BioQuakes

AP Biology class blog for discussing current research in Biology

Author: benzyme

Could Gene Editing be the Key to Perpetual Virus Resistance?

Influenza viruses have spread rapidly despite the vaccines many of us, humans, get (I, for one, just had the flu despite being vaccinated). Vaccines help our bodies recognize certain pathogens and create baseline antibodies to help neutralize them, but, as I learned in AP Bio class, mutations randomly happen. Not only is this genetic variation the key to natural selection in nature, but also for viruses (though viruses also often use the recombination process). As host organisms work as the viruses’ environment that they are trying to survive and reproduce in, natural selection could choose the viruses with mutations that are not recognized by our immune system from the vaccine and potentially create a new virus strand our vaccine is ineffective against.

Potentially more effective and permanent than vaccines, scientists are now exploring gene editing. A step up from the human interference in artifical selection that we learned in AP Bio, where humans choose to breed organisms with specifc traits to create ideal offspring, gene editing changes the organisms themselves. Typically thought of with genetically modified organisms (GMO) referring to plants and plant-based foods, gene editing can also be done on animals.

Take, for example, genetically-modified chickens that protect against avian influenza infections that have run throughout poultry farms at devastating costs. Since the ANP32A gene in chickens codes for the protein that influenza viruses rely on to successfully hijack cells, scientists edited that gene with CRISPR molecular scissors. As the protein is absolutely essential to the virus hijacking chicken cells, no simple mutations should be enough to override the gene editing; thus, chickens should theoretically be permanently resistant to the virus.

CRISPR-Cas9 Editing of the Genome (26453307604).jpg

In multiple studies done, this permanent resistance was almost the case: every typical chicken got the flu when closely exposed to high levels of it (at least 1000 infectious particles), whereas genetically-modifed chickens very rarely got it. In the first study, ten out of ten typical chickens got it, while just one out of 10 edited chickens got it and also at a lower level. In another experiment with an astounding 1 million infectous particles in two separate incubators, all of the typical chickens got it in both incubators and none of the modified chicken got it in one of the incubators, but five out of ten got it in the other. As it turns out, viruses in the latter incubator adapted to use proteins very similar to the protein the edited gene eliminated. There are two proteins very similar to the eliminated protein in chickens, so, to create full flu resistance in chickens, those two genes would need to be edited as well, researchers confirmed. However, editing those genes may hurt chicken development.

Chickens are everywhere, vital to many people’s diet, and can pass the flu to pigs and even us. If we can make chickens resistant to the flu, it could do us and our world wonders  plus, who knows where we will go from there!? Thus, I believe researchers should focus on figuring out if they can edit those three genes in chickens without hurting their development and how to create resistance with this incredible gene-editing ability if not.

We need to make use of our incredible technologies to limit illnesses and improve society; do you have any thoughts on gene editing or possibly even how we can maximize its potential to practically accomplish this task?

Stop Thinking Food Webs are so Simple!!

We have all learned about food chains and food webs: the producers perform photosynthesis to create their own food (autotrophs), the primary consumers eat the producers for energy (herbivores), the secondary consumers eat the primary consumers for energy (carnivores) and the tertiary consumers eat the secondary consumers for energy (carnivores). We also know that animals can often fit into multiple categories in a food web.

However, it is not quite as often that people explore the effects that just one population change of any part of a food web can have on the rest of the food web; that is to say that a producer decreasing in population would indirectly hurt a tertiary consumer’s population. That is the case because producers are how the food chain gets all its energy in the first place, so with less producers, less energy is in the food chain. Furthermore, as we learned in AP Bio class, each trophic level is merely 10% energy efficient in consuming the trophic level below; thus, each higher trophic level has less energy than the last. Not only is this lack of energy efficiency why there are only a few trophic levels in each food web, but that is why it is so vital for there to be enough (energy) producers in the food web. Additionally, with energy so scarce, any organism’s population size changing can have a dramatic effect on the other populations in its food web.

