AP Biology class blog for discussing current research in Biology

Tag: Gene

Preferential Gene Expression: Not As Random As We Thought

Our conventional knowledge of genetics dictates that the activation of genes in our DNA is random. It is equally likely that our body will express our mother’s alleles as it is that our body will express our father’s. In the case that one parent donates a defective copy, it will be silenced; the other parent’s healthy set of DNA takes precedence and becomes activated.

However, a new study indicates that gene expression and activation is not as random as we thought. In certain regions of the body, our genes demonstrate preferential expression.

A team of scientists at the University of Utah found that almost 85 percent of genes in juvenile mice brains displayed preferential treatment. The mice brains activated one parent’s set of DNA over the other’s. This phenomenon was observed in other areas of the body, as well as in primates.

Although the preferential expression came to a close within ten days, it could provide explanations for vulnerability to brain diseases such as schizophrenia, ADD, and Huntington’s. The temporary preferential treatment to one parent’s copy of DNA could trigger a host of problems specific to that cell site that lead to such disorders, if the parent had given a defective copy of genes.

The study has the potential to alter our basic understandings of genetics, and how we are more prone to certain specialized diseases.

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The Grey Area of Human Gene Editing

The process of Human Gene Editing developed with the goal to prevent future generations from suffering from genetic diseases present in past generations, like our own. Human gene editing, provided it is done only to the correct disease, alters the DNA in embryos, eggs, and sperm to the when reproduction occurs, the gene for the disease or disability is not inherited. However, two weeks ago the National Academies of Sciences and Medicine issued a report stating that human gene editing is being used to enhance people’s health or abilities. This is considered unethical according to organizers of a Global Summit on human gene editing.

Human gene editing has been given a “yellow light” because the process is not yet approved to be done on people. There are high hopes that diseases caused by only 1 genetic mutation such cystic fibrosis and Huntington’s disease will be eliminated due to this process. Unfortunately diseases that are caused by more than one genetic mutation, such as autism or schizophrenia, are not curable by this process.

National Cancer Institute

Gene Editing on humans is such a controversial topic right now: is it ethical to change genes? should the practice be used to change physical appearances? Ultimately, if Human Gene Editing is approves, who decides when it becomes too much, or unethical. This grey area is presented to be somewhere between when it is appropriate to help aid the life of a human, ridding them of a disease, and when enhancements are made.


XRN1: The Virus Hitman

When I think of the words killer and assassin, my mind drifts to shady men in all black equipped with sniper rifles. However, recent research conducted by the University of Idaho and the University of Colorado Boulder has indicated that I should expand that mental list to include XRN1, a gene in saccharomyces cerevisiae which, according to a recent study, kills viruses within the yeast. Upon stumbling onto this subject, I was intrigued because it was a fairly simple procedure that led to a huge discovery. To grasp the significance of such a discovery, one must understand it on a molecular level. XRN1’s duty in yeasts is to create a protein which breaks down old RNA. The image below shows the generic process of the creation of a new protein through gene regulation.

Wikipedia- Regulation of Gene Expression

Wikipedia- Regulation of Gene Expression

Yeasts also contain viral RNA since practically all yeasts are infected by viruses. When scientists removed XRN1 from the yeasts, the viruses within yeasts replicated much faster, and when they expressed high amounts of XRN1, the virus was completely eradicated. This is because the XRN1 gene was inadvertently breaking down the viral RNA, mistakenly taking it for the yeast’s RNA. Scientists continued the research by using XRN1 from other saccharomyces yeast species. The virus continued replicating rapidly but the XRN1 did continue its job of breaking down the yeast’s RNA. This shows that the XRN1 from each yeast species evolves to attack the specific viruses that occur in its host while still maintaining their basic role as the RNA eaters. Scientists are hopeful about this study’s human health implications. Viruses such as Polio and Hepatitis C work by degrading XRN1 and not allowing it to break down RNA, respectively. Dengue Fever also occurs when XRN1 is unable to perform its function of RNA breakdown. These studies on Dengue Fever and Hepatitis C elaborate on the implications of XRN1 not breaking down RNA. Scientists hope that this discovery could lead to the triumph of XRN1 over these viruses. Could this really be the discovery that leads to the first ever Hepatitis C vaccine? Do you think that XRN1’s success against virus in yeasts guarantees eventual success against viruses in humans?


