Team:NYU Shanghai/Notebook

Home

Team Members Attributions Description Design Notebook Protocol Results Piezoelectric Notebook Parts Overview Human Practice Collaboration Medal Criteria Competition Results

Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13 Week 14 Week 15 Week 16 Week 17 Week 18&19

In the lab this week: Yuma, Jialu, Siyi, Tiger, Sally

Tasks:

• Make Detailed Proposals/Protocols
• Order Genes (pSoxR/pSoxS)
• Meet Lab instructors to discuss the schedule

[05.29] Wednesday

• Wednesday: 9 AM Meet with Jeffery (Lab Technician)

[05.30] Thursday

• Thursday: Meet with Xu (Lab director)

In the lab this week: Yuma, Jialu, Siyi, Tiger

Tasks:

• Assembly first

[06.06] Thursday

• Weekly Meeting (9am-)
• Washing scales (10am-12pm)
• Made stock solutions: 1L of 1.0M NaCl, 1L of 50mM Tris HCl, 0.5L of 0.5M EDTA, 1L of 0.5M NaOH)

In the lab this week: Yuma, Tiger, Yifan, Siyi, Sally, Sichen, Jialu

Tasks:

• Fabricate Fish scale nanogenerator
• Examination

[06.10] Monday

FSC treatment (Scale, 50mM HCl Tris, 0.5M EDTA, 0.5M NaOH, 1.0M NaCl, Electric leads, silver paste, PP film): One set (step 4 for 15 min) and another sample (~step 3)

FSCNG Fabrication with PP film (Treated fish scale, silver paste, PP film: Only one fabrication

PDMS Fabrication (PDMS elastomer, curing agent, plastic container, hotplate, box knife, cutting mat)

Make more 0.5M EDTA solution (in pH 8 sol) -> 500 mL

  

[06.11] Tuesday

FSCNG Fabrication with PP film (Treated fish scale, silver paste, PP film, adhesive tape (transparent one)) -> silver on one side

FSCNG Examination (Fabricated Scale, voltage/current sensor)

PDMS Fabrication (PDMS elastomer, curing agent, plastic container, hotplate, box knife, cutting mat) -> an oven/dessicator is in Rm 703

  

[06.12] Wednesday

FSCNG Fabrication with PP film (Treated fish scale, silver paste, PP film, adhesive tape (transparent one))

PDMS Fabrication (PDMS elastomer, curing agent, plastic container, hotplate, box knife, cutting mat)

  

[06.13] Thursday

Weekly meeting @ 9:30 AM

FSCNG Fabrication with PP film (Treated fish scale, silver paste, PP film, adhesive tape (transparent one)) -> PP film did not work, PDMS is more stable

FSCNG Examination (Fabricated Scale, voltage/current sensor)

PDMS Fabrication (PDMS elastomer, curing agent, plastic container, hotplate, box knife, cutting mat)

FSC treatment with EDTA -> start from 11:30AM for 24 hours sample

  

[06.14] Friday

Pick up Treated fish scales

PDMS Fabrication (PDMS elastomer, curing agent, plastic container, hotplate, box knife, cutting mat)

FSCNG Examination (Fabricated Scale, voltage/current sensor)

In the lab this week: Yuma, Sally, Yifan, Sichen, Jialu, Siyi

Task:

• FSCNG examination with different EDTA treatment timing
• Examination on Fish scale piezoelectricity in the solution

[06.17] Monday

FSCNG lamination (FSCNG, PDMS uncured agents)

  

[06.18] Tuesday

Voltage exam on FSC with PDMS film -> deltaV = 100mV but skeptical

  

FSCNG Examination with Sounds (FSCNG, voltage/current sensor, capstone software, sound source)

Agar plate preparation (agar, Petri dishes, antibiotics)

  

[06.19] Wednesday

Voltage exam on FSC with PDMS film (fish is treated by EDTA for 24 hrs) Bending: deltaV = 100mV Tapping: deltaV = 100mV Sound: deltaV = 20mV   

E.coli. transformation (LB broth, agar plate, plasmid, competent bacterial cell, shaker, water bath, 37C incubator) - Finish at 4pm

FSCNG fabrication with thin PDMS film (silver paste, FSC, thin PDMS)

  

[06.20] Thursday

Voltage exam on FSC with PDMS film -> it was not very clear if the gold ring touches to the silver paste -> maybe Polypropylene film is better? Tapping: deltaV = 50mV   