In the African savanna, Jake Goheen and his colleagues at the University of Wyoming and the Ol Pejeta Conservancy in Laikipia, Kenya, have taken investigating food web relationships to another level. They have spent about 15 years examining how acacia ants (genus Crematogaster) impact a food chain that they are not even a part of consumer wise. They have found that acacia ants protect whistling thorn trees from elephants, which would rip the trees apart: the ants, abundant in the savanna area, consistently protect the trees by swarming in the elephants’ nostrils and biting them from the inside out.

Whistling thorn acacia in Masai Mara

However, with the arrival of a new invasive species theorized to have arrived along with the shipping of human goods, called big-headed ants (Pheidole megacephala), acacia ants have been massively killed off in certain areas. Although the acacia ants are not part of the food chain consumption wise with the whistling thorn trees, the loss of the protection for the trees allows elephants to eat them. Then, much more grassland is opened up. According to Goheen and his colleagues, this open land, with approximately 2.67 times higher visibility than the land typically has (according to a separate study they did), hurts the diet of a higher trophic level predator, lions:

Goheen and his colleagues found that higher visibility in land with less whistling thorn trees helped one of the lions’ main prey sources, zebras, more than it helped them: their chance of taking down a zebra dropped from 62% to only 22% in areas with big-headed ants and thus minimal whistling thorn trees, according to Goheen’s study. Thus, lions pivoted to eating buffalos, which became 42% of their diet. Eating buffalos instead of zebras hurts lions because buffalos are more likely to injure them than zebras are, but buffalos and zebras are still both primary consumers, meaning they both have 10% of the energy of the producers that they eat; that is to say, although buffalos are more dangerous than zebras to lions, lions do not lose energy with their diet swap.

Regardless, more lion deaths from lions having to kill buffalos suggests that the invasive species of big-headed ants that killed off the acacia ants truly caused massive indirect changes in a food web that it and what it killed had nothing to do with consumer wise: to me, it seems apparent that there is much more to food webs than the basic, linear way people usually think about them.

What other ways do you think food webs are affected that we do not realize?

The Revolutionary mRNA COVID Vaccines

Biochemists Katalin Kariko and Drew Weissman have won the 2023 Nobel Prize in medicine/physiology. Why? Because they were the people behind the vaccines that just allowed us to control the worldwide COVID pandemic.

Usually, vaccine development takes about 5 to 10 years. However, more resources were put into the urgent battle of fighting the rapidly spreading COVID-19 than ever before: in record time, after the genetic sequence of the SARS-CoV-2 virus was discovered, several pharmaceutical companies, namely Moderna and Pfizer, created messenger RNA vaccines. Then, for the first time ever, the FDA approved mRNA vaccines.

Covid Vaccine

Typical vaccines consist of weakened viruses or bacteria that provoke the immune system to make antibodies to protect against future infections:

As I learned in AP Bio class, once those weakened pathogens are allowed to get through the body’s innate defenses (skin, mucus, tears, saliva, etc.), macrophages and dendritic cells engulf the antigens of the foreign pathogens (the spike protein for coronavirus) through phagocytosis, which the phagocytes can display on the outside of their plasma membranes on MHC proteins, while simultaneously releasing chemical messengers called cytokines. Activated by the cytokines, certain T-helper cells then recognize the antigens displayed on certain MHC proteins and call for an appropriate response. If this process is in a cell, T-helper cells activate cytotoxic T cells and T-memory cells. However, if it is in the blood, T-helper cells activate B-plasma cells and B-memory cells. B-plasma cells are the cells that create antibodies, which effectively neutralize pathogens and B-memory cells remember how to create those antibodies significantly more effectively for better future protection.

