BioQuakes

AP Biology class blog for discussing current research in Biology

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Secretive Bacteria: A Revolutionary Discovery in Bacteria

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On April 7, 2025

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For decades, scientists believed that genetic code was like an open book. They believed that each gene is neatly stored in the chromosomes. However, a groundbreaking study from Columbia University has flipped this idea on its head. Researchers have discovered that bacteria can create free-floating, ephemeral genes, or genes that don’t permanently reside in the genome but still play important roles in survival. This raises important questions. Could similar floating genes exist in humans, hidden from our current understanding of genetics? If so, this discovery could change how we think about genetic information, evolution, and gene therapy.

Bacterias

The research, led by Samuel Sternberg and Stephen Tang, focused on an unusual bacterial defense system against viral infections. Instead of cutting up viral DNA, like the well-known CRISPR system, this new defense involved an enzyme called reverse transcriptase, which synthesizes DNA from an RNA template. 

Using a new experimental technique, the researchers found that this enzyme repeatedly copied a small loop of RNA, producing long, repetitive strands of DNA. At first, they thought it was a mistake, but after more digging, they realized that this mysterious DNA was actually a functioning, temporary gene that played a vital role in stopping viral infections. When bacteria were exposed to viruses, this free-floating DNA made a protective protein that prevented viral replication, acting as a defense shield.

This discovery challenges the traditional understanding of molecular biology, which states that genetic instructions flow in a plain sequence from DNA to RNA to protein. The existence of genes that function without being permanently stored in chromosomes could mean that our understanding of the human genome is incomplete. It raises the possibility that humans might also have hidden genetic instructions that only appear under certain conditions. If such genes exist, they could provide insight into diseases, immune responses, or even the evolution of complex life.

The study also has implications for gene therapy. CRISPR, a revolutionary gene-editing tool, has already transformed medicine by allowing scientists to cut DNA precisely. However, it has limitations because even though it can remove or disable genes, it cannot efficiently add new genetic material. The bacterial reverse transcriptase described in this study could help overcome this hurdle by allowing researchers to “write” new DNA sequences directly into the genome, leading to more advanced genetic treatments for diseases.

In AP Biology, we learned about gene expression and regulation, including how DNA is transcribed into RNA and then translated into proteins. This study challenges that structure by showing that genetic information isn’t always locked inside chromosomes. Gene regulation is complex and involves transcription factors, promoters, and enhancers, which determine when and how much of a gene is expressed. The discovery of floating genes suggests that gene expression might be even more involved, with certain genetic instructions appearing only when needed. This discovery also ties into endosymbiotic theory, which explains how some of our cellular structures, like mitochondria, originated from ancient bacterial ancestors. This theory proposes that early eukaryotic cells engulfed bacteria that eventually became permanent parts of the cell. The idea that bacteria have temporary genes that can be activated when needed suggests that early life forms may have exchanged more genetic material than we’ve previously thought. 

If free-floating genes exist in bacteria, could they exist in humans? What if our cells produce hidden genetic instructions in response to environmental triggers? Could these genes hold the key to curing genetic disorders?

What do you think? Could hidden genes in human cells play a role in health and disease? Drop your thoughts in the comments!



Exciting New Advancements in Gene-Editing Technology

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On April 7, 2025

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In the past 15 years, advances in the gene-editing technology known as CRISPR-Cas9 has provided significant information about the roles that specific genes play in various diseases. However, as of March 25, 2025, this technology, which allows scientists to use a “guide” RNA to modify DNA sequences and analyze the effects, has only been able to delete, replace, target or modify only single gene sequences with a single “guide” RNA, limiting ability to evaluate multiple genetic changes at the same time. How interesting!

File:CRISPR CAS9 technology.png

Recently, however, Yale Scientists have created a series of high-level mouse models using CRISPR (“clustered regularly interspaced short palindromic repeats”) technology that permits them to simultaneously evaluate genetic interactions on a host of immunological responses to many diseases such as cancer. In general, gene editing technology allows scientists to implement enzymes, in this case, Cas9 (CRISPR-associated protein 9), as a “molecular scissors” that can accurately remove or modify sections of RNA or DNA, increasing understanding regarding the role these genes play in disorders. According to Sidi Chen, an associate professor of genetics and neurosurgery at Yale School of Medicine and a trailblazer in the field of CRISPR technology, the new tool, CRISPR-Cas12a, can aid researchers in simultaneously analyzing the effect of many genetic changes involved in multiple immune system responses. By using these new tools, Chen’s lab was able to induce and track modifications in many immune system cells in response to gene editing and was also able to tweak sets of genes in different directions simultaneously. Would you ever be interested in going into research similar to this study?

This article connects to AP Biology as it is related to gene expression and regulation which are essential to how organisms function. Even though all cells in an organism contain the same DNA, different cells express different genes depending on their role. Specifically, cells are able to regulate which genes are turned on and off and when that “turning on and off” happens. Regulations include epigenetic controls such as DNA methylation and DNA acetylation that affect the transcription stage of protein synthesis by influencing whether DNA is loosely or tightly wound. Tightly wound DNA (DNA methylation) works by turning off the genes in that region, while  loosely wound DNA (DNA acetylation) can be transcribed more easily. Once a gene is accessible, transcription factors such as enhancers influence whether a gene is transcribed. Following transcription, RNA processing occurs which includes RNA splicing which increases proteome diversity by removing the introns (non-coding regions) and keeping exons (coding regions) which form a mature mRNA molecule that is ready for translation. In this study particularly, researchers explore how gene networks interact to control expression patterns. As learned in AP Biology, changing one gene may have limited effects because of redundancy of others. However, by changing many genes in a system, researchers can observe how epistasis occurs (when one gene affects the expression of another). In AP Biology, we first learn about this regulatory complexity when learning about different operon models in prokaryotes (trp and lac), or the roles of enhancers, and transcription factors in eukaryotes. We study how one change in one part of the system can silence, activate, or modify other genes. By modifying genes involved in the immune response, the researchers in the study watch how the cellular regulatory system reacts or adapts. These reactions reveal how interconnected gene expression is, showing that genes operate as a part of a controlled system that determines the behavior of cells and ultimately a whole organism.

I found this article particularly interesting because it shows how often scientists are inventing new technologies and advancing every day- this article was written around just a week ago!

 

 

 

 

Simultaneous Tracking: CRISPR’s Major Upgrade

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On April 7, 2025

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Software updates on your iPhone can often feel unnecessary. Waiting for your smartphone to complete an increasingly lengthy update, only to discover seemingly minimal changes in one area—like fixing bugs or improving compatibility—can be frustrating.

People using smartphones at a railway station

Smartphone users at a railway station.

For the past decade, scientists have been able to edit DNA with remarkable precision, revolutionizing genetic research with the use of CRISPR-Cas9 technology. Specifically, CRISPR-Cas9 technology is a type of gene editing technology that allows scientists to use enzymes to molecularly cut and/or modify specific portions of DNA or RNA to discover the roles these genes play in a variety of disorders and diseases. According to the National Library of Medicine, CRISPR-Cas9 “makes it possible to correct errors in the genome and turn on or off genes in cells and organisms quickly, cheaply, and with relative ease.”

This is what makes CRISPR technology so amazing! The technology’s ability to, according to the Broad Institute, “easily be matched with tailor-made “guide” RNA (gRNA) sequences designed to lead them to their DNA targets,” makes the technology distinctly efficient and customizable in a way other gene-editing tools are not.