Weekly meeting @ 9:30 AM

FSCNG Examination (FSCNG, voltage/current sensor, capstone software, sound source): it was not clear if the gold ring touches the silver paste

Picking up colonies and inoculation (Agar plates with colonies, LB broth, Culture tubes, shaker)

  

[06.21] Friday

Voltage exam on FSC with PP film (deltaV = 20mV)   

FSCNG examination

DNA purification (Shaked culture tube, miniprep kit, nanodrop)

(GFP purification)

(Gel Electrophoresis/SDS-PAGE)

In the lab this week: Yuma, Jialu, Sichen

[06.24] Monday

Voltage exam on FSC with PP film   

• FSC with pp lamination:
1. One FSC: test tapping (using weight)/ soundwave (speaker in the physics lab), compare which one has better impact on the piezoelectricity
2. Four FSC (simply piled up): tapping and soundwave, compare with one FSC

  

[06.25] Tuesday

• FSC with pp lamination:
1. One FSC: test tapping (using weight)/ soundwave (speaker in the physics lab), compare which one has better impact on the piezoelectricity
2. Four FSC (simply piled up): tapping and soundwave, compare with one FSC

  

[06.26] Wednesday

5 pm ~: Colonies picking up & inoculation (transformed cell plate, culture tube, LB media, 37C shaker)

  

[06.27] Thursday

Morning:
Agar Plates Preparation - Amp (100ng/mL), Pyo (2.5uM), Fcn (10uM) with 1% agar plate in 90mm dish.
5PM:
Spread 400ul of E. coli. sample to each plate, agar plates voltage application (0.5V) begins for DH5a and BL21 with BBa_K2862021 (for 16 hrs)

Weekly Meeting @ 9:30 AM

10:30 am~: Agar plate preparation with electrodes/FSC (agar, autoclave, LB powder, antibiotics (pyocyanin, ferricyanide, ferrocyanide)), power supply, long wires

5 pm ~: Agar plate voltage application (potentiostat, transformed cells, positive/negative control agar plate with redox modulators and antibiotics, incubator) -- apply 13 hrs *added 400ul

  

[06.28] Friday

9 AM Results DH5alpha: both with/without electrodes did not glow so much BL21: both with/without electrodes did glow very well except around electrodes.      

Plate fluorescence level examination (voltage applied plate, fluorescence analyzer)

In the lab this week: Yuma, Sally, Frank, Jialu, Sichen, Jessica

Tasks:

• Further examination on pSox Promoter with electrodes and redox modulators
• Design new parts

[07.01] Monday

Discussed what has gone right and what has gone wrong

...
1. NaSO3 was not added -> add it
2. Agar was not covering the graphite electrodes wholly -> dig shallower
3. Introduction of voltage might have been too long -> compare 3hrs, 6hrs, and overnight
4. Ferrocyanide was too much? -> adding Ferricyanide and compare

  

Agar plates preparation

E. coli. Inoculation for BL21 (5 PM)

Read more   

[07.02] Tuesday

Morning:
Agar plates preparation, two 90mm plates for each set (with/without voltage):

Set1: Ferro/Ferri 2.5mM, Amp (100ng/mL), Pyo (2.5uM), sodium sulfite (0.03%)

Set2: Ferri 5mM, Same others

Set3: Ferro 5mM, Same others

*Plate with + sign is the one with voltage, and + sign indicates the positive potential 5 PM:

Inoculate transformed BL21 colonies

  

Agar plates preparation (Na2SO3, agar, autoclave, LB)

E. coli. inoculation (5 PM)

  

[07.03] Wednesday

10 AM: spread 100ul of BL21 in each dish

1 PM: check samples (3hrs): set1, set2, set3

6 PM: check samples (6hrs): set1, set2, set3

Electrodes examination with the different drug (Ferro and ferricyanide) - 3hrs, 6hrs, 20hrs (Thursday morning), 100ul of E.coli cell

1. Set1: Ferricyanide 5mM, pyocyanin 2.5uM, sodium sulfite 0.03%, ampicillin 100ug/ml
2. Set2: Ferrocyanide 5mM, same others
3. Set3: Ferricyanide 2.5mM, Ferrocyanide 2.5mM, same others

  

[07.04] Thursday

9 AM: check samples (23hrs, overnight): set1, set2, set3
Conclusion: They are all glowing at some point, but the dish with Ferri and both are glowing more than the dish with Ferro.

