madnahallicase – BioQuakes

A group of researchers at the University of Zurich have completed a study to test whether CRISPR gene editing technology can be used to correct the DNA sequence error in people with chronic granulomatous, a rare genetic disease that causes white blood cells to be unable to kill certain pathogens. They found that the technology was successfully able to insert the two nitrogenous bases, that are missing in people with this disease, into the DNA sequence. While this process was successful, they also found that, at the same time, it caused further damage to the DNA.

After performing the gene editing process, the scientists found new defects in the newly repaired cells. In certain cells, the entire section of the DNA where the editing took place was missing. This is due to the NCF1 gene and its characteristics. It shows up three times in the DNA; once as an active gene, and twice as pseudogenes, which are sections of DNA that resemble active genes but are in fact nonfunctional. The CRISPR technology cannot distinguish between the two versions of the gene and therefore ends up editing multiple portions of the DNA, resulting in gene segments being misaligned or missing. The consequences of such errors are still not fully understood and can be unpredictable. Therefore medical professionals are hesitant to use this method of treatment for chronic granulomatous disease. Other research teams have continued this work to find a safer method of treatment using CRISPR. Do you think that CRISPR should be used to cure diseases like chronic granulomatous despite possible risks?

Model of DNA Structure

This connects to the AP Biology subjects of DNA structure and function. The CRISPR technology performs edits to DNA sequences such as adding or removing certain nitrogenous bases, which is closely related to DNA structure. It also relates to DNA function as changing the sequence of the DNA will alter what the DNA codes for. This changes how certain portions of DNA affect cell processes by, for example, producing different proteins.

New Research Suggests Adopting C4 Plants’ Photosynthesis Could be the Key to C3 Crops’ Survival During Climate Change, and a Simpler Process than Previously Thought

By madnahallicase

On March 7, 2025

In Student Post

Researchers have recently discovered the specific evolutionary changes that occurred within C4 plants that allow them to perform photosynthesis in the specific way they do. The proteins that regulate the genes that are responsible for C4 plants’ specific photosynthesis are found in both C3 and C4 plants, meaning that in the future, scientists will be able to transition C3 plants to start performing C4 photosynthesis.

C3 plants can be less efficient at photosynthesis than C4 plants as they are prone to accidentally perform photorespiration occasionally. This slows down the process of photosynthesis and wastes the plant’s energy. C4 plants do not have to face this issue as they use bundle sheath cells, which are the cells that form a layer surrounding the veins of the leaf, to perform photosynthesis along with the mesophyll cells which are normally responsible for the majority of photosynthesis. This allows C4 plants to avoid photorespiration completely and increase water-retention. Overall the way that C4 plants have adapted to perform photosynthesis has many benefits and the potential to help C3 plants when faced with more extreme climates due to global warming.

Cross section of a C4 plant highlighting bundle sheath cells in purple and mesophyll cells in green

In order to figure out how C3 plants were initially able to evolve into C4 plants, researchers used single-cell genomics technology to analyze the differences between specific C3 plants and C4 plants. They found that it was not a change in the genes of the plants that caused them to become C4 plants, but rather a change in the process of regulatory proteins turning on or off certain genes within the cell. The specific family of these proteins are called DOFs, and the scientists found that they are present within both C3 plants and C4 plants. They even bind to the same section of DNA. The researchers found, however, that in C3 plants, the section of DNA was only associated with bundle sheath identity, while in C4 plants, it was also associated with photosynthesis. This allows both genes to be turned on within C4 plants at the same time, and therefore for bundle sheath cells to have the ability to photosynthesize. Since this ability was not a result of the addition or removal of a specific gene, scientists are hopeful that the process of adding this C4 photosynthesis ability in C3 plants will be relatively simple. What do you think of this discovery? Do you think it will be able to help with the growth of crops in the future as we combat climate change?

This relates to the AP Biology subjects of photosynthesis and molecular fitness. Both C3 plants and C4 plants perform photosynthesis in order to create glucose and other sugars from the sun’s energy. C4 plants’ adaptation to also perform photosynthesis within bundle sheath cells is an example of molecular fitness, as it allows them to survive long enough to reproduce in more extreme environments.

New Explanation for how Certain People’s Immune Systems Prevent them from Contracting Covid-19

By madnahallicase

On December 16, 2024

In Student Post

Researchers have completed recent studies of people’s immune responses to Covid-19 pathogens. They found that certain innate immune responses work better at preventing infection of the virus than others. In addition, the researchers were able to recognize patterns relating to the receptors on T-cells which may be able to help in the creation of new strategies to fight infections.

