AP Biology class blog for discussing current research in Biology

Author: namurthy

Glow in the dark proteins???

Recently scientists have discovered Glow in the dark proteins that could help diagnose viral diseases. Scientist rely on a chemical reaction using the luciferase protein, which “catalyze the oxidation of the substrate in a reaction that results in the emission of a photon”, which then causes the glow in the dark effect. The luciferase protien is then put into sensors that show a light when they find their target. Although these sensors are simple and would make point-of-care testing much easier, scientists have “lacked the sensitivity required of a clinical diagnostic test”. The gene editing tool CRISPR could provide this for them but requires many steps. According to MedlinePlus gene editing is a “a group of technologies that give scientists the ability to change an organism’s DNA“. A well known type of gene editing is called CRISPR, it is supposed to be more efficient and accurate than other genome editing methods. Scientist Maarten Merk decided to use CRIPSR related proteins and combine them with a bioluminescence technique whose signal could be detected. During testing scientists discovered that if a specific viral genome that was being tested for was present, the two CRISPR proteins would bind to the specific nucleic acid sequences and come close to each other, this would then cause the luciferase protein to shine a blue light.

AP Bio Connection

Exons are the coding regions of a gene that are translated into functional proteins. These contain the information needed for the synthesis of a specific protein. Introns are the non-coding regions of a gene that do not code for proteins. Introns are transcribed into RNA along with the exons, but they are removed from the final RNA transcript. Gene editing techniques, such as CRISPR-Cas9, rely on specific recognition of DNA sequences by the Cas9 enzyme. To achieve targeted gene editing, the Cas9 enzyme needs to be guided to a specific site in the genome using RNA molecules called guide gRNAs. gRNAs are designed to bind to a specific sequence in the genome, typically located in an exon, which is then split by the Cas9 enzyme.CRISPR logo

A tree stump that should be dead, found alive!!!

A tree stump in New Zealand that should be dead, was found alive. Martin Bader and Sebastian Leuzinger, professors at the Auckland University of Technology discovered the tree stump during a hike in West Auckland. The stump didn’t have any foliage, which according to Merriam-Webster dictionary is
a cluster of leaves, flowers, and branches“. The two professors decided to investigate how the nearby trees were keeping the stump alive. It was found that the water flow to the tree stump “was strongly negatively correlated with that in the other trees”. It was then found that roots of the stump were grafted to the surrounding trees. These grafts, (“thick underground roots that are pressed together”) are solely what was keeping this stump alive. But now the question is why would the other trees want to keep this stump alive? There might be a possible explanations. Professor Leuzinger says that grafts were formed before the tree became a stump. Trees do this in order to access more nutrients from other trees. When this tree became a stump the grafts stay in tact. So when the other trees are receiving nutrients they are transferring to the stump unknowingly to keep it alive. This discovery could change the way scientists deal with survival of trees throughout climate change as well as the ecology of the forest.


Trees constantly go through photosynthesis in order to survive. Photosynthesis in trees takes place inside the chloroplasts that are in the mesophyll of the tree. The leaves pull in carbon dioxide and water and use energy from the sun in order to feed the tree. The carbon dioxide and water are then converted into chemical compounds, like sugar, which fuels the trees life. Trees that have grafts then take the nutrients and transfer them to surrounding trees. The trees surrounding the tree stump took the nutrients gained from photosynthesis as well as nearby water to feed and keep the stump alive.

Adansonia digitata

Lab-Made Covid-19 Variant?!

COVID-19 has been a part of life for over three years now. Throughout this time, new variants arose from this viral respiratory disease caused by a SARS-associated coronavirus” (WHC 1). This October, scientists at Boston University created a new variant of SARS-CoV-2. They combined different features of pre-existing strains. The lab-made variant reminded people and caused them to question if the original COVID-19 was made in a lab and released or if it was natural. Controversy about this experiment grew, forcing the U.S. government to investigate if what these scientists were doing followed protocol. It turns out that they were trying to figure out how the Omicron BA.1 strain could “escape the protection provided by the immune system and vaccines”(Park 1). They did this by focusing on the Spike Protein, which “is located on the outside of a coronavirus and is how SARS-CoV-2 (the coronavirus) enters human cells”(UNMC 1). They hoped to figure out if the spike protein made Omicron defiant against the vaccine or a different part of the variant. Unfortunately, in the middle of their studies, the scientists accidentally created a very lethal variant to mice, which forced the U.S. Department of Health and Human Services to look into this case. Since the experiment was funded through the university and not the government, it was allowed to continue. This experiment concluded that spike protein in Omicron was the reason it was so resistant to the vaccine. Although what the scientists at Boston University were doing was important, what they created amid the experiment was highly dangerous and not worth the risk. 

Sars cov2Connection to A.P. Biology

The immune system is a very complex space that is supposed to protect the human body from dangerous invaders. There are two types of immunity, Innate and Adaptive. Innate immunity is the body’s first response to foreign substances, and Adaptive develops after exposure to an unknown invader. The scientists questioned why Omicron, a variant of COVID-19, managed to avoid being destroyed in bodies that previously had the vaccine and developed adaptive immunity. But since learning that it was the Spike protein that mutated in Omicron, the human body saw it as a foreign invader, and adaptive immunity was of no use here. 

Can extinct animals be resurrected?

Recently the CIA has been looking into “resurrecting” extinct animals, specifically Mammoths. Colossal Biosciences, a company based in Texas, believes they can genetically engineer the mammals’ DNA. Although it would be virtually impossible to bring Mammoths back from the dead, their goal is to insert their distinctive traits into present-day Elephants. For this process, scientists need to use “CRISPR,” a method used to replicate gene sequences. According to MedlinePlus, CRISPR “is a group of technologies that give scientists the ability to change an organism’s DNA…and allow genetic material to be added, removed, or altered at particular locations in the genome”. While some scientists are for this idea, others believe it is impossible and the time and money spent could be allocated elsewhere. Ben Shapiro, a professor of ecology and evolutionary biology at the University of California, stated “The biggest misconception about de-extinction is that it’s possible.” Even if scientists were able to collect preserved DNA from the animal, it is nearly impossible to replicate them using technology.

AP Biology Connection

All animal cells need oxygen, food, and water, so when they are deprived of it, they die. Cells consume these through a process called endocytosis. Endocytosis is a process in which cells pull substances from the outside and then engulf them in a vesicle. Without this process, not only would the cell die, but so would all of its contents. DNA is the cells “carrier of genetic information“. DNA itself is very fragile, and under no circumstances will it survive from the extinction of the Mammoths to the present day. Ancient DNA, such as the ones we have from Mammoths, has gone through many environmental issues. Elements such as sunlight, water, and heat can accelerate the DNA degrading process. Unless very well persevered by freezing and sealing it, the DNA will not be functional. The rupturing of cells, when dead, release nucleases causing damage to DNA. Although “bringing back” the Woolly Mammoth would be a great scientific revelation, it seems infeasible due to the inner workings and preservation of the cells.  Woolly mammoth (Mammuthus primigenius) - Mauricio Antón

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