BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: protein

Could A Computer Detect Your Sick Gut?

Photo by Nicola Fawcett (photo source)

 

The human gut microbiome is a system specially revolved around the genetic makeup of an individual person. These gut biomes are the subject of many studies by scientists who are interested in the small world of bacteria living inside of our stomachs and its relation to our health or illness. Many humans have the ability to recognize a healthy or unhealthy human gut microbiome, however, is it possible for a computer to have this same ability? According to the impressive research results developed by a group of scientists at the University of California San Diego, it is possible for a computer to be trained to differentiate a sick gut microbiome compared to an unhealthy one.

In order to reach this innovative conclusion, these scientists utilized metagenomics, a gene sequencing technique, to break up the DNA of hundreds of microbes residing in the human gut. The scientists took gut bacterial samples from the stool samples of thirty “healthy” and thirty “unhealthy” people. The unhealthy people whom had samples taken from them were either diagnosed with autoimmune Inflammatory Bowel Disease. With these 60 samples total, the scientists were able to sequence 600 billion DNA bases and put the information into a computer. After that, the scientists underwent a complex process of translating reconstructed DNA of the hundreds of microbes into thousands of proteins, which were then categorized into thousands of protein families. The tedious differentiation and categorization of certain proteins allows the scientists to see the activity of the bacteria and then program it into the computer so it, too, would be able to recognize these proteins and bacteria. Bryn C. Taylor, One of the scientists involved in this research says that, “You can try to categorize healthy and sick people by looking at their intestinal bacterial composition…but the differences are not always clear. Instead, when we categorize by the bacterial protein family levels, we see a distinct difference between healthy and sick people.” Incorporating this method of distinction with the storage of healthy and unhealthy patient data into computers is an effective way of “training” a computer how to detect a sick or healthy human gut due to a distinguishable difference in bacterial activity, protein presence, etc..

Overall, it seems that these scientists at the University of California San Diego have made groundbreaking progress in the future usage of computers in the detection of an unhealthy or sick human gut microbiome. Do you think the development of a computer’s ability to detect a sick gut will be ultimately more beneficial to the world of health and science, or will it just be an unnecessary new trick that computers can learn? The next time you feel like you’ve got a stomach bug, you just might be scheduling an appointment with a computer instead of your doctor.

https://commons.wikimedia.org/wiki/File:Wild_garden_of_the_gut_bacteria_3.jpg

 

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?

 

Original Article: http://phys.org/news/2016-10-yeast-gene-rapidly-evolves-viruses.html

 

Could non-gluten proteins play a role in celiac disease?

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Gluten refers to the proteins found in wheat endosperm. Wheat endosperm is a type of tissue produced in seeds that’s ground to make flour.  It is composed of two different proteins: gliadin (a prolamin protein) and glutenin (a glutelin protein). Today, there are many questions being asked about whether we should be consuming gluten.

In today’s society, one of the new healthy trends is to be gluten free. However, for those with celiac disease, it is necessary to be gluten free. Celiac disease is a condition that damages the lining of the small intestine. It prevents the intestine from absorbing parts of food that are important for staying healthy. In this article, questions are raised regarding research that claims that people with celiac disease also have reactions to non-gluten proteins.

From research, scientists have discovered that when someone with celiac disease eats gluten (group of proteins), it causes an immune reaction. Such symptoms are diarrhea, abdominal pain, anemia, and nutritional deficiencies. The current treatments are to avoid all gluten-containing foods. Armin Alaedini, Susan B. Altenbach, and their colleagues wanted to further investigate this.  They found that people with celiac disease and dermatitis herpetiformis (a rash associated with the disease) had an immune reaction to five groups of non-gluten proteins. From this, Scientists concluded that further studies regarding celiac disease and gluten should test and include non-gluten proteins.

In addition, according to the National Institute of Diabetes and Digestive and Kidney Diseases, the way to test for celiac disease is through a blood test and then a follow up biopsy on the small intestine. When people have celiac disease and it goes untreated, their body is not receiving the necessary nutrients in order for the body to grow.

I chose this article because I try to be extremely conscious of making healthy eating choices. I have found that a lot of foods don’t agree with me but bread/ gluten has never been a concern. I know people who have celiac disease and are gluten-free. However, I also know people who do not have celiac disease and eat a gluten-free diet anyway. In some cases, people who have done this have found that it damages their stomach and ruins their ability to eat gluten. I researched this topic because I wanted to learn the truth behind a gluten-free diet and when that diet is truly necessary and appropriate.

Are you gluten-free? Do you have celiac disease? Have you ever tried gluten-free products?

 

http://celiac.org/celiac-disease/what-is-celiac-disease/

http://www.livescience.com/39726-what-is-gluten.html

http://en.wikipedia.org/wiki/Gluten

http://www.niddk.nih.gov/health-information/health-topics/digestive-diseases/celiac-disease/Pages/ez.aspx

Article Link: http://www.biologynews.net/archives/2014/11/05/could_nongluten_proteins_play_a_role_in_celiac_disease.html

 

 

The Ability to Control Genes with Your Thoughts

A research group led by Martin Fussenegger, a professor of Biotechnology and Bioengineering at the Swiss Federal Institute of Technology, has developed a method by which brainwaves control the creation of proteins from genes. The technology wirelessly transfers brainwaves to a network of genes that allows the human’s thoughts to control the protein synthesis of the genes. The system uses a uses an electroencephalogram (EEG) headset, which records and transmits a human’s brainwaves and sets it to the implant in the gene culture.

