BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: biotechnology

Unlocking Genetic Mysteries with CRISPR!

At Oak Ridge National Laboratory, researchers are tackling the challenge of enhancing CRISPR, a groundbreaking gene-editing tool sort of like molecular scissors. While CRISPR has revolutionized genetic engineering in larger organisms such as mammals and fruit flies, its effectiveness in smaller organisms is limited. This limitation prompted a team to jump into the complex world of quantum biology, an area of study that investigates how quantum mechanics influence biological processes.

CRISPR logo

In AP Biology, we were introduced to the complexities of cellular structures and genetic mechanisms, and CRISPR is a topic of connection. CRISPR operates at the DNA level, precisely targeting and modifying specific sections of the DNA molecule. The passage highlights how CRISPR can be used to alter an organism’s traits by editing its DNA. This concept ties directly to the unit on genetics, where we learned about how changes in DNA sequence can lead to variations in phenotype. CRISPR technology allows scientists to make precise changes to the genetic code, providing a powerful tool for studying gene function and genetic disorders. In their search to understand why CRISPR behaves differently across various organisms, the researchers explored the movement of electrons within cellular structures, drawing insights from some principles of quantum mechanics. This exploration led them to develop a deeper understanding of the underlying mechanisms influencing CRISPR’s efficiency.

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Based on their discoveries, the team launched to develop a sophisticated computational model. This model, which integrates elements of artificial intelligence and quantum chemistry, is designed to predict the most effective targets for CRISPR within microbial genomes. Basically, they are leveraging the principles of quantum biology to enhance the precision and efficacy of CRISPR editing in smaller organisms. The implications of this research have promise for addressing genetic diseases and advancing biotechnological applications in human health and agriculture. Through their efforts, they inspire new pathways for harnessing the power of CRISPR to solve new mysteries and pave the way for a future characterized by innovation and discovery.

CRISPR-Cas9 – The Human Editor

What is CRISPR-Cas9? CRISPR-Cas9 (Clustered, Regularly Interspaced Short Palindromic Repeats) is a powerful technology that allows geneticists to modify or “edit” parts of the target genome by adding or removing whole sections of the DNA sequence. Currently, CRISPR is the most versatile and accurate DNA modification tool globally. This tool allows scientists to fix flaws in most organisms’ DNA and has minimal risk of off-target damage.

Cas9 cleavage position

CRISPR-Cas9 has two main molecules that carry out the change in DNA, an enzyme called Cas9, and a piece of RNA called guide RNA (gRNA). The Cas9 enzyme locates the target area and can cut the DNA in a specific location in the genome so that small pieces of DNA can either be added or removed. The gRNA is made of a small piece of a lab-designed RNA sequence, roughly 20 bases long, located within the RNA scaffold. To ensure that the Cas9 enzyme cuts at the right point in the genome, the scaffold binds to the DNA, and the lab-designed sequence pilots the Cas9 enzyme to the correct location. The gRNA has RNA bases that match those of the target DNA sequence in the genome. The Cas9 enzyme follows the gRNA to the specific area and makes a precise cut across both strands of the DNA. During this stage, the cell recognizes that the DNA has been damaged and will try to repair itself. Scientists use this DNA repair system to add or remove changes in one or multiple genes. This technology is consistent with our most recent AP Biology Unit, DNA Replication, and Gene Expression/Replication.

In my opinion, CRISPR-Cas9 is an incredible technology as it has so many practical applications. The future of this technology has potential in many diverse fields such as genetic engineering, bioengineering, and molecular biology, among other areas of study.

The technology has been tested on dogs with Duchenne Muscular Dystrophy, a gene mutation adversely affecting muscle proteins. In this case, a CRISPR gene-editing treatment demonstrated promising signs of permanently fixing the genetic mutation responsible for this disease, which in humans, affects approximately 1 in 3,500 male births worldwide. The mutation prevents an organism from producing an appropriate level of functioning dystrophin which causes muscles to be weak and not respond efficiently. Researchers at the University of Texas Southwestern found that gene editing restored the functioning dystrophin levels in the dog’s muscles and heart tissue. The increase in the dystrophin levels would need to be more significant for it to work in humans, but researchers have been making substantial progress in advancing this developing CRISPR-Cas9 technology.

