BioQuakes

AP Biology class blog for discussing current research in Biology

Author: clalvincycle

Can Technology Ketchup To These Super Tomatoes?

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On March 30, 2022

In Student Post

Sicilian Rouge tomatoes are one of the first foods made with CRISPR-Cas9 technology to be sold to the public. An article by Emily Waltz, of Scientific American, goes in depth on how these tomatoes are taking Japan by storm. Sanatech Seed, a company based in Tokyo, has edited the tomatoes to have a large amount of GABA(γ-aminobutyric acid).  According to the company, GABA supposedly lowers blood pressure and promotes relaxation when ingested orally.

In Japan, GABA is a popular addition to many foods, drinks and other products such as chocolates. Hiroshi Ezra works as both the chief technology officer at Sanatech and a plant molecular biologist at the University of Tsukuba. He says that “GABA is a famous health-promoting compound in Japan. It’s like vitamin C…That’s why we chose this as our first target for our genome editing technology. “

 

CRISPR has been used in a myriad of ways by plant bioengineers. Non-browning mushrooms and drought-tolerant soybeans are just a few examples of this. However, Sanatech’s Sicilian Rouge tomato was the first CRISPR-edited food known to be commercialized.

 

But what is CRISPR and why has it become so popular? Yourgenome.org effectively explains what the different parts of the CRISPR-Cas9 technology do. The system is made of two parts: the enzyme and RNA. The enzyme is called Cas9 and its role in gene editing is to ‘cut’ the specific genome in strand of DNA so that the mutation can be made. The RNA acts as a guide for the enzyme, which is why it is called gRNA. The piece of RNA is made of an approximately 20 base sequence that is a part of the longer RNA ‘scaffold’. When the strand binds to the DNA the 20 base sequence guides the Cas9 to the part of the genome that is meant to be cut. The scaffold is able to find the correct genome because its bases are made to be specifically complementary to the target genome. Once the genome is cut the cell recognizes the cut in the DNA and repairs it. It is when this repair takes place that the changes/mutations to the genome occur. 

4.3. The CRISPR Cas 9 system III

The processes of CRISPR are similar to what we learned about in biology too. During DNA replication, small complementary strands of RNA act as primers so that DNA polymerase can add to anc continue the chain. DNA polymerase also ‘proofreads’ strands of DNA for any mistakes which it would cut out and replace with the correct nucleotides. The Ligase then reforms the phosphodiester bonds which hold the nucleotides together. This process of error correction is what takes place once the Cas9 cuts the genomes.

 

Another type of DNA editing is called TALENs or transcription activator-like effector nucleases. A company called Calyxt commercialized TALENs through their genetically edited soybean oil that is free of trans fats. Gene editing hasn’t only been bound to plants, but also animals too. In October of last year Japan approved CRISPR two gene-edited fish. One was an edited tiger puffer which “exhibits depressed appetite suppression”. The other was a Red Sea bream which was edited to have “increased muscle growth”.

 

From super-crops to super-fish, it appears as though there are no limits for CRISPR in our daily lives. It’s amazing how precise technology has allowed us to alter the nutrition of the food we eat. I wonder what other possibilities lie in the future of CRISPR and how they will affect our society.

Customizing Cancer?

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On February 16, 2022

In Student Post

Oncologists are moving toward a future in which cancer treatment is customizable and specific to each patient. This is achieved through genomic testing. Medical News Today: Pancreatic cancer splits into four types, says genome study

As genes differ from person to person, the information from genomic testing is unique to each. This speaks to what we’ve learned recently in bio class about how cellular mutations cause cancer. Changes to the DNA of a cell, specifically to genes that control the cell cycle, could result in oncogenes. But, I digress. The drawback of this type of treatment is that oncologists are met with so much information that it becomes not useful,  making the treatments less personal than they should be.

