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Effect of environmental toxins on GATC methylation in E. coli May 3, 2011

Posted by ljsteele in Biology, Chemistry, Ecology, Environment/Conservation, Evolution, Genetics, Health, Marian University curriculum, Physiology.
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With the end of the semester drawing near it is becoming that time again when the results are piling in from research you have been working on all semester. As we speak, the final data collection and analysis is taking place in biochemistry, a team of student researchers are exploring of environmental toxins of DNA methylation  in the bacterium E. coli. 

The Bacterial Genome

Bacteria exist throughout the world and can survive in almost any climate . Bacteria are unicellular and can consist in a wide range of environments such as a pond all the way to soil.  One unique attribute of the bacterial genome is that it contains adenine methylation , opposed to mammalian organisms which contain cytosine methylation at GpC islands.  Adenine methylation is when a methyl group becomes attached to the adenine nucleotide on the DNA. When a methyl group is donated from SAM to form a covalent attachment, it is made on the adenine which can cause steric hindrance of transcription factors and differential effects of DNA binding proteins, which can contribute to a change in gene expression.  In previous studies  it has been shown when E. coli is exposed to different carbon sources (ie glycerol or glucose).  Some areas of the genome become demethylated.  In the bacteria E. coli almost every adenine (A) in the GATC sequence is methylated.  To block the methyation at the GATC sequence, a protein must be present to inhibit the DAM methyltransferase from depositing a methyl group on the adenine.

What does Methylation do?

Adenine methylation has many roles in bacteria. Methylation can effect gene expression, cell cycle, virulence, and how proteins interact with the DNA. For the research we are performing, we are concerned with what effect the environment has on changing adenine methylation on the GATC repeats. There are about 20,000 GATC repeats in the E. coli genome and under normal log growth conditions almost every single repeat is methylated. It has been found that when bacterial cells are in a log growth phase there are 6-10 sites which are not methylated. These nonmethylated sites lie up and down stream of promoters of different genes. The lack of methylation may allow DNA binding proteins to modulate their function to allow a functional change in gene expression.

Pollutants and the Genome

In the study we are performing we wanted to see how three classes of chemicals pollutants commonly found in the Midwest affect adenine methylation at the GATC site. We choose three pollutants to represent chemicals that fit into the families of common water pollutants, which are heavy metals, chlorinated compounds and nitrogen rich compounds.Gel Electrophoresis

The above families of compounds will be compared to samples collected from different areas around the campus of Marian University, Indianapolis, IN. Supplements will be added to all the samples to generate a rich liquid media that will facilitate bacterial growth.  With 6 different test groups and 2 controls we are going to seek to determine if any of our known compounds or a compound present in our environmental sample has an effect on the methylation.  The determination of methylation can be done by using restriction enzyme digest with endonuclease selecting specifically for the nonmethylated site.  The enzyme we have chosen was MBO and AVI.  When all the genomic DNA from the bacteria is extracted and digested, then it will be ran on a gel to be imaged to determine if the bands of digested DNA differ depending on the chemicals present during growth.  This is a time efficient way to examine if any changes in methylation levels have occurred.

What Does It All Mean?

For conclusion, the relevance of this study includes a few things.  This study will provide evidence to show if environmental toxins have an effect on bacterial DAM methylation. One role bacteria play in an ecosystem is influencing the flow of nutrients which support plant and algae growth. The results of our proposed study may display that toxins have an effect on methylation patterns which could lead to an increase the mutation rate of the bacteria genome itself.   Destructive mutations may decrease bacterial populations leading to a disruption in the ecosystems nutrient flow, hence disruptions in plant and algae growth with effect additional aquatic and terrestrial organisms.

April 5, 2011

Posted by Dr. O in Biology, Ecology, Environment/Conservation, Institute for Green & Sustainable Science (IGSS), Marian University curriculum, Physiology, Science Education.
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Congrats to Marian University’s very own, Cassie Freestone! Check out her spread (click on picture to expand) in the Spring 2011 issue of Marian University’s magazine, The Magnet.


Cassie Freestone has participated in numerous independent research endeavors at Marian University from a rigorous summer research course at the Institute for Green & Sustainable Science, to taking independent research credits. Her research experience has given her the toolkit to attract and succeed in internship opportunities like this international marine research study.



