Revision as of 21:18, 19 October 2019

Phage infection assay · Benchling

Phage infection assay

Project: Phage multiplication

Authors: iGEM_GO_Paris_saclay

Tuesday, 16/7/2019

AIM: As a first step in proving the RNA World concept, we wanted to create an “RNA cell”, in which replicating RNA, rather than DNA, would be the support of genetic information.

Principle: In order to carry out this substitution of DNA, we clone and expresse 3 nucleases: A1, gp3 and yqcg and see if they can efficiently degrade bacterial DNA. In addition to these nucleases, we infecte the cells by the MS2 phage and produce new virions, which would result from the replication of RNA and its translation into proteins, since MS2 is an positive-sense single-stranded RNA phage.

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MS2 phage titration : Hugues

Incubate K12 Hfr in 5mL LB-amp (0,2%) initial OD600=0,1 at 37°C

Cultivate with agitation to OD600=0,8

Melt agar, add CaCl2 and MgCl2 (1mM final), keep the mix at 42°C

Pour 3mL agar-CaCl2-MgCl2 in sterile glass tubes

Add 100µL bacteria (K12 Hfr) + 100µL MS2 phage

Pour the 3mL agar(CaCl2-MgCl2-bacteria-phage on the LB plate, spread the mix

Incubate at 37°C

Thursday, 18/7/2019

MS2 infection : Hugues

KeioZ1, KeioZ1 F' MoClo, KeioZ1 F' A1, KeioZ1 F' T7

Dilute these 4 strains in LB (amp if necessary) in 12 mL LB at 0D600=0,1

Add CaCl2 and MgCl2 (1 mM final)

Incubate at 37°C with agitation (200rpm) to OD=0,4

40min after the incubation of the 4 strains, dilute K12 Hfr strain in 12mL LB at OD=0,1 (no CaCl2, MgCl2)

When Keio strains are at OD=0,4, add arabinose (0,2% final) and incubate at 37°C for 30min

Mesurate OD600 then add phage volume equals to : V(µL) = [5*vol culture bacteria (in mL)*OD600*5*10^8]/phage concentration

-> OD600 30min after arabinose

	A A	B B	C C
1 1	KeioZ1	0,65	466,5µL
2 2	KeioZ1 F' MoClo	0,78	559,8
3 3	KeioZ1 F' A1	0,49	551,7
4 4	KeioZ1 F' T7	0,56	401,9

Table7

Take off 0,5mL of bacteria at time 0, 1 hour, 2h and 18h. Take OD600 for each culture

	A A	B B	C C	D D	E E
1 1		t0	t1h	t2h	t18h
2 2	KeioZ1	0,65		2,6	4,5
3 3	KeioZ1 F' MoClo	0,78		0,47	2,7
4 4	KeioZ1 F' A1	0,49		0,51	1,6
5 5	KeioZ1 F' T7	0,56		0,40	0,6

Table8

With the 0,5mL, centrifugate at 13000rpm 5 min

Take off 180µL of the supernatant, put in a microplaque

Dilute 10 fold in series the supernatant (20 in 180) (No dilution to 10^-9)

Prepare 3mL soft agar (3mL for each LB plate needed)(50% solid LB + 50% liquid LB + 1mM CaCl2 + 1mM MgCl2, 100µL K12 Hfr (at OD=0,4))

Pour the 3mL onto LB plate

Once soft agar dry out, drop off 5µL of each dilution (+ND) on LB + soft agar plate. 37°C

Friday, 19/7/2019

MS2 phage stock : Hugues

Add 10mL phage buffer to a phage titration plate with lysis range. Incubate the Petri dish at room temperature 24h then repipette the phage buffer, filtrate it then stock the MS2 phage stock at 4°C.

The MS2 phage stock has to be titrated.

