BioQuakes

AP Biology class blog for discussing current research in Biology

Author: kriesenbergprinciple

How to Proofread the Genome

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On April 13, 2016

In Student Post

CRISPR-Cas9 is an emerging technology in the field of genetics that has opened an incredible number of  doors and revolutionized the field. It permanently changes the genome of cells while they are alive. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. This sounds confusing but the actual technology is simple. Feng Zhang uses the analogy of proofreading a book to explain it.Let us say you are proofreading your novel and you find the phrase “twinkle twinkle big star”. Now you want to change it to “twinkle twinkle little star”. In this scenario, the words are base pairs and the change from “little” to “big” is a mutation. You can not just delete “big” or just “add” little you must do both. And that is what CRISPR does. It uses an enzyme to cut the DNA and silences that gene. It also can do the opposite and activate certain genes.

A diagram of how CRISPR works

This precise controls of genes have allow scientists to do research faster and cheaper. Its applications go beyond just research however. This technology can be used to treat certain genetic mutations by correcting the incorrect base pairs accurately.

Link to article:

https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answers-about-crispr

Other Links:

https://www.sciencedaily.com/releases/2015/12/151210125648.htm

https://www.addgene.org/crispr/guide/

A Computer Powered By ATP?

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On March 1, 2016

In Student Post

Could supercomputers be powered by ATP the same molecules that power our cells? And could these computers run faster than normal supercomputers? The Dan Nicolau and his son Dan Nicolau Jr. seem to think so. Although this computer is not yet a reality the father and son duo have been working on a model of this bio-supercomputer for seven years. The original drawing looked like “small worms exploring mazes” according to Dan Nicolau. These chips use short strings of proteins instead of electrons and using ATP to power it all.

 

imgres

Molecule of ATP

You may be wondering why this is a big deal. It is because traditional supercomputers spend so much power cooling themselves down they need their own power plant to function. Since ATP is used in biological organisms it does not heat up as much. This could lead to dramatic decreases in the amount of energy a supercomputer uses. The model is promising but the father and son do not have an estimate on when the supercomputer could become a reality. One possibility according to Dan Nicolau is the integration of the bio supercomputer with a traditional supercomputer.

 

Link to Article:

https://www.sciencedaily.com/releases/2016/02/160226133606.htm

Other Links:

http://sputniknews.com/science/20160228/1035493225/biological-supercomputer-unveiled.html

https://en.wikipedia.org/wiki/Biocomputer

Bringing the Human Gut Microbiome into the Light

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On January 9, 2016

In Student Post

The human gut microbiome is an incredible system of symbiotic organisms. These micro-organisms that provide us with vitamins and amino acids as well as break down toxins and protect us from harmful invaders. We could not live without them and they could not survive without their host, us. We carry over 3 pounds of these little helpers in our body and outnumber our cells. Although this system is so important to our survival, it has been hard to study for long periods of time, until now. Judah Folkman, professor of Vascular Biology at Harvard Medical School states, “”Until now, use of traditional culture methods and even more sophisticated organoid cultures have prevented the microbiome from being studied beyond one or two days. With our human gut-on-a-chip, we can not only culture the normal gut microbiome for extended times.”

 Escherichia coli

E. Coli 10000x magnified

https://en.wikipedia.org/wiki/Fecal_bacteriotherapy

The human gut-on-a-chip is constructed from a clear, flexible polymer roughly the size of the a flash drive. This chip simulates the environment of our gut so well that cultures can last up to weeks. This extended period of time can allow for major breakthroughs in the study of the microbiome and what happens when things do not go as planned. Judah Folkman adds, “we can also analyze contributions of pathogens, immune cells, and vascular and lymphatic endothelium, as well as model specific diseases to understand complex pathophysiological responses of the intestinal tract.”

 

The Wyss team thinks that this new technology can help treat patients by eventually culturing there own cells and microbiome on the human gut-on-a-chip to test different treatments. This new technology, although not directly discovering anything about the human gut microbiome, will lead to major discoveries down the line.