Marian University encourages the Town of Speedway to Go Green May 1, 2010

Posted by Colleen in Environment/Conservation, Marian University curriculum, Science & Culture.
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This semester, I have been part of a business creation and development class at Marian University called the A-Team. The A-Team is a student consulting group made up of students that come from a number of different backgrounds and disciplines but come together to work on a specific engagement. The team acts as a consulting group for a business or organization that comes forward with a specific problem or question that they would like us to answer. This semester our team chose to work with the Town of Speedway. Speedway has been having a problem over the past 20 years with their population declining causing an increase in housing stock and a decline in the overall upkeep of some of the houses. They came to us to try to figure out how to get young professionals to move to their town as well as how to deal with the blight that has been beginning in their neighborhoods.

modern windspire to generate energy

solar-panels on house

You may be wondering now what exactly that has to do with a science blog. Well, I’ll tell you. We came to the conclusion that

Speedway should work on becoming a green community. There is nowhere else in the Indianapolis area that can make the claim that they are a green community. We all agreed that if Speedway were green we’d move there in a heart-beat. I personally think that the concept of living in a green town would be really cool! What we did as consultants was work on finding some suggestions for things that they could do. Some of the team members found lots of green grants and tax credits that the citizens could potentially use. There are things as extreme as installing solar panels or wind turbines. This would significantly decrease energy costs for the home. Also, there are other, smaller-scale things we suggested they look into.

go green with energy efficient light bulbs

By upgrading appliances to more energy efficient models, the homeowner saves a lot of money over time as well as doing something good for the environment. Houses can be made more green and energy efficient by installing energy-saving windows and insulation, and most simply by putting in compact fluorescent light bulbs.

We hope that Speedway listened to what we had to say (we gave them our presentation yesterday evening) and will work on going green!

Marian Travels to Pensacola April 5, 2010

Posted by Colleen in Biology, Ecology, Environment/Conservation, Marian University curriculum, Science Education.
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Spring Break….and SCIENCE!

Over Marian University’s spring break, the MU Marine Biology class that I am enrolled in took a field trip to Pensacola, Florida. It’s been kind of difficult learning about marine topics while in a classroom in the middle of Indiana…the nearest ocean is hours away. Because of this, I found our Pensacola trip to be vital to my understanding of the topics we’ve covered so far this semester.

Day one

Our group began our caravan to Florida at 5 AM the Saturday of spring break and arrived to our rented beach house in Pensacola about 12 and a half hours later. As soon as we got there, the whole class ran to the beach across the street, and our learning began!

A jelly fish washed up on the beach, so of course we took pictures.

Day two

The following day, we went to Big Lagoon State Park. One of the first things we did in every new place we went to was to check water temperature and salinity. Here, the water was an icy 15 degrees C and had a salinity of 17 ppt. The water here was somewhat less salty because we were looking at an area that acted as a nursery ground to many young marine organisms. To look at these organisms, some of us took a seining net and walked through the water. Some of the organisms we found included snapping shrimp, jellyfish (one was a moon jelly), juvenile sea trout, croaker and mullet, pipefish (related to seahorses), as well as other juvenile organisms.We also looked at the primary producers in this area. Sea grass and eel grass were the plants we saw in the water and Juncus was a terrestrial plant we saw all over.

Seine nets

Day three

The following day, we took a day trip to Mobile, Alabama to look at the mud flats there. Unfortunately, the Gulf coast only experiences one tide circuit per day (compared to 2 on other oceans).   Low tide had occurred at 5:30 in the morning, but we got there around 11 AM. We did what we could as far as looking at soil samples, but information was difficult to gather here. The temperature of the water was half a degree cooler (14.5 degrees) in Mobile Bay and salinity was 10 ppt. The salinity here was so much lower because of the fresh-water river that flowed into the area.

In Pensacola Bay, right behind the house where we stayed, we looked at fouling communities, which are the communities of barnacles, and oysters that attach to buoys, boats, pilings of piers, and any other surface that they can find to claim as home. The zonation depends on how much time the object spends in or out of the water. Oysters tend to live on things that spend all or most of their time submerged. Barnacles can be higher up and can survive for periods of time out of the water.


The beach by our house

One of the final marine aspects our class explored was to look at the water and beach of the Gulf of Mexico right outside of the house we stayed in. We took measurements of the length of the beach (from waterline to area where plant growth began) so that future classes could come down and compare our data with theirs. The water here had a much higher salinity than anywhere else we had tested at 37 ppt. The temperature was the same as most other places we tested (15 degrees). There were some interesting organisms that we came across here as well. One was the ghost crab. If you see the holes that are along the beach, that is most likely the home of one of these creatures. They range in size from very small to about the size of a fist (if you include its legs). We found a large female crab and brought her in to study, but she must have been old because she died the next day. We also tried bringing in a smaller one we found later on in the week, but there was an accident and the little guy got crushed. A third and fourth were brought back to our house and placed in a tank. On was large and the other was small. Unfortunately for the smaller crab, the big guy got hungry. Before we came home again, we let go our lone surviving crab. I’m sure she was glad to be free again.