AP Biology class blog for discussing current research in Biology

Tag: proteins (Page 1 of 2)

How a Rogue Protein can cause Alzheimer’s Disease

In a study done by NYU Langone Healthy and the School of Medicine, researchers learned more about the types of proteins that cause the tangles in the brain that cause Alzheimer’s. Alzheimer’s disease is a type of dementia that affects the “memory, thinking, and behavior” of the over 5 million Americans who have it, according the the Alzheimer’s Association. The researchers tested tissue sample of 12 subjects with the disease looking for tau knots to “[examine] the bundles to identify the many proteins tangled within”.

File:Histopathology of neurofibrillary tangles in Alzheimer's disease.jpg

Shown is the tangles that are found in and contribute to Alzheimer’s disease 

You might be wondering, what is a tau knot? A tau is a protein that exists mostly in nerves that has the objective of stabilizing microtubules. When this protein is defective, it can become tangled with other molecules which leaders to Alzheimer’s disease.

Although neuroscientists already knew that tau tangles can cause neurodegenerative diseases like Alzheimer’s or dementia, they did not know many of the proteins that cause these dangerous knots. After analyzing the brain tissue, the researchers “found 12 proteins that they say have not before been tied to both tau and Alzheimer’s disease.” These knots were made up of 542 different proteins including those involved in the most essential processes of the cell like “energy production”, “the reading of genetic material”, “and cell breakdown and digestion.” These proteins that work to produce ATP and RNA in the processes of cell respiration and gene transcription (which are necessary parts of cell function); these important proteins are involved in the knotting. It is crazy that along with their existence comes the possibility of them destroying all they have created.

Despite the sad nature of this research, this new information comes along with hope for those suffering from this debilitating illness. According to co-lead author Geoffrey Pires, “Now that we have better insight into possible ‘key players’ in neurodegeneration, we may have clearer targets for potential therapies.” As these researchers gain more and more information, they gain a better understanding of Alzheimer’s and in turn, other similar “tau-linked neurodegenerative diseases, such as Pick’s disease.”

I feel Alzheimer’s is an essential disease to learn more about not only because it is incurable and unpreventable, but because 4 members of my own family have suffered from it. As the study’s senior author Thomas Wisniewski said “Alzheimer’s has been studied for over a century, so it is eye opening that we are still uncovering dozens of proteins that we had no idea are associated with the disease.” It is wild to think that something so common and well known, still has so many mysteries to it and that makes it immensely more fascinating and important to learn about.

A Friendzyme of the Environment

A team of researchers at the University of Portsmouth in England have engineered an enzyme that breaks down plastic six times faster than the previous most efficient plastic destroying enzyme. This enzyme specializes in breaking down PET, polyethylene terephthalate, the material most plastic bottles are made of. They created this by reengineering the previous enzyme, PETase, and combining it with another enzyme, MHETase, to create a ‘super enzyme’. They used a method normally utilized by companies in the biofuel industry, who combine enzymes to break down types of cellulase. Granted, it is still far too slow to be effective in breaking down the vast amounts of plastic waste we are faced with, but it is certainly a step in the right direction.

Enzymes are made of proteins which are made up of amino acids. Amino acids consist of a carboxyl group, an amino group, and a unique R group. Amino acids create chains in which carboxyl group match with amino groups, linking together using covalent peptide bonds, formed after dehydration synthesis. The chains of amino acids begin to fold and create proteins, which are the basis of almost all enzymes.

I think this issue is an important endeavor that should be funded by governments all around the world. We all share the Earth, and it is currently under threat by a number of issues, a prime example being pollution. Up to 8.8 million metric tons of plastic waste may enter the oceans every year. Some studies put the amount of seabirds that contain some form of plastic waste in their system at upwards of 90%. Plastic waste needs solutions before it makes the oceans uninhabitable for more creatures, and a mass produced enzyme may be a valid solution. The Great Pacific Garbage Patch is a large convergence of currents in the Pacific Ocean that has collected so much garbage, a large portion of which is made of plastic, that it is comparable to the size of Texas. Developing an effective enzyme that could quickly break down plastic could become a serious help to minimizing the environmental impact of the Garbage Patch.

While we cannot develop enzymes ourselves, several tips for mitigating our plastic waste are:

-Try to use aluminum cans instead of plastic bottles.

-Always recycle or reuse plastic bottles.

