SVA-NYC

Notebooks

Week 1

DRY LAB 1:

For our first team meeting we distributed handouts, reviewed the Art & Design track guidelines and introduced a few project ideas.

We discussed preliminary research and possible manifestations of a project about testing soil, which included an iPhone case that coordinates with an app to process physical samples in the field and a large (weather like) map showing soil health in Manhattan.

Sites of interest for sampling soil: Parks, retro manufacturers, cemeteries, backyards. *Expand list and make map*

NEXT MEETING:

Check out project NOAH for soil. Also look into previous iGEM projects.

WET LAB 1:

5/18 - First iGEM syllabus meeting
5/19 - Preliminary research on nutrient activated promoter

Week 2

DRY LAB 2:

Distributed lab coats and iGEM pins
Team members signed up for iGEM usernames
Brainstormed project titles
Took group photo
Drafted list of subcommittees and preliminary tasks
Extended sample collecting to other boroughs
Emailed LaMotte handbook to team

Potential names for project:

“SOIL-SCAPE”
“Super Duper Soil SenSomatic!”
“DIRT-BOW”
“SOILED”
“Soil Spectrum”
“ChromaDirt”

Everyone will research their assigned soil topic as well as think about:
What is the definition of soil? The chemicals used in the testing of soil nutrients are toxic- what are non-toxic solutions? is soil toxic? what nutrients are present? can you neutralize soil? what is soil health?

pH- Suzanne
Nitrate Nitrogen - Sebastian
Potassium - Jennifer
Phosphorous - Martica
Humus - Shane
Magnesium - Daniella
Calcium - Tarah
Sulfate - Andrew
Aluminum - Victor
Chloride - Daniella
Ferric Iron - Darya
Nitrite Nitrogen - Beckett
Ammonia Nitrogen - Mike
Manganese - Tiffany

First deadline: JUNE 26TH

WET LAB 2:

5/25 - Research led to the possibility of using microfluidics

Week 3

DRY LAB 3:

- Team members presented their research on assigned soil nutrients to the group.
- Looked at an app that tests soil.
- Discussed the legalities of sampling: taking samples in public is going to need more formalities. Personal spaces and community gardens will be a more realistic place to begin sampling.
- Plotted iGEM deadlines onto a calendar.
- Ordered 6 soil augers, spray bottles, tape measures, location markers, etc. for collecting samples.
- After reviewing the SDS sheets for the LaMotte kit reagents we discussed chemical hygiene and trained new team members on our lab protocol.

After realizing just how toxic the kit is, the team continued to brainstorm about non-toxic sensors. Ideally we will find biological substitutes for LaMotte soil tests - if that is not an option we can greatly decrease the amount of the substance needed for testing, by using a microchannel chip and spectrophotometer, possibly interfaced into a device for a smart phone.

Sebastian explained that exposure time for the biosensors we make would not be an instant result, like the LaMotte kit, but need at minimum a few hours to process. We also discussed how (some of) the biosensors function to change colors- once they bind the to soil sample the molecules change shape, therefore changing the way the light refracts which makes the color visible.

NEXT MEETING:

We will test out the LaMotte soil kit for the first time as a group.

Need to make a map of community gardens and draft a letter to introduce our project and ask for access. How do we encourage citizen participation? Offer participants a survey of data pertaining to their soil.

WET LAB 3:

6/2 - Found Arsenic activated biosensor in biobrick registry

Week 4

DRY LAB 4:

Sebastian leads a demonstration on how to use the LaMotte Soil Kit to test a soil sample for different nutrients, starting with the process of filtering nutrients from soil into container with liquid extraction. We discussed possible ways to streamline and expedite the slow drip extraction, while keeping in mind we must use individual containers and utensils for each sample to AVOID CROSS-CONTAMINATION. Miniature French presses? Centerfuge?

After performing LaMotte nutrient tests, several issues were discovered:
- Some nutrients produced very small quantities, too little to fill cuvette.
- Due to subjectivity in the perception of colored results, it was difficult to read precise amounts for each nutrient. Several tests, like the one involving a black line and shade of grey, exacerbated this problem.

