Difference between revisions of "Team:NCHU Taichung/js/protocol.js"

Revision as of 15:56, 16 October 2018 (view source) YoYodeTW (Talk | contribs) ← Older edit		Latest revision as of 04:59, 17 October 2018 (view source) YoYodeTW (Talk | contribs)
Line 118:		Line 118:
	]		]
	},		},
		+	{
		+	"title": "MTT assay",
		+	"content": [
		+	"Plate 1.5x10 4 cells per well in a 96-well plate and incubate with the appropriate stimulus for the desired time (usually 6-48 hours).",
		+	"Remove medium and wash cells with PBS.",
		+	"Add 100 µL of desired drugs or compound in each well.",
		+	"Incubate for 6 to 12 hours at 37°C.",
		+	"Remove the compound and add MTT made up in medium to a final concentration of 0.5 mg/mL.",
		+	"Incubate for 2 to 6 hours at 37°C, until intracellular purple formazan crystals are visible under microscope.",
		+	"Remove MTT and add DMSO.",
		+	"Incubate at room temperature, until cells have lysed and purple crystals have dissolved.",
		+	"Measure absorbance at 595 nanometers."
		+	]
		+	},
	{		{
	"title": "Medium",		"title": "Medium",

---

Latest revision as of 04:59, 17 October 2018

let protocols = [

 {
   "title": "Cultivation of Arabidopsis thaliana seeds",
   "content": [
     "Use 3D Micro Shaker to shake seeds for 15 minutes with 20%/ bleach +1/1000 SDS (Tween20)",
     "Remove bleach completely and add sterile water to wash three times",
     "Storage at 4℃ for 4-7 days for Seed vernalization.",
     "Pipette 100 μl of water and seeds to solid 1/2 M.S medium.",
     "Seeds should be cultivated into plates in enough spaces to grow (Each plate should have 15-18 seeds)",
     "Tilt plates and remove excess water",
     "Seal the plates with parafilm",
     "Put plates to growth chamber at constant temperature of 25 ± 2 ° C with 16/8 h light and dark cycle"
   ]
 },
 {
   "title": "Inoculation",
   "content": [
     "take 8-day plants",
     "choose healthy plants which have complete roots ",
     "Holding plant hypocotyls with tweezers and put plants in the cover of plate",
     "Add proper amount bacteria of OD600=0.4 to cover whole roots and sink 1minutes.",
     "Wash excess bacteria by sterile water for 1-2 second then put plants into new solid M.S medium. (For the test of how long the bacteria could stay in plants and the test of phenotype after inoculating)",
     "Seal the plates with parafilm ",
     "For endophytic test, do further experiment"
   ]
 },
 {
   "title": "Endophytic test",
   "content": [
     "sterilized tools: tweezers(label A、B)、ddH2O、Glass Bead、Disposable pestle",
     "prepared three plates of sterile water(label 1、2、3) and a plate of 10%bleach and a plate of 75% ethanol.",
     "Before picking plants, sterile tweezers by alcohol burner or fuego basic then wait it to cool down.",
     "Put 3 inoculated plants into 10% bleach at the same time, timing 1 minutes
Use tweezer A to take plants out the put back to 75% ethanol, timing 30 seconds
Use tweezer A to take plants out the put back to sterile water1, timing 30 seconds
Use tweezer B to take plants out the put back to sterile water2, timing 30 seconds
Use tweezer B to take plants out the put back to sterile water3, timing 30 seconds
Use tweezer B to take plants out the put to labeled eppendorf
Repeat above-mentioned steps for different OD600 but the same species.
Take 100ul of sterile water3 to LB medium as the control group",
     "renew sterile water1、2、3、ethanol and bleach for different bacteria species experiment",
     "After grinding plants by disposable pestle, use 200ul pipette to drop 100ul to LB medium",
     "Pour glass beads then shake horizontally to make fluid spread",
     "Pour glass beads out to waste bottle.",
     "Growth bacteria in proper temperature and wait 12-16 hours."
   ]
 },
 {
   "title": "Cloning (3A and Gibson Assembly)",
   "content": [

"PCR<tbody></tbody>

KOD plus polymerase	1 μl
dNTP	2 μl
10XBuffer	2 μl
Forward Primer	1 μl
Reverse Primer	1 μl
MgSO4	2 μl
DNA	1 μl
H2O	10 μl

", "Restriction Enzyme Digestion

Restriction enzyme : EcoRI , XbaI , SpeI , PStI

<tbody></tbody>

NEB restriction enzyme	(1μl enzyme can react with 1 μg DNA)
DNA
10x Cutsmart buffer	2 μl
Add H2O	to 20 μl