-Cut the holes of six pack rings before disposing so animals cannot be caught in them.

-Use metal and paper straws as a substitute for plastic straws.


File:PETase active site.png - Wikimedia Commons

^ The enzyme PETase 














Some People Can’t Smell Stinky Fish?!

A New York Times article has just reported a new “mutant superpower.” In Iceland, a brand new genetic trait was discovered, in which 2% of the population can’t smell the stinky odor of fish. 

A study of 11,326 Icelanders was conducted, in which each participant was given six “Sniffin’ Sticks (pens imbued with synthetic odors)” of cinnamon, peppermint, banana, licorice, lemon, and fish. The participants were then asked to identify the odors based on how strong each smell was and how good each Sniffin’ Stick smelled. Across the majority, the fish was rated the lowest in pleasantness. However, a small group of people actually enjoyed the scent, noting that it smelled like caramel or even a rose. 

This small group of participants was discovered to have a genetic mutation that enables the TAAR5 gene to form. TAAR5 (Trace Amine Associated Receptor 5) aids in making proteins that recognize trimethylamine (TMA), a chemical found in rotten and fermented fish, and some bodily fluids, including sweat and urine.  TAAR5 is also a G Protein, meaning that it binds guanine nucleotides. And, like other coding proteins, TAAR5 is a quaternary structured protein that has three subunits. Because this protein is incapable of binding guanine nucleotides, it means that there will be at least one “broken” copy of the gene that codes for the inability to smell fish. 

To simplify: TAAR5 recognizes the chemical of smell in fish (TMA), however, with the mutation that prevents the TAAR5 from forming, the smell of fish (TMA) is unrecognizable.

Interestingly, research has shown that this mutation may be a reaction to the customs of Iceland and a possible next step in the evolution of the region. In Iceland, fish takes a prominent place on most menus including dishes like “rotten shark.” These cultural and possibly smelly dishes may explain why this mutation is much more prominent in Iceland compared to Sweden, Southern Europe, and Africa (where the study was repeated). Bettina Malnic, an olfaction expert at the University of Sao Paulo in Brazil, commented on the luck of the region study took place, saying, “if they hadn’t looked at this population, they might not have found the variant [of TAAR5].”

I am VERY sensitive to smell and, at the same time, a lover of sushi, so it definitely fascinates me that there are people out there who don’t have to deal with the odor of smelly fish. This mutation is definitely one I wish I obtained. What do you think about this? Do you think you could have this mutation?!


Does This Protein Trigger Alzheimer’s Disease?

Research done by scientists at the Instituto de Neurociencias de Alicante, in Spain has revealed that the way people with Alzheimer’s process a key protein may lead to the creation of new tests and maybe even treatments. Alzheimer’s disease is a common form of dementia, where memory and thinking skills are progressively lost.

People with Alzheimers have a build up of insoluble plaques made of beta-amyloid and tau, both are proteins. Beta-amyloid is a part of a much larger protein called amyloid precursor protein, which is otherwise known as APP. APP is broken down by enzymes into either a beta-amyloid fragment, which is harmful, and causes Alzheimers, or another harmless fragment.

The process of the beta-amyloids forming insoluble plaques.

Glycosylation is the process of adding sugars to proteins, to form a glycoprotein, during production and the location of these sugar molecules is important in determining the ultimate destination of the protein in the cell. The glycosylation of the amyloid is altered in the brain of an Alzheimer’s patient, research suggests. Therefore, the protein is being processed in such a way where more beta-amyloid is being produced. This mutation no matter how small, can play a huge role in how the protein functions. Proteins have a unique shape determined by the interactions of their side chains. The shape the protein forms usually has to match with another molecule or structure. If the structure is mutated in any way, the protein may not remain the same shape and therefore not match the shape of another molecule or structure. This causes a change in the function. Therefore in this case with amyloid, how the protein is glycosylated will determine where it ends up in the cell membrane, due to shape and this will determine if an enzyme will break it down or not. 

The research found a difference between Alzheimer and non-alzheimer patients in terms of how APP is glycosylated. The patterns of APP glycosylation were evidently different. The patterns of proteins are so crucial to their function and structure. So, researchers were able to perform a chemical analysis and found that these different patterns may be a result of different processing of the protein. By processing APP differently, it may trigger Alzheimers. The protein structure is changed and the protein will not act the same. Therefore, with this knowledge, by looking for APP that has an altered way of being glycosylated, it may be easier to detect Alzheimers and inspire treatments in the future. This research is so exciting and important because one day it can help with Alzheimer’s treatments. Not only will it be a great detection test, but the by preventing the creation of beta-amyloid Alzheimers may be preventable in the future or easier to spot. Do you think this sounds like a promising next step to Alzheimer’s detection and treatment?