Although this type of genetic technology has led to significant discoveries regarding the roles of genes in cancers and autoimmune disorders, CRISPR has had a key limitation: it could only target one gene at a time. However, in a recent study, researchers at Yale University discovered a new upgrade in CRISPR technology that allows for simultaneous genetic modifications and tracking across multiple genes at once, a notable change from past CRISPR abilities.

CRISPR-Cas9 Editing of the Genome

Illustration of CRISPR-Cas9 Editing of a Section of DNA.

The research team’s new tool, called CRISPR-Cas12a, has the ability for researchers to “simultaneously assess the impact of multiple genetic changes involved in a variety of immune system responses.” Led by Dr. Sidi Chen, the team of researchers developed four mouse models that used this new technology to fine-tune and track changes in the mice’s immune system cells. The team distinctly focused on inducing and editing sets of genes in “different directions simultaneously.”

These models essentially allowed the scientists to study the genetic interactions of the mice’s immune system cells that contributed to diseases like cancer and even autoimmune and neurological disorders. In this way, Chen’s team was able to create an entirely new way of studying immune responses at the genetic level not only for mice cells but for human cells as well, which could eventually develop into the creation of new remedies and therapies for certain types of medical conditions and diseases.

This research directly connects to what we’ve studied recently in AP Biology. CRISPR-Cas12a and other gene editing technologies relate directly to the ability to manipulate transcription and translation during protein synthesis through gene regulation. Moreover, we learned in class that genes control traits by coding for different types of proteins and that cells can turn their genes “on” or “off” through a series of regulatory processes. CRISPR-Cas12a connects to our classwork because this technology allows scientists to modify multiple genes at once and observe how those changes can affect how certain cells function and what phenotypes are shown as a result. By editing multiple genes, scientists can study how genes work together to create traits!

Cas12a (Cpf1) in complex with crRNA and target DNA

Structure of CRISPR-Cas12a with a guiding RNA (cRNA) and target segment of DNA.

Ultimately, CRISPR-Cas12a and other types of genetic technology have great implications for the future of medicine and genetic testing. The ability to edit multiple genes simultaneously has created promising hopes for the development of new, personalized medicinal treatments and the improvement of scientists’ understanding of genetic diseases and immune system disorders.

It is clear that the future of medicine is continuing to be crafted, one gene at a time—or in this case, many at once!

Mice and Mutations- A new gene editing tool in the fight against Alzheimer’s

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On April 7, 2025

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Certain genetic mutations have the ability to alter a protein’s whole amino acid sequence and warp proteins into toxic, misfolded shapes which disrupt cellular functions. These mutations can eventually lead to diseases such muscular dystrophy, Huntington’s disease, and Alzheimer’s. 

In most areas, genome editing technology has become a critical tool in targeting toxic proteins and fighting against diseases such as cancer, HIV, and sickle cell anemia. CRISPR technology (clustered regularly interspaced short palindromic repeats) is frequently utilized, employing a Cas9 protein and guide RNA to target specific and edit specific DNA sequences. 

Neurodegenerative diseases including Alzheimer’s and Parkinson’s are strongly associated with accumulation of misfolded proteins in the brain. This specific protein misfolding is influenced by a variety of factors and is seen as very complex. While CRISPR/Cas9 has potential for correcting the protein misfolding associated with neurodegenerative disorders, another new gene editing tool SPLICER, is coming in hot to address this problem. 

To test the capability of SPLICER’s promise in gene editing for neurodegenerative disorders, a research team from the University of Illinois conducted a study to test if SPLICER can reduce plaque accumulation in the brains of live mice, potentially lowering the risk of Alzheimer’s disease. 

SPLICER is a gene-editing tool that utilizes exon skipping, a technique that modifies gene expression by skipping and splicing certain exons during the protein synthesis process. Built upon the CRISPR gene editing platform, SPLICER offers greater flexibility. Traditional CRISPR-Cas 9 gene editing systems require a specific DNA sequence to latch on, bind, and edit genes, limiting which genes can be edited. However, SPLICER employs newer Cas-9 enzymes that function without these restrictions. Additionally, there are two important sequence areas, one at the beginning and end of a gene, that make cellular machinery aware of which parts of a gene to use for protein synthesis. While CRISPR and traditional exon skipping tools use only one of these sequences, SPLICER edits both, allowing the exon-skipping process to be more efficient. 

Alzheimers disease beta-amyloid plaque formation-2

The Illinois team targeted a specific exon in an Alzheimer’s related gene that codes for an amino acid sequence within a precursor protein. Usually, this protein would undergo a modification where it gets cleaved to form amyloid-beta, a peptide which accumulates to form plaques on neurons in the brain. While analyzing the DNA and RNA output in SPLICER treated mice, it was discovered that there was a significant decrease in amyloid-beta production. The researchers found that the targeted exon was reduced by 25% in the SPLICER-treated mice, demonstrating the effectiveness of this technique. 

As a part of our recent Molecular Genetics Unit, we have learned the process of gene expression, where a portion of DNA is transcribed into an mRNA strand, which is then translated into a peptide chain and forms a protein. However, after the transcription of the mRNA, RNA splicing occurs where a spliceosome cuts out the introns (non-coding sequences) and joins the ends of exons (the coding/expressed sequences) together. The purpose of SPLICER is to remove specific exons or coding sequences from the mRNA, potentially producing a modified but still functional protein after the translation phase and reducing the formation of misfolded and toxic proteins. 

The study concluded that SPLICER, which combines newer base editors with the dual sequence editing, enabled exon skipping at a much higher rate than older available technologies. By efficiently skipping target exons in the mice, the tool reduces amyloid-beta production, leading to less plaque buildup and a lower likelihood of developing Alzheimer’s or other neurodegenerative diseases. 

However, this approach does have limitations. Exon skipping only works if the product protein is still functional, meaning not all diseases can be treated this way. However, for diseases like Alzheimer’s, Parkinson’s, Huntington’s or Duchenne’s muscular dystrophy, this approach holds a lot of potential. Further research is needed to confirm that removing targeted exons is safe and does not lead to the production of toxic and nonfunctional proteins. While SPLICER represents a significant advancement in gene editing, continued research and refinement are necessary before it can be considered for human application. 

As part of my Independent Service Project, I will be volunteering with adults who are suffering from dementia and other neurodegenerative diseases. Even before beginning this work, witnessing and understanding the challenges they face each day has strengthened my hope for advancements in treatment. While continued research and refinement are necessary before SPLICER technology is considered for human application, I am grateful that we are making progress to combat these devastating diseases. 

https://www.sciencedaily.com/releases/2024/12/241223153410.htm– original article

https://www.xiahepublishing.com/m/1555-3884/GE-2024-00002–  additional research on CRISPR technology

CREME: Revolutionizing Gene Expression Analysis for Drug Discovery

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On April 7, 2025

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DNA / Naturalis Leiden

CREME is an AI-powered virtual based on CRISPRi, developed by Cold Spring Harbor Lab Assistant Professor Peter Koo and his team, allowing geneticists to run thousands of experiments simply with the click of a button. 

To understand CREME, we first need to understand CRISPR and CRISPRi (CRISPR interference). CRISPR uses a protein called Cas9 to cut certain DNA out of a genome, similar to how introns are cut out in RNA processing. CRISPRi, on the other hand, uses a modified Cas9 called dCas9 not to cut out certain DNA sequences but to block them during RNA transcription, acting similarly to a repressor. During transcription, CRISPRi can interfere with RNA Polymerase during transcription initiation or transcription elongation.