A handful of team members took augers home to get samples from their yards. Next week we will hear feedback from those that used the augers and begin drafting protocol and assembling a kit for sample taking: including recording of gps/time/temp, etc. Environmental limitations: nearby buildings, trees, dog pee, rain within 48 hours.

WET LAB 4:

6/08 - Transformed mRFP1 from kit-4 well-2F ("SVA 1").
6/10 - Preliminary testing of La Motte soil kit.
6/11 - Majority of biobrick registry research to create potential cassettes.

Week 5

DRY LAB 5:

Victor talks about the acquisition of his samples, the type of soil, the process, and his reflection upon the experience of extraction:
- Need the address or geotag location of every collected sample for verification purposes.
- Between each sampling of soil, it is important to clean the auger with DISTILLED WATER, as tap water has trace elements and minerals that may get absorbed into the soil of the next sample, providing false or altered readings.
- When not in use soil should be stored in dark spaces with the bag open, to prevent photobleaching and allow aeration.
- Sebastian blows everyone's mind with science when he casually mentions the "dew" that forms in the plastic bags of soil when they are sealed is not caused by humidity, but by BACTERIA!
- A scientist and a photographer try to agree on how to standardize and optimize the process of photographing the samples and results.
- The Universal Extraction Buffer (used in many of these nutrient tests) is essentially vinegar. It NEUTRALIZES the alkalinity of the sample to even out the pH. This process leads to an opaque reaction that forms a PRECIPITATE that will not dissolve. Because of this, the color will remain. Just keep refrigerated.
- The sample requires a relative reading. I.e. any lighting can be used, so long as the sample and the control are read (or photographed) at the same time.
- The white flakes from a fresh fire are called Pot Ash. It's another name for Potassium.

NEXT WEEK:

- Start drafting outreach email to faculty and students that have back yard access.
- Draft list of places we can post open invitational flyers.
- Make list of potential sponsors and contact.

WET LAB 5:

6/15 - Transformed Mer Operon from kit-5 well-21N ("SVA 2")
6/15 - Miniprepped SVA 1
6/16 - Transformed Limonene Synthase from kit-4 well-3I ("SVA 9")
6/17 - Miniprepped SVA 2

Week 6

DRY LAB 6:

- Drafted an ‘all concerned’ email blast to SVA community, which will be sent out this week.
- Discussed the pros and cons of letting random participants take the samples, instead of sending a team member to the location. Consensus is that coordinating and instructing outsiders to take the samples wouldn’t be any less work and could potentially jeopardize our data.
- We looked at all the different sections we will eventually have published on our site and determined which sections we currently have content for and who will manage. We will host the content in google drive until it has been greenlighted. Tarah will make a shared website folder for content. Raul drafted a spreadsheet to manage website content.
- Updates to our project description - focus our efforts on community gardens and backyards in our urban environment.
- Missed opportunities to connect with community garden contacts and we all agreed (approved) letter addressed to sites of interest should be a priority for the next meeting, as reaching out requires waiting on others to respond.
- Discussed how to get the most pure and accurate sample from a single site. We do not have the resources to test each site multiple times, however- we could take multiple samples from each site, and process the combination of samples to get an average. - Sebastian and Tarah drafted responses to an iGEM survey about our lab and about our project.
- Made our very first iGEM submission deadline on 06/26/25!
- Jen updated us on her progress of converting the LaMotte sample forms into 2 separate custom forms for our project- one designated for out in the field and another for processing back in the lab. Jen has been drafting standardized answers to select from as well as creating a visual guide of different types of soil. Steph recommended instead of printing pictures of soil on each form have a laminated photo card in each kit.

NEXT MEETING:

- Review everyone’s 100 word bio and take individual head shots of the group for the team page.
- Gather all available info and images and continue sorting into website folders to create a workflow of approving and adding content to the website.
- Finalize forms for sampling and processing soil.
- Gather information about soil processing procedure and begin designing our soil collection kit. Create forms and questionnaire for field sampling.

