BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: technology

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

 

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.

Stop Taking Notes

Put down your pencils. Stop taking notes. Scientists have recently proven that you are less likely to remember something once you write it down. Now you all have scientific explanations for not bringing a backpack to school. Scientists began by researching the effects of technology on our memories. Unsurprisingly, they concluded that people who saved information on the computer were less likely to remember it than those who were told the facts verbally. More of this study can be seen in the article “Poor Memory, Blame Google”. It brings up a larger concern; what will the mental capacities of our society come to in our increasingly technological age? This brought Professor Susan Greenfield to investigate the affects of all information processing tactics and their effect on human memory.

She began with the most simple and popular of memory methods, note taking. They split a population of undergraduate students into 2 groups, one that took notes and one that relied on straight memory. They showed them pairs of cards and instructed them to memorize the location. One group wrote it down and the other did not. After the study time, the note-taking group had their notes taken away and the full group was tested on the cards’ location. Surprisingly, the note-taking group performed very poorly in the exercise, far underperforming the memory group.

The scientists concluding that by taking notes, the students were relying on an external form of storage rather than their own synapses. So keep those pencils down, your memory will thank you.

Original Article: http://www.wired.com/2014/11/paper-effect-note-something-youre-likely-forget/

Contrary Study:

http://library.wcsu.edu/dspace/bitstream/0/65/1/dewitt.pdf

Screen Shot 2014-11-14 at 3.08.22 PM

The Ebola Epidemic: When Will it End?

Ebola Virus

The Ebola epidemic in West Africa has captivated international audiences the last few weeks.  Ebola Virus Disease is an often fatal disease which is systemic meaning it attacks all organs and tissue in the body. It can be spread through any human to human contact, making this disease highly contagious. The countries of Liberia, Sierra Leone and Guinea have been heavily affected by this disease. On tuesday September 23th the Center for Disease Control (CDC) based in Atlanta Georgia released new projections on the Ebola epidemic in Africa based on computer modeling.  The CDC released a best-case scenario being that if proper measures are taken the disease could be eradicated by January 2nd and a worse-case scenario that if disease is left unmonitored and continues as is, there will be approximately 1.4 million cases by January 2nd.   Doctor Thomas R. Frieden, the director of the Ebola epidemic, has stated that since the data was received in August conditions have improved slightly due to increased aid to the affected regions. Another report was released by the World Health Organization (WHO) which stated more conservative figures but also acknowledged that there could possibly be more due to unreported cases. The WHO report brings about the idea that the epidemic may not end and the Ebola virus will perpetuate in West Africa. It is obvious to health officials, such as Dr. Jack Chow, that even in a medium case scenario the amount of hospital beds and aid are rapidly being surpassed by the number of cases. The CDC does acknowledge this impending lack of bed and isolation unit crisis. One solution to this problem is to educate citizens on home care and send home care packages to support this movement.  Although some are dubious, Frieden states that home care had been effective in the smallpox crisis in the 1960s in Africa.  In addition to homecare, Doctor D. A. Henderson explains that funds and food play a huge roll in the containment and elimination of disease because when you give victims money and food there is no need for them to beg or go out to the market for food where they might encounter other human contact. How should this epidemic be handled? Is homecare an effective solution? Where should money be allocated, homecare or hospital expansion?

 

Link to Article:

http://www.nytimes.com/2014/09/24/health/ebola-cases-could-reach-14-million-in-4-months-cdc-estimates.html?ref=health&_r=1

 

The Brain that Looked like Jello

Scientists at Stanford University made an entire mouse brain and part of a human brain that is the same consistency as Jell-O. The brain model is transparent so that neurons sending and receiving information can be highlighted and in in the same complexity as 3-D, but without having to slice the model. This new process, called Clarity, preserves the biochemistry of the brain so well researchers can reuse the same model over and over again.

Why Now?

