BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: infection

The Fluorescent Frontier: Glow in the Dark Proteins in Disease Research

We all know that although science is improving rapidly on a global scale, diagnostic tests for diseases remain sensitive and require complicated techniques. One evident example is the tests for COVID-19. This complexity can range from their preparation to an interpretation of their results. However, recent research from the American Chemical Society has developed a method that is able to analyze viral or infected nucleic acids in less than 30 minutes and in just one step. This is all due to “glow in the dark” proteins.

Bioluminescence is a scientific phenomenon that powers many animals: a firefly’s flash, an anglerfish’s glowing head, and even phytoplankton’s blue color.  Here a chemical reaction occurs, involving the luciferase protein. This protein essentially causes the “glow in the dark” effect. The protein is incorporated into sensors which emit a light when a target is located. Although the simplicity of these sensors is idyllic for clinical diagnostic testing, they still lack the sensitivity

One solution to this problem is presented by a particular gene editing technique: CRISPR. The Broad Institute defines CRISPR as; Clustered Regularly Interspaced Short Palindromic Repeats. It is essentially an efficient and customizable alternative to other existing genome editing tools. With this new technique, Maarten Merkx and his coworkers wished to use CRISPR-connected proteins while combining them with a bioluminescence form whose glow could be seen by humans, through a digital camera for example.

CRISPR CAS9 technology

To ensure that there was an ample amount of DNA or RNA to analyze, they used a technique known as Recombinase Polymerase Amplification, or RPA. This is a simple method which works continuously at a temperature of 100 F. With this  two CRISPR proteins specific for different parts of a viral genome each have a different fragment of luciferase attached. In other words, the new treatment known as LUNAS (Luminescent Nucleic Acid Sensor), takes two CRISPR proteins for different parts of a viral genome and has a distinct fragment of luciferase added to each.

Moreover, if one specific viral genome that the researchers were testing was present, the two CRISPR proteins would bind to the targeted nucleic acid sequence. This would allow them to come together and promote the full luciferase protein to form and glow. Additionally, to account for the luciferase being depleted, the researchers used a control reaction which turned green. In the event of a positive viral detection the color would change from green to blue. To prove the validity of this method, the researchers tested LUNAS on clinical samples of nasal swabs testing COVID-19. The method successfully detected the virus in less than 20 minutes, even at low concentrations. With this, the LUNAS method holds great potential in detecting other viruses in a concise and efficient manner.

Zika-chain-colored

To connect to our AP Bio class, we learned about how specific proteins code for specific actions or results in our bodies. At their tertiary and quaternary structures, proteins have a myriad of functions ranging from acting as a receptor to interacting with an enzyme. This parallels with the luciferase’s specific function of creating a glow affect. Additionally we learned about cell communication and how interaction with a receptor would result, or cause a specific occurrence. This connects to luciferase’s binding to its sensor, causing the glow affect. This cell communication also connects to the two CRISPR proteins attaching to a specific nucleid acid sequence. If the nucleid acid holds the viral genome and the luciferase, it would connect and form a glow response – a direct example of intercellular communication. Continually, we learned about DNA manipulation and alteration and how segments can be added in, substituted, or even removed. This occurs in CRISPR gene editing’s nature as a genome editing tool. It exemplifies all these manipulations to both DNA and RNA. We also learned about ideal protein function at a variety of temperatures, pHs, and environmental settings. This idyllic setting in seen in RPA’s function at a continuous 100 F.

To close, I feel that the use of luciferase, or “glow in the dark” proteins fronts an entirely new way of combating diseases and supporting disease identification. It would provide a new way for doctors and scientists to diagnose patients in a time efficient manner. And frankly, the idea of being diagnosed by something “glow in the dark” is entirely lightening and provides some relief to the gravity of the situation. I invite any and all comments regarding this specific method of disease identification or any other relevant discussion points.

Can Your Lungs Work Against COVID-19?

Within the last two to three years there has been an immense focus in the field of science, COVID-19. This pandemic has sparked a myriad of research opportunities as well as brought up questions we didn’t even know we needed answered.

