BioQuakes

AP Biology class blog for discussing current research in Biology

Author: binturtong

CRISPR Causes Cancer? Or Does It?

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On March 20, 2022

In Student Post

CRISPR illustration gif animation 1

The ground-breaking scientific break through of gene editing is finally here with the technique called CRISPR. CRISPR, or gene cutting, is the method of cutting a strand of DNA and letting the DNA repairer function repair the cut by itself. But it is at this instant where scientists introduce some changes to the genes, which the DNA will reproduce; DNA naturally grows back the mutated Genes. This CRISPR sounds great in the world of science, where certain genes can be modified onto a person. Though there are different opinions on gene-modifying, CRISPR has yet to be fully perfected. One of these hurdles is P53; a tumor suppressing protein. P53 is known as the “guardian of the genome” as this protein determines “whether the DNA will be repaired or the damaged cell will self-destruct” (MEDICINEPLUS). While this is good news, it is observed that “a dataset of >800 human cancer cell lines identified additional factors influencing the enrichment of p53-mutated cells.”(aacrjournals). So a lot of cancer cells have had a mutated P53 protein. So why does this happen? Why is the guardian of the genome being mutated?

 

P53 mutations are “missense mutations,” meaning they mutate in relation to a gene being edited, which creates different amino acids. By creating a whole new set of amino acids, the cell completely changes and in this case, mutates the P53. By mutating the P53 protein, P53 can no longer stop the cell division cycle, immensely increasing the chance of cancer cells. Although I make CRISPR sound like a dangerous operation to do(*I am not a scientist*), Researchers at Karolinska Institutet say to” have found new links between CRISPR, p53 and other cancer genes that could prevent the accumulation of mutated cells without compromising the gene scissors’ effectiveness.”

Another new research point mentions that although a lot of P53 mutations occur when subject to CRISPR, “cells with mutations are there from the start.” This is still a huge unknown to scientists, as CRISPR does cause P53 to mutate, there are already mutated P53 cells beforehand. Though this does prove that P53 is affected by other factors instead of only affected by CRISPR. Scientists still have much to uncover about gene-editing and in the future, they could possibly change somebody’s genes for a good cause.

 

 

 

Starfish are Strong?

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On February 15, 2022

In Student Post

When on the beach, sometimes you can see a starfish on the beach. Assuming it was brought by the tides of the water, if a starfish is able to be pushed by water, how does it survive in the water that is pushing it around?

Well, Starfish are actually quite strong. Their anatomy is essentially a central disk which grows out arms, commonly 5, that have spikes on them.  They have an endoskeleton consisting of many ossicles, made of Calcite,  which strongly boost the structural integrity of the starfish.  But to understand the strength of a small starfish, we need to look into the ossicles and calcite that make up a starfish. This is helpful to humans as starfish have inspired ideas like hydraulic movement.

Simple Sea Star Body Plan

Since Calcite, made of carbons and calcium, make up the ossicle, the integrity of a starfish is dependent upon the placements of carbon molecules. Similar to a diamond, the carbon molecules of the starfish are strongly bonded by covalent bonds, giving strength to each surface. Diamonds are one of the hardest structured natural material. More so, each calcite in the ossicles resemble a stack of carbon hexagons. Because calcite cannot be uniformly bonded, pushing on areas of a starfish will break these calcite bones. Although the starfish does have its integral flaws, the diamond-like structured ossicles make up for most of it. The strongly covalent bonds of carbon atoms create a mesh-like surface and hold the starfish together.

By studying the starfish’s simple yet complex anatomy, we may be able to make breakthroughs for “creating stronger porous materials” like ceramics says Material Scientist Ling Li at Virginia Tech. Starfish seem frail and pushed upon, by the water, but in reality, starfish are strong predators which root from their complex anatomy.

The Science Behind COVID Tests

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On January 17, 2022

In Student Post

My family and I have had a lot of questions about the COVID test, such as if I take the COVID vaccine and do a test, will it come positive? Well to answer a question like this we need information on how tests work.

Lets start with the basics:

There are two types of molecular tests, antigen tests and nucleic acid amplification tests. Rapid tests are known as Antigen Tests while PCR tests are known as nucleic acid amplification tests. I will talk about PCR tests first. The PCR tests test for DNA. However, the COVID-19 genetic code is actually RNA. So how do PCR tests pick up positive or negative results?

Test de antígenos Covid 3

When your swab of DNA is sent back to the lab, they will isolate RNA and DNA with the process called gel electrophoresis. After isolating the RNA, it is mixed with enzymes (DNA polymerase and reverse transcriptase), DNA building blocks, cofactors, proves and primers. The RNA is transcribed into DNA by the reverse transcriptase. This transcription creates a complimentary DNA. The goal is to isolate the DNA now, and the DNA polymerase does so. The enzyme breaks up the RNA and isolates the complimentary DNA. That DNA is duplicated in order to amplify the molecule. Remember that this DNA is duplicated from the virus RNA.

To amplify the DNA for the equipment to read, the DNA is first heated, denatured, in order to separate the DNA strands. When cooled, primers and probes bind to the DNA strands. The DNA polymerase assembles new DNA strands from the DNA building blocks and when fully reconstructed, it has been successfully amplified. This is done repeatedly with the RNA and thus, creates many complimentary DNA’s ready to amplify.

If SARS-CoV-2 complementary DNA is present in the sample, primers copy the infected regions while probes, signaling proteins, stick to it and release a visual signal read by the equipment. Because there are millions of amplified DNA, there will be lots of signals being produced by the probes. If their is no virus, the probes do not stick and this no signal release and a negative result shows. Thanks to the power of signaling and cell communication, lab instruments can pick up on it and give us a positive or negative result.