The Obama Administration recently announced it’s interest in discovering the secrets of the brain. While this project was not part of the Obama Administration’s new initiative, Dr. Thomas Insel, director of the National Institute of Mental Health said that Clarity will help build the foundation of the Obama administration’s brain initiative.

The Clarity technique also works with brains that have been preserved for years.

One of the challenges of studying a preserved brain is making it clear enough to see into it. Unlike previous methods, Clarity makes the brain clear enough to see its inner workings.

Imagine if you could see through this brain!

 

How it Happened 

There are many was to make a tissue transparent. Clarity uses hydrogel, a substance of water held together by other molecules to give it solidity. The hydrogel forms a mesh that permeates the brain and connects to most molecules other than lipids. The hydrogel brain is then put in a soapy electrical solution, where a current is applied, driving the solution to the brain and getting rid of the lipids. The brain is then transparent with its biochemistry still in tact, so it can be infused with chemicals that will show the details of its structure.

The hardest part of the procedure is obtaining the correct ratio of temperature, electricity and solution. More work is needed to be done before this method can be applied to an entire human brain.

The Benefits 

The Clarity technique gives scientists a more exact image of what’s going on in people’s brains. This process may discover physical reasons for debilitating mental disorders, such as PTDS, schizophrenia, and autism.

Wait, you don’t hear that ringing, too?

Defined as “the perception of sound in one or both ears or in the head when no external sound is present” by the American Tinnitus Foundation, tinnitus affects 50 million people in the US and forty percent of veterans.  It can be caused by everything physical trauma or long-term exposure to loud noises (i.e. combat veterans or teenagers with iPods) to hormonal imbalance or aspirin use. Currently, there are many treatments available, although the success rate of these treatments varies. The main reason for this is that the best way of treating tinnitus would involve delivering medication to the inner ear, the site of the problem. Currently, doctors have no way of putting medication in the inner ear, but this could change  in a few years thanks to the the beginning of a new project by the US Department of Defense, who has commissioned Draper Laboratory to work out a

concept for a small delivery device inserted near the membrane-covered window—no more than three millimeters in diameter—separating the middle ear from inner ear. Once at the membrane the device … would release a drug into the cochlea… The plan is to embed wireless communications into the capsule so that a patient or doctor can control the dosage. After the capsule finishes delivering its supply of drugs, it would dissolve. 

 

Courtesy of: http://www.lesliewong.us/blog/2009/01/23/sony-mdr-v6-and-sennheiser-cx300-headphones/
These may be setting up my generation for a tinnitus epidemic many years from now.

 

The project is only in its beginning stages, so it will be years before patients can actually reap any benefits from this technology. However, I take comfort in knowing that should I develop tinnitus, I could possibly have access to better treatment than is available today. This is especially relevant to my generation; everywhere you look, there are teenagers blasting their iPods, unknowingly (or not caring) causing permanent damage. Despite the warnings received from adult, many teens will not listen, and will continue to cause damage with loud noise. Should this treatment be developed, the tinnitus that will be inevitable developed by a large portion of my generation will treated, and possibly cured.

This project also holds a personal significance for me.  As someone who wants to eventually enter the armed forces, I am relieved to know that such a common issue among veterans is coming a step closer to being eradicated. Despite the technology used today to prevent noise damage,  I know of Iraq and Afghanistan war veterans who are experiencing tinnitus, and even hearing loss. I’m glad that research is being conducted on a condition that, while it may not sound terribly crippling, can actually have a huge effect on one’s quality of life.

So, readers, do any of you have or know someone with tinnitus  If so, how did you or the person you know develop it? And, if you have it, would you consider one day utilizing this kind of treatment?

Post, discuss, talk with your friends. Discussion breeds awareness, which is key to arriving at a cure. 

 

 

http://www.scientificamerican.com/article.cfm?id=tinnitus-treatment

Walking on Walls

 

Photo Credit: dirk huijssoon flickr

Have you ever wished you could walk on walls? Ever wished you could get your new plasma TV on the wall and be able to easily move it later? Well, now you can do both of those things. Using the gecko‘s feet as a model, scientists were able to replicate the adhesive mechanism that geckos use to get around.