 

Main Article:

http://www.sciencedaily.com/releases/2015/12/151214165918.htm

 

Other Articles:

http://www.sciencedaily.com/releases/2014/07/140707103641.htm

http://www.britannica.com/science/human-microbiome

https://en.wikipedia.org/wiki/Human_Microbiome_Project

Printing More Than Just Pictures

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On November 18, 2015

In Student Post

3-D printing is an increasingly accessible technology that is bringing manufacturing into the home. Now these marvels of technology are being used in medicine. With children growing rapidly, expensive prosthetics are not an option for most families. Customized 3-D printed prosthetics are becoming more common and are helping out these families by making prosthetics less expensive.

15643030820_77278f25b4_b

 

3-D Printed Prosthetic Hand

Usually, 3-D printers only print hard material such as plastic and metal. This is very useful while creating bone replacements and customizable prosthetics, but is not ideal for printing organic tissue.

Bioprinting, or the printing of organic tissues, is a rising and feasible option in medical treatments. This advance would be a huge improvement to many practices such as medical testing and organ transplants. The ability to print organic tissue would eliminate the need for long donor list that many people wait on, but never receive an organ. With bioprinting doctors would be able to test their medicine on organic human tissue rather than animals. This all may sound like science fiction, however it is happening right now.

Carnegie Mellon recently bought a commercial 3-D printer for around 1,000 dollar and after some modifications began to print soft materials. Associate professor at Carnegie Mellon Adam Feinberg and others have developed a way to print soft materials in-expensively. The main problem with printing soft materials is the prints would collapse on the weight of itself. To prevent this the researchers at Carnegie Mellon created a process they now call FRESH (Freeform Reversible Embedding of Suspended Hydrogels). In this process the nozzle prints with a gel inside a petri dish filled with a supportive gel. Then they heat up the petri dish and the supportive gel melts away leaving the print.

As this technology is open source and inexpensive, hopefully many patients will be receiving their very own custom printed organs soon.

 

Original Articles:

http://news.discovery.com/tech/biotechnology/hearts-and-arteries-could-be-3d-printed-cheaply-151026.htm

http://www.cnbc.com/2015/11/02/bioprinting-the-new-frontier-in-medicine-that-makes-human-tissue.html

More Information:

http://lifesciences.ieee.org/articles/feature-articles/332-printing-body-parts-a-sampling-of-progress-in-biological-3d-printing

While studying the brain there arises the need to activate or inhibit certain cells. The most common process for doing this in the past was optogenetics. Optogenetics is the use of light to activate or inhibit cells. While optogenetics is very precise, it has some drawbacks and limitations. Light is scattered in the brain and to reach deep in the brain scientists usually insert a fiber optic cable which is highly invasive. This practice is still used today, but there has been a new development: sonogenetics. Researchers at the Salk lab have been working on this new technique. Sonogenetics use sound waves, low-frequency ultrasound waves to be more specific, to activate the neurons. This new method allows scientists to reach neurons deep in the subject’s brain without having to perform a surgery to implement a fiber optic cable. It also has the potential to have no effect on the surrounding neurons. In the Salk laboratory, the scientist used worms to study the use of sonogenetics. Worms would normally be impossible to work with as performing surgery to implement a fiber optic cable is nearly impossible, but with the use of sonogenetics the scientist were able to activate certain neurons. The sound waves were aided by microbubbles outside the worm that oscillated in size in conjunction with the wave. The scientist then discovered TRP-4, an ion channel which can be affected by the sound waves. They found that the sounds waves along with the microbubbles can open these channels and activate the cell. Though this process they activated cells that would normally not have been activated by ultrasound. Although it all sounds very promising, sonogenetics has only been used on Caenorhabditis elegans neurons.

imgres

 

A picture of Caenorhabditis elegans

 

https://en.wikipedia.org/wiki/Caenorhabditis_elegans#/media/File:CelegansGoldsteinLabUNC.jpg

The next step in the research would be to get the sonogenetics to work in a mammal’s brain. This could potentially lead to therapies that are non-invasive for humans. However, how comfortable would you feel with doctors using sound waves to control neurons in your brain? Sonogenetics sounds very promising and contains a lot of upside, however, the research is not far enough along yet to completely tell.

 

Original Article: http://www.salk.edu/news/pressrelease_details.php?press_id=2110

 

For More Information: http://dujs.dartmouth.edu/news/sonogenetics-the-latest-in-mind-control#.VhMJimRViko

 

By

On October 5, 2015

In Student Post

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