", "Gel extraction THERMO Gel extraction

1. Excise gel slice containing the DNA fragment using a clean scalpel or razor blade
2. Put into Eppendorf (remember to keep the gel weight in 100-200mg)
3. Add equal volume of binding buffer , vortex
4. Incubate it until all the gel is dissolved in the buffer
5. Transfer all the solution to the purification column then centrifuge for 15,000rpm, 1min
6. Discard the flow-through and add 100μl binding buffer then centrifuge for 15,000rpm, 1min
7. Discard the flow through and add 700μl wash buffer then centrifuge for 15,000rpm, 1min
8. Discard the flow through and repeat (7) process
9. Discard the flow through and centrifuge for 15,000rpm, 7 min
10. Transfer the purification column to the 1.5ml eppendorf
11. Incubate it in 50-55℃ for 10 min
12. Add 20μl H₂O (prewarm) or Elution buffer into the center of the column and wait for 2-3 min
13. Centrifuge for 15,000rpm, 7 min
14. Use nanodrop to quantify the nucleic acids’ concentration

", "DNA clean up (after cutting, if the residue is in 5-8bp you can use DNA clean up) Genemark DNA clean up kit

1. Add 3 volumes of binding buffer, mix completely
2. Transfer the solution into purification column, centrifuge for 1 min in top speed
3. Discard the flow-through and add 700μl of wash solution, centrifuge for 1 min in top speed
4. Discard the flow-through and repeat step (3)
5. Centrifuge for 7 min in top speed
6. Incubate in 50-55℃
7. Add rewarmed H₂O or elution buffer into the center of the column, wait for 2-3 min
8. Centrifuge for 7 min in top speed
9. Use nanodrop to quantify the nucleic acids’ concentration

", "Ligation Promega T4 ligase

1. Calcμlate the vector and insert ‘s ratio $${ng\\ of\\ vector\\times\\ kb\\ size\\ of\\ insert\\times molar\\ ratio\\ of\\ insert\\over kb\\ size\\ of\\ vector\\ vector} = ng\\ of\\ insert$$vector : insert = 1 : 3 is quite optimal
2. Add 10X buffer
3. Add T4 ligase
4. Add H₂O till 20μl in total volume
5. Put it in 4℃ overnight or 22℃ for 3 hr

", "Transformation Use DH5alpha E.coli comercial competent cell

1. Add 10μl DNA into 40 μl competent cell
2. Put it on the ice for 20-30min
3. 42℃ heat shock
4. Put it back onto the ice for 3 min
5. Add 250 SOC medium and 37℃ incubate for 1 hr
6. Plate all of the transformation and equally distribute it onto a 10 cm LB agar plate containing the appropriate antibiotic
7. 37℃ incubate overnight

", "Gibson assembly

1. 2–3 Fragment Assembly DNA 0.02-0.5 pmols, Gibson Assembly Master Mix 10μl, Add H₂O to 20μl in total volume
2. Incubate in 50℃ for 15 min when 2-3 fragment assembly, store on ice or in -20℃ for transformation

"