No need to buy fragrances, we can just create them: a new way of creating everyday items from scratch.

Gene modification.

In a rapidly developing industry, genome editing technology has been growing to a point where “food, drugs, cosmetics, and biofuels” can be synthesized by microbes. Eric Rhodes investigates this phenomenon through the use of CRISPR/Cas9 gene editing technology. Emmanuelle Charpentier and Jennifer Doudna’s findings reveal how scientists can target specific segments in genes and then inactivate, delete, insert, and alter to however the scientist pleases.

At a closer look at what CRISPR technology is, Rhodes, elaborates and shows that multiple genes can be edited. It can be altered to produce any of the approximately 30 biosynthetic gene clusters to produce any natural product. Some popular compounds that are produced include carotenoids, citric acid, 1,3-propanediol, phenylethanol, and squalene. This can make great strides by making common commodities more accessible to the average human. Whether it is pigments (cartenoids), flavoring agents (citric acid), cosmetics (phenylethanol), or components in vaccines (squalene), the opportunities are endless.

We had recently done a bio lab on E.coli and through independent research, we found E.coli’s importance to our digestive system. CRISPR technology too can be used in the engineering of enzymes similar which have seen massive practicality in the modern world. In biology class we learned about epigenetics and how gene expressions can be more pronounced or repressed. In the case of CRISPR technology, CRISPRa involves fusing a catalytically inactive Cas9 (dCas9) protein to a transcriptional activation domain, which can attach transcriptional things to a specific promoter and enhance gene expression.

Perhaps a more pressing matter that this CRISPR technology can target is finding greener alternatives in our world. Rhodes claims that “CRISPR can also be used to modify microbes to grow at lower temperatures” this way high demand species that are endangered will have less pressure of being threatened. This could pose a creative way of solving some endangered species problems by simply providing a cleaner alternative.

The growing potential of genome editing technology, specifically CRISPR/Cas9, to produce a range of useful products from common commodities to components in vaccines, presents endless opportunities for the future of industrial biotechnology, and may help address issues related to endangered species.

Adapted Bacteria vs AI

In a recent article it has been found out by researchers at Washington State University that it is possible to find antibiotic resistant genes in bacteria with machine learning and game theory.

In the world of health and medicine one of, if not the biggest discovery is antibiotics. They were the most simple way of clearing out or slowing down the reproduction of bacteria in the human body. People a long time ago had been dying left and right to bacterial deseases and antibiotics helped the expectancy of everyone’s lives. However eventually after it started being used bacteria with DNA that has antibiotic resistance survived and reproduced. Eventually it could be problematic as there’s many ways to acquire resistances as said here. With certain bacteria that many people used to be infected with a lot and since people used antibiotics for it certain bacteria had vast resistances as there’s very limited antibiotics to kill one type of disease. If there was a strand of bacteria completely used to antibiotics it could wipe out the human race. If you want to learn more on that it could be found here

 

Although it isn’t too bad and we haven’t run into many bacteria that resist antibiotics, it can also be very dangerous if a person takes an antibiotic that the bacteria in their body is resistant to. The bacteria then wouldn’t die and thy would also expand and live on to reproduce and make the problem worse since it was technically not treated. However with what the people in Washington state university are doing computers would more and more be able to find the bacteria that have genes resistant to certain antibiotics.  The AI would learn more and more what genes are likely to be ones that resist antibiotics and they will be able to apply that to other situations. This method used worldwide would really help people know what type of antibiotics to give sick people. If a strain of bacteria is treated with antibiotics that most of it is resistant to not only could the person die but the existing bacteria in that persons body could be extremely dangerous if it reproduces as said before. So knowing if that bacteria does indeed have a resistance could be pivotal in many peoples lives. This could also happen at new speeds since that is one of the biggest advantages of using AI.