Tuesday, 23/7/2019

MS2 phage infection : Hugues

Start a culture of KeioZ1, Z1 F' MoClo, Z1 F' A1, Z1 F' T7 in 12mL LB (+amp if necessary) + 1mM CaCl2 + 1mM MgCl2 at OD600=0,1 then incubate at 37°C

Start the culture of K12 Hfr in 12 mL LB 30/40min after the first culture

Wednesday, 31/7/2019

See the protocol "Infection assay" below.

Protocol-phage-infection1.docx

Precultures of LB plus 10µL of ampicilline and 100µL of glucose (except for KEÏO Z1 and Hfr) were used to inoculate 10 mL of each of our strains. 583 µL of preculture A1 was put into 15mL of LB, 600µL of MoClo, 588µL of T7 and 619µL of Keio Z1.

The CACL2, MgCl2 were added after 30min of culture.

The final OD600nm used for the infection were:

	A A	B B	C C	D D	E E
1 1	Strains names	KEIO Z1	MoClo	A1	T7
2 2	OD 600nm	0.5	0.35	0.42	0.32

Table1

According to the formula from the protocol, the amount of phages used was with a concentration of 4.18*10^5 PFU/mL:

○

Keio Z1 : 281 µL in 10ml medium plus bacteria

○

MoClo: 263 µL

○

A1: 275 µL

○

T7: 233 µL

Hfr cells had an OD_600nm of 0,79 when they were poured into soft Agar containing 1mM of CaCl2 and MgCl2.

Serial dilutions started from 10^-1 to 10^-9, 20µL of undiluted supernatant was put into 180µL of phage buffer.

The ODs were taken for 0min, 60 min and 120 min:

	A A	B B	C C	D D	E E
1 1	Strains	OD 600nm Keïo Z1	OD 600nm Keïo Z1 F' pBAD24-MoClo1	OD 600nm Keïo Z1 F' pBAD24-A1	OD 600nm Keïo Z1 F' pBAD24-T7
2 2	T=0min	0.28	0.28	0.28	0.2
3 3	T=60min	0.8	0.7	0.58	0.29
4 4	T=120min	1.4	0.69	0.55	0.21
5 5	T= Day after	3.1	2	0.9	2.16

OD600nm every 1 hour for MS2 infection and the day after

HFR stayed all night long on table and then mixed with soft agar for the last time point (day after).

Bacteria and phages mix wasn't put at 37°C in LB + ARA directly, stayed in ice

Results of the infection assay :

Phage titration & infection 01082019- corrected Laetitia.xlsx

Friday, 2/8/2019

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Phage infection (Clara_Arnaud)

Results: the point "day after" wasn't good, couldn't count anything, maybe because of the HFR stayed all night long on the bench.

Thursday, 8/8/2019

See the protocol "Infection assay"

Precultures of LB plus 20µL of ampicilline and 200µL of glucose (except for KEÏO Z1 and Hfr) were used to inoculate 20 mL of each of our strains. 769 µL of preculture A1 and MoClo was put into 15mL of LB, 741µL of T7 and 667µL of Keio Z1.

The CACL2, MgCl2 were added at a final concentration of 1mM.

The final OD600nm used for the infection were:

	A A	B B	C C	D D	E E
1 1	Strains name	KEIO Z1	MoClo	A1	T7
2 2	OD 600nm	0,41	0,49	0,42	0,38

Table2

According to the formula from the protocol, the amount of phages used was with a concentration of 4.18*10^5 PFU/mL:

○

Keio Z1 : 294 µL in 20ml medium plus bacteria

○

MoClo: 352 µL

○

A1: 301 µL

○

T7: 273 µL

After 1hour in ice, LB + 0,2% arabinose and 100 µg/µL of ampicilline was added to the mix of phages and bacteria. Normally, the strain KEIO Z1 shouldn't have received Ampicilline since it is sensitive to it.

Hfr cells had an OD_600nm of 0,67 when they were poured into soft Agar containing 1mM of CaCl2 and MgCl2.

Serial dilutions started from 10^-1 to 10^-9, 20µL of undiluted supernatant was put into 180µL of phage buffer.