A successful experiment of the system included humans controlling gene implants in mice. When activated by brainwaves, the gene implant culture would light up by an installed LED light. The researches used the human protein SEAP as the protein that would be generated in the culture and diffused into the blood stream of the mice. The humans were categorized by their states of mind: “bio-feedback, meditation and concentration”. The concentrating group caused an average release of SEAP. The meditation group released high concentrations of the protein. Finally, the bio-feedback group produced varying degrees of SEAP, as they were able to visually control the production of the protein as they could view the LED light turning on and off during the production process. The LED light emits infrared light, which is neither harmful to human nor mice cells. The system proved successful in its ability to translate brainwaves into gene control and protein production and its potential for harmless integration into the living tissue of humans.

The research group hopes that in the future a thought-controlled implant could help prevent neurological diseases by recognizing certain brainwaves at an early stage of the disease and translating the brainwaves into the production of proteins and other molecules that would work to counteract the disease.

Lights of ideas

Proteins Keeping Fishes Alive

 

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Words To Know:

notothenoids: the arctic ice fish

practical application: how organisms adapt through natural selection

superheating: solid is above its melting point but does not actually it to melt at this point

Origins: 

     Fish in Antarctica have been forced to evolve natural antifreeze proteins to stay alive.  These proteins are mainly found in the notothenoid fishes, which are found in freezing temperatures. Arthur DeVries discovered these fish, their ice- binding-proteins and also figured out how they work in the 1960s . The proteins bind to small crystals and also protect cells by binding to their cell membranes. They are anti-freezing proteins that allow fish to survive and adapt to harsh and cold conditions of arctic waters.

Recent Discoveries:

          Paul Cziko, among other researchers in the United States and New Zealand, published in The Proceedings of the National Academy of Sciences that these ‘anti freeze’ proteins’ are also ‘anti melting’. Cziko and his team wanted to understand the antifreeze ability and examined if an anti-freeze protein (that was attached to an ice crystal inside the fish) would melt when the temperature rose. Instead, they found that the ice crystals did not melt. Ice above the melting is point is considered superheated. Cziko’s research basically says that even when it is way past its melting point, the ice (that’s latched on to the protein) still stays frozen inside the fish. These ‘anti-freezing’ proteins are also ‘anti-melting’ proteins that cause ice crystals to accumulate in the fish’s body.

The study shows evolution, not practical application, and this is a typical case of ‘evolutionary trade off’. There are difficulties that get solved, but there’s also a price to pay. Cziko’s research has not indicated any unfavorable effect due to the crystals, but the crystals could potentially block up the blood vessels of the fish and provoke an inflammatory reaction.

Personal Statement: 

      Personally, I really liked the NY Times article. I actually didn’t realize that we had to find additional articles until I re-read the assignment sheet. I found other articles because I was genuinely curious as to how this worked and came about. I was initially attracted to the word ‘protein’ in the article’ title -since it relates to what we are learning in class- but stayed because of the evolutionary aspect. It has always been hard for me to think of evolution as something. It is such a difficult-to-grasp concept since you can’t really see it happening . But, in some way- this made me think that I did see evolution. Instead of making me think of evolution as a concept or theory that I learn at school, it made me think of it as a reality, and as something that actually happens.     

Original Article: http://www.nytimes.com/2014/09/23/science/antifreeze-proteins-keep-antarctic-fish-alive-and-icy.html?ref=science&_r=0

Additional Article: http://thewestsidestory.net/2014/09/23/17354/antarctic-fish-anti-freeze-anti-melt-proteins-keeps-freezing/

Additional Article: http://www.scienceworldreport.com/articles/17326/20140923/antarctic-fish-antifreeze-blood-ice-crystals-bodies.htm

Study Shows Link Between Enzyme and Spread of Breast Cancer

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 “40,000 women in America will die of breast cancer in 2014.” This is a truly terrifying projection. Breast Cancer is an extremely deadly, and extremely prevalent cancer that affects the lives of millions each year. In my personal experience, I have many friends and family members that have battled against this cancer. So many are affected, and there is still no concrete cure. There is no cure, however, researchers at the University of California, San Diego School of Medicine have identified an enzyme that is closely related to the metastasis of breast cancer cells. This is great news, for it suggests the possibility of further research using this finding to end breast cancer for good. Xuefeng Wu, a lead scientist involved with this research, has stated that the team has been able to “target breast cancer metastasis through a pathway regulated by an enzyme“. This enzyme is called UBC13 and it regulates the activity of a protein called p38.