With this, recent research at the University of Sydney shows that our lungs contain a protein that blocks the COVID-19 infection and works to create a protective barrier within our body. The way it works is that a protein receptor found in our lungs sticks to the virus, and then pulls it away from the targeted cells. The protein is known as the Leucine-Rich Repeat-Containing Protein 15 or in short, LRRC15. For context, leucine is an essential amino acid for protein synthesis as well as many other biological functions. The protein is a built-in receptor inside of our bodies that binds to the COVID-19 virus and doesn’t pass on the infection.

Lungs diagram detailed

Initially, the research was published on February 9, 2023, in the PLOS Biology Journal. Led by Professor Greg Neely and his team members, the findings serve to open a new sect of immunology and COVID research, specifically around the protein, LRRC15. Moreover, it creates a path to develop new drugs and treatments to prevent infections such as COVID-19. Greely states that ” This new receptor acts by binding to the virus and sequestering it which reduces infection,” essentially the receptor is able to attach to the virus and “squish” it before it moves to infection. He also pushes the idea that the new receptor can be used to “design broad-acting drugs that can block viral infection or even suppress lung fibrosis.” Continually Dr. Lipin Loo, one of Greely’s team members, mentions, “We think it acts a bit like Velcro, molecular Velcro, in that it sticks to the spike of the virus and then pulls it away from the target cell types,” here he outlines the stickiness of both the receptor and the virus as well as the receptor’s nature to latch onto the virus and “hold” it. In addition, Loo states, “When we stain the lungs of healthy tissue, we don’t see much of LRRC15, but then in COVID-19 lungs, we see much more of the protein,” here he fronts the idea that COVID-19 lungs are far richer in the LRRC15 protein than normal lungs, this may be due to a result of the protein’s ability to immobilize the virus.

To outline COVID-19 infects us by using a spike protein to attach to a specific receptor in our cells. It mainly uses the ACE2 receptor to enter human cells. Moreover, our lung cells have high levels of ACE2 receptors, which is why being infected can often cause severe problems in our lungs. Similar to ACE2, LRRC15 is a receptor for COVID. But, LRRC15 does not support infection, instead, it sticks to the virus and immobilizes it. This prevents other cells from becoming infected. LRRC15 attaches to the spike of the virus and pulls it away from certain target cell types. The LRRC15 protein is widely present throughout our body, it is in the: lungs, skin, tongue, fibroblasts, placenta, and lymph nodes. However, the researchers observe that the lungs “light up” with LRRC15 after infection. They think the new protein is a part of our body’s natural response to combatting the COVID-19 infection. It creates a barrier that separates the virus from our lung cells most susceptible to COVID-19 infection

SARS-COV-2

To connect to our AP Bio Class, we learned about adaptive immunity where we develop an acquired immunity after being exposed to pathogens, a specific response. I see some similarity here in that the LRRC15 protein is specific to immobilizing the COVID-19 infection. Additionally, in our Cell Signalling Chapter, we focused on signal transduction and its stages, reception, transduction, and response. Specifically in the reception stage, we focused on intracellular and transmembrane receptors. I think that LRRC15 would be transmembrane in order for it to efficiently bind to the COVID-19 Spike. With this, however, I would like to see more about the transduction component of the LRRC15 receptor. Lastly in our Enzyme Unit, we learned about how different factors can affect enzymatic activity; heat, pH, and even general surroundings. I wonder which factors work to hinder and work to stimulate the purpose of the LRRC15. I invite any and all comments with additional info relevant to the topics discussed.

How COVID-19 Antibodies Are Causing Long-Term Effects

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!

HIV > CRISPR-Cas 9

https://commons.wikimedia.org/wiki/Category:HIV#/media/File:HIV-infected_H9_T_Cell_(6813314147).jpg

HIV Infecting a Cell

CRISPR-Cas 9 is an extremely advanced gene editing tool. This tool has efficiently created ways to make precise and targeted changes to the genome of living cells. However, in a study in the journal Cell Reports, scientists from the McGill University AIDS Center in Canada discovered drawbacks in using CRISPR to treat HIV. Instead of simply removing the virus from affected cells, the process of using CRISPR can also strengthen the infection by causing it to replicate at a much faster rate.

