BioQuakes

AP Biology class blog for discussing current research in Biology

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CRISPR Gene Editing Provides Hope for Patients on Transplant List

Do you know anyone who has needed an organ transplant? Hopefully, the answer is no. However, many medical dramas on television have shown us the awful process patients go through when waiting on a transplant list for a heart, lung, kidney, etc.

For years, scientists have experienced many trials and errors. They explored pig parts and ways to supplement them as human organs. However, a huge advancement in gene editing has just reinstated hope for many suffering patients.  On March 16th, Richard Slayman received a pig kidney. He had type two diabetes and had been on dialysis. He had a transplant several years ago, but the organ showed signs of failure. Doctor Winfred Williams explained that Slay would not have survived if he had to wait another five years for a human kidney transplant.

National Guard Kidney Transplant 099

Eventually, the idea was proposed for Slayman to receive a genetically engineered pig kidney from eGenesis, a biotechnology company.  Their goal is to generate human-compatible organs that can be used in transplants. In Slayman’s case, this kidney had been genetically altered 69 times using the CRISPR-Cas9 gene editing system, which allows certain parts of a genome to be removed or even added. Slayman’s new kidney was made suitable for him in a very meticulous way. Firstly, three genes that are typically found in pigs that attack human immune systems were removed. These were genes that code for the synthesis of certain carbohydrates. Additionally, seven human genes were added to the genome that prevent an immune response that may lead to transplant rejection. Certain pig viruses were also removed as they pose a harm to humans.

This is very relevant to one of our last AP Biology units. We just learned about mRNA processing. This step occurs following mRNA transciption, with the goal of making certain proteins. After the nitrogenous bases are transcrribed from template DNA, the mRNA is processed in several ways. A Guanine cap is added to the front of the strand and a Poly-A tail is added to the end. Additionally, parts of the mRNA are cut out. In CRISPR editing, this same process is done by scientists artificially, rather than our natural processes. The parts of mRNA that are cut out that will not make a protein are called introns, while the kept parts of mRNA are called exons. mRNA splicing can also take place where different combinations of bases are organized to make certain amino acid chains.

4.5. The CRISPR Cas 9 system as a laboratory tool

This new advancement will not only help patients receive new organ quicker, but it is the doctors’ hope that this will solve a larger cultural issue, in that ethnic minorities often struggle to receive organ transplants. This new process will hopefully benefit the healthcare system both medically and culturally.

Unlocking Cancer’s Secrets: The Power of CRISPR

Is there a cure for cancer? 

MIT researchers have developed a novel technique using prime editing, a variant of CRISPR genome-editing, to screen thousands of mutations in cancer genes, such as the tumor suppressor gene p53, more efficiently. This method allows for the identification of harmful mutations previously overlooked, shedding light on their role in tumor development and response to treatment. Unlike previous approaches, which introduced artificial versions of mutant genes, this technique edits the genome directly, providing more accurate insights into mutation effects.

Breast cancer cell (2)

The researchers demonstrated the effectiveness of their approach by examining over 1,000 mutations in the p53 gene found in cancer patients, revealing previously unknown harmful mutations. By enabling the generation of various mutations seen in cancer patients and testing their response to therapy, this technique holds promise for precision medicine, potentially revolutionizing cancer treatment strategies. With further exploration into other cancer-linked genes, the researchers aim to uncover new therapeutic targets and eventually personalize cancer therapies based on individual genetic makeup, marking a significant advancement in cancer research and treatment.

In AP Bio’s Unit 6 on Cell Cycle and Mendelian Genetics, we briefly touched upon the topic of cancer, but I found myself captivated and eager to delve further into its complexities and implications. In learning about cancer, I discovered that its development stems from cells breaking free of normal controls, leading to unregulated division and tumor formation. Unlike normal cells, cancer cells disregard signals that regulate division, perpetuating their growth indefinitely. Furthermore, cancer spreads through a process called metastasis, where tumors manipulate blood vessels to obtain nutrients and travel to distant parts of the body, contributing significantly to cancer-related deaths. Treatments target the diverse population of cancer cells, aiming to eliminate them; however, the high mutation rate often leads to drug resistance and tumor recurrence.

