Category Archives: Uncategorized
Day 40 and rolling!
Last Thursday Wendy and I went out to collect our day 40 samples! So far so good- we have collected at day 12, 24, and 40, with one more to go. Here we are, returning with the treasures. What we do … Continue reading
New Deployment!
We have been quiet but we have been busy. After the FTIR analysis (showing signs of degradation in the plastic) and PCR of the colonies grown from the plastic on ChromAgar Vibrio (showing interesting but not pathogenic Vibrios), we decided … Continue reading
Poster presentation accepted for ASM2017!
ASM Microbe conference! Needless to say, we are very excited. Just received some preliminary FT-IR data (this is a chemical analysis technique that can expose changes in the structure of materials) for one of the plastics, LDPE (that would be the … Continue reading
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Tagged conferences, news
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Extracting DNA
Few days ago we used the MOBIO Biostic kit to isolate DNA I extracted from microbial colonies grown on ChromAgar Vibrio with the goal of identifying them using PCR. Colonies had been collected and frozen at -20 oC. Super excited … Continue reading
Re-Analysis and Validation!
Thanks to your contributions, we were able to purchase the Geneious software package to validate our analyses. I’m still in the midst of pre-processing for our sequences–since we have millions of reads and low quality data can result in inaccurate species identification, it’s … Continue reading
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Tagged bioinformatics, data, ngs
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Moving forward!
View of Dana Point Harbor, just North of our sampling site. The team has been quiet since the ISME conference, but that does not mean we have been idle…on the contrary! We have been teaching and dealing with a number … Continue reading
ISME impressions and poster link
ISME16 started yesterday afternoon with the keynote address and today it was in full swing. It is my first time and so far I have been impressed with the scheduling (there seems to be plenty of time to attend the presentations, and … Continue reading
Information Overload!
This week Ana and Rachel attended a workshop on metagenomics hosted by Liz Dinsdale at San Diego State University. From DNA extraction all the way through sequencing and analysis, we were able to produce metagenomes from shotgun sequencing from some … Continue reading
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Tagged bioinformatics, lab work, ngs, sequencing, workshop
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We made it!
Sunrise over the Atlantic. We hit our funding goal yesterday, thanks to all of you who donated to this project…thank you! We are so touched by the number of people who felt moved by the project and supported us. So … Continue reading
Microbes on PET bottles
Reproduced from the article: Fig 5. PET and glass biomarkers identified by linear discriminant analysis This article just appeared in PLOS One: Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris A quick read showed … Continue reading