CHALLENGING GENETICS

The reason for this is due to the inability to identify which test will be most useful for each patient. When genetic data is obtained, what it means for the patient isn’t exactly clear. The example given in an article by Andrew Ip states that “several inhibitors of the enzyme anaplastic lymphoma kinase (ALK) have proven effective in treating lymphoma, non-small cell lung cancer, and neuroblastoma, while other findings suggest one of the inhibitors can treat pediatric oncology patients”. Although information was found from research specifically for ALK, it appears that much more is affected by these inhibitors making it less “personalized” than intended. 

Another reason as to why genomic testing is so difficult is accessibility. It can be difficult to get the treatments to patients due to health insurance limitations. In another instance, according to Andrew, “oncologists in community settings … had difficulty handling tumor samples, faced long turnaround times for laboratory tests, and had limited access to targeted therapies. To make it more difficult, next-generation sequencing results are often provided as a pdf, which cannot be digitally integrated with a patient’s electronic health records”. It appears altogether that oncologists are hindered by the lack of seamless integration of genomic testing into daily scenarios.

THERE IS HOPE

Although it appears that oncologists are overwhelmed, there is progress being made to support them. 

At the Hackensack Meridian Health John Theurer Cancer Center, where Andrew practices oncology, genomic testing was put into action. An ill patient had two separate biopsies done, and the findings of both contrasted each other greatly. One specified that the cancer identified was incurable, while the genomic sequencing depicted the cancer as curable. The patient was treated with chemotherapy and made quick improvement. 

The Genomic Testing Cooperative joined with Hackensack Meridian Health to implement an “in-house genomic profiling center”. As stated in Andrews article, the center “analyzes 434 genes for solid tumors, searching for DNA and RNA mutations and chromosomal structural abnormalities. For blood cancers, the service generates a 177 gene panel hematology profile”.

This isn’t all. A new database to which will aid oncologists in using the genomic results, cancer types, cancer medicines and patient outcomes is being built there as well.

FUTURE ADVANCES

In order to fully take advantage of genomic sequencing, companies are turning toward artificial intelligence. The goal is for AI to be able to use information from genomics, drug trials, patient demographics, and past scientific research to provide its own efficient course of action. This is called a clinical decision support system or CDS. IBM Watson was to be a CDS but did not suffice.

Until then oncologists take what Andrew describes as a “holistic approach to care”. This involves working with multidisciplinary teams made up of radiologists, pathologists, medical oncologists, radiation oncologists, and surgeons. Altogether they are known as molecular tumor boards. It’s fascinating to see just how much goes into making cancer care especially personalized to each patient.

We’ve Been Programmed to Fight Coronaviruses since 6 Years Old

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On December 20, 2021

In Student Post

It was previously thought that after initial infection your body creates antibodies tohelp your immune system in the future. But did you know that a common cold you had at a young age can affect how your react to covid today? Depending on the specific spike protein, your body may have a positive or negative response to future variants. An article by Rachel Brazil describes this as “original antigenic sin”(OAS) and has been linked to the differing immune responses to COVID-19.

THE HISTORY BEHIND OAS.

In 1960, Thomas Francis Jr, a US epidemiologist, noted that the immune system seemed to be ‘permanently programmed’ to produce specific antibodies against the first strain of flu it encountered. These antibodies would then reactivate when a flu virus shared similar epitopes to that of the first strain. Relating to SARS-CoV-2, the varying coronaviruses cause different immune responses from person to person. Similar to this, we learned about memory cells in AP Bio. Once the adaptive immune response takes place memory B, helper T, and cytotoxic cell are created to support future immunity to that specific virus.

child sick

Microbiologist at the University of Pennsylvania in Philadelphia, Scott Hensley, spoke with the author of the original article about his team’s work with OAS. “Much like flu, most of us are infected with these common coronaviruses by the age of five or six,” says Hensley. It’s surprising to learn that a coronaviruses have been around for many years before the pandemic. What’s even more surprising is that a simple cold we had as a kid can affectus even today. Hensley and his group analysed blood serum samples taken before the pandemic. Their findings were that the samples had antibodies that defended against a ‘common cold’ coronavirus called OC43. These antibodies could also bind to the SARS-Cov-2 spike protein. Hesley’s group then took samples from before and after SARS-Cov-2 infection for testing. Results showed that infection boosted the production of the antibodies that bind to OC43. They also found that these OC43-binding antibodies bound to the S2 subunit of the SARS-CoV-2 spike protein(due to its similar structure to that in OC43). On the other hand, the antibodies did not bind to the S1 region of the SARS-CoV-2 spike and were unable to stop the virus entering cells.