Growing up, I heard stories of my family’s experiences with cancer, especially the loss of my mother’s birth father to a rare liver cancer when she was just a child. His passing at such a young age left an indelible mark on our family. Unfortunately, his story isn’t the only one. Cancer has touched other members of my family too, reminding me of the importance of understanding this disease. Instead of feeling weighed down by sadness, I’ve chosen to embrace curiosity and become proactive in learning about cancer. It’s my way of honoring their memories and empowering myself to make a difference. As I prepare for college this Fall, I’ve been reflecting on my career aspirations. My goal is to make a meaningful and purposeful impact in the field of medicine, so I’ve decided to pursue a career in nursing. This path resonates with me as it aligns with my passion for helping others and allows me to realize my professional ambitions.

The innovative technique developed by MIT researchers, along with my personal journey, has inspired me to join the fight against cancer. With a newfound understanding and determination, I eagerly look forward to pursuing a nursing career, driven by the belief that every effort contributes to better treatments and outcomes for those impacted by cancer.What’s your take on CRISPR genome-editing? Share your thoughts or any interesting facts you know!

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

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

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

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

A Future without Dialysis? Oink-credible!

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

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

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

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

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

**Used Grammarly as a tool***

CRISPR Gene Editing: The Key to Pharmaceutical Development

Sickle Cell Anemia

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

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

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

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

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

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

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

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

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

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

Unraveling Genetic Secrets: CRISPR’s Dance with p53 and Cancer

An article titled, New findings on the link between CRISPR gene-editing and mutated cancer cells, discusses how researchers at Karolinska Institutet in Sweden have discovered that during gene editing with the CRISPR technique (Clustered Regularly Interspaced Short Palindromic Repeats). CRISPR is a component of bacterial immune systems that can break DNA and has been repurposed as a tool for gene editing. During this process, they discovered a protein called p53, which protects cells from DNA damage and gets activated. However, cells with mutated p53 have an advantage in surviving this process, which can lead to cancer.

P53 Schematic

This relates to Unit 7, Molecular Genetics, in AP Biology because we learned about how genes mutate. Gene mutation refers to a change in the nucleotide sequence of a gene. The researchers’ discovery shows how genes mutate, specifically the p52, and how that can interact with the CRISPR technique. 

Furthermore, the study shows that by temporarily inhibiting p53 could minimize the buildup of mutated cells while keeping CRISPR’s efficiency intact. With this research, scientist are on the right path to creating more specific cancer treatments in the future.

Additionally, researchers discovered a network of genes associated with p53 mutations, which contribute to cell enrichment. However, temporarily blocking p53 can reduce this enrichment. The study created CRISPR experiments on isolated cells and examined a database. More study is needed to determine the scope of this problem in healthcare settings. Several research organizations funded the study.

The CRISPR technique for gene editing is beneficial to my own life as I have many family members who have battled cancer. It is extremely discouraging to watch, especially since there is no cure; however, with this technique, I am hopeful that the future will bring advancements to cancer treatment and hopefully one day put an end to the disease. SO, who else is excited to see how far in cancer studies the CRISPR technique can take us?

Dark Side of the CRISPR

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

The Promise and Danger of CRISPR

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

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

Ethics.jpg
CC BY 2.0, Link

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

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

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

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

 

 

New Technology Can Detect Cancer Using Blood Samples

With over 150,000 diagnoses per year, cancer is the leading cause of illness and death in Australia. Cancers in organs such as the liver and kidneys often require surgery for a diagnosis, however, researchers have recently created a device to diagnose cancer that does not require invasive biopsy surgeries.

biopsy can take many different forms. Some examples include a needle biopsy, the most general type, which is when a small needle is inserted into the skin to collect cells or fluid. An image-guided biopsy can include an x-ray, MRI, or ultrasound. A surgical biopsy is a surgery that includes making an incision in the skin in order to remove suspicious tissue. The complexity of the surgery varies depending on the the part of the body. Biopsies can be difficult for many reasons such as the price, the amount of risk, its consuming of time, and the possibility of bad side effects; however before this new method was finalized, they were necessary for a definite diagnosis and effective treatment.

Scientists have created a device called the Static Droplet Microfluidic device, which identifies the metabolic signature of cancer cells to identify ones that have broken away from a tumor and entered the bloodstream. Professor Warkiani states that the device has 38,400 chambers, which are capable of classifying the tumor cells, making it easier to distinguish a single cancer cell among billions of normal blood cells. This device is also crucial in discovering metastasis, which is when cancer cells travel through the blood and grow in different parts of the body. Metastasis leads to 90% of cancer-related deaths.