WET LAB 6:

6/22 - Transformed RBS from kit-4 well-1N ("SVA 3")
6/22 - Transformed Double Terminator from kit-3 well-3F ("SVA 4")
6/22 - Transformed mCherry from kit-2 well-18D ("SVA 5")
6/22 - Transformed ArsR from kit-3 well-10O ("SVA 6")
6/23 - Transformed aeBlue from BBa_K1033929 ("SVA 7")
6/23 - Transformed eforRed from BBa_K1073023 ("SVA 8")
6/26 - Liquid Culture of SVA 4,5 and 6

Week 7

DRY LAB 7:

- Began receiving lots of responses from our outreach email. Off to a great start!
- Submitted and proofed bios and Raul took headshots for our team page.
- Sebastian showed us plasmid maps for the parts we hope to contribute.
- Opened a twitter account, which Andrew will maintain.
- Discussed a logo for pins- which Steph will design.
- Picked a font called “Brown” for our main website and our header image of “Soiled” written in dirt. Mike will cut a few different sizes out of plexi.

NEXT MEETING:

Getting ready for the following deadlines:
July 15th - must submit our project description to our official iGEM wiki.
August 1st - We would like to have all soil samples submitted for processing.

WET LAB 7:

6/29 - Miniprepped SV 4 & 5 (SVA 6 yielded no growth)
6/29 - Agar stabbed SVA 1, 2A, 2B, 4, 5, and 9
6/29 - First attempt to ligate SVA 4 and SVA 5 (making "SVA 13")
7/01 - Redid SVA 6 liquid culture
7/02 - Miniprepped SVA 6

Week 8

DRY LAB 8:

We are continuing to receive a lot of interest from NYC residents that would like their soil tested! We began scheduling appointments and created a database to manage locations and times of participant’s availability.

We reviewed the judging rubric that was recently released and elaborated on different elements our project will be judged on. It is confirmed that we will be given some type of installation space, but no details about dimensions, lighting, etc.

- Contacted iGEM headquarters of what to expect for installation.
- Shared the draft website Raul and Mike have been working on.
- Added profile pictures and posted to our new Twitter account.
- Linked twitter with “SVABioArt” Instagram.
- Brainstormed logo concept - a round logo with the teeth of the gear replaced with nyc skyline and a color wheel of some sort in the center.
- Steph found a reasonably priced supplier for pins that has a minimum production of 50.
- Darya began experimenting with growing seeds in a “Soiled” plexi cutout. She will resume documenting a few different versions with Mike’s help.
- Continued to brainstorm how to precisely collect samples. After physically taking samples in different locations Steph and Darya stressed that there are a handful of details we still need to work out.
- 07/11 The very first official soil sample (#1 + #2) are collected from participant’s residence.
- 07/12 Adjusted soil sample protocol to make the procedure more efficient on field.

NEXT MEETING:

Must finish all edits on Project Description!!!!
Since we would like to get all samples in by August 1st- we need to finish hammering out the collection kit instructions and supplies ASAP.

WET LAB 8:

7/06 - SVA 3 transformation again (ran out)
7/06 - Transformed LacI Operon ("SVA 14")
7/07 - Remade SVA 13 using proper restriction enzymes
7/07 - Preliminary Mercury tests on Mer Operon + GFP
7/07 - Ligated SVA 7 onto SVA 4 to make SVA 15
7/08 - Liquid cultured SVA 14
7/09 - Transformed SVA 16, 17, & 18

Week 9

DRY LAB 9:

- Continued to manage replies and schedule appointments with participants.
- Created a smart map to more efficiently visit sampling locations within close proximities.
- Team members are out visiting participating locations and taking samples.