Trade Your Treadmill for… a Protein?

As humans, we have recognized that regular exercise has many benefits for everyday life. It helps our physique, our muscle and bone health, and it also is responsible for the release of endorphins that improve our mood. However, exercise is time consuming, and some of us just lack the motivation for regular physical exertion.  Scientists at Michigan Medicine have been researching the protein Sestrin in mice and flies, and they have found that “it can mimic many of exercise’s effects,” potentially creating a way to gain the benefits of exercise without actual exertion.

In their experiment, the Michigan scientists used two groups of flies. One group of flies was deprived os Sestrin, while the other group’s Sestrin levels were enhanced. When put through an extended period of exercise, the flies that lack Sestrin did not have any of the typical muscle development and endurance that comes from working out. The flies that received amplified amounts of Sestrin also didn’t progress. However, the Sestrin-boosted flies didn’t receive the benefits of exercise from exertion, because they had already acquired those benefits  from their increased Sestrin levels. In performing the same experiment with mice, “Mice without Sestrin lacked the improved aerobic capacity, improved respiration and fat burning typically associated with exercise.” According to the article “Sestrins are evolutionary conserved mediators of exercise benefits,” “in vertebrates, endurance training leads to increased mitochondrial biogenesis/efficiency, decreased triglyceride storage, improved insulin sensitivity, and protection of both muscle and neural functions.” Basically, if Sestrin indeed proves to be the magic exercise replacement, it could help alleviate some of the negative physical consequences of aging.

However, our scientists have 2 main problems in turning Sestrin to a mass produced supplement: it’s a very large molecule, and we are still unsure of how the body naturally produces sestrin during exercise. Therefore, we are not yet at a point where our exercise replacement is a reality, but the probability of future promising results is high.

Personally, I will have to see this protein work on humans before I take seriously the idea of an exercise replacement. A successful Sestrin supplement may be able to mimic the physical benefits exercise, but obtaining physical results through minimal work could be detrimental to the public’s general mentality. Receiving physical benefits through hard exercise teaches cause and effect, mental toughness,  the value of goals, and the satisfaction of well deserved rewards. If this supplement ends up being the fantasized work out supplement everyone is looking for, how will that result-without-the-work mentality impact how we treat other aspects of society? That’s why I don’t see this discovery as a total positive, but I’m excited to see what future studies bring in the development of this long fantasized product.

If you have anything other information or opinions on this topic, feel free to drop a comment below!


And The Nobel Prize in Medicine Goes To…

On October 7th, it was announced that the Nobel Prize in Medicine would be awarded jointly to scientists William G. Kaelin Jr., Sir Peter J. Ratcliffe and Gregg L. Semenza for their contributions in the discovery of how cells detect and react to the levels of oxygen in their environments. Each contributor will be receiving 1/3 of the prize share for their work in this topic.

The “Textbook Discovery”

Before we are able to understand the gravity of the discovery being awarded one of the world’s most prestigious scientific prizes, let’s set up some essential vocabulary we will need to break this concept down. Firstly, HIF-1α is the main protein that has been found to be essential to the identification of Oxygen. We have known that there exists an EPO gene which encodes for a steroid known to increase levels of Oxygen but the discovery of the HIF-1α protein is what is so astounding. What this protein does is regulate the activity of the EPO gene. Another factor which plays a large role in this discovery is the VHL gene, a gene known to be responsible for preventing occurrences of cancer. It was discovered that VHL had a link to the regulation of oxygen when low levels of the gene were linked to low level of oxygen (hypoxia). However, as more VHL was reintroduced, oxygen

levels were restored to normal.

How do HIF-1α proteins, VHL genes and EPO genes come together to create an understanding for how cells react to oxygen variation? Well, for HIF-1α to degrade, a peptide known as ubiquitin must link onto the HIF-1α and begin proteasomal degradation. It just so happens to be that VHL codes for a complex which tags proteins with ubiquitin allowing them to degrade. Finally, it was discovered that Oxygen was what binded theses two together, moving ubiquitin from the VHL over to the HIF-1α protein, thus degrading it. In other words, the more oxygen there is present, the more HIF-1α which gets degraded. Finally, the mechanism by which oxygen levels are controlled has been uncovered.