Diagram showing cancer cells spreading into the blood stream CRUK 448.svg
By <a href=”//commons.wikimedia.org/wiki/User:Cancer_Research_UK_uploader” title=”User:Cancer Research UK uploader”>Cancer Research UK uploader</a> – <span class=”int-own-work” lang=”en”>Own work</span>, CC BY-SA 4.0, Link

As learned in AP Biology, cancer cells are created when a cell loses its ability to regulate cell division. This inability could be caused by mutations that affect the activity of the cell cycle regulators. For example, a mutation could cause a lack of activity of cell cycle inhibitors, which allows the cell to continue to divide without limits. There could also be too much activity of positive cell cycle regulators, which can lead to cancer because it causes the cell to divide too much.

Differently from normal cells, cancer cells can continue to divide whether they have growth factors or not. Some have growth factors that are always “on,” some have the ability to make their own growth factors, and some can use neighboring cells to make growth factors for them. They also have “replicative immortality,” which is their ability to replicate many more times than the average cell. The enzyme telomerase is created, which reverses the shortening of chromosomes that normal cells experience during cell division. This characteristic is why cells have a limited life span. Cancer cells are difficult to stop because they do not undergo apoptosis (programmed cell death) like normal cells.

The Static Droplet Microfluidic Device will allow doctors to diagnose and treat cancers in a safe and cost-effective way. I have family members who have undergone painful surgeries in order to officially diagnose cancer, and technology using blood would have greatly improved their process of diagnosis. I invite any and all comments to share experiences or other information!

 

 

 

Researchers Discovered a Possible Antidote for the Most Deadly Mushroom

There is a reason why it is not advisable to eat wild mushrooms; Amanita Amanita phalloides 2011 G3phalloides, nicknamed death cap mushrooms, closely resemble edible mushroom variants—but are deadly if ingested. If a person chances upon one and happens to eat it, regardless of whether it is cooked, there is a high likelihood that they die.

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

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

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

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

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

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

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

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

CRISPR illustration gif animation 1.gif

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

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

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

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

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

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

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

Unlocking Genetic Mysteries with CRISPR!

At Oak Ridge National Laboratory, researchers are tackling the challenge of enhancing CRISPR, a groundbreaking gene-editing tool sort of like molecular scissors. While CRISPR has revolutionized genetic engineering in larger organisms such as mammals and fruit flies, its effectiveness in smaller organisms is limited. This limitation prompted a team to jump into the complex world of quantum biology, an area of study that investigates how quantum mechanics influence biological processes.

CRISPR logo

In AP Biology, we were introduced to the complexities of cellular structures and genetic mechanisms, and CRISPR is a topic of connection. CRISPR operates at the DNA level, precisely targeting and modifying specific sections of the DNA molecule. The passage highlights how CRISPR can be used to alter an organism’s traits by editing its DNA. This concept ties directly to the unit on genetics, where we learned about how changes in DNA sequence can lead to variations in phenotype. CRISPR technology allows scientists to make precise changes to the genetic code, providing a powerful tool for studying gene function and genetic disorders. In their search to understand why CRISPR behaves differently across various organisms, the researchers explored the movement of electrons within cellular structures, drawing insights from some principles of quantum mechanics. This exploration led them to develop a deeper understanding of the underlying mechanisms influencing CRISPR’s efficiency.

CAS 4qyz
Based on their discoveries, the team launched to develop a sophisticated computational model. This model, which integrates elements of artificial intelligence and quantum chemistry, is designed to predict the most effective targets for CRISPR within microbial genomes. Basically, they are leveraging the principles of quantum biology to enhance the precision and efficacy of CRISPR editing in smaller organisms. The implications of this research have promise for addressing genetic diseases and advancing biotechnological applications in human health and agriculture. Through their efforts, they inspire new pathways for harnessing the power of CRISPR to solve new mysteries and pave the way for a future characterized by innovation and discovery.

Big Cat, Little Bird

A fishing cat in a bird's nest

Credits: Allama Shibli Sadik & Muntasir Akash / De Gruyter

 

Cats don’t hate water, contrary to popular belief. In fact, there is a species of wildcat evolved to hunt in water. 