CREME is, in a sense, an AI-powered virtual CRISPRi. This is a major advantage to CRISPRi because, as Koo explains, “CRISPRi is incredibly challenging to perform in the laboratory,” further saying that “the number of perturbations and the scale” also limit CRISPRi in the laboratory. 

However, by using CREME, the aforementioned limitations seemingly disappear, as it becomes possible to do “hundreds of thousands of perturbation experiments.”

Koo and his team also demonstrated that CREME could be used to help discover genetic rules. To do this they tested CREME on another AI-powered genome analysis tool called Enformer. Enformer is good at making accurate predictions on gene expression, but we don’t know what rules of gene regulation Enformer or other models like Enformer are basing their predictions on.

With CREME, Koo and his team found several rules that Enformer based its predictions off of. These findings are compelling in the possibilities in drug discovery. By understanding how different genes are expressed, drugs can be more easily discovered.

Do you have any ideas on how changing gene expression can impact public health?

Beyond Genetic Scissors: How CRISPR-Cas12a Is Editing the Future of Medicine

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On April 7, 2025

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Cas12a (AsSpf1) in complex with crRNA and target DNA

Imagine if your DNA came with a backspace key — thanks to CRISPR, it kind of does. This idea may seem crazy, and it is, but let me explain. CRISPR is a unique technology that allows scientists to edit parts of the genome by removing, adding or altering sections of the DNA sequence. How does it do this? Well it’s a little complicated. The CRISPR-Cas9 system has two fundamental molecules, the enzyme Cas9 and a piece of RNA called guide RNA (gRNA). gRNA is a small piece of pre designed RNA that contains bases complementary to a specific DNA sequence. This means that the gRNA will only bind to the targeted sequence and will “guide” the Cas9 to the right part of the genome. Cas 9 is playfully referred to as “genetic scissors” as it makes precise cuts in both strands of the DNA at the targeted spot in the genome. When the cell recognizes its DNA is damaged it activates repair mechanisms, allowing scientists to swoop in and insert, delete, or modify genetic material at that site.

Seems amazing right? The one catch is that CRISPR can only target, delete, replace, or modify one gene sequence at a time using a single guide RNA, making it difficult to study multiple genetic changes at once. However, a brand new study at Yale school of medicine has developed a new technologie that can help researchers simultaneously assess the impact of multiple genetic changes involved in a variety of immune system responses. This new tool is called CRISPR-Cas12a, and seems to have huge implications. Sidi Chen, an associate professor of genetics and neurosurgery at Yale School of Medicine and a pioneer in the field of CRISPR technology, led the lab in making four specially engineered mouse lines that allowed the scientists to study “complex genetic interactions and their effects involved in many disorders.”

Using Cas12a Chen’s lab was able to induce and monitor changes in the immune cell in response to gene editing, fine tuning sets of genes in different directions at the same time. The researchers were also able to generate rapid production of new disease and treatment models, including genetic disease in the liver, lung cancer, and skin cancer.

This all represents a huge step forward in the world of CRISPR gene editing, as according to Chen these developments will be a powerful tool for scientists developing new treatments for a wide range of diseases, from cancer and metabolic disorders to autoimmune and neurological conditions.

In fact CRISPR treatment has already been utilized with real patients. A clinical trial launched by the University of Pennsylvania in 2019 used CRISPR to engineer T cells that could better detect and attack cancer cells. The treatment entailed removing three genes that interfered with the immune system’s response to cancer and adding one gene that helped the T cells recognize cancer cells. While the trial focused on safety and the results were modest, the trial proved that CRISPR treatment can be done in a safe and meaningful way. This coupled with the work done in Chens Lab at Yale lays the groundwork for groundbreaking discoveries in the future. 

As a student of AP bio the work being done in the world of CRISPR gene editing is especially interesting as we recently just finished our unit on molecular genetics which centered around DNA, RNA, and Gene Regulation/Expression, topics that are very relevant to CRISPR technology. Having this background made me more curious as I researched the topic. For example we learned in class that before DNA can be transcribed, helicase needs to “unzip” the DNA, which made me wonder what unzips the DNA so the gRNA can bind to the complementary bases? Does Cas9 unwind the DNA due to its job as the “genetic scissors”? Or is helicase itself involved?

Another question I had connected to what I learned in AP bio was about frame shifts. If CRISPR cuts targeted spots in the genome, then how do researchers prevent frame shifts that could cause totally different proteins to be produced? 

If you know the answer to any of these questions please let me know in the comments!

For People with DMD, the Average Lifespan is 20 years. CRISPR Gives them Hope.

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On April 7, 2025

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DMD stands for Duchenne muscular dystrophy. In short, it is a genetic disorder carried on the X chromosome responsible for improper growth of muscles. DMD is a type of dystrophy, a general term used to describe muscular disorders. In order to thoroughly understand what causes this atrocious malfunction, it is essential to recap what we learned in AP Biology class – particularly mutations.

A frameshift mutation shifts all the bases in an RNA or DNA sequence up or down, caused by an insertion or deletion of a base. As a result, all the codons that should be present are not, as all of them changed by one base down the line of DNA/RNA. So, the protein that the sequence codes for is completely different from what it should be, most often causing complete failure for the protein to function properly. The protein wastes energy being made and could possibly have further adverse effects. Meanwhile, a point mutation is less severe, as it involves the switching of a base for another. It could be harmless, as in silent mutations, where the changed base does not change the amino acid the codon codes for. Or, the point mutation could be missense, changing just one amino acid that may change the protein’s function. Even worse, a nonsense mutation changes the codon from an amino acid to a stop codon, halting the rest of the protein’s production.

Now I didn’t mention all types of mutations for no reason: we don’t waste time here. DMD can be caused by any one of them except the silent mutation, because any change in the dystrophy gene on the X chromosome can cause colossal changes in muscle development. This disorder is significant when it happens extremely early in development, because that’s when it can cause most of the entire body’s muscle cells to develop improperly. Furthermore, frameshift mutations can be absolutely devastating as they often make most muscles in the body trivial in function. 

Previous research has determined the mutation “hotspots” – areas of the dystrophy  gene that are most common to have a mutation. They located precisely the exons (2-10 and 45-55) where this often occurs. Building upon this progressive research, Esra Erkut and Toshifumi Yokota looked into how CRISPR can play a role in alleviating the problem in their paper published in the National Library of Medicine.

Prior to reading this blog post, you have probably heard of CRISPR as a gene editing technology online or elsewhere across this feed. Therefore, I won’t delve too much into the specifics of its function; I will only cover what is necessary and relevant to its implications in DMD.

CRISPR Cas9

CRISPR is able to enter a cell, cut out a gene, and replace it with a different one. It knows where to cut based on an RNA sequence artificially selected for it. In the case of DMD, it is already evident where the CRISPR needs to start and end cutting due to previous findings on the most common mutation locations (note: it is technically cas9 that does the cutting). So, researchers were able to match an RNA sequence to the start of these exons to initiate CRISPR there, and properly end it where they needed to. Afterward, they can insert the proper gene from a patient’s functioning muscle cells or elsewhere. And viola! The muscle cells are back to functioning properly. But not so fast, it’s not that easy. Still, due to the tremendous progress in this area, a clinical trial has been approved by the FDA and is currently in action. So hopefully, if all goes well, the lifespan for patients with DMD will be much closer to the average 77.5 years, over 50 years more than what they are expected to live now.

With all this CRISPR technology rapidly growing in effectiveness and becoming ever more ubiquitous, there are evidently some societal concerns that arise. From choosing the traits of a child to complete human cloning, so many things are possible right now. While cloning is technically illegal, the technology to do it is easily available and someone has probably (secretly) cloned somebody before. This is very creepy to think about, but issues like these are inevitable with technology like this. There is a tradeoff: better healthcare, but more health dilemmas.

