BioQuakes

AP Biology class blog for discussing current research in Biology

Author: joelesterol

CRISPR Quits Coronavirus Replication

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On March 22, 2022

In Student Post

The gene-editing CRISPR has now been utilized by scientists to prevent the replication of Coronavirus in human cells, which can ultimately become a new treatment for the contagious virus. However, since these studies were performed on lab dishes, this treatment can be years away from now.

Firstly, CRISPR is a genome-editing tool that is faster, cheaper, and more accurate than past DNA editing techniques whilst having a much broader range of use. The system works by using two molecules: Cas9 and guide RNA (gRNA). Cas9 is an enzyme that acts as “molecular scissors” that cuts two strands of DNA at a specific location. gRNA binds to DNA and guides Cas9 to the right location of the genome and ultimately makes sure that Cas9 cuts at the right point.

 

CRISPR'S Cas9 enzyme in action

CRISPR’S Cas9 enzyme in action

In this instance, CRISPR is used to allow the microbes to target and destroy the genetic material of viruses. However, they target and destroy the RNA rather than the DNA. The specific enzyme they use for this is Cas13b, which cleaves the single strands of RNA, similar to those that are seen in SARS-CoV-2. Once the enzyme Cas13b binds to the RNA, it destroys the part of the RNA that the virus needs to replicate. This method has been found to even work on new mutations of the SARS-CoV-2 genome, including the alpha variant.

COVID-19 vaccines are being distributed around the world, but an effective and immediate treatment for the virus is necessary. There are many fears that the virus will be able to escape the vaccines and become a bigger threat. Although this treatment is a step in the right direction for effective treatment of COVID-19, this technique will ultimately take a long time for the treatment to be publicly available.

CRISPR is greatly relevant to AP Bio, as seen through its use of enzymes in DNA replication. CRISPR utilizes Cas9, an enzyme that is similar to helicase. In DNA replication, the helicase untwists the DNA at the replication fork, which after the DNA strands are replicated in both directions. 

This article is fairly outdated since there have now been immediate treatments created for COVID-19. But, what do you think about the use of CRISPR for future viruses and pandemics? Personally, I believe that CRISPR will ultimately become a historical achievement in science due to its various uses. Thank you for reading and let me know what you think in the comments! 

 

How Do Guard Cells Attain Energy?

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On February 15, 2022

In Student Post

Ever since we were young, we understood that plants utilize photosynthesis for energy, releasing oxygen in the process. But, we did not learn which parts of the plant actually perform photosynthesis. This is highlighted by guard cells, the cell located in the upper epidermis that controls the concentration of Carbon Dioxide in the plant. So how do they contribute to photosynthesis?

Stomata & Guard Cells

The team of Dr. Boon Leong Lim at HKU wanted to observe the real-time production of ATP and NADPH in the mesophyll cell chloroplasts, which was done by using planta protein sensors in a model plant, Arabidopsis thaliana. This plant is specifically used due to its small genome, short life cycle, simple process to mutagenize, and easily identifiable genes. Shockingly, the Guard Cells Chloroplasts have not detected any ATP or NADPH production whatsoever. Looking for answers, the researchers decided to contact Dr. Diana Santelia, an expert in cell metabolism. Throughout a decade of research and collaboration, they finally have an answer.

Unlike mesophyll cells, photosynthesis in the Guard Cells is inadequately regulated. This is because synthesized sugars from the mesophyll cells are imported into the Guard cells, in which is used ATP production for the opening of the stomata. Additionally, Guard Cells chloroplasts take cytosolic ATP through nucleotide transporters on the chloroplast membrane for starch synthesis throughout the day. At night, though, Guard Cells degrade starch into sugars for the opening of the stomata. Mesophyll Cells, on the other hand, synthesize starch and export sucrose at dawn. Thus, the chloroplasts of Guard Cells ultimately serve as starch storage for the opening of the stomata. Their function is closely linked to that of MCs in order to effectively coordinate CO2 absorption through stomata and CO2 fixation in MCs. 

Although the Guard Cells seem redundant, their role in the overall process of photosynthesis is absolutely necessary. As seen in AP Bio, the stomata are essential for gas exchange for photosynthetic reactions. The stomata’s main role is to take in Carbon Dioxide and release Oxygen, both of which are necessities for the reaction to occur. 

Thank you so much for reading this blog, and let me know what you think in the comments below!

Bacteria May Not Be As Simple As We Once Thought

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On January 17, 2022

In Student Post

Bacteria biofilms are ubiquitous in our world, living in various conditions that allow bacteria to build up, such as sewer pipes or even our own teeth. New studies have shown that bacteria not only have intelligent systems for communication but also have the ability to remember things.