The ODs were taken for 0min, 20min, 40min,60 min, 80 min, 100 min and 120 min:

	A A	B B	C C	D D	E E
1 1	Strains	OD 600nm Keïo Z1	OD 600nm Keïo Z1 F' pBAD24-MoClo1	OD 600nm Keïo Z1 F' pBAD24-A1	OD 600nm Keïo Z1 F' pBAD24-T7
2 2	T=-60min	0.41	0.49	0.42	0.38
3 3	T=20 min	0.54	0.64	0.58	0.33
4 4	T=40min	0.38	0.87	0.56	0.23
5 5	T=60min	0.25	0.94	0.55	0.15
6 6	T=80min	0.22	0.5	0.59	0.15
7 7	T=100min	0.15	0.27	0.59	0.11
8 8	T=120min	0.14	0.23	0.57	0.1

Table3

Results of the infection assay :

Phage titration & infection.xlsx

For the ODs 600nm, these results weren't expected, we don't know what went wrong --> look for it.

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Titration of Ms2 phage (Laetitia)

Phage has been titrated by folowing Titration phage protocol.

100 μL of a 1 mL 10^-5 to 10^-9dilution has been plated.

Results :

	A A	B B	C C	D D	E E	F F	G G
1 1		10-5	10-6	10-7	10-8	10-9	Phage titration
2 2	Phage already titrated at 4.10^10 phage/mL	non exploitable	confluent	88	12	4	8,8.10^9
3 3	Phage with unknown titration	Confluent	Not down	Not down	8	Not down	8.10^9 ?

Table4

Friday, 9/8/2019

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Glycerol stock of Hfr and KeioZ1 : Arnaud

Glycerol stock 0.5ml (333.4 µL bacterial culture and 166.6 µL Glycerol 60%)

Tuesday, 13/8/2019

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Preparation of the experiment (Clara)

220 mL of soft agar without MgCl2 and CaCl2 was prepared and put at 60°C overnight

Hfr and KeïoZ1 strains were precultured into 3ml of LB.

Keïo Z1 F' cells containing the following plasmids were precultured into 3 mL of LB plus ampicilline (Cf=100µg/µm) and 0.2% glucose

-pBAD-A1

-pBAD-T7

-pBAD-B.subtilis

-pBAD-MoClo

Wednesday, 14/8/2019

The soft agar which was made the day before had a little thing inside, then we were suspicious about contamination. So we made another one.

See the protocol "Infection assay" for more precise information.

Precultures of LB plus 20µL of ampicilline and 200µL of glucose (except for KEÏO Z1 and Hfr) were used to inoculate 20 mL of each of our strains. 541 µL of preculture A1 and 435 µL of preculture MoClo , 741µL of T7, 667µL of Keio Z1 and 667 µL of B. subtilis were put into 20mL of LB.

The CACL2, MgCl2 were added at a final concentration of 1mM.

The final OD600nm used for the infection were:

	A A	B B	C C	D D	E E	F F
1 1	Strains name	KEIO Z1	MoClo	A1	T7	B. subtilis
2 2	OD 600nm	0,4	0,48	0,50	0,34	0.26

Table5

According to the formula from the protocol, the amount of phages used was for a concentration of 8.8*10^9 PFU/mL :

○

Keio Z1 : 409 µL in 20ml medium plus bacteria

○

MoClo: 464 µL

○

A1: 511 µL

○

T7: 348 µL

○

B. subtilis: 266 µL

After 30 min in ice, LB + 0,2% arabinose + 100 µg/µL was added to the mix of phages and bacteria. Normally, the strain KEIO Z1 shouldn't have received Ampicilline since it is sensitive to it.

Hfr cells had an OD_600nm of 0.42 when they were poured into soft Agar containing 1mM of CaCl2 and MgCl2.