However, it is a very costly and tedious process for scientists to get loads of the coronavirus and weaken it for vaccines. The way Pfizer and Moderna created working COVID vaccines so quickly, based on the research that Kariko and Weissman began in 2006, is by creating vaccines with mRNA that tells cells how to create weakened coronavirus proteins; this process is instead of scientists manually putting weakened proteins into vaccines and is significantly more efficient since our bodies are already good at making proteins based on DNA/RNA code.

The reason why mRNA vaccines have never been FDA approved before the COVID vaccines is because pumping mRNA into the body releases cytokines itself. As mentioned previously, in AP Bio we learned that cytokines trigger helper-T cells. If helper-T cells are triggered when they shouldn’t be, that could create many problems. So, to fix this problem, Kariko and Weissman slightly altered the structure of the RNA to lessen cytokine triggering. Additionally, they encased mRNA in bubbles of lipids. As I learned in AP Bio class, lipids are nonpolar, meaning they can travel through cell plasma membranes. This lipid bubble, therefore, allows the mRNA to travel directly to and inside the nuclei of cells without causing harm elsewhere. Then, the mRNA can tell ribosomes to create the certain weakened coronavirus proteins that trigger the immune response of creating antibodies as previously described.

With the help of the research of the very deserving 2023 medicine/physiology Nobel Prize winners, Weissman and Kariko, the problems with mRNA technologies have finally been resolved (for now). Thus, this more efficient and may we call it, revolutionary mRNA technology is now being looked at to potentially defend other viruses and even cancers. The opportunities for this technology seem extraordinary, but what other challenges will scientists and researchers face when trying to explore these opportunities?

I would argue it is time for them to explore and find out.

Pink Pineapples???

Most days at school, I eat a snack that consists of pineapples — typical, yellow pineapples. However, it has come upon me that my favorite fruit can also be pink?! With the addition of a singular gene, genetically-modified (GMO) pineapples have their yellow inner color turn into bright pink.

Pineapple

In order to add the gene that causes a color change, scientists use a bacterium called Agrobacterium tumefaciens. They use this bacterium since it treats host cells like a virus does and transfers its DNA to the host cell. Thus, by adding Agrobacterium tumefaciens bacteria cells holding the color-changing gene to pineapples, the new gene’s DNA is able to transfer to the genome of a pineapple. I found this DNA transfer process interesting since it illustrates how prokaryotes can work differently:

In the Endosymbiotic Theory that I learned in AP Bio class, it is said that mitochondria and chloroplasts came into eukaryotic cells by being engulfed by them long ago as prokaryotic cells. All prokaryotes have their own DNA, but, different from Agrobacterium tumefaciens, these prokaryotes must have not been able to transfer their DNA to the host cell because the Endosymbiotic Theory is used to explain why mitochondria and chloroplasts have their own DNA separate from the cell, among other features.

Once in the pineapple’s genome, the DNA transcribes RNA, also as I learned in AP Bio class. However, rather than telling a ribosome what protein(s) to make, the RNA here purposefully interferes with the mRNA that pineapples naturally have that tells ribsomes to create an enzyme called lycopene beta-cyclase. This is in order to stop the prodcution of lycopene beta-cyclase, the enzyme which breaks down pineapple’s naturally-occuring pigment of lycopene into beta-carotene and makes pineapples yellow.

With the lycopene beta-cyclase enzyme no longer being synthesized, these GMO pineapples now have a surplus of lycopene; pineapples’ naturally-occuring lycopene is no longer being broken down. Lycopene is the compound that gives many red and pink fruits and vegetables, such as watermelons and grapefruits, their color. Hence, why pineapples high in lycopene concentration shine pink on the inside.

Lastly, if you ever buy one of these pretty pineapples, it came from the company Del Monte in Costa Rica, who patented the GMO pineapples and is therefore the only company allowed to grow them. Fortunately for Del Monte and rightfully so in my opinion, in Costa Rica these pineapples are higher in demand than supply.

Do you want to see more pink pineapples in the world?

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