Biofilms are ancient, with evidence of biofilms dating back to 3.25 billion years ago. While they are able to grow on many different surfaces, these surfaces all share a commonality: they’re wet. Biofilms to humans are a cause 

of concern regarding our health since biofilms can grow on implanted medical devices, which can lead to infections. Bacterial biofilms can also cause infective endocarditis and pneumonia. Furthermore, bacteria that are within a biofilm are also more resistant to antibiotics and other disinfectants and are considered to be 1,500 times more resistant.

Grand Prismatic Spring

The Grand Prismatic Spring is probably the most popular biofilm, as the various bacteria biofilms give the spring its bright colors.

Biofilms have recently been recognized as an advanced community, with the discovery that biofilm cells are organized in intricate designs that plants and animals have been known to use. Süel, a UC San Diego Professor of Molecular Biology, states that this concept of cell patterning is much more ancient than they once thought. This new discovery opens the possibility that this segmentation of cells may go back to over a billion years, and was not just a new emergence from plants and animals.

As found through experiments and mathematical models, the study revealed that the biofilms involved used a “clock and wavefront mechanism,” which sophisticated organisms such as plants, flies, and humans use. A “wave” of nutrient depletion moves across cells, which dresses a molecular clock inside each cell that creates a pattern of distinct cell types as the biofilm expands and consumes nutrients. This breakthrough identified the circuit that the biofilm’s ability to generate community concentric rings of genetic patterns.

As seen in AP Biology, the formation of a biofilm is an example of Cell Communication. With unicellular organisms, they are able to communicate with each other to signal for the availability of food, identify mating types, or detect others for coordinated behavior. For bacteria, they utilize Quorum Sensing, in which they secrete small molecules that are detected by other bacteria. If they sense the population is close enough to perform group behavior, they will begin to do so.

This new discovery opens many doors to various research fields, due to the fact that biofilms are prevalent in our everyday lives. From medicine to the food industry to the military, these biofilm systems can be used to test and investigate the in-depth aspects of the clock and wavefront mechanism. Plants and vertebrate systems are harder to study, but bacteria aren’t because they “offer more experimentally accessible systems that could provide new insights for the field of development,” Süel states. 

Personally, I am very interested in how these studies are going to be used, specifically in a “military” field. Furthermore, do you think there is more groundbreaking information regarding bacteria that can help us put the pieces together for life before humans? Let me know in the comments below and thank you for your time!

 

How COVID-19 Antibodies Are Causing Long-Term Effects

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On December 20, 2021

In Student Post

The COVID-19 vaccine has been essential in flattening the curve of the pandemic, but there have been reports of various side effects derived from the vaccine. These side effects include allergic reactions, heart inflammation, and blood clotting. These symptoms have been commonly thought to be because of the patient’s immune system. But, this question as to why these immune responses to both the vaccines and responses to the virus itself have been possibly answered in a new article in The New England Journal of Medicine.

COVID-19 vaccines (2021) A

Various types of the COVID-19 Vaccine

 

William Murphy and Dan Longo, both Professors of Dermatology and Medicine respectively, believe that the Network Hypothesis by Niels Jerne contains insight as to why these side effects occur. In this hypothesis, Jerne details the process as to which the immune system regulates antibodies. This process is a cascade, in which the immune system launches antibody responses initially to an antigen. These antibodies can trigger an antibody response toward themselves, causing them to disappear over time. Anti-idiotype antibodies, also known as secondary antibodies, bind and deplete the initial antibody responses. They have the ability to act like the original antigen itself, which would initiate side effects to the person. 

SARS-CoV-2

SARS-CoV-2 spike protein, the protein responsible for binding to ACE2 Receptors

SARS-CoV-2, the virus that causes COVID-19, enters the body by binding its protein spikes to the ACE2 receptor, thus gaining entry into the cell. The immune system then reacts by producing antibodies for the virus, which neutralizes the effects of the virus. However, these antibodies can cause immune responses with the anti-idiotype antibodies. These secondary antibody responses clear the initial antibodies, which results in the depletion of the initial antibodies and a weakened efficiency for antibody production. 

 

Murphy states that “A fascinating aspect of the newly formed anti-idiotype antibodies is that some of their structures can be a mirror image of the original antigen and act like it is binding to the same receptors that the viral antigen binds. This binding can potentially lead to unwanted actions and pathology, particularly in the long term.” He and Longo also believe that these anti-idiotype antibodies can also target the same ACE2 receptors. 

