BioQuakes

AP Biology class blog for discussing current research in Biology

Author: blakelement

We Live In a Time Where We Can Hack and Edit The DNA In Diseases, and We Have Only Just Begun…

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On April 23, 2023

In Student Post

CRISPR gene editing, (Clustered Regularly Interspaced Short Palindromic Repeats), is a relatively new biological technology that allows scientists to fix unimaginable flaws with an unprecedented minimal risk of off-target effects. This advanced technology aligns perfectly with our current unit of DNA replication and Gene expression/replication, so it should be a good review to keep reading.

CRISPR gene editing has two main components; the Cas9 protein and a guide RNA (gRNA). The Cas9 protein acts as the Helicase, cutting and unzipping the DNA strand. The gRNA is designed to recognize a specific sequence in the DNA of a cell. Once the DNA is cut, the cell uses a homologous DNA template to repair the break in the DNA molecule. The template DNA, Homology Directed Repair (HDR), is designed to carry the desired genetic modification and incorporate it into the DNA through the natural DNA repair mechanisms. This process alters or even adds new genetic information to the organism. For example, researchers from UT Southwestern Medical Center used CRISPR to treat Duchenne muscular dystrophy (DMD). A genetic disease that causes muscle degeneration and weakness. The team used CRISPR to delete the gene responsible for producing a toxic protein that causes DMD. They then replaced the missing gene with a shorter, functional version, which allowed the muscles to regenerate and become stronger.

CRISPR illustration gif animation 1

This advanced technology has been used to increase crop yield from various crops. In California it was used to create more drought resistant rice. In another state, it was used to eliminate browning of red apples. This process is becoming increasingly useful and popular because of its safety. The gRNA can be designed to target a very specific sequence of DNA, which means that scientists can modify genes with precision and accuracy. This specificity also reduces unintended genes, which remains to be a large concern for other gene-editing processes. This technology has enormous potential in the science world and can safely guide us into disease treatments, agricultural efficiency, and advanced biological research.

DCas SAM system

Is De-Extinction Upon Us? The Woolly Mammoth is Planned to be Introduced Back on Earth by 2027

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On March 15, 2023

In Student Post

You may be familiar with the large Woolly Mammoth’s (Mammuthus primigenius) from the movie Ice Age. These animals had once roamed the Earth for thousands of years, only recently going extinct at the end of the Pleistocene Period. Scientists Ben Lamm and George Church are leading the research into the second ever human provoked de-extinction, planning to release the Mammoth’s in Siberia. With an initial $15 million dollars in private funding, the team has received an additional $60 million to help achieve the 2027 deadline.

The closest living relative to these Mammoths is the Asian Elephant. Having once shared an ancestor 6 million years ago, scientists are working on pinpointing the genetic differences that set the ancient species apart from their modern (living) cousins. Fragments of Mammoth DNA have been retrieved from their ancient fossils (One of my previous blogs I wrote about DNA in fossils!), making it possible for scientists to modify the genome of an elephant to produce something that would look and act like a mammoth. The team will try to create an elephant embryo with its genome modified to resemble an ancient mammoth. To do this, the scientists will need to remove DNA from an elephant egg and replace it with the mammoth-like DNA. Some traits the Mammoth’s will need is dense hair and thick fat to withstand the cold environment. Siegsdorfer Mammut

Some other challenges to this de-extinction process is the actual birth of a fetal Mammoth. Scientists have been able to create a sealed bag that can support a fetal lamb up to four weeks, but for the Mammoth to be successfully birthed, it will require an artificial uterus big enough to house a fetus for around two years, reaching a weight of 200 pounds (~22~ months). While this may seem like an impossible task to many, the researchers behind this operation have stated that they’re eager and confident that their expertise will prevail, showing the world that editing DNA can bring extinct species back to life.

This article connects to our most recent unit in AP Bio of genes, genetics, and DNA. As we know genes in DNA are what make each person different from the other. Physical traits are mostly represented through gene pools (genetics), such as the thicker fat needed for the mammoth to survive. DNA editing is a crucial step to bringing back this animal and the scientists are working carefully to create the closest representation of the extinct species. This goal cannot be succeeded without the things we learned in this unit!

The presence of Wooly Mammoths in todays world can help the Siberian tundra as it has been overruled by moss. The moss acts as an insulator for the permafrost soil from the cold temperatures, thus melting the permafrost and releasing harmful gasses such as methane and Co2 into the atmosphere. Mammoths are considered “ecosystem engineers” because they feed on the moss and provide a natural fertilizer with their waste. With the moss being broken up, it would allow the grasslands to come back which keep the soil from eroding and melting. Ecologists have imported bison into the tundra in an attempt to help the tundra return to grasslands, but they believe the Mammoth’s will be much more effective.

While the team is multiple steps away, facing many challenges not yet conquered, they are continuing to push on with their research, inching closer and closer to making this reality. If this mission is a success, it will open the door to numerous DNA editing opportunities, restoration of the Siberian Tundra, and will remain a great feat of human advancement.

Siberian tundra 05

There Are More Viruses On Earth Than Stars In The Universe. Why do only some infect us?

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On January 16, 2023

In Student Post

Scientists have estimated that there are 10 nonillion (10 to the 31st power) viruses currently on our planet. They are everywhere. Many viruses are beneficial for their host, many inflict no harm, but why do so few viruses affect us and even fewer severely affect us? The short answer: “These pathogens are extraordinarily picky about the cells they infect, and only an infinitesimally small fraction of the viruses that surround us actually pose any threat to humans” says virologist Sara Sawyer.