7/15 - Soil sample #3 is collected
7/17 - Soil sample #4 is collected
7/18 - Soil sample #5 and # 6 are collected

WET LAB 9:

7/13 - Liquid cultured SVA 16, 17, & 18
7/14 - Miniprepped SVA 16 &17
7/14 - Ligated 17 onto 4 and 16 onto 4 (SVA 21 & 22)
7/15 - Miniprepped SVA 18
7/15 - Ligated SVA 7 onto 4 and SVA 8 onto 4 (SVA 19 & 20)
7/16 - Ligated SVA 6 onto 18 (SVA 12) (SVA 18 is replacing planned SVA 3 which constantly had no growth would not transform properly)
7/16 - Transformed SVA 19, 20, 21, 22 & 3

Week 10

DRY LAB 10:

- We gathered to discuss some issues that occurred during our field trips - Some participants have canceled and there's been poor weather conditions, slowing the process of soil collection.
- Take pictures, fill out forms, give survey to plot owners/caretakers, get weather report from National Oceanic and Atmospheric Administration (NOAA), and use GPS to get longitude/latitude, ask how old the property is.

Discussed outside sources and ways to expand our participants list:
- Brooklyn College soil lab and Hydroponics company
- LaMotte sponsorship
- Contact friends of friends
- Written consent of use of soil
- Reach out to Sustainable South Bronx (rooftop gardens)
- Contact the Friends of the NATLAB email list
- Add a “refer a friend” line in the survey paper so we can increase our spread
- Growing plant seeds in vitro using soil extract as medium
- Growing wheat seeds in soil of donor

07/21 - Soil samples #7,8, 9, 10 and 11 are collected
07/22 - Soil sample # 13 and 14 are collected
07/23 - Soil samples # 12 and 15 are collected
07/24 - Soil sample # 16, 17, 18, 19 and 20 are collected

WET LAB 10:

- Spectrophotometer calibration: specific wavelength goes up and down based on concentration. Needs a known reference: "blanking" with just LB (eg) set 537 nm for Magnesium.
- Concentration correlates to the highest peak on the graph, each referring to a different color.
- Some display inverted peaks and require more calibration.
- Should yield accuracy within a mL.
- Using 14 chemical tests (all from La Motte except humus).

7/20 - Researching GlnA operon for Nitrogen-sensitive promoters
7/20 - Transformed SVA 12
7/21 - Miniprepped SVA 3, 19, 20, 21, & 22
7/23 - Liquid Cultured SVA 12

Week 11

DRY LAB 11:

- Narrowed sample collections down to five boroughs of New York: urban gardening, rooftop gardens, backyards, and community gardens.
- How are we going to efficiently and accurately test large quantity of soil samples? Assembly line of one person per test, repetitive and familiar process expedites work flow? Work in pairs to monitor mistakes?
- Reviewed soil reports and decided to ad cue card of images of different types of soil to standardize description recordings
- When soil testing, we should include the question: "Where do you get your soil?" - Make a list of sponsors (Possible sponsors: High Line, Davinci, Union Square Farmers Market, LaMotte)
- Formulation of calendar
- Updating field test sheets
- Continue brainstorming apparatus that would encase chemicals to avoid contact with personnel.

7/29 - Soil samples # 21,22, 23, 24, 25, 26, 27 are collected
7/30 - Soil samples #28, 29, 30, 31 are collected
7/31 - Soil samples # 32, 33, 34 are collected
8/01 - Soil samples # 35, 36, 37 and 39 are collected

WET LAB 11:

Ash/Beckett/Sebastian will alternate chemicals and focus on microfluidics, paper encapsulates it like a litmus test (paper test).

7/29 - Ligated SVA 5 onto 3 and SVA 7 onto 14 (Making SVA 23 and 16, respectively)
7/31 - Transforming SVA 16 & 23
- Began research and skeleton design for complex multi-colored biosensor

Week 12

DRY LAB 12:

- Discussed Steph’s logo sketches
- Reminded team the banner deadline September 1st - everyone will submit at least one draft for us to vote on
8/08 - Soil sample # 40 is collected

WET LAB 12:

8/03 - Liquid cultured SVA 16 and 23
8/03 - Calculated molarities and ppm of our spectrophotometric standards for our 15 different nutrients
8/04 - Miniprepped SVA 16 and 23, again
8/07 - Catalogued all genetic devices constructed on SnapGene program

Week 13

DRY LAB 13:

- Discussed possible installation and art works based on our wet and dry lab processes to date, and on where we foresee the project going.
- Several ideas and sketches were presented by the team and critiqued.
08/13 - Soil sample # 42 is collected.
08/17 - Soil sample # 41 is collected (rescheduled).