Not only is this new method very fast it is also very efficient. The researches at Washington state had been able to determine this at an accuracy rate ranging from 93% -99%. These constant advancements in health and technology show how the implementation of tech into health has changed life as we know it and will continue to forever.

Advanced new understanding of lung abnormality… thank you turtles!

A recent study of an unusual snapping turtle with one lung was found to share similar characteristics to humans born with one lung who survive infancy. “These shared traits include an enlarged single lung with a more homogenous distribution of respiratory parenchyma(the gas exchanging tissues), an opposing bronchus that ends where the opposite lung should be and malformations of the spine (such as scoliosis),” said Dr. Schnacher an Assistant Professor of cell biology at Louisiana State University. This study is important because there is very little known about lung morphogenesis.But we do knowthat mutations in genes cause severe, even lethal, lung malformations and lung formation. It is possible that similar genetic mutations are at play in both the turtle and in humans! What an interesting parallel!

 

 

 

 

 

The snapping turtle was found in Minnesota and brought to a wildlife rehabilitation center because of a deformity on its shell. However, it wasn’t long until the turtle’s second abnormality was discovered, its singular lung. The turtle was passed down to the hands of Dr. Schnacherand it went through computed tomography(CT) and microCT imaging. The images created 3D models of the area. For comparison, images of a normal turtle specimen were also taken. The comparison was conducted to observe the negative spaces within the lungs– the bronchial tree, lung skeleton, and lung surface. The architecture of the spaces and the patterns inside the lung were compared to the “normal” turtle. In addition, these models also facilitate a visual of specific structures that are very difficult to see in living animals, such as blood vessels and air spaces. What is so innovative about this technology is that qualitative and quantitative comparisons can be made between organisms with absolutely no harm to the specimens! For animal lovers like me this is a huge breakthrough.

So, what was the big reveal? The primary difference between the turtle with one lung and the normal turtle was that the normal turtle had an larger surface area and density value in regard to its gas exchanging tissue. The tissue originates from the secondary airways, thus the 14.3% increase is very signifigant. However, this abnormality had no effect on the turtles survival rate, it only effected aquatic locomotion and buoyancy control. How does this relate to humans now? The turtle represents an example of a non-fatal congenital defect and a clear pathway of how the turtle adapted to compensate for it. This increased understanding of soft tissue structures reveals key breakthroughs to one day understand and improve diagnoses in humans! I think the future holds big answers, what do you think?

 

The Brain that Looked like Jello

Scientists at Stanford University made an entire mouse brain and part of a human brain that is the same consistency as Jell-O. The brain model is transparent so that neurons sending and receiving information can be highlighted and in in the same complexity as 3-D, but without having to slice the model. This new process, called Clarity, preserves the biochemistry of the brain so well researchers can reuse the same model over and over again.

Why Now?

The Obama Administration recently announced it’s interest in discovering the secrets of the brain. While this project was not part of the Obama Administration’s new initiative, Dr. Thomas Insel, director of the National Institute of Mental Health said that Clarity will help build the foundation of the Obama administration’s brain initiative.

The Clarity technique also works with brains that have been preserved for years.

One of the challenges of studying a preserved brain is making it clear enough to see into it. Unlike previous methods, Clarity makes the brain clear enough to see its inner workings.

Imagine if you could see through this brain!

 

How it Happened 

There are many was to make a tissue transparent. Clarity uses hydrogel, a substance of water held together by other molecules to give it solidity. The hydrogel forms a mesh that permeates the brain and connects to most molecules other than lipids. The hydrogel brain is then put in a soapy electrical solution, where a current is applied, driving the solution to the brain and getting rid of the lipids. The brain is then transparent with its biochemistry still in tact, so it can be infused with chemicals that will show the details of its structure.

The hardest part of the procedure is obtaining the correct ratio of temperature, electricity and solution. More work is needed to be done before this method can be applied to an entire human brain.

The Benefits 

The Clarity technique gives scientists a more exact image of what’s going on in people’s brains. This process may discover physical reasons for debilitating mental disorders, such as PTDS, schizophrenia, and autism.

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