#urbanmicrobiome

[greenlabnotebook-blog]

Whoops, haven't had a post since before the holidays...

Today and tomorrow I'm finishing up the library prep for Gwynne's Urban sampling. I'll send those off for 16S sequencing later this week.

[greenlabnotebook-blog]

Ran a PCR on the Urban air samples I extracted last week. Gel visualization revealed faint bands in each of the air samples and solid bands in each of the settling dish samples. No contamination present in 2 of the extraction controls I ran. Overall, very promising and indicates successful extraction. I'll prep the full sample set for 16S Illumina sequencing next week.

[greenlabnotebook-blog]

Urban air sample extractions

Nov 12:

DNA extractions on Urban Park's vs Parking lots air filter samples (n = 30) with MoBio PowerWater extraction kits. Extraction order was randomized. Made the following modifications (similar to previous air filter extractions for Lillis):

After adding PW1 (cell lysis buffer) freeze-thaw each sample in liquid nitrogen and heat at 65 °C for 10 min. Helps to break up filter for more efficient extraction.

Final elution volume of 50 µL and let sit for 5 min before spin down.

Also ran 2 extraction controls: EC1, EC2.

Nov 13:

DNA extractions on settling dishes from Urban air (n = 30) with MoBio PowerWater kits. Extraction order was randomized. Each dish (lid and base) was swabbed with pre-moistened (sterile PBS) nylon-flocked swabs and added to the bead tube. The following kit modifications were made (similar to swab extractions for Lillis):

After adding PW1 heat sample in water bath for 10 min at 65 °C.

Bead beat for only 2.5 min (vortex adapter) to prevent shearing unprotected DNA

Final elution volume of 50 µL and let sit for 5 min before spin down.

Also ran 2 extraction controls: EC3, EC4.

[greenlabnotebook-blog]

This week's efforts went towards:

Skin interactome proposal with James O'Dwyer, Tom Sharpton, and Brendan Bohannan

Potential partnerships with Josh Snodgrass & Brendan Bohannan on the Shuar Health and Life History Project

Helene Morlon's lab discussion featuring Fabien Condamine's ongoing project on predicting diversification rates, as a function of environmental change, over evolutionary timescales

Reading and preparing for next week's workshop on Cities Unseen [partially using Pinterest and Scoop It]

Lillis dust ms revisions

Our "Healthy Schools" EPA proposal with Gwynne, Charlie, Bart, and Deb

Josh Ladau and Katie Pollard project on predicting beta-diversity patterns via species perimeter-area ratios

[greenlabnotebook-blog]

Spent most of the day drafting and submitting a second round of peer-review journal reviews.

Contributed to the GBMF seagrass microbiome grant review responses with Jonathan Eisen & Jay Stachowitz.

Checked in via Skype with Gwynne, James and Josh about the #UrbanMicrobiome project. Next steps include considering potential of building on the PGP/1000 homes project. Have plans to connect with Katie Pollard about this once she returns from travel the week of October 1. Will follow up with Graham Rook’s suggested epidemiology contacts.

[greenlabnotebook-blog]

I spent lots of time dealing with data from built environment studies going into the QIIME DB, and trying to prepare before we meet today. Then in the afternoon I was able to work on pickle box analysis for a while. I should have lots of results to go into manuscript soon.

Discussed VOCs and health with Josh and Gwynne - we're trying to figure out exactly what data to collect in that context:

lots known about bad effects of VOCs but very little about benefits

well known what VOCs you might experience based on land cover and proximity to given sources (like plants vs industrial vs roads etc)

assumed that most come from plants - assumed that little comes from plant microbes and some comes from soils, with some individual VOCs known and well tracked

But likely little known regarding small scale spatial dynamics in urban environment with regards to beneficials.

Some research on benefits - mostly forest bathing and essential oils research.

So we are considering collecting VOCs from urban gradient (but determining the appropriate scale) for predictive model since we have lots of good info about health effects for bad VOCs and some on beneficials.

Found great VOC database for mining health research: http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB

[greenlabnotebook-blog]

Auguest 28, 2013

I spent most of the day finishing up our big submission to the QIIME database (lillis dust, air, and surfaces). All metadata are now in order for all 3 projects, and they are working on entering data so that sequences can be input before our Berkeley Indoor Evolution meta-analysis meeting.

Additionally I worked for part of the day with Adam on the lab notebook website, and we think it is about ready to launch after we test it for the next couple of days.

Josh, Gwynne and I met with Chris Gray (Fierer lab in UCBoulder) about VOCs and health. We came away with the impression that quite a bit of work has already been done, and that our plans might actually be accomplished with a big review article tying several lines of evidence together. However a niche modeling approach in urban centers might be a really nice addition to existing literature. This would likely include spatial sampling of VOCs to inform a predictive model. And it appears that we might be able to partner with a lab that already is well set up to analyze VOCs on GC-MS.