 

In an article published by The Conversation, the ACE2 receptors play an important role in the immune response against SARS-CoV-2. The authors, Krishna Sriram, Paul Insel, and Rohit Loomba, write that the “SARS-CoV-2 virus binds to ACE2 – like a key being inserted into a lock – prior to entry and infection of cells. Hence, ACE2 acts as a cellular doorway – a receptor – for the virus that causes COVID-19.” Personally, this fact baffles me, since it’s truly both amazing and terrifying that non-living viruses are able to manipulate and finesse their way into infecting the host cells. 

 

Returning to the main article, the ACE2 receptors could be responsible for the long-lasting effects being reported to both the vaccine and the virus itself. These responses can also answer why these long-term effects can occur, even long after the infection has passed. 

 

These terms are apparent in our AP Biology classroom, specifically regarding the Immunity System. The immune response used to combat SARS-CoV-2 is Adaptive Immunity, which develops after exposure to pathogens including bacteria, viruses, toxins, or other foreign substances. Due to the complexity of SARS-CoV-2, Adaptive Immunity is used because it’s a specific but slower response to the virus. Both B Lymphocytes and T Lymphocytes are used in the response against COVID-19 but during different stages of the infection. When the virus first enters the body, the Immune System performs Humoral Response, in which B Cells bind to the antigen and secrete antibodies that are made by B-Plasma cells, and these antibodies are stored in the B-Memory Cells to prevent future infection. In the case that COVID-19 enters and infects a cell, the Cell-Mediated Response is used to kill off infected cells using T-Killer Cells and T-Memory Cells are created to prevent future infection.

How do you think this research will be implemented for the prevention of these long-term effects? Let me know in the comments below and stay safe!

This Parasite Can Change Agriculture for the Better

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On October 27, 2021

In Student Post

When parasites take control of a host, it may seem like all is lost for the unfortunate animal. However, a newly discovered parasite uses a mechanism that actually slows down plant aging, and may offer new ways to protect crops that were once threatened by diseases. 

Prior to this discovery, very little was known on how this parasite functioned on both a molecular and mechanistic basis. The Hogenhout group at the John Innes Centre and collaborators published in Cell have identified a manipulation molecule produced by Phytoplasma bacteria, which hijacks the development of plants. This protein breaks down key growth regulators, which as a result causes abnormal growth.

According to an article published by FronteirsIn, phytoplasmas and their associated diseases cause severe yield loss globally. For example, Aster Yellows cause major yield losses in crops such as lettuce, carrots, and cereals. As stated in the article, “Phytoplasma diseases of vegetable crops are characterized by symptoms such as little leaves, phydolly, flower virescence, big buds, and witches’ brooms.” These effects ultimately cause the host plants to die over time. 

Phytoplasma Growing on a Plant

Professor Saskia Hogenhuot said that “Our findings cast new light on a molecular mechanism behind this extended phenotype in a way that could help solve a major problem for food production.” One of these findings includes the bacteria protein entitled SAP05, which manipulates the plant’s molecular structure. This manipulation targets the process of the proteasome, which breaks down obsolete proteins inside plant cells. SAP05 causes the plant proteins that are used for regulating growth and development to be thrown out. With the absence of the proteins, the plant’s development favors the bacteria, which in turn triggers vegetative growth and pauses the plant’s aging process.

Specifically, SAP05 directly binds to the plant developmental proteins and the proteasome. Proteasomes hold a very important role in the cell regarding the degradation of proteins, with Professor Gonzalez writing, “proteasomes perform crucial roles in many cellular pathways by degrading proteins to enforce quality control and regulate many cellular processes such as cell cycle progression, signal transduction, cell death, immune responses, metabolism, protein-quality control, and development.” Conversely, SAP05’s direct binding is a newly discovered method of degrading proteins, unlike the usual fashion of proteins degraded by proteasomes that are tagged with ubiquitin beforehand. 

To further study SAP05, the research team wanted to see if SAP05 affects the insects that carry the bacteria plant to plant. Turns out, SAP05 does not affect the insects due to the structure of the host proteins in animals differing enough from plants. This research also enabled the team to identify the two amino acids in the proteasome that interact with SAP05. If these two amino acids in the plant proteins were switched to the amino acids found in the insect protein, they would prevent abnormal growth. 

In a polypeptide chain, every amino acid is important to how the chain functions. Specifically, an amino acid’s unique side-chain gives it different characteristics, which plays a role in how the protein is structured and its function in the cell. In this case, these two amino acids from plant to insect proteins ultimately change the way SAP05 interacts with the polypeptide chain, which as a result changes the effect. 

Personally, I feel that this discovery is groundbreaking since it enables countless possibilities regarding the prevention of mass yield loss. How do you think this research will be utilized in the future? Let me know in the comments!

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