Weekly meeting @ 9:30 AM

Inoculation (11 AM)

Agar plates preparation

1. Set1 & 2: Ferricyanide 10mM, pyocyanin 2.5uM or 0uM, sodium sulfite 0.03%, ampicillin 100ug/ml
2. Set3: Ferrocyanide 10mM pyocyanin 2.5uM, sodium sulfite 0.03%, ampicillin 100ug/ml

Culture tube preparation

1. Set1 & 2: Set1 & 2: Ferricyanide 10mM, pyocyanin 2.5uM or 0uM, sodium sulfite 0.03%, ampicillin 100ug/ml
2. Set3 & 4: Ferrocyanide 10mM pyocyanin 2.5uM or 0uM, sodium sulfite 0.03%, ampicillin 100ug/ml

Spread cells to agar plates and culture tube and incubate (agar: 1.0V electrode, culture tube: shaking without electrodes. NOTE: 200ul of a cell to the plates, 100ul to the tubes

[07.05] Friday

Checking results (16hrs)

Team member Photoshoot

In the lab this week: Jialu, Sichen, Sally, Siyi

Tasks:

• Finish fish scale experiment/modeling/data analysis
• Schedule

[07.09] Monday

Make samples of 1 fish scale / 4 fish scales (pile & spread)

Determine the magnitude of the force we should apply to fish scale

  

[07.10] Tuesday

Knock the fish scale

  

[07.11] Wednesday

Try the soundwave

  

[07.12] Thursday

Weekly meeting @ 9:30 AM

  

[07.13] Friday

Modeling & data analysis

In the lab this week: Tiger

[07.19] Friday

Make agar plates for control (empty pUC57 vector):

• Set1: 5mM Ferri, 2.5uM Pyo, 0.02% Sodium Sulfite, Amp x2
• Set2: 5mM Ferro, 2.5uM Pyo, 0.02% Sodium Sulfite, Amp x2
• Set3: 5mM Ferri, 0.02% Sodium Sulfite, Amp x2
• Set4: 5mM Ferro, 0.02% Sodium Sulfite, Amp x2
• *2 plates for each for with/without electrodes

• make control plates for comparison to make sure target gene is functioning well (Tiger)
• LB Broth autoclave, pour the plates
• 4 plates: 5mM Ferri+ 5mM Ferro+ Pyo +0.02% Na2SO3+ ampicillin (2 with electrodes, two without )
• 4 plates: same but without Pyo

In the lab this week: Shaoting, Tiger

Tasks:

• PUC57 empty vector arrived.
• Transformation of the empty vector into BL21 E.coli
• Culture with/without electrodes, compare

[07.22] Monday

• Morning: Transformation: BL21 + empty pUC57 vector
• 5PM: Culture transformed cells (not the plates with drugs, but the plate with just Amp)

• PUC57 empty vector arrived.
• Transformation of the empty vector into BL21 E.coli
• Culture with/without electrodes, compare

[07.23] Tuesday

4:28pm: 4 sets of E.coli

• Set1: 1ml LB + colony from LB21+ plate + 10μl amp
• Set2: 1ml LB + colony from LB21+ plate + 10μl amp
• Set3: 1ml LB + colony from LB21- plate + 10μl amp
• Set4: 1ml LB + colony from LB21- plate + 10μl amp

• pick up colonies and culture, pour the plates, culture overnight

[07.24] Wednesday

• compare results

In the lab this week: Shaoting, Tiger

Tasks: More control groups to compare with week 9 experiments

[07.29] Monday

• Discussion about the Control experiment

[07.30] Tuesday

• Prepare for the plate and agar

[08.01] Thursday

• Weekly meeting @ 9:30 AM

In the lab this week: Shaoting, Tiger

Tasks: electric shock for 1 hr followed by overnight culturing -> plates with parts worked properly

[08.05] Monday

Making plate for electric culturing: 100ml in total:(100ml dd water + 2.5g agar + 5mM FeCN(O)+ 5mM FeCN(R) + 100μl amp + 0.02g Na2SO3 + 1.25μl pyo)

[08.06] Tuesday

50μl cells + 350μl LB

Culture the cells with electric shock for 1 hr, then culture without electric overnight

[08.08] Thursday

Talked about human practice: we should do NEW APPLICATION TRACK
1. Because our project is focusing on the new application of FSC.
2. Waste management is related to our project because the new application is one of the waste reuse.
3. Additionally, fish scale optimization can be the integrated HP because we will ask supermarkets, local markets, and vendors which fish species is the most wasted and we can determine which one is the most cost-effective one to use in our experiment.