This p38 protein, when not in use, prevents metastasis. By identifying the enzyme that prevents the use of p38, researchers have come one step closer to preventing the spread of breast cancer in the body, and therefore defeating it. With the use of a lentivirus injected into the mammary tissues of mice, the scientists were able to suppress the functions of both UBC13 and protein p38. The mice grew primary tumors, as was expected, however the primary tumors did not metastasize and spread breast cancer cells throughout the bodies, which means the cancer was stopped from spreading throughout the body. This prohibition of the cancer cells to spread is a major breakthrough in breast cancer research and will without a doubt contribute greatly to the ending of breast cancer.

Protein Structure May Lead to Cure for Ebola

For those who haven’t been keeping up with the latest in viral outbreaks, Ebola has been spreading throughout West Africa and has already taken the lives of 2,600 people since the outbreak in March 2014.  According to the World Health Organization , there are currently no certified vaccines or treatments for Ebola but a new breakthrough may have answers to developing a cure or vaccine for the deadly disease

Scientists at the University of Virginia have gotten their hands on a crystalized structure of the Ebola Nucleoprotein C-Terminal domain, which is an important protein used in replicating the virus.  The tertiary fold of the C-terminal is “unique in the RNA virus world,” claims structural biologist Dr. Zygmunt Derewenda, and this unique fold could ultimately lead to the foundation of drugs to prevent further infections.

The team was able to produce the protein by using E Coli as the protein factory.  So far, the protein demonstrates traits that are extremely unique and unlike other known proteins.  Evidence thus far has shown that the viral nucleoapsid is self assembled by the domain.  Insights and new research that the UVA team is conducting is paving the way to an Ebola anti-viral drug.

 

Ebola Virus Particles

 

Protein Might Help Fight Deadly Diseases

The enzyme “Cholesterol-25-Hydroxylase,” or CH25H, might help fight against human viruses such as Rift Valley Fever, Niphah and HIV. CH25H converts cholesterol to an oxysterol called 25HC, which can permeate a cell’s wall to prevent a virus from getting in. The CH25H enzyme is activated by interferon, an anti-viral cell signaling protein produced in the body.  Researchers have known that interferon has been part of the body’s defense mechanism against viruses, though it does not have any antiviral properties itself.

This discovery is revolutionary because other antiviral genes have not been able to be used for treatment of viruses in humans. According to Yang Lui, a student at the David Geffen School of Medicine at UCLA, most antiviral genes are difficult to use in therapy because the genes are difficult for cells to express. However, CH25H is different because it is naturally synthesized.

HIV Replication within a cell

The discovery of CH25H is relevant to the efforts to develop broad antivirals against an increase of emerging pathogens. In a collaboration with Dr. Lee, another UCLA professor, it was discovered that the 25HC produced from CH25H can inhibit HIV growth in vivo. The researchers initially found that 25HC inhibited HIV growth in cultures. When implanted mice with human tissues, the 25HC reduced the HIV in within 7 days and reversed T-Cell depletion caused by the HIV. It was also discovered that 25HC inhibited the growth of other diseases such as Rift Valley Fever Virus and Ebola.

There are still some weaknesses with the study. It’s difficult to deliver 25HC in the large doses needed to fight viruses. Researchers also need to compare 25HC to other antiviral HIV treatments.

Fighting Cancer with Protein P53

Despite the amazing diagnostic technologies, pharmaceuticals, and procedures of modern medecine, cancer still takes the lives of more than half a million people in the US every year. Characterized by the unmediated reproduction and metastasis of tumorous cells, the various forms of the disease have proved difficult to slow and often nearly impossible to cure. Treating cancer usually requires rigorous chemotherapy or invasive surgery, each involving painful side-affects and long recovery periods.

Chemotherapy, while effective, indiscriminately attacks cells that divide quickly. Thus, the fast-dividing cells lining the mouth and intestine as well as the cells that cause hair to grow are also affected, causing an array of side affects. Scientists have been searching for a new way to fight cancer that would only target cancer cells while letting healthy cells function unhindered. A team at University of California, Irvine may have found that method in protein P53, mutated forms of which are implicated in “nearly 40 percent of diagnosed cases of cancer.

P53 is responsible for repairing damaged DNA and causing apoptosis, or programmed cell death, in cells that are damaged beyond repair. In a mutated form, P53 does not function properly, allowing cancerous cells that would normally be destroyed to proliferate. A therapy that reactivated mutated proteins could potentially surpress tumors without causing the nasty side affects of current drugs. Also, since P53 is present in so many cancer cases, a single treatment could be used against many different forms of the affliction. However, since P53 proteins “undulate constantly, much like a seaweed bed in the ocean,” sites where medicinal compounds could bind are difficult to locate.

The UCI team had to reach across disciplinal boundaries, enlisting computer scientists, molecular biologist and others to find a usable binding site. With the help of molecular dynamics, the group constructed a simulation of P53’s movements, eventually locating a transient site that could bind with stictic acid, one of forty-five small molecules they tried. Unfortunately, stictic acid is not a viable compound for pharmaceuticals, but the scientists at UCI think that other small molecules with similar characteristics will likely have similar effects and make effective treatments.

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