BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: biochemistry

For Cancer Cells, it’s Halloween All Year Long– New Research Finds That They Masquerade as Normal Cells by Covering Themselves in “Sugary Costumes”

Dr. Rachel Willand-Charnley and her team of biochemist researchers at South Dakota State Univerity have achieved a “sweet victory” in cancer research. Their recent findings determine how cancer cells utilize sugar to deceive our immune systems. Their research suggests that cancerous cells mimic normal cells’ glycans due to genetic mutations, and because of this similarity, the immune system then confuses the cancer cell for a normal, healthy cell. This is because glycans on cell membranes of the cell are inspected by T-cells belonging to the immune system

Macs killing cancer cell

This is revolutionary to understanding the behavior and function of cancer cells which could help create more effective cancer treatments. Potential new treatment methods include stripping or altering the sugary layer of the cancer cell, allowing the immune system to recognize it as a threat and take care of it itself.

Milestones in cancer research are significant because as of right now, there is no cure for it. As we have learned in AP Biology, normal cells comply with signals that direct themselves into apoptosis, or programmed cell death. This process involves the expulsion of lysosomal enzymes into the cytosol which kills off the cell. This occurs when the cell is deemed inefficient or unable to function. If cancerous cells are detected by the immune system, those cells could avoid destruction by evading apoptosis signals and continue to progress within the human body which often leads to death. 

How could a cancer cell bypass something like this? Well, it seems that their newly adapted sugary coating could play a role in avoiding those signals. This is because T-cells from the immune system inspect glycans in the extracellular matrix for deviations. When deviations are present, an immune response is triggered, which could also trigger apoptosis of the deviated cell. So, the modified glycans on the cancer cell’s extracellular matrix help cancer evade a process like apoptosis.

Isn’t it astonishing that a single genetic modification could actually make cancers resistant to immunotherapy and chemotherapeutics? What do you think about this discovery?

 

How a Dash of Salt in the Summertime Helped Bring About Life on Earth

As humans, one of the most challenging and provocative questions we can ask is how life on earth came to be. We know about evolution, survival of the fittest, the one fish brave enough to walk. But how did the first microorganism suddenly wriggle its way out the world of the inanimate and mark the beginning of life on earth? Researchers from Saint Louis University, the College of Charleston and the NSF/NASA Center for Chemical Evolution think they have a new clue regarding the Earth’s environment at the time, and it sounds a lot like barbeque and pool party weather!

One of the keys to the creation of life is proteins. Proteins are strings of amino acids held together by peptide bonds, and they are responsible for carrying out countless tasks in the cell from catalyzing reactions as enzymes to protecting against diseases as antibodies to controlling movement and muscle contractions. Previous research has found that subjecting amino acids to “repeated wet-dry cycles”creates an ideal environment for the formation of peptide bonds. The more peptide bonds, the more complex polymer proteins that form and carry out biological processes needed for sustaining life. According to our original article, “Were hot, humid summers the key to life’s origins,” scientists imagine that the pre-life climate on earth consisted of hot, sunny days broken by heavy rainstorms. However, when Luke Bryan said that “rain is a good thing,” I don’t think he was referring to the cultivation of peptide bonds, because too much rain can actually have an opposite effect on our pre-biological proteins.

Pictured above is two amino acids joining to form a dipeptide through dehydration synthesis (removing an H2O molecule to join two monomers)

While water is the basis for all biological function, too much water added to a solution can result in hydrolysis, the decomposition of polymers due to the insertion of water molecules between bonds. If the Earth’s early climate involved large rain storms, the rain would flood the amino acid mixture and prevent the formation of peptide bonds. So, what kind of climate would then be required to spark the creation of life? Angela M. Hessler, in her article “Earth’s Earliest Climate,” tells us that “evidence points to an unfrozen — perhaps balmy — Archean Earth” due to “100–1000 times more CO2 than present atmospheric level,” which gives the Earth a “greenhouse atmosphere.” This greenhouse climate consists of high temperatures and humid weather- basically summer weather! This humidity in the air allows the amino acids to receive the ideal amount of water for forming complex proteins. However, our researchers have also discovered another factor that aids the formation of proteins, the process’s own sort of catalyst that pairs perfectly with the humid climate of pre-biological Earth.