Aptly named “fishing cats,” Prionailurus viverrinus is a species of South Asian cat that has evolved to fish. Unlike other felines, they have slightly webbed forepaws and double layered water-resistant fur. This gives them an edge over others as it means they won’t freeze when they fish, giving them an opportunity to pass this trait down and allows them to stay reliant on their fishing diet, unlike other cats who primarily rely on land prey. They are medium sized cats with yellowish fur, and black tabby stripes that gradiate into mottled spots.

They catch their prey by idling on the edge of a body of water, and scooping the fish out of the water. Very rarely do they wade in and put their head underwater to fish.

But their diet does not solely consist of fish. They are also known to eat small rodents, lizards, amphibians and birds in addition to fish.

The only problem is that with the monsoon season, it is nearly impossible to fish as the land prey is gone, and their usual waters are flooded or destroyed. These cats live in areas prone to flooding and the lack of infrastructure means that the prey cannot flee (also fish cannot sustain on land).

So what does the brilliant cat do?

It climbs trees and preys upon the bird colonies. It has been seen preying upon waterbirds (ie. herons, moorhens, cormorants) high within the tree canopy, snapshotted with camera traps.

This might just be its secret to success since the local population also relies on the fish and (since people have more power than these felines) will deter (and kill) these cats. These waterbirds are not just the cats’ benefit, but the benefit of the locals as well!

Unfortunately, due to brackish waters and the urbanization of wetlands, the clever species is slowly dying out. But that’s another article.

There isn’t a lot known about these guys, but there are ongoing research projects with them.

A “CRISPR” Way to Test for Melioidosis

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

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

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

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

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

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

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

Where else do you think CRISPR can be used?

Had you ever heard of Melioidosis before?

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

The Effect of Ethylene Gas on Plant Growth

Researcher Brad Binder, Professor of Biochemistry & Cellular and Molecular Biology, University of Tennessee, and his team, through their study, accidentally discovered that treating seeds with ethylene gas (C2H4) can enhance the plant’s growth and stress tolerance. This discovery can be a potential breakthrough for improving crop yields and improving plant’s resilience to environmental stress. Where in most cases one gets traded for the other, this revealed that by exposing germinating seeds to ethylene in darkness it is possible to increase growth and stress tolerance.

Plants produce ethylene as a hormone to regulate growth and stress responses. The accidental discovery occurred during an experiment where seeds were exposed to ethylene gas during germination in darkness. The plants exposed had larger leaves, longer root systems, and sustained faster growth throughout their lifespan compared to non-ethylene-exposed plants. The researchers extended their investigation to various crop species, such as tomatoes, cucumbers, wheat, and arugula, and all of them increased growth and stress tolerance after their short-term ethylene treatment.

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The observed effects indicated that brief exposure to ethylene during seed germination can lead to long-lasting growth and stress tolerance benefits. The researchers proposed that ethylene priming enhances photosynthesis, particularly carbon fixation, leading to increased CO₂ absorption and higher levels of carbohydrates like starch, sucrose, and glucose. These molecules contribute to both increased growth and improved stress resilience in plants.

In AP Biology we learned all about the Calvin Cycle! The Calvin Cycle is a series of biochemical reactions that occur in the stroma of chloroplasts during photosynthesis. The cycle starts when the enzyme RuBisCO captures carbon dioxide from the atmosphere, which is then attached to RuBP, forming a six-carbon compound. This compound splits into two molecules of 3-PGA, each containing three carbon atoms. Then ATP and NADPH are reduced, which generates light-dependent reactions that are used to convert 3-PGA into G3P, a three-carbon molecule. Some G3P then continues to cycle and is reused to regenerate RuBP, while the rest contributes to glucose production for cellular respiration. The Calvin Cycle is vital in converting carbon dioxide into glucose for plant growth and sustenance.

I chose this topic because I really loved the photosynthesis unit, and my favorite part about it was memorizing the Calvin cycle, and comparing it to the Citric Acid Cycle.

What specifically about the ethylene gas causes an increased efficiency in Carbon Fixation?

Gut bacteria effects the development of allergies!

Have you wondered why some people have allergies and some don’t? Well, researchers have found that the lack of certain gut bacteria can play a role in the development of allergies and autoimmune diseases.

