BioQuakes

AP Biology class blog for discussing current research in Biology

Author: avahesion

Overcoming a Critical Limitation of CRISPR

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On April 23, 2023

In Student Post

Recent research demonstrates that CRISPR Spherical Nucleic Acids (SNAs) can be delivered across the cell membrane and into the nucleus, all while retaining bioactivity and capability of gene editing. Gene editing is technology which allows a scientist to change an organism’s DNA. 

The work displayed in this article builds on a 25-year study to uncover the properties of SNAs and the factors that distinguish them from the blueprint of life. SNAs are structures typically composed of spherical nanoparticles covered with DNA or RNA, giving them chemical and physical properties different from those forms of nucleic acids found in nature. 

Core-filled and Core-less Spherical Nucleic Acids 01

A variety of SNAs exist, with cores and shells of different chemical compositions and sizes. SNAs are also now being evaluated as potent therapeutics in human clinical trials, such as trials for brain cancer and skin cancer. 

According to nanotechnology pioneer Chad A. Mirkin, “these novel nanostructures provide a path for researchers to broaden the scope of CRISPR utility by dramatically expanding the types of cells and tissues that the CRISPR machinery can be delivered to.” “We already know SNAs provide privileged access to the skin, the brain, the eyes, the immune system, the GI track, heart and lungs. When this type of access is coupled to one of the most important innovations in biomedical science in the last quarter-century, good things will follow.”

Mirkin’s team used Cas9 (protein required for gene editing) as the core of the structure, and attached DNA strands to the surface to form a new type of SNA. These SNAs were also preloaded with RNA capable of performing gene editing and fused with peptides to control their ability to navigate compartmental barriers of the cell, making it the most efficient. In AP Biology, we learned that peptides are molecules containing two or more amino acids. Peptides that contain several amino acids are called polypeptides or proteins. These SNAs effectively enter cells without the use of transfection agents, and display high gene editing efficiency between 32% and 47% across several human and mouse cell lines. 

Advancing Toward Artificial Photosynthesis

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On March 6, 2023

In Student Post

Scientists have succeeded in synthesizing fumaric acid, a raw material for plastics, from CO2 powered by solar energy. This new artificial method of photosynthesis using sunlight can reduce CO2 by combining it with organic compounds, which can be converted into material, such as plastic. 

In the natural process of photosynthesis—as we learned in AP Biology class—CO2 is bound to organic compounds, such as RuBP, and converted into sugar. This is what we call carbon fixation, which takes place in the Calvin Cycle. Carbon fixation is the addition of carbon dioxide to organic molecules to prevent it from remaining in its “free state” in the atmosphere, which, in turn, creates energy. CO2 is not directly reduced in natural photosynthesis. This new discovery reveals that CO2 can synthesize fumaric acid using renewable solar energy. Fumaric acid is an important chemical which is mainly produced by petroleum-based chemical synthesis; however, these findings reveal that it can be synthesized from CO2. 

This research is progressing to the practical application of artificial photosynthesis, as it has effectively used visible light, a form of renewable energy, as its power source. What do you think of this new artificial process of photosynthesis? The scientists aim to collect gaseous CO2 and use it to synthesize fumaric acid directly through artificial photosynthesis. 

Natural Photosynthesis vs the Bionic Leaf

Why Artificial Photosynthesis?

Artificial photosynthesis is a strategy to convert sunlight, an unlimited and sustainable energy source, into chemical fuels. This artificial process of photosynthesis mimics photosynthetic organisms by using sunlight to yield high-energy chemicals with higher efficiencies. Producing plastics from solar energy and CO2, rather than fossil fuels, is also beneficial to our environment. This is because the more plastic we create using fossil fuels, the more fossil fuels we use, which ultimately harms climate change.

“Secret Doors” Are Not So Secret Anymore! 

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On January 16, 2023

In Student Post

In AP Biology class, we learned that an allosteric interaction is when an effector (some other kind of molecule) inhibits or activates an enzyme at its allosteric site. When an allosteric enzyme binds to an effector molecule, a conformational change occurs. The allosteric effects of many mutations that cause diseases, such as cancer drivers, cause them to be pathological. Allosteric sites are very difficult to locate because the rules governing how proteins work at the atomic level are hidden out of sight.

EnzymeActiveandAllostericSites

A recent discovery reveals newly discovered “secret doors” that control protein function and which could potentially be targeted in order to improve the conditions of cancer, dementia, and infectious diseases. Proteins play a crucial role in all living organisms by fighting diseases, speeding up reactions, acting as messengers, etc. A protein’s structure is essential to its function, and with one change in its sequence if amino acids could result in devastating consequences to a human’s health. 

Researchers have previously found success in targeting active sites, and now, with this new method, allosteric sites are identifiable as well. Several treatments have been designed that target a protein’s active site; however, active sites of different proteins look very similar, causing medications to bind and inhibit many different proteins at once. This leads to potential side effects. In contrast, allosteric drugs are one of the most effective medications available today due to the specificity of allosteric sites. The new method in targeting allosteric sites has been used to chart the first map ever of these allosteric sites in two of the most common human proteins. This new approach may be a game changer for drug discovery, leading to more effective medications, and enabling researchers to locate and exploit vulnerabilities in any protein—even those previously thought to be untreatable! 

