Tag: Science

Not your Granddad’s genes

Shewyon ironShewanella oneidensis growing on a metal (iron oxide) from https://asknature.org/strategy/bacteria-reduce-iron-oxide/#.WUA49GjyvIU

From the depths of Lake Oneida in New York comes a very interesting type of bacterium, Shewanella oneidensis.  Shewanella is special organism in that it can survive with, or without oxygen.  As humans, our metabolism requires that we take in food and oxygen to produce carbon dioxide and water.  Shewanella also has this ability, but when oxygen is not present in the environment, they are able to use minerals and metals in the environment for what we as humans need oxygen for.  For example, when we break down glucose, we make energy.  The byproducts of that reaction eventually end up needing to go somewhere, and the cells in our bodies use oxygen as that place, making water.  Obviously, humans cannot survive without oxygen, but Shewanella can!  When they break down a food source to make energy, they also need to get rid of the byproducts…but wait, they don’t have oxygen.  The cool thing about Shewanella is that they have proteins on their surface that allow them to pass those byproducts to things in the environment by contact.  When the byproducts are passed to the environment, it produces an electrical current.  So, our goal is to harvest the electricity produced, but in E. coli.  The proteins that allow Shewanella to do this are encoded for in the genes that we are going to put into E. coli!  Why would we use E. coli and not just Shewanella?  One reason is that what we are doing has never been done before!  It’s pretty awesome to think that we are taking genes from one organism and putting them into another to get a result that has never been observed, EVER!!!  Also, scientists use E. coli for these types of tests because it’s easy to use.  So many studies have been done on E. coli that we know so much about it, and in a lab setting, we can pretty much try and make it do whatever we would like.

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So, where to begin?

A lot of people may think that we scientists just walk into the lab, start mixing these brightly colored chemicals together, and call it an experiment.  The TV commercials that you see with all of the pretty colored mixtures is not indicative of what we do at all, and spoiler alert, it’s Gatorade in those flasks.  What actually goes on in a lab is much different.  Experiments can either take 10 minutes, or your entire day.  Prior to doing any type of experimentation, we need to do a lot of research on our project in order to decide what to do.  For some, including myself, reading research articles that are published in scientific journals is one of the hardest parts of starting your project.  We have to go through a great deal of reading to learn as much as we can about how the organisms and genes we are working with function.  For anyone who is interested in checking out what these journals look like, you may find that in order to read articles, you need a license to that specific journal.  Luckily, science is becoming more open with the community and labs are publishing their work in what are called “open access journals.”  These journals allow anyone to read the research articles that are published on their site.  A link to a list of open access journals on a bunch of different subjects from Wikipedia can be found at the end of this post! Anyways, the reading stage is exactly where I am at right now, and I will be back in a few days to fill you all in with some more background information about the project!  I’d also like to take this time to set up what I’d like to call a “Life Science Live Mailbag.”  If you ever have any questions about the project or want to know information that is a little bit more in-depth, feel free to comment on posts and ask.  If there are questions at the end of each week, I will go through and answer them in a final post for the week!

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

Electric E. coli?!

Post 1

Hello, my name is Kody Duhl.  I am a Ph.D. student at Michigan State University studying biochemistry and conducting research in the TerAvest lab.  Over the summer, I will be taking you all along with me as I journey through a brand new research project!  The idea of the project is to make E. coli produce electricity.  Wait, did I just say E. coli and electricity in the same sentence? Yes, and the best part about it is that the E. coli that I will be working with is not harmful at all.  Unfortunately, E. coli has a bad reputation.  Like me, you have probably heard the scary news stories about the things it does (cough, cough….Chipotle), but for biology, it provides a massive amount of research for us to conduct. The cool thing about E. coli is that it allows us to take genes from other organisms and put those genes inside it.  The E. coli will then make the proteins that are encoded in those genes.  This ability is exactly what we want to take advantage of in this project.  Now, there is already a type of bacterium that can produce and electric current, and our plan is to take the genes that allows this bacterium to do so, and put them into E. coli.  Why would we want to do this, you ask?  It’s because we live in a world that is constantly looking for new sources of renewable energy.  Fossil fuels are a limited source of energy and create pollution as a byproduct.  By attempting to make E. coli produce electricity, we are providing the beginning steps to being able to utilize a renewable energy source that will not pollute our beautiful Earth.  So, I hope you all are interested and tag along as I work through this project throughout the summer!  The best thing about it is that I don’t know much about this subject, so you all get a “live look-in” into how we work in a lab, and you’ll be learning about this project at the same time that I am!