I’m curious, a little off topic, but nonetheless, how many clones do you think exist in the world right now due to CRISPR technology?

CRISPR-Cas9: The Future of Genetic Medicine

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On April 7, 2025

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One of the most important discoveries in modern biology is CRISPR-Cas9, which has transformed our ability to precisely edit genes. It was once discovered to be a bacterial immune system, but it has now evolved into a cutting-edge tool that can treat hereditary illnesses that were previously believed to be incurable.

Deoxyribonucleic acid (DNA) orbit

In an interview with biochemist Virginijus Šikšnys, he discusses how CRISPR-Cas9 has made its way from the lab to clinical settings. Šikšnys was one of the authors of the groundbreaking 2012 paper that demonstrated how the Cas9 protein could be used to precisely edit DNA. He and his colleagues showed how Cas9, an efficient genetic modification tool, could be reprogrammed to target and cut any desired DNA sequence, making it an effective genetic modification tool.

What’s incredible is how quickly these discoveries have moved from basic research to real-world treatments. Sickle-cell disease is one of the first illnesses to be treated with CRISPR. This gene-editing technology has already been used to correct mutations in blood cells, offering hope for those suffering from genetic disorders that were previously untreatable.

CAS 4qyz

Despite its success, CRISPR-Cas9 is still evolving everyday. Current treatments are often performed ex vivo, which means that the patient’s cells are removed, altered in a lab, and then returned.. The next step for CRISPR is to be used in vivo, or  directly within the human body. This will require overcoming challenges such as effectively delivering the CRISPR machinery to the right cells and tissues in the body.

CRISPR-Cas9 directly ties into several important topics that we’ve explored in AP Biology, especially those about DNA structure and gene expression. CRISPR relies on our understanding of DNA’s double-helix structure and how the genetic code is stored in nucleotide sequences. This system uses the precise targeting of specific DNA sequences, allowing for gene editing by cutting or modifying the genetic code, which connects to how mutations affect gene function, a concept we’ve studied in gene expression and regulation.  Additionally, CRISPR’s origins in bacteria as an immune system illustrate key ideas from our lessons on prokaryotes and their genetic systems, showing how bacteria store viral DNA to protect themselves from future infections, which is a mechanism that has been repurposed for gene editing in humans.

Cas12a (Cpf1) in complex with crRNA and target DNA

I chose to write about CRISPR because it fascinates me how a discovery meant to protect bacteria from viruses has now become a tool with the potential to cure diseases in humans. The topic of editing genes to treat illnesses like sickle-cell disease or cystic fibrosis makes me feel hopeful for the future of medicine and biology.

Sickle Cell Disease (SCD)

What are your thoughts on the potential of CRISPR to revolutionize medicine? What ethical concerns do you think need to be considered as CRISPR technology advances? What other diseases do you think CRISPR might be used to treat in the future? Leave a comment below!

CRISPR Vision: Editing Typos in DNA for a Clearer Future!

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On April 7, 2025

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Leber Congenital Amaurosis (LCA) is a rare genetic disorder that leads to severe vision loss or blindness from birth or early childhood. It is primarily caused by mutations in the CEP290 gene, which plays a crucial role in the development and function of photoreceptor cells in the retina. These mutations disrupt the gene’s function, leading to impaired photoreceptor cells and resulting in significant vision impairment.​

As we learned in AP Biology, mutations in a single gene can lead to significant changes in protein function, thereby disrupting essential cellular processes. Specifically, protein structure is determined by four levels of organization: primary, secondary, tertiary, and quaternary structures. When a gene mutation alters the sequence of amino acids (primary structure), it can disrupt hydrogen bonding and other interactions that dictate the protein’s folding into alpha-helices and beta-pleated sheets (secondary structure). If the misfolding continues, it affects the overall three-dimensional shape (tertiary structure), which is crucial for the protein’s function. Some proteins also rely on multiple subunits coming together (quaternary structure), and a mutation can prevent proper assembly. These structural disruptions can render a protein nonfunctional or cause it to mislocalize in the cell, leading to diseases. In the case of LCA, mutations in the CEP290 gene lead to the production of a dysfunctional protein, which adversely affects the structure and function of photoreceptor cells in the retina. This disruption impairs the cells’ ability to respond to light, resulting in severe vision loss or blindness. This directly connects to the concept of protein structure-function relationships that we studied, where alterations in the amino acid sequence can profoundly impact the protein’s overall shape and functionality.​

Traditional treatments for LCA have focused on managing symptoms and providing supportive care, such as using visual aids or enrolling in specialized education programs. While these approaches can improve quality of life, they do not address the underlying genetic cause of the disease. However, recent advances in gene editing are offering hope for a more definitive treatment. CRISPR-Cas9, a revolutionary gene-editing tool, has made it possible to target and correct specific mutations responsible for genetic disorders like LCA.​

In a groundbreaking clinical trial known as the BRILLIANCE trial, researchers used CRISPR-Cas9 to edit the CEP290 gene in patients with LCA. This process involved delivering the CRISPR machinery directly into the retinal cells to correct the genetic mutation. The trial included 14 participants, and the results were promising: approximately 79% of participants experienced measurable improvements in vision. These improvements were assessed through various measures, including visual acuity tests and the ability to navigate obstacles under different lighting conditions. Importantly, there were no serious adverse events related to the treatment, indicating a favorable safety profile.

This trial also provided valuable insights into the challenges of gene editing in humans. While the results were encouraging, researchers noted that further studies are needed to optimize dosing, assess long-term efficacy, and determine which patient populations may benefit the most. Additionally, ongoing monitoring is essential to ensure the safety and durability of the treatment effects. ​

Lezeres Szemmutet AR Budai Szemeszeti Kozpont 849

In conclusion, CRISPR technology holds significant potential for treating genetic diseases like Leber Congenital Amaurosis. By directly targeting the underlying genetic mutations, CRISPR-based therapies could offer a more definitive treatment, reducing or eliminating the need for lifelong supportive care. The success of the BRILLIANCE trial paves the way for future gene-editing treatments for a variety of genetic disorders, such as Duchenne muscular dystrophy or sickle cell disease, highlighting how gene editing could be the next frontier in personalized medicine.​

I’m excited about the promise of CRISPR in treating Leber Congenital Amaurosis because it offers real hope for patients who have long faced the challenges of severe vision impairment. I chose to write about this topic because I recently learned about the BRILLIANCE trial and was inspired by the potential of scientific advancements like CRISPR to transform the future of treatment for these patients.

What are your thoughts on CRISPR and its potential to treat Leber Congenital Amaurosis and other genetic diseases? Do you think we’ll see more gene-editing therapies become available in the near future? I’d love to hear your opinions in the comments!

CRISPR Breakthrough: FDA Approves First Gene Therapy for Sickle Cell Disease

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On April 7, 2025

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Gene editing just made history! The FDA just approved Casgevy, the first-ever CRISPR-based gene therapy for sickle cell disease. This is a massive step forward in genetic medicine and brings hope to thousands of people dealing with this painful and life-threatening disorder.

CRISPR logo

Sickle cell disease (SCD) is a genetic blood disorder that messes with hemoglobin, the protein responsible for carrying oxygen in red blood cells. Instead of being round and flexible, the cells become sickle-shaped and get stuck in blood vessels. This leads to extreme pain, organ damage, and a shorter lifespan. Until now, treatment options were pretty limited. The only real cure was a bone marrow transplant, but finding a matched donor is tough.

