Jimmy Louis performing a DNA Extraction at Lawrence Berkeley National Laboratory
As DNA Everywhere begins a 12-month routine monitoring program exploring the microbial community interactions of SOIL’s compost, Jimmy Louis, Port au Prince’s Sanitation Coordinator came to visit DNA Everywhere and the Thermopile Project at Lawrence Berkeley National Laboratory. On the way to the airport, Jimmy shipped 18 DNA samples he had extracted from SOIL’s compost just days before and raced them to California. Jimmy conducted all the downstream processing of the samples alongside DNA Everywhere Project Manager, Gabby Pecora.
“Jimmy picked up the DNA extractions so quickly when Gary and I were in Haiti. We were thrilled to have him at LBL and are so confident in his ability to teach others how to perform the extractions when he gets back. He’s such a natural in the lab!” said Pecora, “I’m really glad that Jimmy had the opportunity to work at LBL and see what we do with the samples he sends us. I think being able to be in the lab, running PhyloChips really helps close the loop and conceptualize the whole system.”
Jimmy Louis and CalRecycle’s Reinhard Hohlwein talking “compost” at the Thermopile Pile Build on May 3, 2014
The 18 samples were brought to PhyloChip within the two weeks Louis spent in California and he participated in the preliminary analysis of the results. “Jimmy learned very quickly and I think he will be a valuable resource to have back there in Haiti as we continue with this project. We have a lot more work to do for analysis of these samples but it is clear that the DNA extraction that was done there worked perfectly and that gives us a lot of confidence as we go forward.” said Dr. Gary Andersen.
In addition to participating in the downstream processing of the SOIL DNA samples, Louis participated in a Thermopile compost pile build with the help of the Ignacio Rotary Club and taught 7 members of the Club how to extract bacterial DNA from compost. “We are so glad Jimmy could come up here and successfully take what we had taught him and be able to teach the Rotary members how to perform very successful DNA extractions on their first attempt.” said DNA Everywhere Project Director, John Hulls, “This demonstrates complete technology transfer within DNA Everywhere.”
Jimmy Louis and Gabby Pecora discussing PhyloChip data from the first 18 DNA samples shipped from Haiti at Lawrence Berkeley Lab
Jimmy’s trip was a huge success and we look forward to our ongoing partnership with the SOIL organization. A big thank you for your support!
March 29, 2014- DNA Everywhere helped Lawrence Berkeley Lab’s Dr. Eric Dubinsky count a record breaking number of species during the National Geographic BioBlitz in Golden Gate National Recreational Area on Saturday. Dubinksy and company collected water and sediment samples from Lobos Creek and Baker Beach early Friday morning and extracted bacterial DNA using the DNA Everywhere method at the Chrissy Field Center Friday afternoon. DNA was brought back to LBL and analyzed over night using the Berkeley PhyloChip.
National Geographic’s BioBlitz is a 24-hour event where volunteer scientists, students, families and other community members work to find as many species of plants, animals, microbes and any other organisms as possible. Each year the BioBlitz takes place in a different national park.
The event came to a close at 4:00pm on Saturday, March 29 with a final species count of 2034. Of the 2034 counted, LBL counted 916 species of bacteria and 68 species of archaea, which accounted for almost half of the total species inventoried. Check out NatGeo’s coverage of DNA Everywhere and the PhyloChip here:
Gabby Pecora (left) and Dr. Gary Andersen (right) at the SOIL composting facility in Port au Prince
With support from the 11th Hour Project, DNA Everywhere’s Gabby Pecora and Lawrence Berkeley Lab’s, Dr. Gary Andersen traveled to Port au Prince, Haiti in October to implement the first stage of the DNA Everywhere project. After training six members of the SOIL organization to extract DNA from SOIL compost, Pecora analyzed the samples at LBNL for contamination and DNA yield, finding the samples sufficient for PhyloChip analysis.
“This gives us the ability to try new designs and see if we can further optimize the composting process,” says Dr. Sasha Kramer, co-founder and Executive Director of SOIL on the DNA Everywhere technology. “Cholera is on everyone’s mind here, and anything that we can do to reduce this risk will save lives.”
In addition to training SOIL staff on the DNA Everywhere extraction protocol, Andersen and Pecora were toured through many of SOIL’s sites in both Port au Prince and Cap Haitien, including communities with public toilets, private family toilets, compost sites, agricultural farms and compost research sites. “SOIL efforts are really astounding, they have such a presence in so many areas of Haiti, everyone knows who they are.” says Pecora after traveling to Cap Haitien. “We went down there to implement the DNA Everywhere project, but we learned so much about their composting operation in the process that is invaluable to our Thermopile Project” Pecora states. In fact, as a result of this trip, the SOIL organization has agreed to discuss implementing a Thermopile test cell in Haiti to provide further analysis for both the Thermopile Project and SOIL.
DNA Everywhere is currently in the process of running samples from Haiti and planning a twelve-month analysis schedule where SOIL will ship DNA samples to LBNL for routine PhyloChip analysis. DNA Everywhere is also hoping to expand DNA extraction capabilities to the Cap Haitien operation as well as part of the Project’s next stages.