BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: molecules

This Parasite Can Change Agriculture for the Better

When parasites take control of a host, it may seem like all is lost for the unfortunate animal. However, a newly discovered parasite uses a mechanism that actually slows down plant aging, and may offer new ways to protect crops that were once threatened by diseases. 

Prior to this discovery, very little was known on how this parasite functioned on both a molecular and mechanistic basis. The Hogenhout group at the John Innes Centre and collaborators published in Cell have identified a manipulation molecule produced by Phytoplasma bacteria, which hijacks the development of plants. This protein breaks down key growth regulators, which as a result causes abnormal growth.

According to an article published by FronteirsIn, phytoplasmas and their associated diseases cause severe yield loss globally. For example, Aster Yellows cause major yield losses in crops such as lettuce, carrots, and cereals. As stated in the article, “Phytoplasma diseases of vegetable crops are characterized by symptoms such as little leaves, phydolly, flower virescence, big buds, and witches’ brooms.” These effects ultimately cause the host plants to die over time. 

Phytoplasma Growing on a Plant

Professor Saskia Hogenhuot said that “Our findings cast new light on a molecular mechanism behind this extended phenotype in a way that could help solve a major problem for food production.” One of these findings includes the bacteria protein entitled SAP05, which manipulates the plant’s molecular structure. This manipulation targets the process of the proteasome, which breaks down obsolete proteins inside plant cells. SAP05 causes the plant proteins that are used for regulating growth and development to be thrown out. With the absence of the proteins, the plant’s development favors the bacteria, which in turn triggers vegetative growth and pauses the plant’s aging process.

Specifically, SAP05 directly binds to the plant developmental proteins and the proteasome. Proteasomes hold a very important role in the cell regarding the degradation of proteins, with Professor Gonzalez writing, “proteasomes perform crucial roles in many cellular pathways by degrading proteins to enforce quality control and regulate many cellular processes such as cell cycle progression, signal transduction, cell death, immune responses, metabolism, protein-quality control, and development.” Conversely, SAP05’s direct binding is a newly discovered method of degrading proteins, unlike the usual fashion of proteins degraded by proteasomes that are tagged with ubiquitin beforehand. 

To further study SAP05, the research team wanted to see if SAP05 affects the insects that carry the bacteria plant to plant. Turns out, SAP05 does not affect the insects due to the structure of the host proteins in animals differing enough from plants. This research also enabled the team to identify the two amino acids in the proteasome that interact with SAP05. If these two amino acids in the plant proteins were switched to the amino acids found in the insect protein, they would prevent abnormal growth. 

In a polypeptide chain, every amino acid is important to how the chain functions. Specifically, an amino acid’s unique side-chain gives it different characteristics, which plays a role in how the protein is structured and its function in the cell. In this case, these two amino acids from plant to insect proteins ultimately change the way SAP05 interacts with the polypeptide chain, which as a result changes the effect. 

Personally, I feel that this discovery is groundbreaking since it enables countless possibilities regarding the prevention of mass yield loss. How do you think this research will be utilized in the future? Let me know in the comments!

A Super Self-Assembling Vaccine Booster to the Rescue!

Vaccines: a topic on the forefront of the minds of scientists, researchers, and the general public. With the novel coronavirus and fiery online debates led by coined “anti-vaxers” about the effectiveness and dangers of vaccination, biologists are racing to discover more methods to improve these life-saving injections. An essential component of many vaccines, including ones used to prevent cervical cancer, influenza, and hepatitis is the adjuvant: a “booster” ingredient that helps the vaccine create a longer-lasting, stronger immune response in the patient. Recently, a team of scientists in Japan discovered a new adjuvant—a molecule called cholicamade—that was equally as effective in treating influenza in mice as its predecessor, Alum. The emergence of this new ingredient is exciting, but the real novelty lies in the process these biologists used in discovering chloicamade: looking at molecules that could self-assemble.

What is the self-assembly of a molecule, or multiple molecules? Multiple molecules are said to self-assemble if they are able to organize into a defined pattern without the intervention of an external source, such as heat. These molecules will form ionic or hydrogen bonds with each other, similar to the joining of water molecules, since they don’t share electrons equally, as we learned in AP Biology. Identifying molecular structures that self-assemble is a common practice in materials science, but not often used in researching adjuvants. This team of biologists and chemists hypothesized that utilizing molecules that form in this fashion for disease treatments may be effective because pathogens in viruses also form through self-assembly. They wondered if a similar method in structural formation between a treatment and its virus would trigger a similar immune response.  

And it did! Cholicamide self-assembles through ionic bonds to create a structure which looks almost identical to a virus, triggering the same immune system cells to react. The structure of the molecule

An image of the influenza virus, which the treatment would attempt to replicate.

lends itself to the formation of ionic bonds because of its inherent polarity and electronegative elements. The molecule can be injected directly into vacuoles that will connect it with the specialized receptors which will trigger the appropriate immune response. A vacuole’s ability to store water and other nutrients (as we learned in AP Biology) as well as transport these nutrients throughout an animal cell is vital in ensuring the treatment binds to the correct receptors. Uesugi, a leading scientist in the study, hopes “the new approach paves the way for discovering and designing self-assembling small molecule adjuvants against pathogens, including emerging viruses.” What do you think about this new method in discovering vaccine treatments? How do you see the future of vaccines changing as more adjuvants are researched? I believe there is nothing more exciting than not only confirming the effectiveness of a new treatment, but also conducting the research with a new approach or perspective.