Sickle cell anemia

Casgevy changes the game by using CRISPR-Cas9 technology to edit a patient’s own bone marrow stem cells. Scientists take these cells, tweak them in a lab to boost fetal hemoglobin production (which helps prevent sickling), and then put them back into the patient. The result? Healthier red blood cells that drastically reduce pain and hospital visits.

This approval is huge for a few reasons. First, it’s basically a functional cure. Early trial results show that most patients treated with Casgevy are almost symptom-free afterward. Second, it removes the need for a donor, unlike traditional bone marrow transplants, which lowers the risk of rejection. And finally, it sets the stage for future CRISPR-based treatments for genetic diseases like cystic fibrosis and muscular dystrophy.

Even though this approval is a big deal, CRISPR research is still pushing forward. Scientists are working on making gene editing even safer and more precise. There are still ethical concerns, especially about who will have access to these treatments and what the long-term effects might be. But one thing is clear: this is just the beginning of a whole new era in medicine.

This connects directly to AP Bio’s Unit 6: Gene Expression and Regulation. In this unit, we learn how DNA controls protein production through processes like transcription and translation. CRISPR takes that concept to another level by directly editing DNA to change how genes are expressed. Understanding how this works gives us a deeper look at how cells function and how we might one day treat even more genetic diseases. The science we’re learning in class isn’t just theoretical—it’s shaping the future of medicine in real-time.

When I read about the FDA’s approval of Casgevy, the first CRISPR-based therapy for sickle cell disease, and it totally blew my mind! It’s amazing to think that gene editing can actually go into someone’s DNA, change it, and potentially cure a genetic disorder that’s been around for centuries. I always thought genetic diseases were something we just had to manage, but this shows that we might be able to change them at the molecular level. It’s honestly so cool to see science moving in this direction, where we can directly alter genetic codes to improve health outcomes.

It makes me wonder: Could we use this technology to treat other genetic diseases, even ones that are currently considered untreatable? And what could the long-term effects be of altering someone’s genes in such a precise way? Could this be a step toward eradicating certain genetic disorders entirely, or will there be challenges we haven’t even thought of yet? It’s exciting, but it also leaves me wondering what the ethical and practical limits might be for gene editing in humans.

What do you think—could CRISPR-based therapies like Casgevy eventually become a routine treatment for other genetic diseases, or do you think there are too many risks and ethical questions to consider before it becomes widely used?

CRISPR Gene Editing Disables Key Herpes Virus Genes

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A new study, has introduced a promising new application for gene drives—this time, targeting viruses instead of insects. The researchers developed a CRISPR-based gene drive system that spreads through herpes simplex virus type 1 (HSV-1), potentially opening the door to a future treatment or even a cure, researchers report in Nature Communications.

Herpes Simplex Virus Type 1: Procapsid and Mature Capsid

3D model of herpes simplex virus type 1 (HSV-1)

 

Gene drives are designed to copy and spread specific genetic information through a population. In this case, scientists engineered a gene drive virus that could insert itself into the genome of other herpes viruses during co-infection. They tested this in mice by introducing a standard HSV-1 virus that glows yellow and a gene drive virus marked with red fluorescence. Within four days, nearly 90% of the viruses in certain tissues were replaced by the gene drive version, confirming that it had successfully spread between viruses inside the body.

Most notably, the gene drive spread to latent HSV-1 already hiding in the neurons of previously infected mice. This is a major breakthrough since herpes viruses are known for their ability to become dormant and evade treatment. Existing antiviral medications can only suppress symptoms—they can’t eliminate the virus. A gene drive that targets latent infections could change that.

The system works by using CRISPR to cut the virus’s genome and insert its own DNA, essentially rewriting it. In this study, the gene drive targeted UL23, a gene that helps HSV evade the host immune system. Disabling UL23 and replacing it with a red fluorescent marker made the virus easier to track and less virulent.

The schematic diagram of CRISPR-Cas9

Cas9, guided by a complementary RNA strand (sgRNA), binds to the target DNA sequence and makes a precise double-stranded cut, disabling the viral gene.

While this technology is still in early stages, the results show that viral gene drives can work in mammals and may one day be used to treat chronic infections. However, safety concerns remain—researchers must prevent resistance, off-target effects, and unintended spread to others. Future versions will need to be made safer and more controlled before clinical testing.

This article connects to what we’ve learned in AP Biology about transcription, complementary base pairing, and CRISPR gene editing mechanisms. Researchers created guide RNAs (gRNAs) that are complementary to essential HSV genes, UL8 and UL29. These gRNAs were made through in vitro transcription, in which RNA polymerase reads a DNA template strand 3’ to 5’ and builds an RNA strand 5’ to 3’ with matching bases. The gRNAs were then packaged into lipid nanoparticles and delivered into infected neurons. Once inside, each gRNA binds to a Cas9 protein, forming a CRISPR-Cas9 complex that searches for matching viral DNA sequences via base pairing—similar to how tRNA anticodons pair with mRNA codons during translation.

When the gRNA finds a matching sequence in the viral DNA, the Cas9 enzyme makes a double-stranded cut at that site. The host cell attempts to repair the break using non-homologous end joining (NHEJ), an error-prone mechanism that often results in insertions or deletions—leading to frameshift mutations that disrupt the gene’s reading frame. These mutations render the targeted viral genes nonfunctional. Since UL8 and UL29 are essential for HSV replication and reactivation, the virus is effectively disabled. This demonstrates how scientists can use complementary RNAs to target and silence specific genes by inducing disruptive mutations, showing that gene expression can be permanently shut down through physical edits to the DNA itself.

I find it fascinating how genes can be edited to serve a specific purpose, especially in targeting and disabling viruses. I think CRISPR technology has the potential to completely transform the way we approach treatment for persistent infections like HSV-1. What do you think about this mechanism? Do you believe CRISPR is an ethical tool with the potential to benefit human health? Leave a comment sharing your thoughts!

Disease Prevention and Containment With CRISPR

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Mosquito CRISPR gene-editing technology has transformed the way scientists approach disease prevention  with one of the best applications being the modification of mosquito DNA to combat the spread of deadly infections. Mosquitoes are the primary carriers of diseases such as malaria, dengue fever, and Zika virus, which affect millions of people each year in continents like Africa and Asia. Traditional methods of mosquito control such as pesticides and bed nets have had some success but are limited by environmental concerns and the ability of mosquitoes to develop resistance. CRISPR presents an innovative alternative by allowing researchers to precisely edit mosquito genes to reduce their ability to transmit diseases.

One of the most significant breakthroughs in this field involves the use of CRISPR to make mosquitoes resistant to the malaria parasite. Researchers have modified the DNA of Anopheles mosquitoes so that they are unable to carry Plasmodium, the parasite responsible for malaria. Without a suitable host, the parasite cannot spread to humans, effectively cutting off one of the major transmission routes. Similarly, scientists have also explored using CRISPR to sterilize male mosquitoes, which do not bite humans but are essential for reproduction. By releasing genetically modified sterile males into the wild, mosquito populations can be reduced over time, lowering disease transmission rates without relying on chemical insecticides. Another powerful strategy involves gene drives, a method that ensures an edited gene is passed down to nearly 100% of offspring. This allows beneficial genetic modifications to spread rapidly through an entire population of mosquitoes, enhancing disease resistance or reducing reproductive rates with long-lasting effects. Also, recent studies have displayed the effectiveness of these approaches in controlled environments. A study conducted at the Imperial College London showed that gene drive technology successfully eliminated a malaria carrying mosquito population in laboratory trials. Another study published by the National Institutes of Health highlighted the potential for CRISPR to be used in controlling other mosquito-borne diseases, including dengue and Zika, by altering mosquito immune responses to viruses. Despite these promising results, there are concerns regarding the ecological impact of releasing genetically modified mosquitoes into the wild. Some scientists worry about unintended consequences, such as disrupting ecosystems or causing unforeseen mutations. Public acceptance and regulatory approval also remain significant hurdles, as widespread use of CRISPR-modified organisms requires careful risk assessment and ethical considerations.

