BioQuakes

AP Biology class blog for discussing current research in Biology

Author: nucliyatide

The Quest to CRISPR Vision

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On April 17, 2024

In Student Post

Retinitis Pigmentosa is a genetic disorder that causes severe vision loss. The tunnel vision and narrow sight progressively damage the retina and as the condition progresses, daily life becomes more and more of a challenge. This condition affects over one million people worldwide and causes inherited blindness in 1 out of every 4,000 people. But what if this condition could be cured using gene editing?

Retinitis Pigmentosa is the progressive deterioration of photoreceptor cells that line the back of the eye and convert light into electrical impulses that are sent to the brain. The condition is caused by genetic mutations and it can be hereditary. At least 100 genes are associated with the disease, one being phosphodiesterase 6b. This protein-coding gene is a huge part of the phototransduction pathway as it converts light into an electrical signal that the brain interprets as vision. The mutation affects the cone photoreceptor cells and the loss of these cells leads to the irreversible deterioration of vision.

Consecutive OA in retinitis pigmentosa

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is gene editing technology that targets specific DNA sequences. It uses specialized cellular machinery to make precise cuts in the DNA strand which allows the removal of mutated genes, replacing them when non-mutated ones.

CRISPR Cas9

A study in China used CRISPR gene editing to restore the vision of mice with retinitis pigmentosa. The researchers used PESpRY to correct the mutation in the PDE6b gene through precise edits while not being limited by PAM interferences. This corrected the activity of the gene in the retinas of the mice, while also preventing the death of the cone photoreceptors and restoring their electrical responses to light. Tests proved the mice sustained good vision into old age and the photoreceptors were preserved.

This relates to what we have learned in AP Bio because of the relation to gene expression and genetic disorders. Gene expression is the process where DNA sequences are transcribed into messenger RNA and then translated into a protein. This process is tightly regulated but can be influenced by genetic mutations, such as retinitis pigmentosa. In this case, scientists are able to manipulate the DNA to fix specific genetic mutations which highlights the importance of understanding genetic mechanisms.

The use of CRISPR gene editing is a promising approach for treating genetic diseases in the retina, and with more testing could be used for humans as well. So, would you try this out if it could help fix your vision?

 

 

Teaching Cancer to Fight Itself

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On February 27, 2024

In Student Post

Many of us know someone who has suffered from cancer and we have watched loved ones undergo the harsh treatments for it. With treatments such as chemotherapy, the side effects are hard to bear. So, what if your body could be taught to treat cancer on its own without having to experience the hair loss, fatigue, nausea, and anemia that external treatments can cause.

Cancer cells are very different from normal cells as they hide from the immune system which usually eliminates damaged or abnormal cells. Cancer cells also trick the immune system to help cancerous cells stay alive and grow. But, what if these cancer cells could be altered to teach the body’s immune system to fight the cancer that the cells come from?

7 Most Deadliest Cancers

In an experiment done by Stanford Medicine researchers used mouse leukemia cells to train T cells to recognize cancer in a way that could mimic the natural occurrence in the body, similar to vaccines. T cells recognize pathogens due to special antigen presenting cells (APCs) gathering pieces of the pathogen to show to the T cells what to attack. In cancer, the APCs would gather up the many antigens that characterize a cancer cell so T cells could be trained to recognize cancer antigens and wage a multi-pronged attack on the cancer.

Killer T cells surround a cancer cell

The researchers programmed mouse leukemia cells to be induced to transform themselves into APCs.  When they tested the cancer vaccine strategy on the mouse immune system, the mice were able to clear the cancer. The immune system was able to remember what the cells had taught them and when they reintroduced cancer to the mice 100 days they were able to have a strong immunological response to protect them. Additionally, they tried to see if the tactic used with leukemia would work with solid tumors so they used the same approach by using mice fibrosarcoma, breast cancer, and bone cancer. They found that the solid tumor transformation was not as efficient to that of leukemia, but it still had a positive result. With all three cancers, there was significantly improved survival rates.

They then went back to leukemia, but this time they studied acute leukemia in human cells. When the human leukemia cells APCs were exposed to human T cells from the same patient, they observed all of the signs that indicated the APCs were teaching the T cells how to attacked the leukemia.