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Harmless Mosquitoes…Yes Please

What are the most annoying things on Earth? Why, mosquitoes of course. They bite you and their bites are extremely irritating. Mosquitoes also carry life-threatening viruses, such as Malaria. However, scientists have come up with a way to get rid of mosquitoes carrying Malaria with the help of gene drives.

A gene drive is a self-generating “cut-and-paste system” that can sterilize mosquitoes. Well how do gene drives work? They operate using CRISPR/Cas9, precision molecular scissors that cut DNA. Scientists used CRISPR/Cas9 to disrupt the genes that are active in mosquito ovaries. If a female mosquito is missing one of these genes, they become sterile. Gene drives insert themselves into a target gene to assimilate every unaltered gene they pass. They break normal inheritance rules by being able to pass themselves into over 50% of an altered animal’s offspring.


The first gene drive that was made stopped mosquitoes from transmitting Malaria. This new gene drive would eliminate Malaria-carrying mosquitoes in the future by making the females sterile, unable to reproduce. This gene drive is not 100% perfect yet, but scientists are hoping to perfect it soon to be able to release it. They hope that this gene drive will be able to control different insect populations, not only mosquitoes.

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The Gene Switch

Researchers at the Stowers Institute for Medical Research have created a high-resolution mechanism to “precisely and reliably map individual transcription factor binding sites in the genome.” This new technique, published in Nature Biology today, has proven to be more efficient and successful than those previously studied.

All of the cells in an organism carry DNA; however different cells in the body express different portions of it to function properly. For instance, nerve cells express genes that facilitate them carrying messages to other nerve cells. This process is known as gene expression and is responsible for making our bodies function the way we do. Despite our limited knowledge on gene expression, researchers are aware that it is is controlled by proteins called transcription factors that bind to specific sites around a gene and,  in the right order, allow the gene’s sequence to be read.

Transcription factor binding sites in DNA are extremely difficult to locate but, thanks to new technology, it is becoming easier to track their location. “The transcription factor binding sites that are likely functional leave behind clear footprints, indicating that transcription factors consistently land on very specific sequences. In contrast, questionable binding sites that were previously detected as bound showed a more scattered unspecific pattern that was no longer considered bound.”

These techniques are implemented through a method called chromatin immunoprecipitation or ChIP, a tool that determines the relativity of the proteins to their positions on the DNA, cuts the DNA into reasonable sizes, and then isolates the sections that are bound by the proteins. While the research is largely preliminary, scientist Zeitlinger attests to the significance of this creation; ”If we do this kind of analysis for lots of transcription factors, we will gather information needed to better understand gene expression.”


chIP mechanism

Identical Twins, Identical Lives, Different Disease

Jack and Jeff Gernsheimer are identical twins. Jack has Parkinson’s disease, and his twin Jeff does not. Up until recently, because they have identical genomes, it would have been a mystery as to why Jack could develop Parkinson’s but not Jeff. However, with the discovery of epigenetics, scientists know that genes alone cannot explain why some people get Parkinson’s and other do not. While there are some genetic mutations linked to Parkinson’s, 90 percent of cases are “sporadic”, meaning that the disease did not run in the family. Even twins often do not develop Parkinson’s in tandem. Naturally, if genes don’t explain the development of Parkinson’s, scientists look to environment. There are several environmental factors that are known to link to the disease. People who were POW’s in WWII, for example, have a higher rate of developing Parkinson’s. But, and here’s the interesting part, Jack and Jeff have lived almost identical lives. For almost all of their lives, they have lived less than half a mile apart. Throughout their lives, they have been exposed to the same air, water, pesticides, etc. When they grew up, they built homes five minutes apart (by walk) on their father’s farm in Pennsylvania. Then, when they entered the professional life, they co-founded a design firm, working with their desks pushed up against each other.


This anomaly, where a pair of humans exist with the same genetics and the same environment yet only one of them got sick is a research “bonanza” for scientists. All expected variables are being held constant, thus whatever is left must be deeply linked to the origins of Parkinson’s. However, there was a small difference in their lives that could provide insight into this anomaly. in 1968, Jack was drafted into the army and Jeff was not. This led to a series of unfortunate events in Jack’s life: first he served two years stateside in the military, got married, had two children, became involved in a long divorce, and suddenly his teenage son died. After this traumatic event, Jack went on to develop Parkinson’s, glaucoma, and prostate cancer, none of which Jeff has.