CRISPR-based mosquito modification connects to AP Biology through gene regulation, specifically acetylation and methylation which can control whether a gene is turned on or off. Acetylation loosens DNA, making genes less likely to activate. On the other hand methylation silences them by tightening the DNA strands that code for the specific genes. Similarly scientists can use similar mechanisms to control genes in mosquitoes, either activating ones that prevent malaria transmission or silencing those that help the parasite survive. By altering these genetic switches, CRISPR ensures that the modifications can be passed down through generations, changing inheritance patterns and affecting population dynamics to help reduce disease spread.

 

While challenges remain, CRISPR-based mosquito modification represents a revolutionary step in global disease prevention. If successfully implemented, this technology could significantly reduce reliance on chemical insecticides and vaccines, offering a sustainable solution to controlling mosquito-borne illnesses. As research progresses, scientists continue to refine these approaches to ensure they are both effective and ecologically responsible. With further advancements, CRISPR has the potential to reshape public health strategies and provide a powerful tool in the fight against some of the world’s most persistent diseases.

 

How CRISPR is Changing the Way We Treat Illness

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Introduction: Imagine a world where genetic diseases like sickle cell disease (SCD) are no longer a life sentence. Recent advancements in gene editing, particularly using CRISPR technology, are turning this vision into reality. As an AP Biology student fascinated by genetics, I was captivated by a groundbreaking therapy that utilizes CRISPR to treat SCD, a condition we’ve explored in our studies on genetic mutations and their physiological impacts.

 

Summary of Main Research Article:

 

A recent article titled “Cutting Edge Gene Therapy” discusses the development and approval of Cassava, a CRISPR-based gene therapy for individuals suffering from sickle cell disease (SCD) and transfusion-dependent beta-thalassemia (TDT). Researchers discovered that higher levels of fetal hemoglobin (HbF), which has a higher oxygen affinity than adult hemoglobin, can alleviate symptoms of these diseases. Casgevy works by editing blood-forming stem cells to promote HbF production, thereby reducing the impact of SCD and TDT. Clinical trials indicated that 93.5% of SCD patients did not experience pain crises for at least a year post-infusion. Notably, this therapy became the first CRISPR-based treatment to obtain FDA approval in December 2023. 

Orginal Article: https://time.com/7094725/vertex-pharmaceuticals-and-crispr-therapeutics-casgevy/

Additional Resources:

 

  1. Innovative Genomics Institute: CRISPR Clinical Trials Update https://innovativegenomics.org/news/crispr-clinical-trials-2024/

 Provides an overview of ongoing CRISPR clinical trials and their implications.

 

  1. Nature: CRISPR genome-editing grows up https://www.nature.com/articles/d41586-024-04102-w

 Discusses the maturation of gene-editing technologies for treating various disorders.

 

Connection to AP Biology:

 

In our AP Biology curriculum, we’ve studied the central dogma of molecular biology, which describes the flow of genetic information from DNA to RNA to protein. Sickle cell disease is caused by a point mutation in the β-globin gene, leading to the production of abnormal hemoglobin S. This mutation results in red blood cells adopting a sickle shape, causing blockages in blood vessels and leading to pain and organ damage. The CRISPR-based therapy directly relates to our discussions on gene expression and mutation impacts, as it involves editing the genome to reactivate the production of fetal hemoglobin (HbF), which can compensate for the defective adult hemoglobin. This therapeutic approach exemplifies the practical applications of our understanding of gene regulation and expression.

 

Personal Reflection:

 

The potential of CRISPR to cure genetic diseases is both exciting and thought-provoking. Learning about Chevys success in treating SCD patients without pain crises for extended periods is inspiring. However, it also raises questions about accessibility and long-term effects. How can we ensure that such groundbreaking treatments are available to all who need them? What ethical considerations should guide the application of gene editing in humans? I’d love to hear your thoughts on these issues.

 

Tags: CRISPR, gene editing, sickle cell disease, gene therapy, fetal hemoglobin

 

Images:

< Diagram explaining steps behind simple CRISPR-based diagnostics

 

This figure shows how CRISPR can be used for quick diagnostics in addition to gene editing. Scientists can develop extremely sensitive, field-deployable diagnostic assays by employing CRISPR proteins to identify particular viral or bacterial DNA sequences. Even though I wrote a piece about gene therapy, this demonstrates how CRISPR technology has many uses outside of medicine and is changing the way we identify illness.

 

 

 

CAS 4qyz

 

The Cas9 protein, the molecular “scissors” in CRISPR systems, is depicted in this 3D model. Cas9 finds and cuts specific DNA sequences under the guidance of RNA, allowing for accurate modifications. The physical complexity of this protein reminds me that even the tools we use to rewrite DNA are themselves the result of evolution — making CRISPR a case of biology editing biology.

 

CRISPR-Cas9

 

This picture explains the CRISPR-Cas9 mechanism: a guide RNA (gRNA) directs the Cas9 protein to a particular DNA sequence, where it chops the strand. After that, the cell fixes the damage, either causing the gene to malfunction or enabling researchers to introduce a corrected form. It helps connect what we study in class with actual medical advancements and effectively illustrates the mechanism underlying treatments like Casgevy.

 

How CRISPR-Cas12a is Changing Medical Research

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Gene editing technology has evolved dramatically over the past decade and the latest advancement from Yale University is set to revolutionize how we approach disease modeling and genetic research. The newly developed CRISPR-Cas12a tool enhances the capabilities of the traditional CRISPR-Cas9 system, offering the ability to assess the impact of multiple genetic changes simultaneously. This innovation could greatly accelerate medical research and therapeutic developments.

The schematic diagram of CRISPR-Cas9

The traditional CRISPR-Cas9 system, which has been a fundamental tool in genetic engineering, uses a guide RNA to target and modify specific DNA sequences. In the CRISPR system, “spacer” sequences are transcribed into short RNA sequences known as CRISPR RNAs that guide the system to specific DNA sequences. Once the target DNA is located, the Cas9 enzyme, produced by the CRISPR system, binds to the DNA and cuts it, effectively silencing the targeted gene. Alternatively, by using modified versions of Cas9, researchers can activate gene expression instead of cutting the DNA. These methods allow researchers to study the gene’s function.

In AP Biology, we recently learned about transcription, gene expression, and gene regulation. Just as transcription factors in eukaryotic cells help initiate and regulate the transcription of DNA into RNA, the CRISPR system uses crRNAs to identify and modify specific DNA sequences, showcasing a direct application of these biological principles in advanced genetic engineering. Both transcription factors and CRISPR systems achieve their targeted function by recognizing specific DNA sequences through RNA interaction.