The rapid test works in a very different way. Antigen rapid test takes about 15 minutes. The goal is to detect the spike protein of the coronavirus. The liquid drops onto the droplet. Antibodies are on the test pad, with three sets.

The testing pad, we’ll call pad, consists of the location for liquid drops, and a C and T line. At each segment of the pad there are different antibodies. Those antibodies will bind to the spike protein as well as the other antibodies. When the liquid is dropped in, capillary flow allows the liquid to move down the pad. The first antibodies will attach to the virus, which then move down the pad. Then the antibody will bind to primary and secondary antibody, not the virus. The combining of antibodies create the line which results in the positive or negative outcome.

 

To answer my question, no. The PCR and rapid tests should not test positive if one has taken the vaccine recently. This is because both tests are checking for active viruses and polymerase. Not immunity.

 

If you feel any symptoms take a rapid test, sometimes it comes negative when you really have COVID and that’s because at the early stages of COVID development in the body, there will not be enough active viruses going around.  But that does not mean you are not contagious, please be safe and stay healthy!

LONG COVID

By

On December 17, 2021

In Student Post

After the long sufferable weeks from catching COVID-19, you would think you are in the clear; until, that is, you feel some extra “health-issues”. The term for these health issues, specifically after COVID-19, are called Long Covid (post-covid). Generally “one in two [covid recovered people] experienced long-term COVID manifestations” and the symptoms included are a diverse field of sickness. Penn State investigators mentioned the trend of symptoms from 250,351 unvaccinated adults and children:

Loss of General Well Being (weight loss, fevers, fatigue)

Decreased Mobility (1 in 5 experienced a decrease in mobility)

Concentration Issues

Lung abnormalities (6 in 10 survivors tight chests and a quarter of patients had difficulty breathing)

Digestive Issues

What could be the reason that COVID-19 is still lurking around in our bodies when the sickness is gone? Researchers at Yale University studying long-COVID have found a pattern of patients having an “unusual level of cytokines” also known as a cytokine storm. Cytokines are a secreted chemical proteins released by cells for communication. In the Immune System process, after a Macrophage, large phagocytic cells, ingests an antigen it releases cytokines, signaling for a t-helper cell to come. After the helper t-cell recognizes the antigen, more cytokines are released and trigger the Cell-Mediated and Humoral Responses (B and T cells). I mention all this because researchers are saying that post-covid patients tend to have patterns of irregular, more-than average cytokines being produced as well as an “unusual pattern of activity by…t cells. The greater than average amount of cytokines suggests a “state of chronic inflammation” and “kill tissues and damage organs.” The unusual activity of t-cells suggests that COVID-19 could still be lurking in the body.

Cytokine Release

Cytokine release and the numerous amounts of it

The treatment for these conditions are mostly to take the vaccine but there are still many unknowns to this Long-Covid problem. These problems are mostly lying in the Immune System rather than other parts of the body that can be tested with machines; which is why solving this problem is very difficult. This problem can only be solved by a matter of time and hope the scientists can figure this out.

 

The Unknown Disinfecting Protein

By

On November 2, 2021

In Student Post

When our body is invaded by a virus, it will send its army to fight it, this army is known as the Immune System. The Immune System uses white blood cells to do most of the pathogen killing work, sending white blood cells in waves. The Immune System records the pathogens signature features and creates antibodies to fight the particular invader. But in some cases, the Immune System’s antibodies “are less effective against pathogens that have already penetrated the interior of the cells.” When bacteria microbes get past the Immune System and get to the cytoplasm, the bacteria will replicate. This is where a protein comes and dissolves the bacteria in the cell.

A less known family of proteins called the Apolipoprotein can actually dissolve bacteria that is in the cytoplasm. Researchers at Howard Hughes Medical Institute at Yale discovered the APOL3 in particular had the ability of dissolving a bacteria. An experiment with un-immune cells, cells that are not protected by Immune System, and the bacteria, Salmonella. Salmonella has a double membrane, similar to mitochondria and chloroplasts, making it very hard for cells to kill it. The APOL3 protein, however, “binds to and destroys the inner membrane of virulent bacteria like salmonella and kills them.” APOL3 only removes the inner layer, with the help of an immune protein called GBP1, GBP1 can remove the outer layer and set up APOL3 for the final shot. The way APOL3 dissolves bacteria is by shooting or surrounding the bacteria with APOL3 molecules and it just goes away. This is probably why researchers called it the detergent. The way APOL3 does this scientifically is by possessing “parts attracted to water and parts drawn to fats.” Since membranes are mostly made of lipids, the bacteria is a sphere of lipids and inside are its organelles. The APOL3 binds to and destroys the lipid membrane, releasing all the cytoplasm organelles out and killing the bacteria. APOL3’s method of dissolving must dissolve some other parts of the cell right? Well, APOL3 actually has a selective target, targeting bacteria lipids and not attacking cholesterol.  As we learned in class, cholesterol is a lipid which is part of the plasma membrane as well as the building block of other steroids. Because APOL3 cannot target cholesterol, our human cells are safe.

Salmonella

“Salmonella” by National Institutes of Health (NIH) is licensed under CC BY-NC 2.0

 APOL3 is a very diverse protein and allows it to be around the whole body. Humans have a very strong defense system, having the Immune System as well as detergent like proteins around the body, lipid based bacteria will have a hard time in our cells.

 

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