This relates to what we have learned in AP Biology because we learned about cell division and how cancer differs from normal cell division. Cancer is a disease where some of the body’s cells divide and grow uncontrollably. This can start anywhere but also spread to other parts of the body very quickly. In its normal process, human cells grow and multiply through interphase and mitosis to form new cells as the body needs. Interphase is the phase in the cell cycle that prepares for cell division by growing cells and undergoing the process of DNA replication. The body has checkpoints that regulate the G1, S, and G2, phases of interphase. There are also checkpoints for mitosis, which is the division of cells that results in two daughter cells. When the cells become old or damaged, they die and new cells are regenerated. When this process breaks down and abnormal or damaged cells grow and multiply when they’re not supposed to, the body goes through a process called metastasis where cancerous tumors are formed. Cancer cells ignore the checkpoints and continue to divide and multiply.

This research has introduced a new way that could eventually treat cancer in a more harmless way while also ensuring that the body can fight off recurrence. So do you think that this will be the new treatment for cancer?

 

Is Diet Soda a Scam?

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On January 7, 2024

In Student Post

If you are like me and your favorite drink is Diet Coke, then you are no stranger to the people around judging your choice and claiming that you are drinking chemicals. “It’s just as bad as the real thing,” they all say. I genuinely think the diet and regular versions of soda taste different, and when it comes to Coke, I just prefer the diet version. However, some people drink it as an alternative to the high levels of sugar in regular sodas.

Recently, studies have come out to prove that the sugar substitutes in diet sodas are just as bad for you as the cane sugar in regular soda. So, is the impression that Diet Coke is healthier than regular Coke a scam?

Drink it in a Coke

First, you need to understand what mimics the sweetness of regular sodas in diet ones. The chemicals that people are referring to are the sweeteners used in replacement of the almost 40g of sugar in a regular coke. The main sweetener is aspartame, which is a dipeptide composed of two amino acids; phenylalanine and aspartic acid. The other is acesulfamm potassium. Acesulfame Potassium, also known as Ace-K, is a potassium salt that is roughly 200 times sweeter than sucrose. Both of these sugar substitutes are synthetic products.

So, are these sugar substitutes better or the same as the real thing?

In a study done by the Research Ethics Committee of the Federal University of São Paulo, 15 healthy participants participated in a blindfolded trial including a Diet soft drink, Regular soft drink, water with sweeteners, water with a low sucrose content, and regular water, in 5 days. The goal of the experiment was to study the aspartame excretion in saliva and the salivary insulin, in response to the ingestion of the beverages. Each day, their saliva was collected when fasted, 15, 30, 60, and 120 minutes after drink intake, to check for the levels of salivary aspartame and insulin levels. The researchers found that insulin levels increased 1 hour after both regular and soft drink digestion. Therefore, the study found that although diet soda is sugar and calorie free, it still influences insulin levels, like regular sodas. So, by avoiding the regular version of a soft drink, you are not avoiding the insulin spike. However, the research only included a 15 participants, so an experiment with a larger sample size would need to be conducted to reach a final conclusion. But, the idea that “no sugar” soft drinks are that much healthier than the real thing, isn’t exactly true.

This connects to what we have been learning in AP Bio because we learned about insulin and glucose levels and how they maintain homeostasis in our bodies. Insulin is a hormone produced in the pancreas that regulates blood glucose levels. Insulin helps blood sugar enter the cells of our body so it can be used for energy along with sending signals to the liver in order to store glucose for later use. However, when insulin levels rise too high, it can cause the cells in our bodies to absorb too much glucose from the blood, and the liver to release less glucose. This causes dangerously low glucose levels in the blood. If this becomes chronic, and there is constantly high insulin levels, it can lead to prediabetes and Type 2 Diabetes.

Do you still think your diet soda is better for you than the regular one, or will you opt for a regular coke next time?

 

 

 

 

Your Genetics May Have Saved You From Getting COVID-19

By

On December 5, 2023

In Student Post

Were you one of the, what felt like fairly few, people who never got COVID-19 when it seemed like everyone else did? Well, maybe you did and you were asymptomatic with COVID-19. I remember when my whole family was sick with this virus, except for me. I always thought it was just luck, and you might have as well, but what if certain gene mutations can prevent the symptoms of this virus.

In a study done by the National Institute of Health, researchers looked into the genetic variations and how they affected T cells in the immune system. The focus of the study was the human leukocyte antigen complex (HLA). The proteins of these genes prevented people from people feeling symptoms of COVID-19. The proteins of HLA helped the immune system react to the SARS-CoV-2 virus by recognizing the infected cells by presenting pieces of pathogens to the T cells.