Deliquescent minerals are salts that absorb humidity out of the air and then dissolve. If deliquescent minerals are present while amino acids bond into polypeptides, they can regulate the wetness of the environment in which polypeptides form, creating a perfect environment for the creation of proteins! I guess we can take the Bible that much more literally when were were told, “For you were made from dust, and to dust you will return.”

Above is dipotassium phosphate, a highly deliquescent mineral that is likely to have been present during the first formation of polypeptides millions of years ago.

While to some it may seem inconsequential, this discovery is important! Think about it: whenever we talk about evolution, we talk about inheriting traits from our ancestors. But we never talk about our oldest ancestor. The ancestor that has no ancestors because they are the first thing to live on this Earth! This discovery gives concrete evidence for a plausible theory regarding the birth of life on this planet, that one cell that fathered everything that now sees and breaths and strives to reproduce. This article gives us the farthest glimpse possible into the past, and with this new information, we can start to learn more about how life rose from the ground to survive and thrive on Earth.

If you have any other ideas or remarks, please feel free to comment on this post! I would love to hear what you all have to say about this exciting, new discovery!

 

Programming protein pairs

Researchers from the University of Washington’s Institute of Protein Design have created a new method to engineer protein dimers, or pairs. Working alongside molecular biologists at Ohio State, the researchers have made it possible “to design proteins so they come together exactly how you want them to,” as the paper’s lead author explains.

Two proteins held together by DNA.

Before, researchers relied on DNA to engineer dimeric proteins, utilizing complementary strands to create helical proteins held together by the hydrogen bonds between base pairs. However, DNA-created proteins lack the functionality of highly active proteins like protease, while also being prone to interference during synthesis. So, longing to create these more complex protein assemblies, the researchers engineered a new way to make them.

 

Using a computer program called Rosetta, the researchers designed hydrogen bond networks for their desired protein complexes, creating complementary bond networks for each pair of amino acids. For this, Rosetta algorithmically determined the ideal shape of each amino acid chain, calculating the best way to balance out intermolecular forces and finding the resulting lowest energy level, the most probable state for each chain. Thus, the researchers could accurately design complementary protein structures, so the two parts would fit together exactly.

As a result, the researchers were able to create highly specific, more active protein dimers that form double helices unencumbered by DNA and do not form unwanted shapes or interfere with other proteins during synthesis.

This new method has the potential to “transform biomedical technology”, as scientists can now have much more control over protein interactions, potentially engineering bacteria to produce energy or designing protein machines to diagnose diseases, among many other tasks. As the researchers set their sights on more complicated, dynamic protein complexes, there is no telling what exciting discoveries await.

NIH program to create 3D map of human tissues

Nervous Tissue

A recent project from the National Institute of Health aims to build a 3D map of human tissues on a cellular level. Known as HuBMAP (Human BioMolecular Atlas Program), the project is largely seen as a successor to the Human Genome Project and will likely yield similarly incredible results.

With the goal of better understanding how cells organize and cooperate in tissues, the researchers involved in the project hope to be able to view the body with molecular level precision, understanding which “genes and proteins are activated in each part of the body” and the effects that has. Although it won’t map the entire body, the project will nevertheless present many challenges in dealing with big data, a very current issue in science research, as the researchers seek to map trillions of cells, compose high-resolution maps of them, and categorize those maps.

Caltech, one of the few institutions chosen for the program, is working on mapping the circulatory system, analyzing differences in the tissues of arteries, veins, and other components on a microscopic scale. Using a new imaging technique known as seqFISH, researchers at CalTech aim to analyze mRNA and in doing so pinpoint thousands of biomarkers across tissues in 3D.

In creating such a detailed and complex atlas of tissue maps, researchers hope to answer big questions in pathology and aging with one particular goal being to better understand how healthy tissues vary on a cellular level. As the project continues into the mid-2020s, one can only hope that HuBMAP enables us to fill critical gaps in our knowledge of cells, tissues, and health.

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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