In the lab this week: Tiger
Task: Ordering the relay cell and receiver cell from the company: this week is a waiting period for the genes to arrive

In the lab this week: Tiger

Tasks:

• Verify New parts
  • GFP phenotype after the electric shock (1hr)
  • Protein purification after the electric shock (1hr)
    1. Coomassie-stained SDS-PAGE gel

[08.29] Thursday

• Meeting
  1. Deadlines: track selection, abstract due
  2. Poster: print in NYC
  3. HP
     • research part… ask experts for modeling of collagen
     • (optional) decoration… ask local markets which fish scale is most cost-effective in terms of our result of our experiment.

In the lab this week: Tiger

• Transform the relay cell and receiver cell gene from the company
• Preparation for co-culture task to see the quorum sensing effect

[09.03] Tuesday

• Check the result

[09.05] Thursday

• Prepare the agar plate and the gel
• Doing transformation, apply on the plate, overnight culturing

[09.06] Friday

Transformation for two parts (relay cell and receiver cell), we successfully get a single colony which means the transformation is a success.

• Check the results, stored at 4 ℃

In the lab this week: Tiger

[09.09] Monday

Conducted liquid culture incubation (inoculation), amplified the transformed cell for future experiment, we have: co-culture tube A, co-culture tube B, relay cell, receiver cell, puc57 empty vector,and empty control, the empty control didn’t have bacteria, which means the incubation is success

[09.10] Tuesday

Making plate for electric culturing: 200ml in total (200ml dd water + 8g LB-agar + 5mM FeCN(O)+ 5mM FeCN(R) + 100μl amp + 0.02g Na2SO3 + 2.5um pyo)

Sets we have:

• co-culture in liquid (+elec+pyo+Fe)
• co-culture in liquid (-elec+pyo+Fe)
• co-culture on plate: (add relay cell and receiver cell separately on one plate)(+elec+pyo+Fe)
• only receiver (cell+elec+pyo+Fe)
• only receiver cell (-elec+pyo+Fe)
• only relay cell (-elec+pyo+Fe)
• Puc57 empty vector (+elec+pyo+Fe)
• Puc57 empty vector (-elec+pyo+Fe)

[09.12] Thursday

Results: no single colony - Maybe applied too much liquid bacteria on the plate?

Result: no glowing for co-culture: (LEFT is the one with two parts; RIGHT is only imperial college part)

In the lab this week: Tiger

Tasks:

1. Confirm the transformation is okay
   • Check whether (only) receiver cell colonies glow
   • Plasmid purification -> Nanodrop
   • using microscope to check the GFP
2. Prepare for the protein purification and SDS-PAGE
Redo the co-culture part
Do the culture without electrode, find the best density of the plasmid solution

[09.16] Monday

Culturing the cell under RT for over 72 hours

See the receiver cell glow(+elec) and see the co-culture one glow(-elec), but apply too much on the plate, it’s hard to scrape a single colony.

• Check the result, talk with Wenshu and Lina
• Scrap single colony, do liquid incubation

[09.17] Tuesday

• Prepare SDS-PAGE agar, Electrophoresis gel
• Using GFP microscope to check the GFP
• Prepare more plate, liquid culture the transformed cell for further experiment
• Using GFP microscope to check the GFP

[09.18] Wednesday

Set up a lot of plate to see the best concentration for growing single colony Sets we have: 20X,10X, 5X, 2X receiver cell(dilute to 100ul,-elec + pyo and Fe) 20X,10X, 5X, 2X co-culture cell(co-culture on plate)(dilute to 100ul,-elec + pyo and Fe)

[09.19] Thursday

Results from last night: 20X dilute set is still blurry, can see the GFP only on receiver cell

Set up more diluted concentration gradient sets: 50X 100X 500X 1000X receiver cell (+pyo +Fe -elec) and 50X 100X 200X 300X 500X 1000X co-culture on plate cell(same condition)

• Redo the co-culture part incubate overnight
• Do the Electrophoresis

[09.20] Friday

As we can see, 1000X dilute can see some small single colony, but the colony is too small, I have no idea how to scrape one.

• Check the results, to see the best culture time
• Check the Electrophore