Jeff and Jack have been more than willing to undergo several studies in hope of finding something that could alleviate Jack’s Parkinson’s. The first study involved collecting embryonic stem cells from the twins. The benefit of stem cell cultures is that they act similarly to how they would in the body even though they are in a petri dish. The mid-brain dopaminergic neurons grown from Jack’s cells created abnormally low amounts of dopamine. Jeff’s produced normal amounts. Surprisingly, even though Jeff showed no signs of Parkinson’s, both twins had a mutation on a gene called GBA. This gene is known to be associated with Parkinson’s. As a result, both of their brain culture cells produced half the normal amount of beta-glucocerebrosidase, an enzyme linked to that gene. Instead of answering questions, this study only raised more to the fascinating case of Jeff and Jack.

I want to add a bit about how Jack’s son died, because it is unimaginably tragic and can show you just how much Jack had to face. Especially if we are considering Jack’s trauma as a contributor to his development of Parkinson’s, it is important to know the story. When Gabe, Jack’s son, was 14 in 1987, he became fascinated with the Vietnam War. Like any good father, Jack rented his son some movies on the war. One of those being The Deer Hunter, in which there is a scene where two prisoners of the Viet Cong are forced to play Russian Roulette. Gabe told his friend that if it were him, he wouldn’t just sit there. He would rather just get it over with. With that conversation, Gabe got his dad’s pistol, that he knew was hidden in the closet drawer, put one bullet in the chamber, put the gun to his head, and shot.

Jack rarely shows emotion. This “pressure cooker” way of dealing with things could explain his illness. Jeff thinks that the parkinson’s is a physical manifestation of how Jack deals with stress, rather how he doesn’t deal with stress. The connection between stress and disease is a very active research topic. And while their lives were very similar, if compared, Jack’s is by far the life with a more stressful environment. Some research might suggest that this stress differential can have a relation to Parkinson’s disease. In 2002, neuroscientists at UPitt subjected rats to stress, and they found that the stressed rats were more likely to experience damage to their dopamine-producing neurons than the non-stressed rats. This led to the term “neuroendangerment”, which means “rather than stress producing damage directly and immediately, it might increase the vulnerability of dopamine-producing cells to a subsequent insult.”

Another hypothesis as to what caused Jack’s Parkinson’s is that it could be linked to chronic inflammation.  Chronic inflammation is the mechanism by which stress can create neurodegeneration. Evidence that suggests this could be the case in Jack and Jeff is presented in their skin. Jack has psoriasis, a condition linked to chronic inflammation, and Jeff does not.

To this day, the search for what caused Jack’s Parkinson’s continues. Last year, NYSCF scientists conducted a study on the twins’ stem cells. They found a few functional differences between their cells. After finding the GBA mutation, they searched harder for other clues as to what might differentiate their brains. They screened 39,000 SNV’s, single nucleotide variants, which are instances where a single nucleotide in the human genome has been altered (either switched, deleted, or duplicated). They found 11 SNV’s, nine of which are linked to Parkinson’s disease. However, all 9 were found in both twins, meaning that this did not explain why Jack was sick and Jeff wasn’t.

Finally, they were able to uncover a relevant difference. Jack had high levels of MAO-B, which is involved in the breakdown of dopamine, whereas Jeff’s levels were close to normal.This hypothesis supposed that there exists a possible molecular mechanism by which stress could lead to neurodegeneration. What’s nice about this finding is that it could present a possible treatment for Parkinson’s. MAO-B inhibitors exist and are actually drugs currently on the market. They were given to Jack, and while it’s too soon to see the effects and to recommend them as treatment for Parkinson’s disease, it’s definitely a start.


