Showing posts with label molecular biology. Show all posts
Showing posts with label molecular biology. Show all posts

Sunday, October 29, 2023

ProteoCool #Pills29: Simple solutions to improve laboratory routine work with few euro/dollars: #1 IKEA


Chain stores with furniture, DIY, decoupage hobbies as 

IKEA, OBI, Leroy Merlin, Bricoman 

 can be a great source for funny and cheap items useful for improve the laboratory organization

Here i report just some examples: 

1) SANDVIVIA OVEN MIT 

                   made in silicone which provides a firm grip and is heat-insulating.

It allow to manipulate and move the hot agarose gel and/or hot culture media removed from microwaves or autoclave.

                                           Avaialble from IKEA (Italy: 3euro - US: 4 dollars )

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2) VEKSEN CART 

It fits in the smallest of laboratory, but there’s plenty of space on the shelves for all  for all those staff that you need to have on hand when you work on the laminar hood

             or in a laboratory with low space 



Assemble the trolley quickly and easily by clicking the parts together without any specific tools.

Available from IKEA (Italy: 10 euro;  US: 9 dollars) 

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TIKSEN Hook with suction cup.

Alternative clothes hanger solution

Available from IKEA (Italy: 7euro/4p; US: 5dollars/2p) 

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                                                                    BEVARA Sealing clip. 

                                                       Cheap clips for use with Dialysis Tubing 

                                         Available from IKEA (Italy 1,5euro/10p: US: 2 dollars/10p ) 




Tuesday, June 15, 2021

ProteoCool Pills#8: Expi-CHO a powerful cell line for transient expression of biologics

 

If in the ProteoCool n°29 I extensivelly show the properties of the mammalian Expi293  expression system, today I would like to briefly report you the further improvement in terms of productivity that I was able to obtain thanks to the ExpiCHO cell expression system.

Example 1: Expression of a mouse igG2a-CL-k recombinant monoclonal antibodies 

 (both heavy and light chain were cloned in pcdna3.4) with 2 different leader peptides)

 

Protocol (in brief):

1)     15 ml of cells were transfected in a 125 cap vented flask

2)     Cultures timelines:



1)     Cell were centrifuged 20’ at 3000g and surnatant was filtered at 0,22uM

2)     Surnatant is added of 1.5ml of PBS 10X

3)     Surnantat is loaded on a Poliprep gravity column containing 300ul of Protein G FF resin

 5b) For the Expi-CHO productions, the Flow-Through from the column was loaded in a 2nd protein column to recover all the mab

4)     Column is washed with 50CV of PBS

5)     Mab was eluted with glycine 100mM ph2.7 on a Tris 1M pH=9 solution

6)     For Expi-CHO cells due to high expression the 

7)     Mab was concentrated with amicon ultra 50Kda and buffer exchanged in PBS

8)     Mab was quantified with nanodrop measuring the 280nm absorbance and the igG quantification mode.

Results:

                      !! ExpiCHO vs EXpi293 --> More than 10 fold improvement!!


Example 2:  Production of recombinant  human CTLA-4 (1-161 domain) 

(carrying a C-terminal 6XHis tag cloned in pcdna 3.4)

Protocol (in brief)

1)     15 ml of cells were transfected in a 125 cap vented flask

2)     Cultures timelines: Same that reported in the Example

3)     Cell were centrifuged 20’ at 3000g and surnatant was filtered at 0,22uM

4)     Surnatant is added of the same volume of IMAC binding buffer (Tris 20mM, imidazole 10mM, NaCL300mM ph=8)

5)     Surnantat is loaded on a Poliprep gravity column containing 300ul of Ni-sepharose FF

6)     Column is washed with 50CV of Binding buffer

7)     CTLA-4 was eluted with 1ml of IMAC elute buffer (Tris 20mM, imidazole 300mM, NaCl 300mM pH=8.

8)    CTLA-4 was quantified with nanodrop measuring the 280nm absorbance. CTLA-4 extinction coefficient was calculated by ProtParamTool

 Results:

Summary:

 

Pro/Cons Expi-CHO vs Expi293

 

Low DNA amount required for transfection (0,5ug/ml vs 1ug/ml)

Low temperature during protein expression(may help production of thermostable proteins)

Use in the preclinical studies the same cell line (eg CHO) that will be used for the manufacturing of clinical lot and that represent the gold standard strain for biomanufacturing and reduce risks associated to strain transition 

High growth rate at 37°C and higher tendency to aggregate: Routine cells passages require more attention to perform the cell count and cell dilution.