Understanding how certain viruses affect humans is crucial for protecting and preventing future outbreaks. COVID-19, the most recent outbreak that experienced a “spillover event,” was initially spread through interactions with an animal that is a “non-human primate”. This is called zoonosis. Multiple outbreaks have been introduced this way, but not can be started this way. Pathogens can also enter through cuts, scrapes, mosquitoes, ticks, etc. Once a virus has entered, it needs to find a way to get inside the cells and replicate. To do this, it must first attach to the surface of a host cell and then inject its genetic material (RNA) into the cell. The virus’s genetic material then takes over the machinery of the host cell, using it to replicate itself and produce new viruses. Viruses with a lot of genetic flexibility, and particularly those that encode their genomes as RNA rather than DNA, are well-suited to crossing the species divide. The majority of pathogens that have infected the human population in recent decades have been RNA viruses, including Ebola, SARS, MERS, Zika, several influenza viruses, and SARS-CoV-2. The more lethal viruses were found to have been hiding in their hosts for longer periods of time before showing any symptoms. This would allow it to replicate and spread to new species.

 

Coronavirus. SARS-CoV-2

So the answer is; that a virus has to be incredibly sophisticated for it to cause harm to a human, pandemics are so rare because of precautionary measures such as vaccines, healthcare, and proper sanitation. The continuous study of viruses and their behavior is an important task for the human population and its future as current viruses are continuously mutating and developing with each given day.

 

Coronavirus and Natural Immunity…Are You Protected?

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On December 8, 2022

In Student Post

Since the start of the pandemic, scientists have vigorously worked around the clock, conducting research experiments and clinical trials to fully understand how this relatively new virus affects us. How long do our antibodies last? Should I get vaccinated? Can natural immunity protect me forever? The UTHealth School of Public Health, located in Houston Texas, conducted a research experiment on 57,000 volunteers (over the age of 20) across the state to grasp a better understanding of natural immunity and the presence of  SARS-CoV-2 antibodies in our system.

Dornbirn-COVID-19 antibody testing-02ASD

In October 2020, these volunteers enrolled in the Texas CARES survey to provide resources to understand antibody quantities over time. Researchers used blood-drawn samples from Oct. 1, 2020, to Sept. 17, 2021, to analyze the data around levels of antibody presence. Some of the variables identified from the data analysis are age, body mass index (BMI), use of smoking and vaping products, and the severity of the previous infection. Suppose you are exposed to Covid-19 for a greater period of time. In that case, you are much more likely to have a more severe infection which would drastically increase the number of antibodies you will eventually produce. The opposite goes for someone who is very briefly exposed to the virus. However, even with these indicated variables, all volunteers showed a similar rate of decreasing antibodies over time. “Our research shows that the level of antibodies in those previously infected increases for the first 100 days post-infection and then gradually declines over the next 500 days and beyond” (Michael Swartz, Ph.D., associate professor and vice chair of biostatistics at UTHealth School of Public Health). The findings were published in The Journal of Infectious Diseases.

Concluding this experiment, it is safe to say that you are most naturally protected from Covid-19 at 100 days after infection. After that period of time, your protection will gradually wane, slowly making you more vulnerable to severe symptoms again (similar to the covid-19 vaccine).  However, the data suggests that you will have some quantity of antibodies for well over a year after infection. As we learned in class this year, antibodies are a naturally formed secondary response from your immune system. The B-plasma cells secrete antibodies and can send them off to surround and immobilize the pathogen, allowing a macrophage to come and digest/destroy the cell. The B-memory cells are there to help prevent reinfection later down the road. This immune response is a way for our body to naturally protect us while storing information from previous infections for long periods of time. This is what keeps us safe!Antibody Opsonization

 

Geneticist Svante Pääbo is the first person to extract DNA from extinct human species.

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On October 21, 2022

In Student Post

Various forms of the human species have been alive for hundreds of thousands of years before us. For the longest time, it was concluded that DNA breaks down over time and cannot be excreted from ancient fossils…until Svante Pääbo joined the research.

Pääbo, the leader of his research team, was able to extract fragments of DNA from the bones of Neanderthals and Denisovans. By extracting mitochondria outside the cell nuclei, Pääbo’s team was able to place the genetic information into the appropriate chromosome locations “by matching each fragment to similar sequences in human DNA” (Bower). As we learned in class, mitochondria contain circular chromosomes of DNA. Pääbo’s team was able to extract the mitochondria from the cell and then analyze the mtDNA in comparison to modern-day humans. With this process, he concluded that humans diverged from Neanderthals about 516,000 years ago.

Another way they were able to identify common genetic information in the present-day Homo sapiens was by putting DNA into a certain bacteria, which would then make copies of DNA fragments. With this effort, they were able to recover 29 out of the 35 genes that they were targeting.

These new techniques brought research teams to conclude that modern-day humans share similar genes to Denisovans such as ones that regulate brain size, help us adapt to altitude, or even make covid-19 more severe in some cases. The evidence around the commonalities of certain genes encourages the theory that at some point there was interbreeding between Homo lineage.

Pääbo’s findings have paved the way for groundbreaking research, identifying commonalities in evolution, and have helped us understand what makes humans so unique. This new state-of-the-art process can hopefully one day expand to multiple labs, research teams, and even countries. This would allow us to learn even more about our sophisticated past and maybe even some things about our future!

Mitochondrial DNA lgNeanderthalensis

 

 

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