Serial dilutions started from 10^-1 to 10^-9, 20µL of undiluted supernatant was put into 180µL of phage buffer. In the same time, 400 µL of the remaining supernatant was put into another tube with 4 µL of chloroform in order to spread it on another plate. This way, we can spread more than a 5 µL drop and get better results for PFU/mL.

The ODs were taken for 0min, 30 min, 60min, 90 min and 120 min:

	A A	B B	C C	D D	E E	F F
1 1	Strains	OD 600nm Keïo Z1	OD 600nm Keïo Z1 F' pBAD24-MoClo1	OD 600nm Keïo Z1 F' pBAD24-A1	OD 600nm Keïo Z1 F' pBAD24-T7	OD 600nm Keïo Z1 F' pBAD24-B. subtilis
2 2	T=0min	Unexploitable results	0.29	0.34	0.22	0.18
3 3	T=30 min		0.66	0.59	0.22	0.29
4 4	T=60min		0.85	0.6	0.16	0.25
5 5	T=90min		0.31	0.58	0.11	0.26
6 6	T=120min		0.31	0.6	0.13	0.25

Table6

Results of the infection assay :

	A A	B B	C C	D D	E E	F F
1 1		Time (min)
2 2	Strain name	0	30	60	90	120
3 3	MoClo	10^-5	10-4	10^-7	10^-7	10^-7
4 4	A1	10-4	10-4			10^-5/ 10^-6
5 5	T7	10-4	10-4	10^-6	10^-5/ 10^-6	10^-6/10^-7
6 6	B.subtilis	10-4/10-5	10^-5	10^-7	10^-5/ 10^-6	10^-5/ 10^-6

Dilutions where we can count lysis ranges

We can generally count lysis ranges between dilution 10^-4 and 10^-7.

OD results:

Phage titration & infection.xlsx

We can see that the optic density for pBAD-MoClo drops after 60min of infection, like the previous experiment. While OD 600nm for pBAD-T7 & A1 increase for 30 min of infection and then remain stable. Finally, pBAD-B.subtilis OD 600nm remain stable for 30 min of infection and after start to decrease slowly.

Tuesday, 20/8/2019

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Preculture of colonies for phage infection

Incubate Keio Z1F, K12 Hfr in 5mL LB at 37°C. Incubate Keio Z1F' pBAD-MoClo, KeioZ1F' pBAD-A1, KeioZ1F' pBAD-T7, Keio Z1F' pBAD-B. sub in 5mL LB+amp(100ug/ml)+glu(0,2%) at 37°C.

Wednesday, 21/8/2019

●

Phage infection

Dilute each strain (K12 Hfr included) at OD600 = 0,1 in LB +CaCl2(1uL/mL) + MgCl2(1uL/mL) (+amp if necessary), incubate at 37°C.

During bacterial growth, prepare soft agar (50% solid agar + 50% liquid agar + CaCl2(1uL/mL) + MgCl2(1uL/mL)).

Once the indicator strain K12 Hfr reaches an OD=0,4-0,8, add 100µL of K12 Hfr into the soft agar.

Pour 3mL of soft agar+K12 Hfr on top of LB plates.

Once the culture reach to OD600=0,4, add arabinose (0,2% final), incubate at 37°C for 5 minutes.

Add the volume of phage equals to : V(mL) = (5* volume (mL) of bacteria culture * OD * 5*10^8)/phage concentration.

Extract immediately 0,5mL of culture for phage titration, this correspond to the timepoint 0, mesure the OD of the culture and reincubate the culture at 37°C.

Extract 0,5mL of culture at t=30min, t=60min and t=120min.

	A A	B B	C C	D D	E E	F F	G G
1 1	Time (min)	KeioZ1	KeioZ1 F' pBAD_MoClo	KEIOZ1 F' pBAD_A1	KeioZ1 F' pBAD_T7	KeioZ1 F' pBAD_B.sub
2 2	0	0.55	0.51	0.4	0.38	0.5
3 3	120	1.84	1.34	0.75	0.3	0.69
4 4	Volume of phages to add (MOI = 5)	394,7	366,0	287,1	272,7	358,9
5 5
6 6
7 7

OD600 + volume of phage for infection assay

For each timepoint, centrifugate the 0,5mL of culture at max speed for 5min.