However, CRISPR/Cas9’s application is somewhat limited, as it can only modify one gene sequence at a time. Also, when CRISPR/Cas9 is applied directly to embryos, it’s not possible to selectively choose the genetic changes, making it difficult to ensure the desired modifications are made without unwanted mutations. The recent breakthrough by Yale’s research team has culminated in the development of CRISPR-Cas12a, which can target multiple genes at once and assess their collective interactions in disease processes. This capability to edit multiple genes simultaneously enhances the effectiveness of “Crispants,” a method for rapidly knocking out genes by targeting several loci at once in the F0 generation of animals. This technique significantly accelerates early validation in preclinical studies, providing a quicker way to evaluate therapeutic hypotheses.

In our AP Biology course, we learned that the F0 generation refers to the first generation of offspring in a genetic study, which is crucial for observing initial traits and mutations.

Yale researchers have used this technology to develop advanced mouse models that mimic human immune responses more accurately, allowing for a better understanding of complex genetic interactions in diseases like lung cancer, skin cancer, and various metabolic and autoimmune diseases.

I find it interesting that new advances are being made that will hopefully lead to improvements in healthcare treatments in the future. Personally, I was diagnosed with autoimmune hepatitis this year, and my mom has hashimotos. I know its very common for women to get these autoimmune diseases and I hope the future of science and healthcare will allow for earlier detection, prevention, and care.

Have you heard about CRISPR before this blog post? Are you interested to see the advancements that can be made in the future and how they may impact you and future generations?

Is There Anything Else out There?

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Throughout the whole year, we have learned of the importance of protein molecules. Of course, enzymes are proteins. Enzymes catalyze our biochemical reactions. In addition, we have recently learned how nucleosomes (Adenine, Guanine, Thymine, and Cytosine) are integral pieces of nucleotides and, by extension, DNA and DNA replication.

Given this information, the finding of 16 out of 20 of the amino acids–building blocks of protein–that are used by organisms on earth and all four nucleosomes is very interesting.

These discoveries were the handy work of NASA. In 2016, NASA OSIRIS-REx, a robotic probe, traveled to the asteroid Bennu to collect data. It is believed that Bennu was once a part of larger asteroid. Bennu’s parent object, as it referred to as, was once a huge cluster of ice and rock. Radioactive elements, eventually, led to the ice melting. The resulting mix of water and rock provided the necessary conditions for ammonia and other compounds to turn into nucleobases.

In September of 2023, the probe arrived back on earth. NASA scientists were analyzing its sample for some time as only a few months ago in January did they release their findings.

Certainly, these findings are of particular note as they may provide insight as to how life originally developed. In the words of Mark Schneegurt, a scientist at Wichita State, “there could hardly be any study more important to our understanding of the origins of life in the solar system.”

Also of interest, many other asteroids have to similar conditions to that of Bennu’s parent body. For example, Ceres and Enceladus also have the same water, rock conditions.

Thus the question is asked: Is there other life in our universe?

Article

CRISPR Gene Editing can have Unwanted Effects

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A group of researchers at the University of Zurich have completed a study to test whether CRISPR gene editing technology can be used to correct the DNA sequence error in people with chronic granulomatous, a rare genetic disease that causes white blood cells to be unable to kill certain pathogens. They found that the technology was successfully able to insert the two nitrogenous bases, that are missing in people with this disease, into the DNA sequence. While this process was successful, they also found that, at the same time, it caused further damage to the DNA. 

After performing the gene editing process, the scientists found new defects in the newly repaired cells. In certain cells, the entire section of the DNA where the editing took place was missing. This is due to the NCF1 gene and its characteristics. It shows up three times in the DNA; once as an active gene, and twice as pseudogenes, which are sections of DNA that resemble active genes but are in fact nonfunctional. The CRISPR technology cannot distinguish between the two versions of the gene and therefore ends up editing multiple portions of the DNA, resulting in gene segments being misaligned or missing. The consequences of such errors are still not fully understood and can be unpredictable. Therefore medical professionals are hesitant to use this method of treatment for chronic granulomatous disease. Other research teams have continued this work to find a safer method of treatment using CRISPR. Do you think that CRISPR should be used to cure diseases like chronic granulomatous despite possible risks? 

DNA Structure+Key+Labelled.pn NoBB

Model of DNA Structure

This connects to the AP Biology subjects of DNA structure and function. The CRISPR technology performs edits to DNA sequences such as adding or removing certain nitrogenous bases, which is closely related to DNA structure. It also relates to DNA function as changing the sequence of the DNA will alter what the DNA codes for. This changes how certain portions of DNA affect cell processes by, for example, producing different proteins.

How CRISPR is Supercharging Crops

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Scientists at the Carl R. Woese Institute for Genomic Biology at the University of Illinois have made a breakthrough using CRISPR/Cas9 to enhance gene expression in rice by altering its upstream regulatory DNA. This approach increases photosynthetic efficiency and could lead to major advances in sustainable agriculture.

Usually, CRISPR is used to knock out genes, but this research boosts gene expression instead. The team focused on a gene called PsbS, which plays a key role in photoprotection (helping plants balance light absorption for efficient energy use). By flipping the regulatory DNA upstream of the gene, they triggered a significant increase in its expression. This method left most other genes unchanged, minimizing unintended effects.

Rice provides 20% of the world’s calories, so even small improvements in its growth efficiency could have large global impacts. Unlike genetically modified crops, this method does not introduce foreign DNA, which eases regulatory concerns and making adoption by farmers faster.

In AP Biology, we learn that gene regulation occurs at the transcriptional level and also after transcription, which means that modifications to promoters, enhancers, and silencers can directly affect gene activity. This research aligns with the concept of epigenetic regulation, which refers to changes in gene expression that don’t involve altering the DNA sequence itself. The CRISPR-based strategy used in this study is an example of how epigenetic mechanisms can be used to modify plant traits without changing the plant’s DNA structure, which makes this method valuable for sustainable agriculture.

Additionally, this research illustrates how photosynthesis itself is a complex process involving both light-dependent and light-independent reactions. The CRISPR modification indirectly boosts photosynthetic efficiency by enhancing a plant’s ability to handle the absorption of light, preventing damage to the photosystem and ultimately improving the plant’s growth and productivity. The role of light in photosynthesis is a core principle in AP Biology, and this research builds on that by demonstrating how plant genes can be modified to enhance energy efficiency.

This discovery opens the door for future applications in climate-resistant crops, higher-yield wheat, and drought-tolerant corn. Scientists are already exploring ways to apply similar CRISPR-based enhancements to other frequently used crops, such as maize and soybeans.

I’d be open to eating CRISPR-edited rice since it enhances natural genes without adding foreign DNA. This research interests me because it connects to what I’ve learned in AP Biology about gene regulation and photosynthesis. I think focusing on modifying existing genes is a smart way to improve crops while avoiding GMO concerns.

Would you eat CRISPR-edited rice? Should scientists focus on enhancing natural genes instead of adding foreign DNA?

Green rice sheaves planted in a paddy field with long shadows at golden hour in Don Det Laos Rice can come in brown, white, red, and black colour.

Rewriting Cancer’s Script

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On April 7, 2025

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Imagine a film editor taking raw footage and cutting scenes to create entirely different movies while using all the same raw materials. This is remarkably similar to how cells process RNA, selectively splicing together different segments to produce various proteins from a single gene. This fine-tuned control is essential for normal cellular function, but when cancer hijacks this system, it rewrites the script for its own survival. A groundbreaking study from The Jackson Laboratory (JAX) and UConn Health, published in Nature Communications, reveals how cancer manipulates RNA splicing and introduces a potential therapy that could disrupt its deadly strategy.

