Current happenings – October 3, 2016
It has been a bit over one year since starting at AWRI and “WOW”. The lab is growing steadily. It is now composed of three graduate students and a part-time lab technician. We have two grant-funded projects happening. The first project is funded through an EPA-Great Lakes Restoration Initiative (GLRI) grant. It is in partnership with The Nature Conservancy and our two collaborators, Jim McNair and Kevin Strychar, at AWRI. This project will assess how different removal strategies are impacting the presence of invasive baby’s breath (Gypsophila paniculata) in Sleeping Bear Dunes National Lakeshore (SBDNL). We are also looking at the genetic structure of these invasive populations throughout west Michigan. The students working on this project spent 2 months in SBDNL working with removal teams from The Nature Conservancy. The teams removed roughly 30 acres of baby’s breath of previously untreated areas. This included 24 manual removal plots and 24 herbicide treated plots. They also collected tissue samples from over 800 plants across 7 populations for genetic analysis. The next step is to start extracting DNA from the plants and getting the molecular work going.
The second project we have is funded through the Michigan Department of Environmental Quality grant in collaboration with Rick Rediske (also at AWRI) and Kevin Strychar. This project will use quantitative PCR (qPCR) to detect and quantify the presence of Microcystis sp. in Muskegon and Bear Lakes, MI. Microcystis is a cyanobacteria that can produce cyanotoxins, which can be harmful to both plant and animals at certain concentrations. The goal of this project is to look at how Microcystis concentrations vary over time within these lakes and see if the production of the cyanotoxin is affected by density or other abiotic factors (temperature, pH, etc). This project has just started and we are currently working out methods for DNA/RNA extractions.
A third project we have in the lab focuses on adapting current methodologies for detecting the presence of fecal contamination around local beaches. One method currently being considered is the use of qPCR to quantify the amount of fecal bacteria DNA present in beach samples. However, one problem with this method is that it can not distinguish live bacteria from dead bacteria and that’s where we come in. Our lab is looking to modify this protocol by adding a chemical called propidium monoazide (PMA) to the reaction before qPCR. This chemical binds to the DNA of dead bacteria and prevents it from being analyzed by the qPCR method. The addition of this step would allow labs to keep the speed of the qPCR method, while being more accurate in its quantification.
OFF WE GO!! – August 28, 2015
This is my 1st post in what will hopefully be a long, joyous, eventful, and successful career in academia. I started my new position at Annis Water Resources Institute at Grand Valley State University exactly 28 days ago, and so far so good! I’ve been busy trying to learn the ropes of this whole “PI thing” (there should seriously be a 2 hour seminar on grant budgets) and getting settled in Michigan. The lab has a few exciting projects that we are working on and I’ll be updating my “Research” section pretty soon. My 1st graduate student starts on Monday and he will soon be integrated into the wonderful world of qPCR. Grant season in in full bloom, although I’m not sure it ever isn’t in bloom, and I have a few new collaborations that I’m really, really excited about. So, overall I give my first month two big thumbs up! Be on the lookout for really awesome things coming out of the newly christened Partridge Lab!!