The Men Behind The Discovery

Over the span of 2 decades of research, three scientists were able to form an understanding on how our bodies respond to one of the most essential molecules in biology.

William G. Kaelin Jr. is a professor of medicine at at Dana-Farber Cancer Institute and Brigham & Women’s Hospital Harvard Medical School. As a cancer researcher, Kaelin’s main contribution was in the creation of a full understanding of the VHL disease which allowed for the link between VHL and HIF-1α to be formed.

Sir Peter J. Ratcliffe is the director of clinical research at the Francis Crick Institute in London. Ratcliffe and his team’s main contribution was establishing the connection between VHL and HIF-1α.

Gregg L. Semenza is a professor in genetic medicine at John Hopkins. His work focused on the EPO gene and how it controlled oxygen levels. He found out how oxygen is regulated, leaving only the cause a mystery.

For even more information on the scientists responsible, look into this New York Times article about them.

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!


Plants Have Memory!

Did you know that flowering plants can remember changes in their environment? I sure didn’t!

Flowering plants use their memory to remember the temperature of a cold winter. By doing so, plants ensure that they will only flower during the warmer temperatures of spring or summer.

The way plants do this is through a group of proteins called polycomb repressive complex 2 (PRC2). In cold temperatures, the proteins come together as a complex and switch the plant into flowering mode. However little is known about how PRC2 senses the temperature changes in the environment.

But according to an article on Science News, a team of researchers from the Universities of Birmingham and Nottingham lead by Dr. Daniel Gibbs discovered a mechanism in angiosperms that enable them to sense and remember changes in the environment so they can adapt to the varying conditions around them, especially during the changing of seasons. The researchers discovered that the protein Vernalization 2 (VRN2), the core of the PRC2, is very unstable.

Why is this important? Since VRN2 is unstable, it can be greatly affected by the level of oxygen in the environment. In warmer months, the plant is already a flower, so it does not need to continue the flowering process. The abundance of oxygen causes VRN2 to break down. Conversely, when there is a lower level of oxygen in the colder months, VRN2 becomes more stable, causing the proteins of PRC2 to come together and switch the plant into flowering mode. As Dr. Gibbs says, “In this way, VRN2 directly senses and responds to signals from the environment, and the PRC2 remains inactive until required.”

By sensing and remembering the changes in their environment, plants can control their life cycle. I find it so interesting that plants have this capability. Plants that are able to adapt to our world’s ever-changing climate will be more successful in surviving.

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.

How Ground Squirrels Are Bracing For The Cold

As we enter the heart of winter, puffy coats, hats, and gloves make it out of our closets to protect us from the frigid air. While we trudge along shivering, the ground squirrel lives happily in the cold weather, resistant to the low temperatures.

The Phenomenon:

A new study shows that when the ground squirrel wakes from hibernation, it is less sensitive to the cold than its non-hibernating relatives. Why? A cold-sensing protein, TRPM8, in the sensory nerve cells is partly responsible for the amazing phenomenon.

The Evidence:

In an experiment conducted with mice (non-hibernating), ground squirrels, and Syrian hamsters (hibernating animals closely related to the ground squirrel), the animals were given the choice between a hotter plate and a colder plate. Whereas the mice gravitated toward the hot plate, the ground squirrel and Syrian hamster did not react to the cold temperature of the plate until it dropped below 10 degrees Celsius.

The Biology:

Part of the squirrel’s and hamster’s intolerance to cold has to do with the TRPM8 protein. TRPM8 is a cold-sensing protein that sends a signal to the brain when something is too cold. Researchers turned to the gene responsible for turning on the TRPM8 protein to find the differences between a ground squirrel and a rat. They found a chain of six amino acids in the squirrel gene that caused the adaptation to cold. When they switched that section with one from a rat, the squirrel was more sensitive to the cold.

It is quite amazing that scientists can extract and switch such small portions of DNA to find the exact cause of a trait. What else do you think this technology could be used for?

The Effect on Life:

Tolerance to cold may help the squirrel and hamster transition from an awake state to hibernation state. This is true because if an animal senses or feels cold, it will expend a lot of energy trying to warm itself up. This process counters they physiological changes needed to transition into hibernation, a state of low metabolic activity. Hence, since the hamster and squirrel don’t sense the cold, it will be easier to hibernate.