In a recent study, scientists not only show how cancer hijacks this tightly regulated splicing and rearranging of RNA but also introduce a potential restorative strategy that could slow or even shrink aggressive and hard-to-treat tumors. In healthy cells, RNA splicing ensures that the right proteins are made at the right time as it removes all the introns and joins the exons back together. A key player in this process is poison exons, which are genetic elements that contain a premature termination codon targeting certain transcripts for decay, decreasing the amount of protein produced. This mechanism prevents excessive or harmful protein production. However, cancer cells have found a way to suppress these poison exons, particularly in the TRA2β gene. The study found that when poison exons are excluded from TRA2β RNA, the resulting protein accumulates, leading to uncontrolled tumor growth. Moreover, researchers observed that lower poison exon inclusion in TRA2β correlates with poor patient outcomes in aggressive cancers such as triple-negative breast cancer, brain tumors, and leukemia.

To counteract this, scientists experimented with antisense oligonucleotides (ASOs), synthetic RNA fragments designed Poison exonto force poison exon inclusion back into TRA2β RNA. By reactivating the gene’s kill switch, ASOs restored the cell’s ability to degrade excess TRA2β RNA and slow tumor progression. Interestingly, when researchers used CRISPR gene editing to remove the TRA2β protein entirely, tumor growth persisted. This suggests that targeting the RNA rather than the protein itself could be a more effective treatment strategy. Furthermore, preliminary results indicate that ASOs are highly specific and do not interfere with normal cell functions, making them promising candidates for future cancer therapies.

This study connects with what we’ve learned in AP Biology about gene expression regulation and alternative RNA splicing. In class, we discussed how alternative RNA splicing is part of how gene activity is controlled in eukaryotes. This gene regulation mechanism is part of RNA processing, which is right after transcription but before translation to make multiple types of proteins from the same RNA by ordering the exons differently. This research on the use of RNA splicing with poison exons to help mitigate tumor growth is a great example of how important a single stage of gene regulation can be. Beyond its scientific significance, this research is personally fascinating because it offers a glimpse into the future of cancer treatment. Traditional therapies like chemotherapy and radiation often come with severe side effects due to their inability to distinguish between healthy and cancerous cells. In contrast, ASOs offer a more targeted approach, potentially leading to treatments that are not only more effective but also less harmful. What do you think? Could ASOs revolutionize cancer treatment as we know it?

New CRISPR Technology Can ‘Press Pause’ on Specific Genes

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Scientists have discovered a new version of CRISPR that is reversible rather than permanent.

This new genetic tool is known as the IV-A CRISPR system. Traditional CRISPR technology works by producing short RNA strands that help the system locate matching DNA sequences. Then, when the target DNA is identified, the Cas9 enzyme binds to it and cuts, disabling the gene. IV-A CRISPR disables the gene without cutting the DNA by continuously influencing it. This system temporarily turns off genes, offering greater control. For example, researchers could turn off a gene and later turn it back on to see the effect it has.

The schematic diagram of CRISPR-Cas9

Diagram of Cas9 enzyme

Looking ahead, Pausch and his team plan to study how CRISPR molecules change while silencing genes, then explore medical applications. The system could enable precise genome editing, temporary gene expression control, or modify epigenetics, changes in gene function that do not involve changing the DNA sequence. Further research and discovery could lead to huge benefits for both medicine and agriculture. I think that it is amazing the range of possibilities that this technology could have for society but I also wonder about potential controversies that could arise. What do you think? If you have any thoughts that you would like to share please write them in the comments!

This relates to the AP biology topic of genetics. It relates to what we have learned about RNA and DNA. mRNA is made from DNA through transcription and then it is used to make proteins. For CRISPR, they use another kind of RNA in a completely different way. They use it to find a matching DNA sequence rather than code for a protein. It also relates to what we have learned about gene regulation. Both traditional CRISPR technology and IV-A CRISPR are essentially repressing for the gene by influencing the DNA, impacting transcription.

Poison Exons May be the Key to Reactivate Cancer’s Molecular ‘Kill Switch’

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On April 7, 2025

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In a study published in Science Daily, researchers from The Jackson Laboratory (JAX) and UConn Health have uncovered a crucial mechanism that cancer cells use to avoid the body’s natural defenses. They have identified a potential therapeutic approach that could slow, or even shrink, aggressive and hard-to-treat tumors. This discovery could be a critical for cancers such as triple-negative breast cancer and certain brain tumors, where current treatment options remain limited.

A crucial finding of the research examines genetic elements called poison exons. In healthy cells, poison exons regulate the levels of key proteins by triggering the destruction of RNA messages before they can be translated into harmful proteins. This process ensures that cellular processes remain tightly controlled.
In AP biology we learned that RNA splicing plays a critical role in gene regulation. It occurs in the nucleus of eukaryotic cells during RNA processing. It is a crucial process where introns are removed from mRNA transcripts, and coding regions exons are joined together to form mature mRNA, enabling protein synthesis.

However, in cancer cells, this critical safeguard is often suppressed. The research team, led by Olga Anczuków, an associate professor at JAX, discovered that cancer cells suppress poison exon activity in a key gene called TRA2β. As a result, TRA2β protein levels rise which causes tumor growth and proliferation. According to the National Library of Medicine, Tra2β protein is a splicing activator. “It binds to exons to regulate their alternative splicing inclusion.”

By analyzing data from various cancer types, the researchers uncovered a correlation between poison exon activity and patient outcomes. “We’ve shown for the first time that low levels of poison exon inclusion in the TRA2β gene are associated with poor outcomes in many different cancer types, especially in aggressive and difficult-to-treat cancers,” said Anczuków. This pattern was observed in cancers such as breast, brain, ovarian, skin, leukemia, and colorectal cancer.

Understanding how cancer suppresses poison exons was the first step. The research team then explored whether they could restore poison exon function and reactivate the natural “off” switch for the gene expression. They found Antisense oligonucleotides (ASOs) to be a possible solution. ASO’s are synthetic RNA fragments designed to increase poison exon inclusion. In an article from PubMed Central researchers Haoyu Xiong, Rakesh N Veedu, and Sarah D Diermeier, found that “oligonucleotide therapeutics are an emerging drug modality, which consists of modified or unmodified short nucleic acid molecules, and includes antisense oligonucleotides. The mechanism of action of oligonucleotide therapeutics mainly relies on Watson–Crick base pairing to targeted mRNAs, resulting in either gene silencing, a steric block, or altered splicing patterns, with the exception of aptamers, which recognize their targets by their three-dimensional structures”

When ASOs were introduced into cancer cells, they successfully tricked the cells into turning off their own growth signals by boosting poison exon inclusion. This, in turn, restored the body’s ability to degrade excess TRA2β RNA and slow tumor progression. “We found that ASOs can rapidly boost poison exon inclusion, essentially tricking the cancer cell into turning off its own growth signals,” explained Nathan Leclair, an MD/PhD graduate student at UConn Health and The Jackson Laboratory.

One of the study’s most interesting findings was that completely removing TRA2β proteins using CRISPR gene editing did not stop tumor growth. This suggests that targeting the RNA instead of the protein may be a more effective strategy.

The schematic diagram of CRISPR-Cas9
While further studies are needed to refine ASO based therapies and explore their delivery to tumors, early results are promising. Preliminary data indicate that ASOs are highly specific, targeting cancerous cells without interfering with normal cellular function. This precision could make ASOs a highly effective and less toxic alternative to current treatments.

The discovery of how poison exons regulate cancer cell growth and how ASOs can be used to restore this natural defense opens the door to a new era of targeted cancer treatments. With continued research and clinical development, this approach may soon transform how we combat some of the deadliest forms of cancer. What do you think about this approach? Could RNA-targeted treatments change the future of medicine?

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