 

 

 

A Computer Powered By ATP?

Could supercomputers be powered by ATP the same molecules that power our cells? And could these computers run faster than normal supercomputers? The Dan Nicolau and his son Dan Nicolau Jr. seem to think so. Although this computer is not yet a reality the father and son duo have been working on a model of this bio-supercomputer for seven years. The original drawing looked like “small worms exploring mazes” according to Dan Nicolau. These chips use short strings of proteins instead of electrons and using ATP to power it all.

 

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Molecule of ATP

You may be wondering why this is a big deal. It is because traditional supercomputers spend so much power cooling themselves down they need their own power plant to function. Since ATP is used in biological organisms it does not heat up as much. This could lead to dramatic decreases in the amount of energy a supercomputer uses. The model is promising but the father and son do not have an estimate on when the supercomputer could become a reality. One possibility according to Dan Nicolau is the integration of the bio supercomputer with a traditional supercomputer.

 

Link to Article:

https://www.sciencedaily.com/releases/2016/02/160226133606.htm

Other Links:

http://sputniknews.com/science/20160228/1035493225/biological-supercomputer-unveiled.html

https://en.wikipedia.org/wiki/Biocomputer

If There Were a Printer for Organic Molecules

This would be the closest thing we have so far. Over at the University of Illinois, Chemistry professor Martin Burke has created a machine that assembles small organic molecules, group-by-group. This rather straightforward way of synthesizing molecules is likened to building with legos: By assembling simple molecular groups, countless shapes (in this case, molecules) can be made. Going even further than that, Burke has designed the machine in such a way that it can take 3-D models of the molecule to create it, taking both technological and hyperbolic advantage of the “3-D printer craze” that just rolled over.

(The University at which the research took place)

The unprecedented advantage such a device would provide to the fields of science is that it would allow practically any non-specialist with an understanding of chemistry to synthesize molecules. Currently, synthesis of certain molecules is something akin to arcane research: incomprehensible and prolonged. Chemists who specialize in chemical synthesis can spend many years trying to figure out how to produce an organic chemical, especially at the more complex level where the specificity of molecular shape and composition can be baffling to produce. Keep in mind, this is all done by humans on a macroscopic scale, whereas what matters in producing the desired substance lies on the atomic scale. This is why such a device could potentially be such a breakthrough! Not only would synthesizers be able to create molecules on the fly, but even non-specialists could dabble with very good chances of success, opening the field of molecular biology to research at a truly profound level of development.

(Molecules like this could be potentially a lot simpler to synthesize in the future)

I doubt, however, that such a device will live up to its miraculous standards. Often, there are many complications with such things, which can lead it to quickly encounter limitations. It is even admitted that the device can only synthesize relatively small, but still complex, molecules. This device operates on a clever, but still not fundamental, scale. The true breakthrough will be when we can manipulate individual atoms to produce anything that is theoretically possible. Nevertheless, congratulations to Martin Burke and his team for developing such a device, which lies on the path of “work smarter, not harder”.

I’m probably quite cynical about this, so I’d like to ask, what are your thoughts on this development?

 

Source Article:

http://will.illinois.edu/news/story/u-of-i-chemists-machine-simplifies-building-of-molecules

Further Reading:

http://www.macroevolution.net/molecule-making-machine.html#.VhGLRDZdE0Q

http://www.technology.org/2015/03/12/molecule-making-machine-simplifies-complex-chemistry/

 

 

Is Type 1 Diabetes Curable?

Right now, on Grey’s Anatomy, one of the plot lines involves Type 1 diabetes and mice. Dr. Miranda Bailey is performing a trial, attempting to create a device with a molecule that can be placed in humans to cure diabetes. She is using mice as the trial guinea pigs. This sounds crazy! However, this same trial is being done in real life!

“Type 1 diabetes is characterized by the body’s inability to manufacture insulin because its own immune system is attacking it.”

Diabetes has doubled in our population in the last ten years. In fact, doctors have found themselves able to predict if someone has or will have Type 1 diabetes ninety percent of the time. The experiment that physicians are now doing on mice started two and a half years a go. Testing different molecules on mice, the doctors have tried to find which molecules will stop the production of Type 1 diabetes. The doctors look for particular structural pockets in the mouse’s body that are lining areas of proteins, and they then place the molecules in those particular pockets. It seems that doctors have tried this experiment on mice with hundreds of molecules in the past, but the one that works is glyphosphine. When the glyphosphine is entered into the mouse’s body, it “enhances insulin presentation”

Mice at the Louisville Zoo, Taken by: Ltshears

and kills the chances of early signs of diabetes in mice becoming Type 1 diabetes. However, if the mouse already has Type 1 diabetes, the treatment is not as effective in getting rid of it, for it has already found a home in the body. In reality, this molecule called glyphosphine is only a preventative molecule, one that can save people who have had diabetes in their family history, or are just unlucky with symptoms of a future diagnosis. This trial has been published in the Journal of Immunology and gives hope to doctors working to fight Type 1 Diabetes.  The clinical trial is to be performed on humans throughout the next five years.

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