Further Research:

There is still a lot unknown about the TRPM8 protein and ground squirrel temperature sensitivities. It is believed that TRPM8 is only a part of their intolerance to cold. Furthermore, the structure and function of TRPM8 is still being studied and could lead to more breakthroughs. Want to learn more about ground squirrels, hibernation, or the TRPM8 protein? Click here to read the full article!

Hair Saving Option with Chemotherapy

Scientists have been finding a way to prevent hair loss after the painful process of cancer treatment, Chemotherapy (Chemo). Hair loss is one of the biggest feared side-effects. A recent study showed that 75% of female patients who had breast cancer feared the side effect of losing hair. Hair loss scored the highest in a Swedish nurse’s study that investigated the quality of life in patients who had breast cancer. With the help of Sung-Jan Lin, a scientist at National Taiwan University, a protein was made that could withstand the distressing effects of Chemotherapy.

There are a few other options for people receiving this treatment. Some will try to put on scalp-cooling caps to freeze the chemo drugs from entering the hair follicles. However, this process is expensive and only works for 50% of the people. The treatment could end up being longer than expected, and can cause mild to severe headaches and discomfort.

Lin describes that part of the problem is that we have such a limited knowledge of how Chemotherapy damages hair follicles.

In short, his team looked at a protein called p53. This protein functions to limit tumor growth, but also helps suppress hair growth (hair cells divide rapidly like tumor cells)

Studying P53, Lin found out that the protein was blocking a hair-promoting protein WNT3A. This stimulated his team to ask the following question. Is injecting WNT3A directly into the scalp while administering Chemo prevent hair loss?

The team decided to experiment with mice with a chemotherapy agent, and soon enough the results matched their hypothesis. One group of mice were injected with WNT3A soaked beads. And sure enough, that group sustained their hair. While the other group that was not given WNT3A loss all their hair.

Lin and his team are now working to adapt his studies on human patients. As stated by Lin it would be unsafe to inject WNT3A in bead form. As a result, they are working to create the protein in a gel or cream solution.

With this new hair saving option, the cancer treatment will seem less fearful for some patients. This treatment could be a big help for the future. Scientists are working to expand their knowledge on how to effectively provide treatment without endangering our human traits.

So after hearing all this, what do you feel about this new idea? Will the “power of proteins” eliminate other side effects provided by Chemotherapy? If so, what kinds? Let me know in the comments below.

Photo link and photographer:

Liz West

Design Your Own Organelle!


All eukaryotic cells consist of compartmentalized organelles, each with a specific function. We’ve all heard of mitochondria, chloroplast, and lysosomes, but, what if we could design a new organelle?! That’s exactly what scientists are working on right now – modifying or hijacking existing organelles to fit new specific functions.


Scientists currently have the technology to alter the DNA of cells to manufacture proteins they couldn’t “naturally” make. However, this technique has a few flaws. The proteins produced or their intermediates could damage the cell and chemicals in the cell could damage the proteins. If we could compartmentalize the production of these new proteins, this problem would be avoided. So, we look to organelles!


Stuart Warriner, a chemical biologist at the University of Leeds, and his colleagues believe peroxisomes are the key. Current techniques allow scientists to manipulate these organelles. Their experiments show that they could deliver certain proteins into the peroxisomes of most cells. These selective proteins are ones that are not usually made; therefore, we say that humans have “hijacked” the cell.

What’s Next?

Scientists are hopeful that future research could lead to the ability to use peroxisomes to manufacture compounds by importing specific proteins into them. Currently, when an organelle is modified, every organelle of that type must be modified. Future research could ensure that modified and conventional organelles could coexist in the same cell. In addition, Warriner and his team are working on the modification of peroxisomes in yeast to produce desirable compounds. Despite these studies, Warriner believes that this technique of hijacking organelles will not be implemented in humans for decades, if not never, because it wouldn’t be particularly useful. To learn more, check out their findings!

Who Cares?

We have the ability to alter DNA and cells! That is amazing! Although peroxisome altercation may not prove to be essential to humans, it is still an impressive exploratory feat and a step toward greater modification in microscopic organisms. What do you think similar cell modification research should be focused on?

