BioQuakes

AP Biology class blog for discussing current research in Biology

Author: benmadryl

CAST is in the past, it’s time for HELIX

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On April 23, 2023

In Student Post

CRISPR stands for clustered regularly interspaced short palindromic repeats.’ The term references a series of repetitive patterns in the DNA of bacteria discovered in the 90s. 20 years later, Jennifer Doudna and Emmanuelle Charpentier discovered that CRISPR-Cas9 could be used to cut any desired DNA sequence by just providing it with the right template, meaning it could be used as a gene-editing tool. To add a desired DNA sequence, one needs an upgraded version of CRISPR editing called CAST, CRISPR-associated transposases. Unfortunately,  CASTs suboptimally insert more DNA sequences than wanted and have a relatively high rate of unwanted off-target integration at unintended sites in the genome. This leads to mutations, the three being, silent mutations, missense mutations, and nonsense mutations. A silent mutation is an insertion or deletion of a nucleotide that doesn’t change the amino acid sequence. A missense mutation is an insertion or deletion of a nucleotide that changes one or more of the amino acids. Lastly, a nonsense mutation leads to an early stop signal.

4.2. The CRISPR Cas 9 system II

Luckily, new research published in Nature Biotechnology tells the reader that an improved CAST system called HELIX now exists. Helix stands for Homing Endonuclease-assisted Large-sequence Integrating CAST-compleX. This mouthful dramatically increased the efficiency of correct DNA insertions, reducing insertions at unwanted off-target sites. HELIX has over a 46% increase in on-target integration compared to that of the CAST system. This discovery is one of many that will continue to help us understand the complexity of our genes.

Hot dogs, Fries, and Chicken Nuggets Aren’t Good For Me?

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On March 15, 2023

In Student Post

Although foods such as soft drinks, chips, and breakfast cereals have been normalized as good meals, these foods are ultra-processed, and new research shows just how dangerous these foods can be. A recent study from the Imperial School of Public Health in London provides new and convincing evidence that ultra-processed foods lead to cancer, especially ovarian and breast cancer.

Now, you may be wondering how one develops cancer. One develops cancer when cells divide uncontrollably. These uncontrollable divisions begin due to a mutation in genes, sections of DNA. Proto-Oncogenes are genes involved in normal cell growth; these genes cause cells to divide. A mutation in a single allele of a proto-oncogene causes a protein to be produced that will exponentially increase the rate of cell division. Tumor suppressor genes are involved in the stopping of cell growth. When both alleles in a tumor suppressor gene are mutated, it leads to an inability to stop cell division.

Cancer

So, how does ultra-processed food cause mutations in your genes? It is believed that these foods can eventually lead to the mutation of alleles in proto-oncogenes and/or tumor suppressor genes. All ultra-processed foods share the commonality of being created by substances extracted from foods: Fats, starches, added sugars, and hydrogenated fats. A diet consisting of these types of food can lead someone to develop type II diabetes. People with type II diabetes are twice as likely to develop liver or pancreatic cancer. These people also have a much higher risk of developing bladder, colon, or breast cancer. When someone has a lot of excess fat around vital organs, it makes it very easy for cancer cells to get the nutrition they need to keep uncontrollably dividing. The fat from glucose is what the cancer cells need to continue to divide; cancer cells are known to metabolize glucose at 200x the normal rate. When one has Type II diabetes, they have increased blood sugar. If the cancer cells have access to blood flow, the increased blood sugar gives the cancer cells even more nutrients to keep dividing. Even though one can not say for sure, it seems increasingly apparent that avoiding ultra-processed foods is best for your health. So, the next time you want a snack, maybe an apple and a glass of water are your best bet.

 

HOLD up COVID-19, HOLD Technology Just Developed A COVID-19 Neutralizer

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On December 8, 2022

In Student Post

At the time of this blog post being written, it has been 998 days since Covid-19 was declared a pandemic. Scientists have been able to lessen the severity of deaths due to COVID-19, but they have not stopped people from falling ill. This post will discuss why and what new technology is being created to stop people from falling ill.

Recycled RoomCoronavirus is not different from many other viruses in that COVID-19 uses a protein on its surface to attach to and enter our cells. So, to battle this, scientists created an mRNA vaccine. mRNA is a genetic material that instructs our cells to make proteins. mRNA is covered in a layer of fat to diffuse through lipid bilayers. Ribosomes read the vaccine mRNA, leading to pieces of the viral surface protein being made and displayed on the surface of a dendritic cell. The dendritic cells release cytokines, which leads to lymph nodes making a copy of the surface protein, leading to  Cell-Mediated and Humoral responses. This leads to the killing of infected cells and the prevention of reinfection, but the coronavirus repeatedly mutates and changes its structure. So, the antibodies that the B cells created don’t fit onto and block the newly mutated coronavirus surface protein. Don’t fret; there is hope, Professor Seung Soo Oh is working on a coronavirus neutralizer.

Professor Seung Soo Oh uses Hotspot-Oriented Ligand Display technology (HOLD) to create this coronavirus neutralizer.  The neutralizer contains a protein fragment and nucleic acids, which strongly bind to the protein spikes of the coronavirus. The HOLD COVID-19 neutralizer is created using technology that operates on the principle of natural selection, which makes it significantly better at dealing with the mutating virus. Professor Seung Soo Oh refers to it as “the world’s first self-evolving neutralizer-developing platform.” His discovery led the neutralizer to be much more effective against the mutating virus. The neutralizer is effective against the Alpha, Beta, Gamma, Delta, and Omicron variants. In fact, it is five times more effective than the current vaccine for Omicron. So, almost 1000 days after COVID-19 was anointed to be a pandemic, Professor Oh has made a tremendous leap in halting the effects of COVID-19.

 

Want To Replicate Cells?

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On October 24, 2022

In Student Post

If you are similar to me in that you aren’t satisfied with the current state of artificial cells and want to “more accurately replicate the gel-like properties of intracellular and extracellular biological environments” you’re in luck. New studies have been published that show how to do this, but first, we must understand what hydrogel is. Hydrogel is made of two polysaccharides: cellulose and chondroitin sulfate. A polysaccharide is a carbohydrate, meaning its elements are CH2O. Carbohydrates are found in sugars and starches, and they’re used for energy. Hydrogel is made by joining cellulose and chondroitin sulfate through a dehydration reaction. Forming a glycosidic linkage.

Hydrogels

Now that we know hydrogel, how do you think it could be used to create artificial cells? The answer is in its backbone. Scientists graft anti-Hist-tag aptamers into the backbone of a bunch of polymers made up of cellulose and chondroitin sulfate, along with feeding nutrients this artificial cell can perform protein expression for more than 16 days. This discovery is used to accurately replicate intracellular and extracellular biological environments.

Here are some examples of how scientists plan to use these artificial cells: therapeutic delivery, biosensing, cell therapy, and bioremediation. Therapeutic delivery is the act of bringing a compound to a specific site in the body. Biosensing detects pathogens, such as E. coli, in food. Cell therapy is the act of injecting healthy cells into a patient. Lastly, bioremediation is when an organism consumes and breaks down pollutants in our environment. It’s astonishing to see every way these artificial cells can be used, and I hope you’re excited about how much these cells can help save lives.

 

 

 

 

 

 

 

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