SARS-CoV-2

The experiment was conducted by researchers from Wellcome Sanger Institute, University College London, Imperial College London, and the Netherlands Cancer Institute. It included a group of participants who had never before been exposed to Covid-19, which was an important detail to the experiment as the researchers wanted to observe specifically the immune responses to pathogens it had not encountered before. Each participant was first purposefully exposed to the virus and then closely observed for a duration of time following that exposure. The researchers monitored the blood and linings of the nasal passages of each person daily, taking note of any immune cell activity. The researchers were then able to use single cell sequencing to create their dataset for this experiment. Single cell sequencing is a method of analyzing the nucleic acids within a cell to understand the function and behavior of different cells. Upon further analysis, the researchers were able to identify immune responses that had not been recorded among people previously infected with Covid-19.

The two most notable of the new immune responses found during this experiment were the activation of specialized mucosal immune cells and a significant decrease in inflammatory white blood cells throughout the body. These immune responses were only present in the people who did not experience infection or symptoms after being exposed to the virus. Typically Covid-19 patients have an immune response that is widespread throughout the body, yet these people showed innate immune responses specifically in the nose. On the other hand, the people who ended up becoming infected presented the opposite immune response, allowing the virus to establish itself in the nose. The researchers also suggest that activity of a certain gene preceding exposure to the virus further helped certain individuals to remain healthy. This gene called, HLA-DQA2, codes for a protein that is a part of the leukocyte antigen system which is an important part of the immune system. Using these findings, researchers hope to be able to develop new, better ways to fight off Covid-19 and other viruses.

This connects to the AP Biology unit of the immune system. The topics being studied in this experiment included innate immune responses. The mucosal cells in the nose and inflammation are both examples of innate immunity. In contrast with adaptive immunity, which is specific to each individual pathogen, these innate immune responses do not recognize differences between pathogens. I think that this research is important and will hopefully help in the creation of new medical technologies. What do you think of this research?

New Molecule, Nanobody NbE, Used to Mitigate the Harmful Effects of Opioid Drugs

By madnahallicase

On October 22, 2024

In Student Post

Researchers from the University of Geneva have recently discovered the molecule, nanobody NbE, which can be used to block the activity of opioids. These molecules are able to do so by binding to the cell receptors that usually bind to opioids. Nanobodies, which are antibody fragments, are much smaller, better at binding to antigens, and more stable in extreme conditions than full antibodies. They are essentially smaller versions of antibodies, the proteins produced by one’s immune system tasked with attaching to harmful substances in the body in order to remove them. Nanobodies, being more simple in structure, have the potential to overcome the limitations of natural antibodies according to scientists’ predictions.

Antibody vs. Nanobody

Nanobody NbE is able to block the harmful activity of opioids by binding with the cell receptors that normally would bind to opioids. Scientists were able to discover the powerful binding ability of this nanobody using “high resolution structural biology methods”. Other than this discovery, researchers also realized that it was only a small portion of the nanobody responsible for actually binding to the receptors. Scientists have now been able to synthesize smaller molecules that possess the same ability as nanobody NbE.

Even though nanobody NbE is much smaller than regular antibodies, it still is a relatively large protein. Nanobodies themselves can be quite costly to produce and their size results in other complications. Because of this, researchers thought of a way to produce a smaller molecule that would provide the same function. These new smaller molecules mimic the portion of nanobody NbE that is actually responsible for binding to receptors. While they are still being refined, the development of these small molecules could potentially help with opioid overdoses and the harmful effects of the drugs.

This connects to the AP Biology subjects of organic compounds and cells. The nanobodies themselves are examples of proteins that have a specific function within the body. In order to be able to bind with receptors, these proteins must at least have tertiary structures and are most often quaternary structures. They bind to opioid receptors, which are embedded in neuron membranes, making them ligands. This relates to not only the function of cell membranes but also specifically neurons. I think that this discovery has a lot of potential to help people and possibly be inspiration for other forms of medicine. What is your opinion on the subject?

BioQuakes

AP Biology class blog for discussing current research in Biology

Author: madnahallicase

CRISPR Gene Editing can have Unwanted Effects

New Research Suggests Adopting C4 Plants’ Photosynthesis Could be the Key to C3 Crops’ Survival During Climate Change, and a Simpler Process than Previously Thought

New Explanation for how Certain People’s Immune Systems Prevent them from Contracting Covid-19

New Molecule, Nanobody NbE, Used to Mitigate the Harmful Effects of Opioid Drugs

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