CRISPR/Cas9 Provides Promising Treatment for Duchenne Muscular Dystrophy

There are nine kinds of muscular dystrophy and of these, Duchenne MD is the most common severe form of childhood MD. It affects about 1 in 5000 newborn males, only in very rare cases has it affected females. DMD is a genetic disorder that causes progressive muscle degeneration and weakness. Patients usually die by age 30 to 40.

DMD is caused by the absence of a protein, dystrophin, that helps keep muscle cells intact. In 1986 it was discovered that there was a gene on the X chromosome that, when mutated, lead to DMD. Later, researchers discovered that the protein associated with this gene was dystrophin. From this information, we can tell that this disorder is sex-linked, which explains why women are mainly carriers.

No one has found an absolute cure for this genetic disorder until now. Even in recent years, people have discovered treatments that will make patients’ lives more bearable, but never reverse the disorder. As a result of these advances, mostly in cardiac and respiratory care, patients are able to live past teen year and as long as in to their fifties, though this is rare. Although there are still drugs being tested like Vamorolone (a “dissociative steroid,” is an anti-inflammatory compound), more treatments on the molecular level are now being considered. However, thanks to recent discoveries and research with the new genetic technology, CRISPR/ Cas9, scientists may have found a treatment for DMD.

This new approach to gene correction by genome editing has shown promise in studies recently. This particular correction can be achieved in a couple ways: one is by skipping exon 51 of the DMD gene using eterplirsen (a morpholino-based oligonucleotide). Studies over four years show prolonged movement abilities, and a change in the rate of decline compared to controls. The newest approach to gene correction using CRISPR/Cas9, which the article I’m writing about focuses on, was performed in this study as next described: the CRISPR/Cas9 system targets the point mutation in exon 23 of the mdx mouse that creates a premature stop codon and serves as a representative model of DMD. Multiple studies in three separate laboratories have provided a path and laid the groundwork for clinical translation addressing many of the critical questions that have been raised regarding this system. The labs also discovered by further demonstrations, that this is a feasible treatment for humans. Functional recovery was demonstrated in the mice, including grip strength, and improved force generation- all of which are very important and hopeful discoveries. It is estimated from these studies that this new method will pass clinical trials and go on to benefit as many as 80% of DMD sufferers. Even greater success rates are expected if this is performed in young and newborn DMD patients.

Protein: A Cell’s Hero or Villain?

The function of the endoplasmic reticulum is to fold and secret transmembrane proteins. Proteins in cells provide a variety of functions; such as speeding up chemical reactions through enzymes, protecting the cell against disease through antibodies, and coordinating organism activities with hormones. Proteins are obviously crucial to cells.

However, recent research shows that although proteins are supposed to help cells run efficiently, in some cases, under stress, proteins can cause cell suicide, or apoptosis. Apoptosis is part of the natural cycle of a cell, but in this case, proteins are truncating the cell’s normal cycle, which can even be disease-inducing.


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When environmental conditions or genetic factors around the ER go awry, a cellular stress reaction called the Unfolded Protein Response (UPR) either triggers or deactivates DR5, Death Receptor 5 Protein, which can lead to cell suicide. The two main factors which control the UPR are IRE1A and PERK. By activating XBP1, which drives expression of cell-survival genes, IRE1A promotes cell survival. PERK actives CHOP, which in turn activates DR5.

The ER activates UPR in order to alleviate cell stress and return the ER to homeostasis, but this instead can lead to apoptosis.

ER stress is central to many diseases, including neurodegeneration, type II diabetes, cancer, atherosclerosis, and liver disease. This finding is so important because now that scientists have found that IRE1A and PERK are the causes of this response, they can better study the phenomenon.

The idea that an organelle can be stressed is very interesting. I usually think of organelles as having clean structures and clean results, but this story shows that the ER can be overstressed through changing conditions and its actions will reflect this stress.

Another interesting part of this article is that when the ER activates UPR, this will either activate or deactivate the DR5, the cause of cell suicide. In science, we usually think of things as reliable and consistent, but this response to the ER can either save the kill or destroy the cell.

Finally, Cancer is a diseased caused by the over-multiplication of cells. If cell stress leads to cell suicide, then maybe scientists can use their new found understanding of the proteins involved in UPR to figure out a way to destroy cancerous cells.

Original Article


Bioengineered Proteins Are Amphibious Adhesives

A group of researchers from MIT recently published their groundbreaking findings on specially engineered proteins that are able to stick to substances both in and out of water. Using naturally occurring adhesives secreted by mussels as a model for their research, the team combined those proteins with biofilms from certain bacteria to create an especially strong and sticky hybrid.