Cornell Medicine researchers have uncovered an intriguing connection between gut bacteria and early immune system development. Their study, published in Science Immunology, reveals that certain bacteria in newborns produce serotonin, a neurotransmitter crucial for educating gut immune cells, particularly T-regulatory cells (Tregs). Tregs, or regulatory T cells, are a specialized subset of white blood cells that suppress immune responses to maintain immune tolerance and prevent autoimmune diseases. Tregs play a vital role in preventing allergic reactions to food and gut microbes during infancy. The findings shed light on the importance of beneficial gut bacteria in early immune system training and may offer insights into combating allergies and autoimmune diseases later in life.

This relates to AP bio through the importance of neurotransmitters in this research. In AP bio, we learned how neurons transport messages using a process involving neurotransmitters. In the process of transport for neurons, neurons communicate messages through a sequence of events involving electrical and chemical signals. When stimulated, a neuron generates an electrical impulse known as an action potential. This action potential travels along the neuron’s length, eventually reaching its terminal branches called axon terminals. Here, neurotransmitters are released into the synapse, the gap between neurons. These neurotransmitters bind to receptors on the neighboring neuron, causing changes in its electrical potential. If the combined effect of these changes reaches a certain threshold, it triggers the generation of a new action potential in the receiving neuron. This process repeats, allowing messages to be relayed from neuron to neuron throughout the nervous system.

Wow! It’s so fascinating how a person’s levels of certain bacteria can influence whether or not a person has allergies. I wonder how else can bacteria can influence a person’s health?

The Mystery of Huntington’s Disease: A Potential Breakthrough in Treatment

In the ongoing search to understand and combat neurodegenerative diseases, scientists have recently made a significant breakthrough in unraveling the complex mechanisms behind Huntington’s Disease. This progress not only sheds light on why this devastating condition progresses slowly but also offers a promising lead in developing effective treatments to halt its fatal course.

Huntington’s disease, a hereditary disorder, is caused by a genetic mutation involving the HTT gene. This mutation results in the repetition of a specific DNA sequence, ultimately leading to the destruction of brain cells and the onset of debilitating symptoms. Until recently, it was believed that the number of repeats in the HTT gene remained constant throughout an individual’s life. However, groundbreaking research presented at the annual meeting of the American Society of Human Genetics has revealed a discovery: in certain brain cells, these repeats can multiply over time, reaching hundreds of copies. This expansion of repeats within vulnerable brain cells is now understood to be a driving force behind the progression of Huntington’s disease.

Geneticist Bob Handsaker of the Broad Institute of MIT and Harvard, who spearheaded this research, emphasized the pivotal role of these repeat expansions in triggering the cascade of events that culminate in the death of brain cells. By examining individual brain cells from both affected and unaffected individuals, Handsaker and his team uncovered a pattern of repeat expansion within a specific type of brain cell known as striatal projection neurons. These expansions, reaching up to 1,000 repeats in some cases, were uniquely concentrated in cells susceptible to Huntington’s disease.

Additionally, the research revealed an important threshold where the activity of thousands of genes within these brain cells changes significantly. This point, reached at around 150 repeats of the disease-causing gene, leads to a quick decline in gene activity, resulting in cell death within months. The exact reasons behind this sudden change are still unknown, presenting a mystery for further study.

However, amidst these uncertainties, the research offers a glimmer of hope for potential interventions. By targeting the process responsible for repeat expansion, namely the malfunction of a DNA repair protein called MSH3, scientists envision a novel approach to slow the progression of Huntington’s disease. By preventing further expansion of repeats, it may be possible to halt the relentless deterioration of brain cells, thereby halting the disease in its tracks.

​​As learned, Genetic mutations are changes in the DNA sequence that can lead to alterations in the proteins produced by genes. In the case of Huntington’s disease, a mutation involving the HTT gene leads to the repetition of a specific DNA sequence, ultimately causing the disease’s devastating effects on brain cells. By targeting the malfunction of a DNA repair protein called MSH3, scientists aim to address the underlying cause of repeat expansion, offering a potential avenue for intervention. This demonstrates how knowledge of genetic mutations can inform strategies for treating genetic disorders.

This research marks a significant shift in our understanding of Huntington’s disease and opens new avenues for therapeutic intervention. It highlights the importance of exploring innovative strategies that go beyond conventional approaches focused solely on reducing levels of the disease-causing protein. As we delve deeper into the intricate mechanisms underlying neurodegenerative diseases, such as Huntington’s, we inch closer to the prospect of effective treatments that could transform the lives of millions worldwide.