The gecko’s feet can stick to almost any smooth surface whether it be vertical, horizontal, slanted, or curved. In addition, they never leave any sticky residue behind and never have trouble moving. The ability to put things, particularly heavy things, on walls and easily remove them later without any damage is something that everyone would like to be able to do. Scientists researched the intricate mechanisms in the geckos feet to determine how the gecko can firmly stick to smooth surfaces and move so easily. They determined that it was a combination of the pads on the gecko’s feet along with the arrangement of tendons and muscles in the feet. This new idea allowed scientists to develop an adhesive, “Geckskin”, that could stick to a smooth surface, hold 700 pounds, and be easily removed. This new adhesive is still being perfected but soon you could actually be able to walk on walls, just like the gecko.

Breathing to create energy

New research has shown that in the future, batteries may not be needed to operate many of the small devices in your body.  Can you imagine simply breathing and being able to power a device that will keep you alive. Researchers have found that breathing can create enough energy to power a small medical device that is already in your body.

Currently the devices that are used to keep us alive are powered by batteries.  Batteries are currently the best and most efficient way to power these devices but they can cause problems for the human body. Also, these batteries do not last forever and when they need to be replaced, the patient must go through extensive surgery. Surgery is risky and every procedure that is made is a risk to the body. Every incision is a risk for infection so by reducing these procedures by finding alternative ways to get energy, lives can be saved. Dr. Wang, has come up with a solution where a battery can gather its own energy and not have a need for a battery.

Dr. Wang believes that the device could use the energy that is already around it. A battery in a vein could use the energy from blood cells colliding, a battery in the foot could gather energy from the foot hitting the ground, a battery in the nose or throat could gather energy from the air that passes over it. Dr. Wang’s idea comes from an idea known as “piezoelectricity.” These materials are able to take very small movements and turn them into energy.

Tests have been done on this idea and scientists have been able to create a device that uses the force of the air from a human breathing to create a strong enough electric current to continue to power a small device. This is a major advancement in technology. The team uses PVDF which is a light flexible material to create a bridge that connects to two larger parts of the device.  When the air passes over this bridge, it is able to convert it into energy. While this is still a work in progress the advancements that has been made are very promising and can lead to many new opportunities in medicine.

iPhone, what’s next?

Credit: creative tools

It seems like every year technology is becoming more and more advanced and phones and computers are becoming capable to do some pretty interesting and exciting things. What is the next thing that your touch screen phone smartphone will be able to do? Some people may find the answer shocking…diagnose your illness! A recent study shows that many people have previously believed that a “USB-stick-sized throwaway device called a lab-on-a-chip” could be used to send tests to a lab without leaving your home but Hyun Gyu Park and Byoung Yeon Won, two scientists at the Korea Advanced Institute for Science and Technology, think that they can take that technology one step further.

Park and Won believe that the super sensitive touch screens on your phone could replace the lab work that would be needed for the lab-on-a-chip device. Park’s idea is to take the lab-on-a-chip with the sample and press it against the phone’s touch screen in order to be analyzed.  The analyzation would take place in an app that would be able to tell whether you have food poisoning, strep throat or the flu just from a small drop of saliva placed on the chip.

Park and Won have begun to do tests on the touchscreen to see if they are able to help in diagnosing our sickness.  In order to do the tests, they took three solutions containing different amounts of DNA from the bacteria that causes chlamydia and put small amounts onto a touch screen the size of that found on an iPhone. They found that the touch-sensing electrodes on the screen were able to tell the difference between the solutions even with the smallest quantities. Park says that this is the first step to creating this new piece of technology.

While this technology is still many years off with many more modifications needing to be made, the development is exciting and the idea of a phone diagnosing an illness is something that would change the lives of many people. What will our iPhones be able to do next?

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