AP Biology class blog for discussing current research in Biology

Author: jouleian

Can Gene Editing Prevent Disease in the future?

There is very exciting news in the world of biology right now. For the first time ever, according to the University of California San Francisco‘s chancellor,  Sam Hawgood, CRISPR gene editing will be delivered to a human in an attempt to study how gene editing can help with asthma.

CRISPR-Cas9 Editing of the Genome (26453307604)

CRISPR-Cas 9 was adapted from a naturally occurring genome that allows bacteria to fight off viruses. When a bacteria was infected with a virus, it would use this genome to take pieces of the DNA from the virus and add them to its own DNA to create a pattern known as a ‘CRISPR array.’ The ‘CRISPR array’ allows the bacteria to remember the virus and cut the DNA of the virus apart.

In 2021, Peter Turnbaugh administered CRISPR into mice in order to target a specific gene and edit it out of the mouses gut. It was this work that inspired the scientists at UCSF to experiment with adding the CRISPR to a human microbiome.

Asthma is the perfect place to start because there is a clear microbial target to attack. There is a molecule that is produced by bacteria in the human gut that can trigger asthma in childhood. The scientists goal is to stop the microbes from producing that molecule, rather than remove the microbe altogether, as that microbe plays other beneficial roles in the human body. By taking a small piece of sgRNA, the scientists would be able to attach that to the target sequence in the DNA of the bacteria that produces that molecule, and ultimately stop the bacteria from producing the molecule that causes asthma.

This can be related to the topic of DNA and Genes that I learned about in AP bio. While reading the UCSF article, I couldn’t help but think about DNA replication, and what implications gene editing would have on DNA replication.

As we learned in AP bio, DNA replication is the process by which a cell copies its DNA before cell division, ensuring that each daughter cell receives a complete set of genetic instructions. During replication, the double-stranded DNA molecule is unwound and separated into two strands, each of which serves as a template for the synthesis of a new complementary strand. The result is two identical copies of the original DNA molecule.

If the scientists at UCSF were able to edit the genes to properly stop the microbes from producing the molecule that causes asthma, would that trait now be passed on to the new complementary strands? Would this gene editing get passed on through DNA replication, and even further would it be passed on to gametes? If both parents were to get this gene edited, would their zygotes now also be immune to asthma, and if so it is almost as if this gene editing is affecting natural selection and evolution.

All of this was very interesting to me and it seems that if/when this becomes a regular part of society, it will have major implications on the way our species sees diseases in the future.

Understanding a Plant’s Stomata to Counteract Affects of Climate Change?!

In mid January, 2023, researchers from the University of California San Diego made an important discovery surrounding photosynthesis, specifically the plants stomata, with climate change implications.

Tomato leaf stomate 1-color

Scientists have understood photosynthesis for many years. As we learned in AP Bio, photosynthesis is the process by which plants, algae, and some bacteria convert light energy from the sun into chemical energy in the form of glucose. The process of photosynthesis can be divided into two stages: the light dependent reactions, and the Calvin cycle.

The light-dependent reactions occur in the thylakoid membranes of chloroplasts and involve the conversion of light energy into chemical energy in the form of ATP and NADPH. During these reactions, water molecules are split  into hydrogen ions, electrons, and oxygen gas. The electrons move through a series of electron carriers and ultimately end up on NADP+ to form NADPH. At the same time, hydrogen ions are pumped from the stroma into the thylakoid lumen, creating a concentration gradient that drives the synthesis of ATP through a process called photophosphorylation.

The Calvin cycle, occurs in the stroma of chloroplasts and involve the conversion of carbon dioxide into glucose. During these reactions, carbon dioxide is fixed into organic molecules by the enzyme rubisco. The resulting molecules are then reduced by NADPH and ATP produced during the light-dependent reactions to form glucose. The Calvin cycle also requires a source of hydrogen ions, which are provided by the light-dependent reactions through the production of NADPH.

The researchers at the university of California San Diego, have furthered this understanding by explaining how the stomata is able to sense when to open and close in order to allow carbon dioxide and water to enter and exit the plant. When the stomata is open for carbon dioxide to enter, it exposes the plant to the outside world, and water from the plant is lost, which can end up drying out the plant.

This research is important because as carbon dioxide in the atmosphere increases, it could lead to the stomata of vital plants being left open too much, which would dehydrate the plant.

Fortunately, the research pointed to a specific protein, known as HT1, that was able to activate the enzyme that opens up the stomata in a low CO2 environment. The researchers also found a second protein that blocked the HT1 from keeping the stomata open in environments with higher CO2 concentrations. This second protein that was found is the reason plants will die when the atmosphere has too much CO2, as the stomata wouldn’t be open for long enough to get the necessary resources for photosynthesis.

This can relate to what we learn in AP Bio, in regards to enzymes and proteins. In AP bio, we learned that proteins are large molecules made of amino acids. Enzymes are a type of protein that catalyze chemical reactions. Enzymes also lower the activation energy needed for a reaction to occur. They interact with specific substrates to form enzyme-substrate complexes. The active site of an enzyme undergoes conformational changes, allowing for catalysis. Specific substrates can only bind to a particular enzyme. Enzyme activity can be affected by temperature, pH, and concentration. Enzymes work most effectively within a specific range of those things. Changes outside that range can affect structure and function. Enzymes and proteins play critical roles in many processes. Examples include DNA replication, protein synthesis, and metabolic pathways. Understanding enzyme-substrate interaction is crucial to understanding how the HT1 that activates the enzyme was able to speed up the reactions that caused the stomata to open up.