In the words of Dr. Leora Fox, Assistant Director of Research and Patient Engagement for the Huntington’s Disease Society of America, this research represents a pivotal moment in Huntington’s research, offering renewed hope. As we continue to unravel the complexities of Huntington’s disease, this latest breakthrough stands as a sign of progress in the ongoing quest to cure this condition. Are you confident in this breakthrough? What are your thoughts?

 

New and Improved Cancer Treatments!

Did you know that new approaches to fighting cancer just use the patient’s own immune system?!                                                                                                                                      In recent years, researching and manipulating the immune system has quickly allowed for new tested and approved treatments that are becoming increasingly popular. This treatment is called Immunotherapy.

Although the immune system can fight cancer on its own, cancer cells can bypass the immune system and spread. Immunotherapy allows the immune system to have a stronger attack on the cancer cells in various ways. One type of immunotherapy treatment is Immune Checkpoint Inhibitors. Unlike other treatments, checkpoint inhibitors work with the immune system to target cancer cells rather than attack them directly. The immune system can distinguish between normal cells and foreign cells (cancer cells) while protecting the normal cells from being attacked. However, as previously stated, cancer cells can exploit the checkpoint proteins on immune cells (T cells) to evade the body’s immune response. In this process, there are two very important proteins involved: PD-1 and PD-L1. PD-1 is a checkpoint protein on the surface of T cells that functions as a regulator, helping to control and restrain the T cells (from attacking healthy cells in the body) when bound to PD-L1, a protein on both normal and cancer cells. So basically, the PD-1 checkpoints act
like a traffic light: green means go, and red means stop! Diagram showing cancer cells spreading into the blood stream CRUK 448

The most common immune checkpoint inhibitor is Pembrolizumab, more commonly recognized by KeytrudaPembrolizumab targets and blocks the PD-1 protein, which triggers the T-cells to find and kill cancer cells. This drug is received intravenously (IV) and is used for multiple cancers, sometimes independently, but it can also be combined with other types of treatment. Pembrolizumab is approved to treat breast cancer, lung cancer, melanoma, kidney cancer, liver cancer, and cervical cancer, among many other types.

 

In our AP Biology class, we discussed what causes cells to become cancerous, how those are then different from healthy cells, and how they metastasize. From learning how cancers develop, I wanted to do more research and found it very interesting how this complex matter is treated. Learning that there are various approaches to treating cancer leaves me wanting to research more. I find it so cool how this newer treatment, Keytruda, supports the body’s immune system because it proves how smart our bodies are, and since immune checkpoint inhibitors continue to be tested and approved, is very encouraging and hopeful as it is an example of science advancing.

What do you think about immune checkpoint inhibitors? Would you expect this kind of treatment to be more or less efficient than treatments you may be familiar with already?

CRISPR and Sickle Cell Disease

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

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

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

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

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

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

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

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

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

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

How many other genetic diseases can CRISPR edit out?

Why are Blueberries Blue?

Have you ever wondered how certain fruits are such vibrant colors? Scientists globally have also pondered such characteristics. Some people think that objects obtain their colors by simply having the pigment inside. However, how our eyes perceive color is much more complicated than simply seeing the pigmentation.

Recently, research has been conducted on the color of blueberries. Blueberries are considered to be a “bloom” fruit, in that it has an epicuticular wax layer and dark pigmentation. This color does not come from smushing the fruit and watching the juice emerge, which led researchers to wonder where exactly it does come from. Researchers have discovered that blueberries are covered by a thin, waxy coating that is two microns thick. The researchers discovered this by removing the waxy layer and recrystallizing it to view the particles within the layer itself.

Within this layer, there are scattered particles in a random crystalline structure that reflect blue and UV light. Photons of light have certain pigments, and only a few of which are visible to humans. The photo below depicts which light is visible to humans. It is also notable that the pigment in blueberries reflects UV light, which is visible to birds.

FIO117: Figure 8.1

This directly relates to our AP Bio Photosynthesis Unit. In this unit we learned the reason why leaves are green. This is because leaves contain certain pigments (one being chlorophyll a) that absorb all wavelengths of light except for green, which is reflected.