WET LAB 13:

8/10 - Made spectrophotometric standards for Cl, SO3, NO3, P, Al, NH4, and Ca
8/13 - Finalized digital models of genetic devices on SnapGene
8/13 - Made spectrophotometric standards for Fe and Mg

Week 14

DRY LAB 14:

- Sketch of soil map of New York City is agreed to be a relevant focus for the creative team.
- Several discussions on concepts emerged.
- Restricted on designing an installation, as there is limited information of the gallery space, dimensions and lighting provided at the jamboree. What we do know is that any soil and chemicals cannot cross state boundaries limiting possibilities for installation materials. Ask iGEM HQ about commercial soil as an installation material.
- The idea of having our creative work designed and made for a New York Gallery (SVA Gallery) was proposed by Shane.

8/22 - Soil sample # 43 is collected

WET LAB 14:

We revised all of the LaMotte protocols to accommodate quantity of samples and volume required for filling cuvettes. We also set up an assembly line to extract the first 35 samples using funnels, filters, conical tubes and universal extraction buffer. Tests for Chloride and pH must be extracted with other solution.

Week 15

DRY LAB 15:

- Focused on concepts of testing soil in NYC, and how we can visually represent the data and process of the scientific work being done.
- Use LEDS to represent location, so information displayed is not static, but can cycle through different results.

8/24 - Soil samples # 44, 45, 46, 47 are collected
8/25 - Soil samples # 48, 49 are collected
8/27 - Soil samples # 50, 51, 52, 53, 54, 55 are collected

WET LAB 15:

- Created Standards and processed soil extraction for Nitrate, Potassium.
- After weeks of contacting suppliers we are a little concerned about getting refills on a few of the reagents needed to finish testing. LaMotte’s tablet pressing machine is out of order and none of the 32 retailers we contacted have any phosphorous tablets!

Week 16

DRY LAB 16:

We gathered to finalize possible installation ideas on how we can represent our final product. At this point all soil sampling is completed and so far we collected 55 samples total from all the boroughs.

Discussed visual representation of the all collected results: - 5 boroughs cutouts with an LED mapping according to location of the each sample.
- Incorporation of the human practices.
- Installation space logistics.

WET LAB 16:

Created Standards and processed soil extraction for Chloride, Magnesium, Ammonia Nitrogen, Manganese, pH. We finally found some replacement phosphorous testing reagents in stock that should be here by the end of the week.

Week 17

DRY LAB 17:

- Installation team continues working on wiring installation, mapping out the LEDs, working on coding.
- Team is processing samples back in lab.
- Organizing all the soil samples images for further placement on the website.
- Archiving all the soil sample documentation.
- Mike and Raul continue to work on the website.
- We 3D printed the final draft of the prototype device, ultimately deciding to pursue a stage-like platform, rather than a phone case.
- Progress on design of microfluidic chip, still determining the best process to manufacture the chip using different ways to transfer the design onto the copper plates with photo-reactive film. The problems we are having are with the channels being neat and clean enough for the chip to function properly.

WET LAB 17:

Created Standards and processed soil extraction for:
Aluminum, Sulfate, Nitrite, Ferric Iron, Phosphorous and Calcium.

We had multiple issues with test results not being as stable as we had previously thought. Many test had to be redone, which has set us back on working on finishing content for the wiki. Many team members have been working nonstop to get everything re-tested and analyzed!

Week 18

DRY LAB 18:

The final week before Wiki Freeze and we are wrapping things up.
- Adding captions to our images.
- Finalizing Notebook and Human Practices.
- Composing time lapse videos of workflow.
- Compiling data from the spectrometer analyzation and converting it into graphs.
- Using the data to plot points on our installation map. Installation almost finished!

WET LAB 18:

Finalizing protocols for fabrication of microfluidic chip, partial etching of PCB boards providing the best results. Concentrated indicators for pH test to get more visibility in microfluidic channels.