. Well, the ways that prairie voles react to their bonds can show us what an evolved brain, which neurologically is wired to have a partner. The studies done on prairie voles inspired scientists to look back closer at the reward structures pf the brain looked at in studies for prairie voles, and it was found that humans had similar responses to the voles. Overall, with much more time to let research and technology develop, studies on prairie voles have definitely taken us one step closer in understanding the science of love.

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