These new adhesives are much more complex than previously engineered proteins. While other scientists used the E. coli bacteria as a template to engineer proteins that resembled the mussel’s protein, leading researcher Timothy Lu described those methods as unable to “capture the complexity of the natural adhesives”. Therefore, the MIT research team uses several types of bacteria to separately manufacture components of different mussel proteins and then combines them with bacterial curli fibers into one complex adhesive.

There are numerous applications of this discovery. Once the team is able to concoct a method of generating the protein in great quantities, it can be used to repair holes in ships as well as to seal wounds after an accident or surgery. One of the team’s subsequent goals is to create “living glues” composed of bacteria that would react to a breach of a material and repair it through secretion of a protein adhesive. The potential of this discovery is demonstrated by the acclaim of the group’s sponsors, which include The Office of Naval Research, the National Science Foundation, and the National Institutes of Health.



Mussel proteins may be the key to a groundbreaking adhesive



Scientists at MIT have created their own adhesive that could revolutionize multiple aspects of life. This adhesive would be used for patching up multiple things ranging from ships to human wounds. The adhesive is made from the proteins found in mussels and the proteins in biofilms. The way mussels stick to ships is because the proteins act as a natural adhesive/glue like material. Biofilm is a group of organisms that stick to each other and other surfaces.

Separate, these both have strong attaching abilities, but when combined, the MIT scientists created the “strongest biologically inspired, protein-based underwater adhesives reported to date”. The new adhesive was created by using the foot proteins in the mussels. More specifically, they used the curli fibers which attach and form larger and stronger fibers, called fibrous meshes. The fibrous meshes can be used both in dry and aqueous solutions making it very versatile.

Timothy Lu, the associate professor of biological engineering and electrical engineering and computer science at MIT, is in charge of the research. Although the adhesive is produced in small amounts, Lu has high hopes as he has plans to make a “living glue” that can tell when there is an opening and secrete the adhesive by itself. This could be very useful if the adhesive is used for human treatment because the adhesive would know exactly when to activate and deactivate itself.

Do you think that this adhesive can make an impact on society?


Additional article:

Hearing Loss Clue Uncovered

In the United States, approximately forty-eight million (twenty percent) of men and women suffer some degree of hearing loss, as it is the third most common physical condition after arthritis and heart disease. While it is most often associated with the population sixty-five and
older, hearing loss effects all ages, as thirty school children per out one-thousand are afflicted in some varying degree. An individual is able to hear sound involving the ear’s main structures. In age-related hearing loss, one or more of these structures is damaged: the external ear canal, the middle ear, and the inner ear. External ear canal impairment is related exclusively to conducive hearing loss. The middle ear, which is separated from the ear canal by the eardrum may be caused by sensorineural hearing loss. Lastly, the inner ear, which contains the cochlea, the main sensory organ of hearing. When the vibrations from the middle ear enter the cochlea it causes the fluid to move and the sensory hair cells pick up this movement. In response to the movement of the fluid the hair cells send an electrical signal up the auditory nerve to the brain where it’s recognized as sound.


Now, how do these different internal departments of the human ear gradually induce hearing loss? While we get older, some may develop presbycusis, which causes the tiny hair-like cells in the cochlea to deteriorate over time. Clarity of sound decreases, as the hairs are unable to vibrate as effectively in response to sound. Recently, otolaryngologists have discovered new evidence that human hearing loss relates to a certain genetic mutations. A study at the University of Melbourne revealed “a novel genetic mutation was first identified in 2010 as causing hearing loss in humans… now discovered that this mutation induces malfunction of an inhibitor of an enzyme commonly found in our body that destroys proteins – known scientifically as SERPINB6. Individuals who lacked both copies of this “good gene” were shown to have lost their hearing by twenty years of age.


Although this discovery is changing the way scientists previously viewed hearing loss, the answer to why this mutation, SERPINB6, is a catalysts for such loss, is inconclusive. However, this mutative gene has created a revelation for many: it is now not unusual to show gradual signs of hearing loss under the age of sixty years.


To better understand the effects of the mutant gene, mice were used in order to imitate the condition from youth to adulthood. At only three weeks of age, mice with SERPINB6 had begun to lose hearing – three weeks is equivalent to pubescent or teenage years in humans. And as we could have predicted, the mice continued to show a decrease in hearing ability, much the same as humans. Researchers examined the mice’s inner ear, which revealed the cells responsible for interpreting sound (sensory hair cells) had died.