Longer culture times (at least 8day vs 4day)

PMT (eg glycosylation profile) may be slightly different from the human cells (eg HEK293 or Expi293)

2 different CO2 incubator shaker are required: shakr n°1 fixed at 37°C 120rpm 8%CO2 for  the cell line propagation a shaker n°2 fixed at 32°C 120rpm 5%CO2 for cell transfection


Expensive or cheaper? 

It depends from the yields. In the reported examples, much cheaper! 

To date culture media and transfection reagents are slightly similar

 

1liter Expi293 mediumà 340euro vs 1liter ExpiCHO medium Ã  466euro

1liter transfection kit Expi293 à1128 euro vs 1liter transfection kit Expi-CHO à1236 euro

  

Those costs may seem very high (about 2000euro/liter) but it depends from yields and complexity of each target.  

 

Expi293 and ExpiCHO allow to you to produce high yields of proteins (eg protein rich of S-S bonds) and/or  full length antibodies those are almost impossible to be produced in similar yields (and correct folding) using less expensive organisms (as E.coli)

 

Sunday, May 2, 2021

ProteoCool Pills#4: Replacement of Ethidium bromide with a safe stain

 

Ethidium bromide thanks to its ability to show an intense fluorescence (ex 300nm/em 620nm) after binding with DNA.

 Ethidium bromide (EB) is inexpensive, sufficiently sensitive and very stable and thanks to this property has been the stain of choice for nucleic acid gel staining for decades.

 However on the other hands, EB is also a known powerful mutagen.

Recent years alternative reagents able to show an intense fluorescence after binding with DNA but not able to permeate cell membrane were developed:

 

My preferred one:

 

Gel REd - Biotium  (VWR cod. 41003) 

   https://biotium.com/product/gelred-nucleic-acid-gel-stain/

 

Safety assessment available at:

 

https://biotium.com/wp-content/uploads/2013/07/GelRed-and-GelGreen-Safety-Report.pdf

 

Cost: About 90€ for 500ul (stock 10000X) à  90€ for 5liter of agarose à 0,9€ for a mini gel (15x2well)

                                                                                                                                  2,5€ for a midi gel (up to 30x2 well)

                                                                                                                                     

Another alternative that I used in the past is the Sybr Safe (thermo cod. S33102) 

https://www.thermofisher.com/order/catalog/product/S33102?SID=srch-srp-S33102#/S33102?SID=srch-srp-S33102 

is another possible alternative. but in my experience, it shows limited stable under UV excitation.

 

More details are available in the following link

 

https://www.blogger.com/video.g?token=AD6v5dxB5wweSgHEks3TU3bm1QoGEYZU6GT8788soF0i7SEVvaQwM2AgHXmDY62fIzukFrMMDbFQEFOPMfSyV4GwvJHPY9U__KiUhmaCsx6NAwneL2yJYbaSu_DV-H4_to6BznMtlE59

Monday, April 26, 2021

ProteoCool Pills#3: Homemade E.coli chemically competent cells

                               

                                         

                               For preparation of 10ml competent cells from 500ml of culture


Day1

 Preculture: Inoculate the *cells in 10 ml of LB (in a 50ml falcon) O/N at 180rpm- 37 °C

 Store in fridge at 4°C the solutions (filtered at 0.22uM) :

-        100 mM MgCl2

-        100 mM CaCl2 with 15 % glycerol) 

*1 peak a single colony from LB-agar or scrape the frozen surface of a glycerol stock

Day2

-        Inoculate 5ml of the pre-culture in 500ml of LB in a 2liter shaking flask (dilution 1:100) and growth at 180rpm- 37°C up to OD(600nm) about 0,4-0,6; 

-        Centrifuge in a sterile tube for 10 minutes at 2500 g - 4 °C

 -        Discard the surnatant (LB) and transfer the tube with the cells in ICE*2.