Prepare 10-fold serial dilutions of the supernatant in phage buffer (10^-1 to 10^-9).

Add 4µL of chloroform to remaining supernatant, stock phages in chloroform at 4°C.

Spot 5uL of the undiluted supernatant and its serial dilutions onto a plate with top agar + K12 Hfr.

Incubate every plate at 37°C.

Phage titration infection 21082019.xlsx

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Preculture of colonies for phage infection

Incubate K12 Hfr in 5mL LB at 37°C.

Thursday, 22/8/2019

Identify the maximum dilutions which permit to get lysis ground.

	A A	B B	C C
1 1	Replicate	1	2
2 2	KeioZ1	10^-5
3 3	KeioZ1 F' MoClo	10^-5	10^-5
4 4	KeioZ1 F' A1	10^-5	10^-5
5 5	KeioZ1 F' T7	10^-6	10^-6
6 6	KeioZ1 F' B. subtilis	10^-6	10^-6
7 7

t=0

Prepare soft agar with CaCl2 (1mM final) and MgCl2 (1mM final).

Dilute K12 Hfr at a OD600=0,1 in LB, wait until OD600=0,5.

Add 100uL of K12 Hfr and 100uL of phages in 3mL soft agar. Each phage dilutions were stocked in chloroform (August, 21th).

Phages come from the chloroform-conserved-phages .

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Preculture of colonies for phage infection

Incubate Keio Z1F, K12 Hfr in 5mL LB at 37°C. Incubate Keio Z1F' pBAD-MoClo, KeioZ1F' pBAD-A1, KeioZ1F' pBAD-T7, Keio Z1F' pBAD-B. sub in 5mL LB+amp(100ug/ml)+glu(0,2%) at 37°C.

Friday, 23/8/2019

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Phage infection : Hugues_Natacha

Dilute each strain (K12 Hfr included) at OD600 = 0,1 in LB +CaCl2(1uL/mL) + MgCl2(1uL/mL) (+amp if necessary), incubate at 37°C.

During bacterial growth, prepare soft agar (50% solid agar + 50% liquid agar + CaCl2(1uL/mL) + MgCl2(1uL/mL)).

Once the indicator strain K12 Hfr reaches an OD=0,4-0,8, add 100µL of K12 Hfr into the soft agar.

Pour 3mL of soft agar+K12 Hfr on top of LB plates.

Once the culture reach to OD600=0,4, add arabinose (0,2% final), incubate at 37°C for 15 minutes.

Add the volume of phage equals to : V(mL) = (5* volume (mL) of bacteria culture * OD * 5*10^8)/phage concentration.

Extract immediately 0,5mL of culture for phage titration and 1mL of culture for gDNA extraction. This correspond to the timepoint 0, mesure the OD of the culture and reincubate the culture at 37°C.

Extract 0,5mL of culture at t=30min, t=90min, t=120min and t=150min.

For each timepoint, centrifugate the 0,5mL of culture at max speed for 5min.

Prepare 10-fold serial dilutions of the supernatant in phage buffer (10^-1 to 10^-9).

Add 4µL of chloroform to remaining supernatant, stock phages in chloroform at 4°C.

Spot 5uL of the supernatant serial dilutions onto a plate with top agar + K12 Hfr.

Incubate every plate at 37°C.