Additionally, we learned in AP Bio that leaves are surrounded by a non-polar, waxy substance. This is the same on blueberries. It is interesting that learn that water will not easily penetrate through the skin of leaves as well as certain fruits due to the repulsion of non-polar and polar substances.

Do you know of any other epicuticular fruits? Can we investigate their pigmentation as well?

Uncovering One Mystery of Tardigrades

Tardigrades, are one of the more well known creatures of the microscopic world. Something that keeps them in the spotlight is their extreme survivability. However, when active tardigrades don’t have their toughness. They only have that survivability when they are dormant, or are in a state called suspended animation, read this blog to find out how they enter this state.

Tardigrades can be called water bears or moss piglets in addition to their official name. This is due to the fact that the location they are found in is typically in water in mossy or muddy areas. They are microscopic eight legged animals that when dormant are close to invincible. When needed, tardigrades can curl into a ball called a tun. One of the reasons they are able to do this is that water bears are invertebrates. When they are in a tun, tardigrades pull in their legs, release water, turn their insides to glass, and nearly stop their metabolism. Once in this state tardigrades can withstand radiation from x-rays and even trips into space.

Derrick Kolling, a chemist at Marshall University found that chemical changes called oxidation to the amino acid cysteine trigger the tun state, and they even found that when this process is reversed, it brings tardigrades out of their dormant state.

 

SEM image of Milnesium tardigradum in active state - journal.pone.0045682.g001-2

Scientists have wondered for a long time what causes tardigrades to go into the tun state, and this finding is an exciting discovery for the biology world. This discovery helps explain some unknown pieces of the biology of water bears as a tun, and there is even hope that this discovery can explain some biological aspects of other creatures in their respective tun state’s.

Kolling started this project almost out ofnowhere. After seeing tardigrades in the news frequently, he decided to find some and test them with an EPR Spectrometer, a device that studies atoms and molecules with unpaired electrons. This relates to our AP Biology class as we also found tardigrades for a lab, and we learned about their toughness, origins, and survivability.

After using the EPR Spectrometer to test a few different things, the researchers found that blocking cysteine oxidation prevented tardigrades from forming tuns triggered by exposure to high levels of salt or sugar. They found that blocking this oxidation also prevented water bears from surviving freezing. This suggests that cysteine oxidation is what triggers the tun state.

Prior to reading this, what did you think caused tardigrades to enter the tun state?

Do you think tardigrades really came from space?

Have you ever tried to find a tardigrade?

Post Includes edits and suggestions made by ChatGPT.

 

Can Alzheimer’s Disease be Transmitted?

https://www.flickr.com/photos/institut-douglas/2677257668

We have long associated Alzheimer’s disease as a condition that could come with aging, but have you ever thought that the disease could also be transmitted? 

 

In most cases, Alzheimer’s disease affects an older population group, as around 1 in every 9 people who are aged 65 or older in the US have Alzheimer’s. However, in January 2024, researchers have reported in the Nature journal that five people who received contaminated injections of a growth hormone in their early childhood years came to develop Alzherimer’s disease unusually early – between ages 38 and 55. This points to the potential that the contamination of the growth hormones to be a cause of the unusually early development of Alzheimer’s disease in the 5 people reported. 

 

These 5 people received hormone injections that are used to treat various growth disorders. The hormones are extracted from pituitary glands of cadavers (a practice no longer used), as the pituitary gland is the location in the body that produces growth hormones that signals the body for growth. However, sometimes these extractions are contaminated with infectious, misshapen proteins, which could cause serious problems in human cells such as preventing the cells from doing its regular jobs to forming clumps in cells. 

 

One of these infectious proteins that came along with the extracted growth hormones from pituitary glands of cadavers is the amyloid-beta protein, which research shows is a hallmark of Alzheimer’s disease as it accumulates in the brain. In class, we learned about the importance of growth hormone proteins in stimulating cell growth. When cells receive growth hormone signals, they are stimulated to keep dividing and growing, and conversely when they don’t, they will stop the cell reproduction cycle. However, for patients who were contaminated with the A-beta growth hormone protein, some harmful cells in their body would be instructed to keep on growing, dividing, and continuing their reproduction cycle, which could be a possible cause of Alzheimer’s disease. 

 

After learning about how it’s possible that Alzheimer’s disease could be developed through medical contaminations, what are some improvements you think should be made in medical settings that could prevent future situations similar to this?



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