-        Re-suspend the cells with 50 ml of 100 mM MgCl2 COLD

*2 From now all the steps have to be performed in ICE and centrifuge need to be COLD, because an heating of the sample may result in decrease of competence level.

-        Incubate in ICE for at least 30 minutes (longer incubation are not an issue)

-        Centrifuge at 2500 g for 10 min a 4°C

-        Discard the surnatant and transfer the tube containing the cells in ICE.

-        Re-suspend the cells with 10 ml of 100 mM CaCl2 with 15 % glycerol (COLD)  

n.b: Vortex can be used for facilitate the cell resuspension with the recommendation to take short steps and not to keep cells out of the ice for too long. 

-        Spilt the cells in aliquots in 1.5ml Eppendorf COLD (100-200ul/Eppendorf)

To maximize the transformation efficiency: If you have DRY ICE available, Cool down empty Eppendorf  tubes in dry ice is preferable to froze immediately the cells before storing at -80°C. Alternatively, cold down the Eppendorf in ICE and just transfer the spitted cells on the -80°C.

The cells competency can be verified performing a transformation test with 20pg of puc19 

Generally, BL21 à show an efficiency of about 10^6 cfu/ml à about 20 colonies 

DH5alpha. DH10B, Top10, MACH1 à shows higher efficiency, about 5-10X10^7 cfu/ml à 50-100 colonies

In case you would like to produce competent cells free of animal components you can use YGR  or Enpresso B animal free (http://enpresso.de/en/products/as) culture media.

More information about YGR and Enpresso are available at the following link:

ProteoCool n°7: High cell density E.coli protein expression using Enpresso B medium

ProteoCool n°32 High cell density E.coli protein expression using YGR medium



Sunday, December 13, 2020

 

                               !! An updated VIDEO PLAY LIST is now available on ProteoCool !!

Click on the ProteoCool TITLE to be re-directed to the video

Proteocool n°

Title

page

1

Cloning methods overview

1

2

Primer Design: Restiction/Ligation

1

3

Primer Design: PIPE Cloning

1

4

PCR Colony screening

1

5

 E.coli high cell density media overview

2

6

Rapid SDS-page coloration/decoloration using microwave

3

7

High cell density E.coli protein expression using EnpressoB media 

2

8

Buffer Exchange methods overview

3

9

2 Common mistakes causing sample lost using the AKTA Systems

4

10

PARAFILM a simple support for sample loading on agarose gel

1

11

Rapid buffer <--> Exchange by PD-10

3

12

EZNA HP MINI KIT II: MIDI KIT YIELDS from a MINI KIT format

6

13

Subctractive IMAC

3

14

Endotrap: A simple and efficient tool for endotoxin removal

3

15

Overview on SDS-page

3

16

3 common mistakes in buffer preparation for protein purification

4

17

Overview on basic bioinformatic tools for DNA sequence analysis

6

18

Simple PCR test for Mycoplasma detection

5

19

Simple bioinformatic Tools for protein sequence analysis

6

20

FAST READ 102: A multi-chamber device to speed up manual cell count

6

21

3 common mistakes in E.coli culture

4

22

Overview on tools for recombinant protein expression  in E.coli

2

23

Taq Nova Red: A cheap master mix TAQ for PCR colony screening 

6

24

DSF a simple and powerful tool for protein QC

3

25

A Simple way to clean and re-generate IMAC coloumns 

7

26

Single channel pipette cleaning

7

27

Overview on Agarose Gel

1

28

Zinc: An alternative cheap and healthy metal for IMAC

3

29

Expi293: A simple and powerful mammalian expression system

2

30

Uniform 15N, 13C and 2H protein labelling using E.coli and more

2

31

Homemade Handrub Sanitizer

7

32

High cell density E.coli protein expression using YGR media 

2

33

Simple TIPS to avoid common mistakes in Spettroptotometry/Fluorimetry/Luminometry

4

34

Inappropriate use of Ultrafiltration  for membrane protein  concentration

4

Click on PAGE number to be re-directed to the PAGE

 
 
 
 
 

ProteoCool37: Densitometric analisys of SDS-page using Image LAB software (license free version)

  A new video exploring how to optimize the densitometric analysis of SDS-PAGE gels using the basic version of Bio-Rad Image Lab is now avai...