●

Genomic DNAs of bacteria infected by phages

At different time points (t0, t30, t90, t120, t150) of the phage infection, 1ml of bacterial culture with phage is withdraw. This is done for the four conditions : A1, T7, Moclo and B.sub. The kit used to quantify the genomics DNA of infected bacteria is "QIAamp DNA Blood Mini Kit (50)" from Qiagen. The protocole is "DNA Purification from Tissues" page 32. We started at step 3. Step 1, 2(a, b, c) and 5a are not done. The elution step is done only one time with 200µL of buffer AE. The final solutions are then analyzed with Nanodrops and put on an electrophoresis gel

Nanodrop results :

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class="daySeparator-date">Thursday, 22/8/2019</span><div class="daySeparator-line"></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1068"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1068" data-index="191" style="margin-left: 0px;">Identify the maximum dilutions which permit to get lysis ground. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1069"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1069" data-index="192" style="margin-left: 0px;"></div></div></div><div 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mediocre-tableEditable-axisCell--header"></td><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--col"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible mediocre-tableEditable-axisCell--header">A</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text mediocre-tableEditable-axisCell--header">A</span><div class="u-flex-display"></div></div></div></td><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--col"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible mediocre-tableEditable-axisCell--header">B</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text mediocre-tableEditable-axisCell--header">B</span><div class="u-flex-display"></div></div></div></td><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--col"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible mediocre-tableEditable-axisCell--header">C</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text mediocre-tableEditable-axisCell--header">C</span><div class="u-flex-display"></div></div></div></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">1</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">1</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-0-0" data-namespace="table-ns1567"><span>Replicate</span></td><td class="cell is-value is-alignRight cell-contents" data-cid="table-note-part1070-0-1" data-namespace="table-ns1567"><span>1</span></td><td class="cell is-value is-alignRight cell-contents" data-cid="table-note-part1070-0-2" data-namespace="table-ns1567"><span>2</span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">2</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">2</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-1-0" data-namespace="table-ns1567"><span>KeioZ1</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-1-1" data-namespace="table-ns1567"><span>10^-5</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-1-2" data-namespace="table-ns1567"><span></span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">3</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">3</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-2-0" data-namespace="table-ns1567"><span>KeioZ1 F' MoClo</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-2-1" data-namespace="table-ns1567"><span>10^-5</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-2-2" data-namespace="table-ns1567"><span>10^-5</span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">4</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">4</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-3-0" data-namespace="table-ns1567"><span>KeioZ1 F' A1</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-3-1" data-namespace="table-ns1567"><span>10^-5</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-3-2" data-namespace="table-ns1567"><span>10^-5</span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">5</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">5</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-4-0" data-namespace="table-ns1567"><span>KeioZ1 F' T7</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-4-1" data-namespace="table-ns1567"><span>10^-6</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-4-2" data-namespace="table-ns1567"><span>10^-6</span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">6</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">6</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-5-0" data-namespace="table-ns1567"><span>KeioZ1 F' B. subtilis</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-5-1" data-namespace="table-ns1567"><span>10^-6</span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-5-2" data-namespace="table-ns1567"><span>10^-6</span></td></tr><tr><td class="mediocre-tableEditable-axisCell mediocre-tableEditable-axisCell--row"><div class="mediocre-tableEditable-axisCell-labelWrapper"><div class="mediocre-tableEditable-axisCell-labelSizer u-overflow-wrap-break-word invisible">7</div><div class="u-flex-display invisible"></div><div class="mediocre-tableEditable-axisCell-label u-verticalCenterItems"><span class="mediocre-tableEditable-axisCell-label-text u-ellipsis-text">7</span><div