HLA-B*2705-peptide in complex with influenza nucleoprotein NP383-391

At the University of California, San Francisco, researchers studied unvaccinated bone marrow donated from The National Marrow Donor Program/Be The Match. Out of 1,428 donors, 136 were asymptomatic for two weeks before and after testing positive COVID-19. The HLA variant, HLA-B*15:01, had a strong association with the asymptomatic donors. The team, along with researchers from La Trobe University in Australia, studied T-cell memory. They found that the T cells in people who had the HLA-B15 gene, and were never exposed to the COVID-19 virus, responded to the NQK-Q8 peptide in the virus and were able to have a faster immune response. Therefore, people who contain the HLA-B15 gene are prone to being asymptomatic to COVID.

In AP Biology we learned about the immune system’s response to viruses, like SARS-CoV-2. We learned that T-cells and Helper T Cells are part of cell-mediated immunity and are crucial for recognizing antigens and releasing cytokines to trigger immune responses. Then, B and T cells create antibodies and cytotoxic cells to kill off the virus. Memory B and T cells are also formed in order to generate a faster immune response if the body is exposed to the same virus again. Therefore, the immune response stimulated when a person contains the HLA-B15 gene is similar to one where the body uses memory cells to fight an infection.

So, have you never caught COVID-19, or are you one of the lucky people to contain the HLA-B15 gene?

 

Is the Gel Manicure worth the Damage to Your DNA?

By

On November 5, 2023

In Student Post

Nail salons are filled with these UV lamps that create the perfect gel manicure which lasts for weeks and dries instantly. These manicures are advertised all around and consumers are sucked in, including myself. I love getting an easy gel manicure and saving myself the hassle of having chipped nails that require at least 20 minutes to dry. However, by placing our hands into these lamps, we are causing ourselves years of permanent damage to our DNA. But how does exposure to UV rays cause these intense issues? It all boils down to one thing; the DNA in our skin cells.

The two main types of skin cancer are melanoma and non-melanoma. Melanoma is less common but more dangerous than non-melanoma. While skin cancer can be hereditary, there is evidence that exposure to UV rays causes skin cancer. PubMed Central explains DNA damage caused by UV rays results in deamination, depurination, and depyrimidination. Deamination is the loss of an amino group from a compound that can convert one base to another, meaning the deamination of cytosine from UV rays would result in the production of uracil. Depurination and depyrimidination are the total removal of purine and pyrimidine bases. This removes the deoxyribose sugars in the cell which causes breakage in the DNA backbone. Exposure to these oxidative stressors can cause double DNA strand breaks which are the most dangerous as they leads to the loss of genetic material. These interferences damage the components of DNA molecules and the normal functions of the cells. The damage that UV rays cause to the DNA in skin cells lead to abnormal growth and the start of benign or malignant growths in the skin, which can ultimately lead to cancer. 

Direct and indirect DNA damage by ionizing radiation

A study done by the University of California used UV lamps that are used to cure gel manicures to study their affects on skin cells. They used three different cells types; adult human skin keratinocytes, human foreskin fibroblasts, and mouse embryonic fibroblasts. They observed that that exposure to the UV lamps for 20 minutes caused between 20-30 percent cell death, and three consecutive 20 minute exposures led to 65-70 percent cell death. Additionally, the exposure caused mitochondrial and DNA damage to the surviving cells. The mutations found in these cells are representative of those found in human skin cancer, proving that the consistent use of these lamps can lead to skin cancer. In another study, Maria Zhivagui, a postdoctoral scholar, exposed three cell types to acute and chronic exposure of UV lights. In both conditions, cell death, damage, and DNA mutations were observed. There was also an elevation of reactive oxygen species molecules which are known to cause DNA damage and mutations that are found in melanoma patients.

UV manicure lamps (15157277325)

Therefore, the study proves how damaging UV rays are to our cells. The risk of using these lamps is not worth the risks they bring to your DNA. Alternatives to UV lamps are just getting normal manicures, press on nails, or powder manicures, which do not require the exposure to UV rays.

This connects to what we have been learning in AP Biology because DNA’s structure is composed of nucleotide molecules. These nucleotides contain a phosphate group, deoxyribose sugar, and one the four nitrogenous bases; adenine, thymine, cytosine, and guanine. UV damage can lead to chemical changes in these nitrogenous bases and to the structure of the DNA. Additionally, this can cause disruptions in the reading of genetic code during protein synthesis which results in incorrect sequence of amino acids. We have learned that altering amino acid structure completely changes the function of the proteins, which is why UV rays lead to mutations such as skin cancer.

So, next time you decide to get a gel manicure will you think about the damage you are causing to your DNA? Is the risk worth it?

 

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