Jenna M. Lang edited Methods.md  about 9 years ago

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#Methods  ## Swabbing instructions:  1. Setup Node-2 Camcorder to capture NanoRacks surface swab Ops throughout the US LAB.   2. Retrieve a clean NanoRacks Swab Kit.  Move to ISS location listed on NanoRacks Swab Kit label.   3. Remove cotton swab from NanoRacks Swab Kit, being careful not to touch the cotton swab tip to avoid contamination.   4. Rub cotton swab vigorously against designated surface. Spin and turn the swab to ensure maximum sample collection.   5. Return cotton swab to NanoRacks Swab Kit and press to close (squeeze excess air out of bag before sealing, FigureX).   Circle number of location swabbed and label with GMT (dd/hh:mm, FigureX).   If swab is contaminated by touching a surface other than the designated location on the label,   Label NanoRacks Swab Kit with a large, "X" and move on to the next location. Notify POIC of NanoRacks Swab Kit S/N that was contaminated   6. Repeat step 2 to step 6 for all 15 locations listed on the NanoRacks Swab Kit label (or reference table below).   NOTE:   An additional large Ziplock Bag is provided (stowed inside the same bag as the NanoRacks Swab Kits) to use per crew preference to separate the used NanoRacks Swab Kits from the clean (unused) NanoRacks Swab Kits for crew efficiency during sampling.   ## Surfaces swabbed:  Astronauts were instructed to swab 15 surfaces on the International Space Station. 

14. Tab used to open, close, and secure the Nomex privacy panel located on the port crew sleep compartment  15. Crew Choice Surface: Audio Terminal Unit (telephone) hand held push-to-talk microphone located in the starboard portion of the Harmony module (Node 2.) 2).  ## Swabbing instructions:  1. Setup Node-2 Camcorder to capture NanoRacks surface swab Ops throughout the US LAB.   2. Retrieve a clean NanoRacks Swab Kit.  Move to ISS location listed on NanoRacks Swab Kit label.   3. Remove cotton swab from NanoRacks Swab Kit, being careful not to touch the cotton swab tip to avoid contamination.   4. Rub cotton swab vigorously against designated surface. Spin and turn the swab to ensure maximum sample collection.   5. Return cotton swab to NanoRacks Swab Kit and press to close (squeeze excess air out of bag before sealing, FigureX).   Circle number of location swabbed and label with GMT (dd/hh:mm, FigureX).   If swab is contaminated by touching a surface other than the designated location on the label,   Label NanoRacks Swab Kit with a large, "X" and move on to the next location. Notify POIC of NanoRacks Swab Kit S/N that was contaminated   6. Repeat step 2 to step 6 for all 15 locations listed on the NanoRacks Swab Kit label (or reference table below).   NOTE:   An additional large Ziplock Bag is provided (stowed inside the same bag as the NanoRacks Swab Kits) to use per crew preference to separate the used NanoRacks Swab Kits from the clean (unused) NanoRacks Swab Kits for crew efficiency during sampling.  ### ISS Crew  Swabbing was conducted during Expedition 39. The crew included NASA astronauts Steve Swanson and Rick Mastracchio and Russian cosmonauts Oleg Artemyev, Alexander Skvortsov, and Mikhail Tyurin. Japan Aerospace Exploration Agency (JAXA) astronaut Koichi Wakata was the commander for this expedition, and is the astronaut who performed the swabbing.  ### When did this happen?  May 9, 2014. ISS Daily Report: http://blogs.nasa.gov/stationreport/2014/05/09/iss-daily-summary-report-050914/  ### Do we have any information on how / why they chose particular sites? (MARK AND I CHOSE THESE SITES - JL)  These surfaces were chosen in an attempt to sample surfaces analogous to those sampled in the Wildlife of Our Homes project \cite{23717552}. Wildlife of Our Homes was a Citizen Science project for which over 1000 volunteers swabbed nine surfaces in their homes: kitchen cutting board, kitchen counter, a shelf inside a refrigerator, toilet seat, pillowcase, exterior handle of the main door into the house, television screen, the upper door trim on the outside surface of an exterior door, and the upper door trim on an interior door. We were not granted access to all corresponding surfaces aboard the ISS. The kitchen surfaces aboard the ISS are in the Russian module, which we did not have permission to access, swabbing the toilet seat was deemed inappropriate due to ???, and the exterior surfaces are accessible only via an "Extra-vehicular Activity" (Space Walk,) Walk),  which was not requested for this experiment. We also sought to collect samples that would be analogous to the cell phone and shoe samples that were being obtained from thousands of Citizen Scientists across the country in a different component of Project MERCCURI. See Table 1 for a list of the ISS sampling sites and to which Earth samples they were intended to be analogous. Upon successful completion of the swabbing on May 9, 2014, http://blogs.nasa.gov/stationreport/2014/05/09/iss-daily-summary-report-050914/  (include link to video of actual swabbing?) ll swabs were stored at -80 deg C in the MELFI freezer onboard the ISS, until transfer to the SpaceX Dragon spacecraft. In the Dragon, the swabs were stored at -80 deg C in a portable freezer, called the GLACIER, that runs off of Dragon's batteries until it is plugged in (either to the ISS or on the ground.) The Dragon re-entered the Earth's atmosphere and splashed down in the Pacific Ocean at 12:05pm PT on May 18, 2014. Samples were transferred to a cooler with dry ice, and shipped to the EMP lab. Insert description of DNA extraction, PCR, sequencing. 

The number of high-quality sequences per sample ranged from 26830 to 77845 (see Table X). The pick\_open\_reference\_otus.py script was used to cluster sequences at 97% similarity. Taxonomy was assigned to each cluster by comparing a representative sequence from each cluster to the gg\_13\_8\_otus reference taxonomy provided by the Greengenes Database Consortium (http://greengenes.secondgenome.com.) No chimeric sequences were identified using the identify\_chimeric\_seqs.py script and there were no singleton OTUs (probably should verify these things). All subsequent beta diversity analyses (comparisons across samples) were performed with all samples rarefied to 26830 sequences.  ###Comparison of ISS surfaces to analogous surfaces in homes on Earth  The sequences and associated metadata from a 40-home pilot study for  the Wildlife of Our Homes Project are available for download from Figshare \cite{885e3742-e0c3-4719-a6a8-dba9930a33ca}. These were used in a combined analysis with the ISS sequences presented here. Because the sequences from the two projects are of different lengths, each dataset was independently analyzed using a closed-reference OTU-picking approach, and the resultant biom tables were merged with the merge\_otu\_tables.py script.