AP Biology class blog for discussing current research in Biology

Tag: proteins

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!




Babies Save the Day?

No, a bionic baby did not come and save today’s world from global warming but in fact, embryonic cells could potentially save those who suffer from Sickle Cell Disease.

Sickle Cell Disease occurs as a result of a DNA letter change in the gene for hemoglobin, the main protein that carries oxygen for red blood cells. It is possible for the single mutation in the amino acid sequence to affect the entire protein because, as I learned in class, the chain of amino acids, formed by peptide bonds, constitutes the primary structure of proteins.

A recent study conducted by researchers at Johns Hopkins have found that sickle cell disease, a disease that can be very debilitating and affects mostly African Americans, can be cured with the use of stem cells. This is important because the only cure that has been found so far is bone marrow transplants, which can be very painful and is not always successful. The researchers isolated a patient’s own bone marrow cells and used them to generate induced pluripotent stem cells, which are adults cells that can be reprogrammed into embryonic cells. These embryonic cells can then be coaxed into red blood cells, through the use of growth factors.

Despite this progress, Dr. Linzhao Cheng states that, “these immature red blood cells still behave like embryonic cells, and as a result are unable to turn on high enough levels of the adult hemoglobin gene” . The cells still need to be coaxed into mature red blood cells.

Even if these cells can be coaxed into maturity, can they be used to cure Sickle Cell Disease? Can babies actually save the day?

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