class="u-flex-display"></div></div></div></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-6-0" data-namespace="table-ns1567"><span></span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-6-1" data-namespace="table-ns1567"><span></span></td><td class="cell is-text is-alignLeft cell-contents" data-cid="table-note-part1070-6-2" data-namespace="table-ns1567"><span></span></td></tr></tbody><tfoot></tfoot></table><div class="mediocre-tableEditable-fillerTableWrapper" style="margin-right: 10px;"><table class="mediocre-tableEditable-fillerTable" style="display: none;"><tbody><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr><tr style="height: 0px;"><td></td></tr></tbody></table></div></div></div></div></div><div class="mediocre-tableEditable-titleBarWrapper"><div class="mediocre-tableEditable-titleBar" style="height: 37px; padding-left: 0px;"><div class="mediocre-tableEditable-tableName u-pointer"><div class="u-flex-grow u-overflow-hidden u-verticalCenterItems"><div class="u-ellipsis-text"><span class="u-ellipsis-text">t=0 </span></div></div><div class="u-flex-none"></div></div><div class="u-flex-none u-tiny-spacing-left u-verticalCenterItems table-floater"><svg class="svgIcon workflowTable-tableCollapser u-pointer"><use xlink:href="#chevron-up_c0f0f77c91b0d9072b0d8255f9f54e3c"></use></svg></div></div></div></div></div></div><div class="mediocre-captionEditable-cell"></div></div><div class="mediocre-captionEditable-row"><div class="mediocre-captionEditable-cell"></div><div class="mediocre-captionEditable-cell"><div class="mediocre-captionEditable-caption--bottom mediocre-captionEditable-caption editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="true" data-cid="note-part1070" data-index="193" style="max-width: 365px; margin-left: 0px;">
 </div></div><div class="mediocre-captionEditable-cell"></div></div></div></div></div></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1071"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1071" data-index="194" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1072"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1072" data-index="195" style="margin-left: 0px;">Prepare soft agar with CaCl2 (1mM final) and MgCl2 (1mM final).</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1073"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1073" data-index="196" style="margin-left: 0px;">Dilute K12 Hfr at a OD600=0,1 in LB, wait until OD600=0,5.</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1074"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1074" data-index="197" style="margin-left: 0px;">Add 100uL of K12 Hfr and 100uL of phages in 3mL soft agar. Each phage dilutions were stocked in chloroform (August, 21th). </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1075"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1075" data-index="198" style="margin-left: 0px;">Phages come from the chloroform-conserved-phages .  </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1076"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1076" data-index="199" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1077"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 35px;"><span>●</span></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1077" data-index="200" style="margin-left: 35px;"><b>Preculture of colonies for phage infection</b></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1078"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1078" data-index="201" style="margin-left: 0px;">Incubate Keio Z1F, K12 Hfr in 5mL LB at 37°C. Incubate Keio Z1F' pBAD-MoClo, KeioZ1F' pBAD-A1, KeioZ1F' pBAD-T7, Keio Z1F' pBAD-<i>B. sub </i>in 5mL LB+amp(100ug/ml)+glu(0,2%) at 37°C. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1079"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1079" data-index="202" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1080"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1080" data-index="203" style="margin-left: 0px;"></div></div></div><div class="daySeparator" data-scroll-id="entryDay868"><div class="daySeparator-inputWrapper"><input class="daySeparator-inputWrapper-hiddenInput" type="input"/></div><span class="daySeparator-date">Friday, 23/8/2019</span><div class="daySeparator-line"></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1081"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 35px;"><span>●</span></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1081" data-index="204" style="margin-left: 35px;"><b>Phage infection : Hugues_Natacha</b></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1082"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1082" data-index="205" style="margin-left: 0px;">Dilute each strain (K12 Hfr included) at OD600 = 0,1 in LB +CaCl2(1uL/mL) + MgCl2(1uL/mL) (+amp if necessary), incubate at 37°C.  </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1083"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1083" data-index="206" style="margin-left: 0px;">During bacterial growth, prepare soft agar (50% solid agar + 50% liquid agar + <span style="color:#344043">CaCl2(1uL/mL) + MgCl2(1uL/mL)).</span></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1084"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1084" data-index="207" style="margin-left: 0px;">Once the indicator strain K12 Hfr reaches an OD=0,4-0,8, add 100µL of K12 Hfr into the soft agar.