As Richard Cyr, the program director stated, “Determining how plants control their stomata under changing CO2 levels creates a different kind of opening — one to new avenues of research and possibilities for addressing societal challenges.” Hopefully this research can result in positive steps for the agricultural community as it takes on the challenge that is climate change.


Universal cure for all variants of Covid-19?


The main issue with COVID-19 since the beginning of the pandemic has always been the various mutations. Someone could get COVID-19 and develop some sort of immunity, but then a new variant would come around and the immunity would be less effective. Scientists at the Pohang University of Science and Technology are working hard to develop a cure for all variants of COVID-19

COVID-19 is a disease caused by the SARS-CoV-2 virus, which is a member of the coronavirus family. In AP Biology, we learned about viruses and how they infect and replicate within host cells. We learned about how COVID-19 is a prime example of how a virus can cause disease in humans. The SARS-CoV-2 virus enters host cells by binding to a receptor called ACE2, which is found on the surface of cells in the respiratory tract and other organs. Once inside the host cell, the virus uses its own enzymes to replicate and produce more copies of itself. This can lead to the death of the host cell and the release of new virus particles, which can then go on to infect other cells. The immune system plays a crucial role in defending the body against viral infections such as COVID-19. When the body is infected with a virus, the immune system recognizes the virus as foreign and mounts an immune response to try to eliminate it. This can include the production of antibodies, the activation of immune cells such as T cells and B cells, and the release of inflammatory molecules.

The reason COVID-19 has been so infectious and is able to mutate so much is because of the ability of the virus to change structure. This structure change increases the strength of its interaction with hACE2 receptors. An hACE2 receptor is the human version of the Angiotensin-converting enzyme 2, the enzyme that serves as the entry point for SARS-CoV-2. As we learned in AP bio, in order for a virus to enter the body, the antigen must bind to a receptor and then travel into the cell. SARS-CoV-2 binds to hACE2. First, the presence of SARS-CoV-2 produces the protein called, IgG. IgG binds to the spike protein on the SARS-CoV-2 cell and that IgG protein binds with the hACE2 receptors in human cells. This binding of IgG is what allows coronavirus to enter human cells.

Understanding this binding process has been key to developing cures for the virus. Most recently, a research team at Pohang University of Science has developed a revolutionary SARS-CoV-2 neutralizer that can adapt to mutations in the virus. This discovery is groundbreaking in the disease prevention world because the type of technology that is used for this specific example can be spread out across the field and used for other viruses. As Professor Seung Soo Oh described: “It is significant that we have developed the world’s first self-evolving neutralizer-developing platform that shows increasingly better performance with the occurrence of viral mutations.” He added, “We plan to develop it into a core technology that can respond to the next-generation pandemic viruses, such as influenza and Hantavirus.”

This neutralizer works by mimicking the interaction between the virus and the receptor, and than once that reaction is mimicked, its protein fragment and nucleic acids can stick to virus, preventing further interaction with the receptor, which eventually prevents the virus from entering the cells.

In all, a neutralizer that adapts with the virus in order to prevent infection and sickness is a groundbreaking discovery that could potentially change the way COVIS-19 (and viruses as a whole) are looked at.


Tardigrades: New findings regarding their durability and survivability while dried out

Tardigrades, also known as water bears, have caught the eye of many biologists due to their immense resilience and their ability to survive under extreme conditions. Tardigrades have been able to survive extreme temperatures, extreme pressures, oxygen deprivation, radiation, starvation, dehydration, and even the vacuum of outer space.

SEM image of Milnesium tardigradum in active state - journal.pone.0045682.g001-2

Among these phenomenons, their ability to survive while dehydrated has caused great confusion for scientists for many years. Recently, however, new research has been done at the University of Wyoming to help understand how Tardigrades are able to survive in a dried out state.

For a long time Scientists thought that Tardigrades did not possess the sugar molecule called Trehalose. Trehalose is usually the molecule found in organisms that can survive with a lack of water, however scientists had not found any evidence of Trehalose in Tardigrades until now. In October of 2022 scientists have finally found trace amounts of Trehalose in tardigrades, only less than the amount found in other organisms.

Trehalose is a disaccharide consisting of two molecules of glucose. It has very high water retention capabilities which is why organisms that synthesize it are able to survive with a lack of water. As we learned in AP BIO, because Trehalose is a disaccharide, the two molecules of glucose were formed together through a process called dehydration synthesis. (the removal of a water molecule to join two monomers) The resulting chemical formula for this would be C12H22O11 instead of C12H24O12 because of the removal of the water molecule. 

Now, with this new information scientists hope that better understanding tardigrades and their synergy with trehalose can help solve problems of water scarcity throughout the world. Understanding Trehalose could help with farming in areas of the world that don’t naturally get the water they need. By applying the adaptation abilities of tardigrades to organisms that wouldn’t otherwise survive under harsh conditions, trehalose could be a massive step in better crop engineering in harsh environments across the world. According to the national library of medicine, “Increasing trehalose accumulation in crop plants could improve drought and salinity tolerance.” An example of this working has already been proven in this study with rice. The scientists had a control plant that wasn’t transformed with trehalose, and several independent transgenic rice plants. The evidence showed that when the rice was fused with trehalose it “exhibited sustained plant growth, less photo-oxidative damage, and more favorable mineral balance under salt, drought, and low-temperature stress conditions.” All of these things make for an interesting future in the world of engineered crops.

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