   ]
 },
 {
   "title": "Protein Preparation and Extraction",
   "content": [
     "overnight culture of recombinant strains was inoculated into 500 mL of fresh LB medium at 37°C, 200 rpm",
     "Until the optical density at 600 nm was 0.8 to 1.0, 1 mM IPTG was added, and the culture was allowed to grow for another 3 to 12 h.",
     "500 mL cells were centrifuged (11,000 x g, 4 °C and 15 min).",
     "The pellet was washed twice with (50mM Tris-Hcl , 0.3M Nacl pH 7.4), and centrifuged at 10000 x g, 4 °C for 10 min.",
     "The cells were then re-suspended in 30 mL of the same buffer, and maintained at 0 °C for sonication.",
     "Unbroken cells and cell wall materials were removed by centrifugation at 22000 x g, 4°C for 30 min",
     "the supernatant was decanted and kept at 4 °C."
   ]
 },
 {
   "title": "protein purification(Immobilized Metal Affinity Chromatography)",
   "content": [
     "use the supernatant from protein preparation step for binding with cobalt column for 20 min",
     "wash with wash buffer (50Mm Tris-Hcl, 0.3M Nacl pH7.4)",
     "elut with elution buffer (50Mm Tris-Hcl, 0.3M Nacl , 0.5M imidazole pH7.4 )",
     "run SDS-Page to check protein purity"
   ]
 },
 {
   "title": "Inoculation of Chrysopogon zizanioides (vetiver plant) with endophytic bacteria",
   "content": [
     "Transplant vetiver plants from field to greenhouse and grow them under same settings for 30 days.",
     "Inoculate vetiver plants by soaking their roots in inocula which were prepared with the isolate Burkholderia cenocepacia 869T2 for 10 minutes.  The inocula were grown under selective conditions at 37 °C on a rotary shaker to an approximate A600nm value of 1.0.",
     "Plant inoculated vetiver plants in pot with TCDD free matrix (control plates).",
     "Likewise, plant inoculated vetiver in the pot with  matrix contain TCDD (TCDD solution was added into the vetiver plants potting matrix and adjust the concentration of TCDD in the matrix to 100 ng-TEQ/ kg.)",
     "Vetiver plants were grown in greenhouse under same settings for 30 days.",
     "Harvest these vetiver plants after 30 days. "
   ]
 },
 {
   "title": "The Growth of Recombinant Bacteria in TCDD Medium",
   "content": [
     "Incubate the recombinant bacteria 12~18 hours without TCDD.",
     "Prepare for the treatment medium (low concentration  of King's B medium) with antibiotics, surfactant Tween 80 (0.1%(v/v)), and different concentrations of TCDD (0ppm, 0.05ppm, 0.1ppm, 0.2ppm) in the 96 wells microplate.",
     "The fresh cultures of recombinant strains are added into the microplate with the OD600nm value 0.05.",
     "The cultures are incubated at 37°C, double orbital shaking in fast speed, and monitor by measuring the OD600nm.",
     "After 2~3 hours, the OD600nm value is about 0.6, add 1mM IPTG if needed."
   ]
 },
 {
   "title": "Preparation of competent cells for endophyte",
   "content": [
     "A frozen glycerol stock of bacteria is picked with a toothpick and spread on a KB agar plate. Place plates inverted at 28 °C for 2-3 days in the dark.",
     "Freshly grown colony is inoculated to 5 ml of LB medium in a 15 ml tube and further incubated at 28 °C for 16 h with horizontal shaking at 200 rpm.",
     "1 ml aliquots is centrifuged twice at 3,500 x g at 4 °C for 5 min.",
     "Each time the pellet is dissolved in 1 ml of filter sterilized and room temperature 300 mM sucrose solution.",
     "The pellet is dissolved in 200 μl of 300 mM sucrose solution and divided into 100 μl aliquots and used the cells immediately for a further transformation step."
   ]
 },
 {
   "title": "Transformation for endophyte",
   "content": [
     "Add ~1 μg of vector into bacteria.",
     "Transfer the mixture of cells + DNA to an electroporation cuvette (0.1 cm electrode gap). Make sure the suspension is at the bottom of the cuvette.",
     "Set the Gene Pulser apparatus at 25 μF the volt at 1.8 kV. Set the Pulse resistance controller to 200 ohms.",
     "Place the cuvette in the chamber slide (Cuvette notch facing away from you).",
     "Push the slide into the chamber until the cuvette is seated between the contacts in the base of the chamber.",
     "Electroporate by pushing the red button.",
     "Remove the cuvette from the chamber and immediately add 1 ml of LB medium to the cuvette and quickly resuspend the cells by pipetting.",
     "Transfer the cell suspension from the cuvette to 1.5 ml tubes and incubate on shaker (200 rpm) at 28 °C for 2 h to allow recovery and expression of the gentamycin resistance marker (Clean cuvettes successively with dH 2 O, EtOH, sterile water, then wrap with aluminum foil then autoclave).",
     "Pipette 200 μl of each transformation on KB agar plates containing 25 ng/ml gentamycin.",
     "Spread the cells with cell spreaders. Place plates inverted at 28 °C for 2-3 days in the dark."
   ]
 },
 {
   "title": "MTT assay",
   "content": [
     "Plate 1.5x10 4 cells per well in a 96-well plate and incubate with the appropriate stimulus for the desired time (usually 6-48 hours).",
     "Remove medium and wash cells with PBS.",
     "Add 100 µL of desired drugs or compound in each well.",
     "Incubate for 6 to 12 hours at 37°C.",
     "Remove the compound and add MTT made up in medium to a final concentration of 0.5 mg/mL.",
     "Incubate for 2 to 6 hours at 37°C, until intracellular purple formazan crystals are visible under microscope.",
     "Remove MTT and add DMSO.",
     "Incubate at room temperature, until cells have lysed and purple crystals have dissolved.",
     "Measure absorbance at 595 nanometers."
   ]
  },
 {
   "title": "Medium",
   "content": [
     "Solid M.S medium:
4.4g/L MS Murashige and skoog Basal Medium (store at 4° C fridge), 1.5 % Sucrose, and 0.8% agar, use HCl or KOH to adjusted pH to 5.7. autoclaved at 120°C for 20 mins.",
     "Low concentration of King's B medium:
Peptone: 6g/L; K2HPO4: 1.5g/L; Glycerol: 7.5 ml/L; 5ml/L 1M MgSO4",
     "LB medium:
NaCl: 10g/L; Tryptone: 10g/L; Yeast Extract: 5g/L"
   ]
 }

]; let $accordion = $('.accordion'); // $.getJSON("./data/protocols.json", (file) => { // protocols = file; console.log(protocols); protocols.forEach((ptc) => {

 let templateString = $('#articleTemplate').html();
 let template = $(templateString);
 title = template.siblings('.title');
 content = template.siblings('.content');
 ptitle = title.find('span');
 ptitle.append($.parseHTML(ptc.title));
 $accordion.append(title);
 olTag = content.find('ol');
 _content = "";
 ptc.content.forEach(step => {

_content = _content + `

${step}

`

 });
 olTag.append(_content);
 $accordion.append(content);

}) $('.accordion').accordion('open', 0); $('#articleTemplate').remove();