Please feel free to leave your thoughts or questions in the comments! 🙂

Memory B Cells in Our Lungs Can Prevent Us From “Coughing up a Lung”  With COVID-19

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On December 8, 2022

In Student Post

Memory B cells are produced in the bone marrow and are mainly found in the lymph nodes and the spleen following infection. However, a recent discovery reveals that they can also be located in the lungs. These memory B cells located in our lungs are highly effective in blocking SARS-CoV-2 virus entry to the respiratory tract!

In AP Biology class, we learned that memory B cells allow immunity to viruses in the future. These cells memorize the characteristics of the antigen (virus) that activated their parent B cell during the infection—hence their name, memory B cell. This triggers a fast, strong, and long-lasting secondary immune response if the memory B cell encounters the same antigen again. 

Aiming to reach a greater understanding of memory B cells’ role in the long-term immune response to respiratory infections, scientists studied mice infected with either influenza or SARS-CoV-2 viruses. The scientists tracked the appearance of memory B cells after infection using fluorescent markers— but not the type we use to draw and color! These fluorescent markers (shown in the image below) are specific molecules that bind to form fluorophores. Fluorophores can re-emit the light that they absorb and emit color, allowing scientists to track particular cells. After tracking the memory B cells, the team performed a single-cell transcriptome analysis, studying the genes expressed in each cell of the sample, which helped them study the function of the animal’s cells. 

S cerevisiae septins

The research revealed groups of memory B cells in the bronchial respiratory mucosa that had formed after the virus left the mice’s bodies. The memory B cell groups were located in a strategic position in which they would be in direct contact with any new virus that entered the lungs! 

COVID-19 vaccines are currently administered intramuscularly. Researchers hypothesize that intranasal vaccination (through our nose) would mimic the natural entry pathway of the virus, moving these lung memory B cells to block the virus as it reaches the respiratory tract, ultimately protecting the body from infection altogether. An intranasal vaccination might not sound too pleasant, so I must add that these are not administered the same way as intramuscular vaccines; intranasal vaccinations are painless, noninvasive, and DO NOT require a needle! Intranasal vaccines are sprayed into each nostril and inhaled, preventing the virus from infecting the body by attacking it at its point of entry. 

Live, Intranasal Influenza Vaccine DVIDS213849

There are several advantages to intranasal vaccination, as it elicits both systemic and mucosal immunity. Systemic immunity induces antibody formation, while mucosal immunity provides protection at the precise site of the infection. In contrast, intramuscular vaccination does generate systemic immunity; however, this tactic lacks the additional benefit of mucosal immunity.

I presume that intranasal vaccination would significantly decrease COVID-19 rates in our nation, as it would better protect us from the initial infection itself. Scientists should continue to work toward finding an effective intranasal vaccine for COVID-19. Do you agree? I would love to hear your thoughts; please feel free to leave a comment!

Advancing Towards a Cure for Mucolipidosis Type II

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On October 24, 2022

In Student Post

Mucolipidosis type II—also known as “I-cell disease”—is a rare life-threatening condition in which the heart and abdomens become swollen, bones deform, and the patient typically does not make it past the age of 7. This lysosomal storage disease is heritable and currently incurable.  

Inclusion cells are non-living substances located in the cell that are not membrane-bound. These non-living substances include glycogen, lipids, and pigments. In mucolipidosis, inclusion cells in growing fibroblasts occupy the cytoplasmic space aside the Golgi apparatus—hence the name “I-cell disease.”

Recent research reveals a new gene, TMEM251, that is defective in humans with symptoms of mucolipidosis type II. TMEM251 is crucial in enabling lysosomes to function appropriately. In AP Biology class, we covered how lysosomes are essential to various cell processes, such as digesting food and breaking down old cell parts enclosed in vesicles. Without the lysosome’s function, this waste will build up, unable to be broken down.

Several enzymes inside lysosomes digest worn-out cell parts (proteins, carbohydrates, lipids, and nucleic acids) of which the lysosome recycles. These enzymes require a signal called the mannose-6-phosphate biosynthetic pathway (M6P) in order to enter the lysosome. TMEM251 activates the M6P. When TMEM251 is defective, there is no M6P to allow the enzymes into the lysosome, thus creating an inability for the lysosomes to function

Researchers tested the link between defective TMEM251 and type II mucolipidosis symptoms by knocking this gene out in zebrafish, ultimately yielding defects in the zebrafish’s abdomen, heart, and skeletal development. These symptoms align with those of mucolipidosis type II in humans, concluding the existence of a relationship between TMEM251 and the disease. 

To treat children with mucolipidosis type II, the researchers propose the idea of “enzyme replacement therapy.” They hypothesize that by supplying enzymes containing M6P modification to TMEM251-deficient cells, the enzymes will be able to filter into the cell through endocytosis, delivering them to the malfunctioning lysosomes. Isn’t that neat? In AP Biology class, we learned that endocytosis occurs when the substances surrounding the cell membrane are transported into the cell. Through the process of receptor-mediated endocytosis, specific ligands (i.e. enzymes) bind to receptors that match their shape.  

A depiction of various types of Endocytosis

I believe that enzyme replacement therapy would efficiently treat mucolipidosis in humans, and encourage further study in this area to seek treatment for this deadly disease that robs young children of their bright futures. Would you support further research in this area? Please feel free to share your thoughts in the comments! 

 

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