The New Source of Mental Illness

a three dimensional recreation of DNA methylation

a three dimensional recreation of DNA methylation

For years scientists were convinced that the root cause of diseases such as bipolar disorder and schizophrenia lay somewhere hidden in the human genome. But the particular genetic sequence that would supposedly be linked to these illnesses remained elusive.  So researches turned to the developing theory of Epigenetics.  Studies from King’s College in London and related in this article have shown that Epigenetic (changes in gene activity caused by the environment) changes might be responsible for bipolar disorder and schizophrenia.  Jonathan Mill and colleagues scanned the genome of 22 pairs of identical twins.  For each pair of twins, one of the twins was diagnosed with either bipolar disorder or schizophrenia. With the understanding that chemical methyl groups attached to particular sites on a genome are responsible for the “turning of” and “turning on” of genes, Mill and his team “scanned for differences in the attachment of methyl groups at 27,000 sites in the genome.”  The researches found variations in the amount of methylation of up to 20 percent in the gene ST6GALNAC1 (which has been connected with schizophrenia) and differences in the amount of methylation of up to 25% in the gene GPR24 (which had previously been linked to bipolar disorder).  Interestingly Mill’s team found that “a gene called ZNF659, showed over methylation in people with schizophrenia and under-methylation in those who were bipolar, suggesting that the conditions might result from opposing gene activity.  These findings certainly support the theory of Epigenetic’s being a real factor in behavior and mental illness.  They also serve to confirm that bipolar disorder and schizophrenia are related disorders.  This relates to our unit in the sense that Epigenetics deals with the expression of the DNA and genetic sequence we are learning about.  While we read about how the nucleotides are sequenced, Epigenetics could potentially be responsible for how DNA is expressed.

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Human Brain Gene Implant Greatly Effects Mice

A study conducted at MIT tested the effect of human Foxp2 gene on mice and observed their ability to navigate through a maze. Foxp2 is found in both mice and humans, but the human form of the gene is related to  learning and language but it has been hypothesized by neuroscientist Ann Graybiel of MIT’s McGovern Institute for Brain Research that perhaps the human gene is related to sub-conscious actions based on environmental cues.

The maze lead to a pile of food, and throughout the maze the scientists placed visual and sensory cues that lead to the end of the maze and to the food. At the end of the study, the results showed that the genetically modified mice would complete the maze 3 days faster than the wild, control mice when visual and sensory cues were both involved.

The significance of the study is the potential connection between specialized learning and the Foxp2 gene. Although the difference between learning how to run a maze and leaning how to speak is massive, tests like this one are the beginnings to analyzing the true significance of Foxp2.


New Breast Cancer Gene Discovered





Today, one of the most talked about cancers is breast cancer. Breast cancer is defined as cancer that forms in the tissues of the breast. There are two types of breast cancer: ductal carcinoma, which is most common and begins in the lining of the milk ducts (thin tubes that carry milk from the lobules of the breast to the nipple) and lobular carcinoma, which begins in the lobules (milk glands) of the breast.

According to a new study done by the Wellcome Trust Sanger Institute and University of Cambridge, a gene has been identified to have a major association in aggressive subtypes of breast cancer. The research suggests that an overactive BCL11A gene causes the development of tripe-negative breast cancer.

The study was conducted in human cells and in mice. The study was important because one in five patients are affected by triple-negative breast cancer. From the conducted research, Dr. Walid Khaled discovered that by adding an active human BCL11A gene to a human or a mouse’s breast cells (in the lab) caused them to behave as cancer cells. Increasingly, Dr. Khaled concluded that “by increasing BCL11A activity we increase cancer-like behaviour; by reducing it, we reduce cancer-like behavior.”

This research and study is extremely important because from the results, the team was able to propose that BCL11A is a strong candidate for development of a possible targeted treatment. Typical treatments of breast cancer include radiation and chemotherapy as well as surgery. The most known surgeries are Lumpectomy/partial mastectomy (large portion of the breast is removed) and a full mastectomy (full removal of breasts)

I chose this article because I know many dear friends that have faced and survived the battle of breast cancer. I believe that spreading awareness and screening early is extremely important. In addition, I am very hopeful that new advances will be made so that others need not endure the excruciating fight of breast cancer.


Bacteria become ‘genomic tape recorders’, recording chemical exposures in their DNA


MIT Engineers have developed a way to create genomic tape recorders out of the Bacteria E. Coli. Timothy Lu, an engineering professor at the university describes the method by which they altered the bacterial DNA in order to allow it to store information. The researchers engineered the cells to produce a recombinase enzyme which can insert a certain sequence of Nucleotides into the genome. However, the trait is useful because the enzyme is activated by specific stimuli. In order to retrieve the information the researchers can either sequence the genome and look for the specific code or look for the trait expressed by the targeted gene by using antibiotics. This process will be useful in the future because of its ability to store long term biological memory. Also, this process transcends previous limitations of genome storage as it is now able to indiscriminately store data as opposed to previous methods that were only able to identify a specific stimulus.

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