Fortunately, this new discovery of a mutant gene in human sensory cells has created new attention to better understand the case of those who are effected by the condition. 



Understanding HIV, one protein at a time

By NIAID/NIH (NIAID Flickr’s photostream) [Public domain], via Wikimedia Commons

In a recent study, scientists at Johns Hopkins University have narrowed down a list of 25 human proteins that HIV viruses target the most. The scientists started by studying the HIV-1virus, which is the most infectious and most common type of HIV. They knew that the virus clings to proteins and membrane as it emerges from an infected human cell in order to disguise itself from the human immune system, but inquired as to whether it was a random process or not. They then searched for types of proteins that they targeted the most, using the HIV-1.

They virus tends to target the CD4+ T cells and microphages which both migrate to sites of inflammation. This makes sense because HIV targets the immune system and  the virus can wait to attack while disguised by these cells. They originally identified 279 proteins that this virus in particular targeted when isolating the HIV-1 with CD4+ T cells, but when they crossed the data from two different cell types, they found that only 25 proteins were shared by viruses from both cell types!

This is an extremely interesting and groundbreaking discovery because of the possibilities behind this discovery. If we can figure out the types of proteins these HIV viruses are hiding behind, we could target and destroy them which could possibly lead to the abolition of HIV.

Gerbils Can You Hear Me?

80 to 90 percent of people suffer from inherited deafness. In a study, scientists have reversed deafness in gerbils. This is a huge step in gene therapy research this month making the possibility of using gene therapy as a cure for deftness one step closer. Genetic therapy is the use of genetic material such as DNA to manipulate a cell and is generally used to treat inherited diseases; in this case scientists used human embryonic stem cells. The gerbils in the study were born deaf. This type of deafness is a birth defect caused by damage to hair cells in the inner ear. These inner ear hair along with auditory neurons which translate sound vibrations from the inner-ear cells to electrical signals are how you can hear. Scientists specifically worked on gerbils whose deafness was caused by a mutation in a gene coding for a protein called vesicular glumamate transporter-3. Even minor alterations to a protein’s primary structure ,such as the movement of a double bond, will cause major defects in the tertiary structure and the function of the protein. The mutated protein in this study vesicular glutamate transporter-3 controls the consumption of glutamate (neurotransmitter) into synaptic vesicles, which join two nerve cells, of the neural cells. This is clearly groundbreaking news this month and has proved the various use of stem cells. How do you feel about the use of embryonic stem cell research? Feel free to comment!!



Gamers solve some of biology’s most difficult riddles?

Who is solving some of biology’s most difficult puzzles and riddles? Obviously scientists, right? Think again. It’s the gamers.

An article recently reported that a revolutionary online game called Foldit, allows anyone, from gamers to students, to help predict the foldings and structures of  various proteins by playing competitively online. Protein folding is one of biology’s most difficult and costly problems, and is even a troublesome task for the most capable computers. A game such as Foldit requires much insight and an intuitive understanding to fold the proteins, allowing human intuition to triumph over a computer’s calculations. As we have learned in class, proteins are very prevalent in the human body. Hormones, enzymes, and antibodies are all examples of proteins, but many proteins are also associated with strands of viruses and diseases.

This is where you, as the gamers, come into the picture.

Since proteins play a large role in the functions of viruses and diseases, gamers playing Foldit can help design new proteins to help treat or provide a cure for the condition. The article reported that gamers have most recently solved the structure of an enzyme crucial for the reproduction of the AIDS virus. Knowing the structure, scientists are now able to find certain drugs to neutralize the enzyme and stop the reproduction of AIDS virus.

In class, we have learned that there is basically an infinite amount of combinations of proteins; there are 20 amino acids and can be combined to form chains of various lengths. We have also learned that the structure of a protein is also correlated with its function. The bonds present in the primary, secondary, tertiary, and quaternary structures of proteins are an important part to the shape and folds of a protein, giving the protein certain properties due to its shape. All of the information we have learned about proteins in our AP Biology class, can be seen and easily applied to the game, Foldit.

Now since we know the vital importance of proteins, do you want contribute to the next cure for a virus or disease? Get your game on and try Foldit out and see what you can do to solve some of biology’s most difficult riddles!




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