HIV has always been a popular disease to conduct research on. Scientists are constantly attempting to come up with ways to kill HIV. Several cures to HIV have been developed such as various as antiretroviral drugs, however, these medicines stop being effective after the patient has ceased to take them. As scientists have started to utilize gene editing tools to remove HIV they have been noticing the huge drawback. They realize that while the gene alteration allows the virus to be killed off in some cases, the resulting scar tissue can lead to the infection becoming stronger! Kamel Khalili, a scientist at Temple University, pointed out that the key to eliminating HIV could lie in attacking the virus at different sites using CRISPR.

Link to Original Study

Link to Original Article 

Link to Original Photo

Animal Overdose and Its Effect on Humans

As we all know, antibiotics can be used to cure infections and kill bacteria, but the also often come with the many side effects that the infomercials so quickly warn us of. However, we often overlook aspects of antibiotics and rely on them to heal us in a variety of ways.

This then causes too much reliance on antibiotics, and in fact, humans are becoming immune to these medicines and too much use takes from their ability to have positive results.

This displays the alignment of veal that has been modified and undergone treatment to fight possiblebacteria.

This displays the alignment of veal that has been modified and undergone treatment to fight possible bacteria.

Animals have been receiving harsh treatment and experience weight gain as a result of being given antibiotics for growth promotion in order to sell more meat without disease.  However, animals experience the same resistance over time. The Environmental Working Group is concerned about this, because most of the meat sold in grocery stores is made up of a large amount of antibiotic-resistant bacteria. This, too, can easily be passed on to humans by consumption, as the Food and Drug Administration states.

Due to this resistance to antibiotics and its misuse, many are concerned that the amount of antibiotics served to both humans and animals needs to be lowered, which is much easier said than done. The ultimate goal would be to continue to fight bacteria as opposed to promoting its resistance, as one would assume. However, it is interesting to know how large of an affect antibiotics have on both the human and animal reactions in their bodily systems, and how misuse can alter the bacteria as well as the reason for their need.

Article Link:

http://www.scientificamerican.com/article/what-are-the-consequences-of-antibiotic-overuse/

Additional Links:

http://www.cdc.gov/narms/animals.html

http://www.pbs.org/wgbh/pages/frontline/shows/meat/safe/overview.html

http://www.fda.gov/ForConsumers/ConsumerUpdates/ucm378100.htm

Image Link:

http://en.wikipedia.org/wiki/Veal#mediaviewer/File:MIN_Rungis_viandes_de_boucherie_veau.jpg

 

Depression Infection?

Melancholy_2

 

Major Depression Disorder (MDD), most commonly known as “Depression”, is typically thought of as a genetic or neurological disease. However, Dr. Tuhran Canli, Associate Professor of Psychology and Radiology at Stony Brook University, suggests that MDD be recategorized as a result of a parasitic, bacterial, or viral infection. Canli’s paper, Biology of Mood & Anxiety Disorders, argues how possible pathways from these infections could cause MDD.

The causes of MDD are still unclear, therefore the research is delving more into the causes over the treatments. Dr. Canli suggests that by redefining MDD as an infectious disease, it will push future researchers to focus their attention on parasites, bacteria, or viruses.

Canli’s three major arguments for this change of MDD’s etiology are as follows:

1. MDD patients have a loss of energy, typically found in an illness. Also, the “inflammatory biomarkers in MDD suggest an illness-related origin”.

2. Parasitic, bacterial, and viral infections alter emotional behavior in humans.

3. The body is an ecosystem, made for microorganisms and genetics. These infections alter that ecosystem.

The redefinition of the causes of MDD could have significant help in finding the cause and eventual better treatment of the disease. Has depression been an infection all along?

 

Original article: http://www.sciencedaily.com/releases/2014/11/141114124307.htm

Picture: http://commons.wikimedia.org/wiki/File:Melancholy_2.PNG

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