</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1085"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1085" data-index="208" style="margin-left: 0px;">Pour 3mL of soft agar+K12 Hfr on top of LB plates. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1086"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1086" data-index="209" style="margin-left: 0px;">Once the culture reach to OD600=0,4, add arabinose (0,2% final), incubate at <u>37°C for 15</u> minutes.</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1087"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1087" data-index="210" style="margin-left: 0px;">Add the volume of phage equals to : V(mL) = (5* volume (mL) of bacteria culture * OD * 5*10^8)/phage concentration.</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1088"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1088" data-index="211" style="margin-left: 0px;">Extract immediately 0,5mL of culture for phage titration and 1mL of culture for gDNA extraction. This correspond to the timepoint 0, mesure the OD of the culture and reincubate the culture at 37°C. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1089"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1089" data-index="212" style="margin-left: 0px;">Extract 0,5mL of culture at t=30min, t=90min, t=120min and t=150min. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1090"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1090" data-index="213" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1091"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1091" data-index="214" style="margin-left: 0px;">For each timepoint, centrifugate the 0,5mL of culture at max speed for 5min. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1092"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1092" data-index="215" style="margin-left: 0px;">Prepare 10-fold serial dilutions of the supernatant in phage buffer (10^-1 to 10^-9).</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1093"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1093" data-index="216" style="margin-left: 0px;">Add 4µL of chloroform to remaining supernatant, stock phages in chloroform at 4°C.  </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1094"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1094" data-index="217" style="margin-left: 0px;">Spot 5uL of the supernatant serial dilutions onto a plate with top agar + K12 Hfr.</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1095"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1095" data-index="218" style="margin-left: 0px;">Incubate every plate at 37°C. </div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1096"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1096" data-index="219" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1097"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 35px;"><span>●</span></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1097" data-index="220" style="margin-left: 35px;"><b>Genomic DNAs of bacteria infected by phages</b></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1098"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1098" data-index="221" style="margin-left: 0px;">At different time points (t0, t30, t90, t120, t150) of the phage infection, 1ml of bacterial culture with phage is withdraw. This is done for the four conditions : A1, T7, Moclo and B.sub. The kit used to quantify the genomics DNA of infected bacteria is "QIAamp DNA Blood Mini Kit (50)" from Qiagen. The protocole is "DNA Purification from Tissues" page 32. We started at step 3. Step 1, 2(a, b, c) and 5a are not done. The elution step is done only one time with 200µL of buffer AE. The final solutions are then analyzed with Nanodrops and put on an electrophoresis gel</div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1099"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1099" data-index="222" style="margin-left: 0px;"></div></div></div><div class="mediocre-item is-text" data-scroll-id="note-part1100"><div class="mediocre-noteEditable multi-editable is-paragraph"><div class="mediocre-noteEditable-indenter" style="width: 0px;"></div><div class="editable selectable is-locked" contenteditable="false" data-allow-at-search="true" data-allow-multiline="false" data-cid="note-part1100" data-index="223" style="margin-left: 0px;">Nanodrop results :</div></div></div><div class="mediocre-item is-captionedTable" data-scale-for-print="print1643" data-scroll-id="note-part1101"><div class=""><div><div class="hiddenFocusEditable editable" contenteditable="true" data-cid="note-part1101-item" data-formattable="true" data-index="224" data-subindex="item"></div><div class="mediocre-captionEditable multi-editable mediocre-captionEditable--table"><div class="mediocre-captionEditable-indent"><div class="mediocre-captionEditable-
+<img src="https://2019.igem.org/wiki/images/1/13/T--Go_Paris-Saclay--Addd1.png">
+<img src="https://2019.igem.org/wiki/images/e/e5/T--Go_Paris-Saclay--Adzdd1.png">
+<img src="https://2019.igem.org/wiki/images/e/ea/T--Go_Paris-Saclay--Addzdd1.png">

Difference between revisions of "Team:GO Paris-Saclay/Phagemultiplication"

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Phage infection assay

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Phage titration & infection 01082019- corrected Laetitia.xlsx

Phage titration & infection.xlsx

Phage titration & infection.xlsx

Phage titration infection 21082019.xlsx