IS THIS A GOOD OR BAD THING?

Hensly’s group once again were studying OAS, but focused on its effects during the 2009 H1N1 pandemic. Their study showed that past infection to other historical flu strains provided protection against the H1N1 virus. While this may seem good, OAS also has drawbacks. The body may produce antibodies that could be used for other virus strains, but they may not be the best fit for the specific virus. As a result of this the ill equipped antibodies bind to the antigens preventing the body from creating more protective response. 

In her article Brazil mentions Aldolfo García-Sastre, director of the Global Health and Emerging Pathogens Institute at the Icahn School of Medicine at Mount Sinai in New York City. García-Sastre observed the levels of the OC43 binding antibodies in patients hospitalized with COVID-19 in Spain. He found an increase in levels of OC43 binding antibodies along with antibodies for HKU1(another betacoronavirus). García-Sastre claimed that, “We looked for a correlation between people mounting higher [levels of] antibodies against these conserved epitopes versus having less protective immunity against SARS-COV-2, and there was a slight correlation”.

THE VERDICT: THERE ISN’T ONE…YET

Because of the varying reactions that follow OAS, the debate on whether or not it is to be seen as beneficial is polarizing. Though th, scientists are still working to find ways to use it in potential vaccines. Comment below to let us know your opinion on the matter!

 

ITS ALIVE!!! Scientists bring their creation to life.

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On November 7, 2021

In Student Post

Cells are the basic units of life, but now scientists found a way to take matters into their own hands and actually create their own Frankenstein of cells. Scientists first created a single-celled organism with only 473 genes five years ago. Unlike the most recent cellular innovation, this simple cell grew and divided into cells of strange and unusual shapes and sizes. In an attempt to fix this, scientists identified 7 genes that when added to the cell, cause them to divide into perfectly uniform shapes. The J. Craig Venter Institute (JCVI), the National Institute of Standards and Technology(NIST), and the Massachusetts Institute of Technology(MIT) Center for Bits and Atoms all together can be accredited with this success.Cell division

How Was It Done?

The first cell with a synthetic genome was created in 2010 by the scientists at JCVI. Rather than building a cell from scratch, they started with cells from a simple bacteria called mycoplasma. The DNA already in those cells were destroyed and replaced with computer designed DNA. Thus lead to the first ever organism on Earth to have an entirely synthetic genome. It was named “JCVI-syn1.0”. Since then scientists have been working on stripping it down and reaching its minimum genetic components. Now scientists added 19 genes into this cell(including the 7 genes needed for proper cell division) and call it JCVI-syn3A. This cell variant also has fewer than 500 genes(a human cell has about 30,000). To find those 7 genes the JCVI synthetic biology group, led by John Glass and Lijie Sun, constructed multiple variants by adding and removing genes. NIST had to observe and measure the changes under a microscope. The difficulty here lay in observing the cells while they were alive, which made imaging them harder because of how small and fragile they were. Even the smallest of force could rupture them. Strychalski and MIT co-authors James Pelletier, Andreas Mershin and Neil Gershenfeld designed a microfluidic chemostat to remedy this. The article by NIST best describes this as a “sort of mini-aquarium where the cells could be kept fed and happy under a light microscope”. They discovered two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, were all required together for cell division. As we learned in AP Bio, organelles like mitochondria and chloroplasts are also autonomous. That simply means that they are self replicating similar to this man-made cell.

 

The ability to create synthetic cells could lead to potential cells that produce drugs, foods and even fuels. Others can detect disease and the drugs to treat it all while being inside your body. It’s amazing to think that humans are capable of creating synthetic life on a molecular level. One can only hope that this power is used for good in the future. Do you believe that what these scientists are doing is ethical or is “playing God” tampering with forces unknown? 

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