Showing posts with label laboratory. Show all posts
Showing posts with label laboratory. 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 ) 




Monday, June 5, 2023

ProteoCool Pills#27: DSF an useful tool for Monoclonal antibodies selection, optimization and developabiltiy assesment

 

DSF 

(Differential scanning fluorimetry previously named also Thermofluor)

is a very simple tecniques that exploit the ability of a fluorescente probe,  typically either SYPRO Orange or 1-anilino-8-naphthalenesulfonate (ANS) – that is quenched in an aqueous environment but becomes strongly fluorescent when bound to exposed hydrophobic groups of a protein. Therefore, the thermal unfolding of a protein of interest in the presence of such a dye, can be followed spectrophotometrically.

DSF is a 96 well based assay that could be performed on a RT-PCR thermocycler, it is inexpensive,  fast, and require relatively little sample. All these advantages have made this approach attractive for screening applications in drug discovery  and also for protein stability formulation

In the ProteoCool n°24 in suggest as in my opinion the DSF may become an essential assay todetermine lot to lot concistenciy in QC department of company producing recombinant proteins (e.g recombinant vaccine and/or enzymes)

In this post i would like to share with you 2 examples that show as DSF may play an important role also in antibody screening, optimization and developability assesment. 

DSF thanks to its excellent throughput and minimal material consumption (about 50ul of antibody at 0,3 mg/ml for each point) allow to readily compare the thermal stability of:

- different antibodies in the same buffer:

-  different  Fab mutants or Fc mutants in the same buffer;

-  different  antibody formulations; (optimize pH, salt concentration, excipients)


Example 1: 

Comparision of thermal stability of different mabs 

Full length human IgG1-Clk mabs  in PBS may show 1 or 2 separate transitions on the basis of the Fab stability. 

Mabs with lower Fab stability show in general a single transition while mabs with high stability show 2 separate transitions, 1 at about 69°C for the Fc and 1 at higher temperature for the Fab.


Example 2:

Comparision of thermal stability of different Fc mutants

In recent years the enhancement or elimination of the Fc-effector function has led to a growing interest in Fc-engineering, to give antibodies specific mechanisms of action and therapeutic properties.  

Even if several Fc modification, as:

-   LALANA, LALAPG, LALAGR mutations to remove effector function;

-  SDIE, GAALIE mutations as well as afucosilation to enanche the effector function

 were already reported, few data about developability of those solutions are still available and there is a lot work  to do to select an enanched Fc combining the best effector function and good manufacturability, stability and pharmacokinetics.

Those are just 2 examples that show as in short time and using a limited amount od samples, thanks to DSF we can obtain  essential informations to guide our decision in antibody during the screening, desing, formulation phases.

Of course, thermal stability itself do not Guarantee that the selected antibody has good developability profile but  some of the following other tecniques as:

- DLS;

- PEG solubility;

- Self-interaction determined by BLI;

those provide informations about antibody  aggregation propensity 

- Hydrofobic interaction chromatografy (HIC)

those provide informations about antibody hydrofobicity

have to be peformed to complement the DSF data. 


A great thanks  to

 Luca Sorrentino





 

Friday, January 13, 2023

ProteoCool Pills#22: Tips for cleaning the OMNISEC RALS/LALS flow cell if get dirty after the passage of biological samples

 

                                                                           OMNISEC 

is an advanced GPC/SEC system combining a pump, degasser, autosampler for mobile phase delivery and sample injection module with an integrated multi detector incorporating refractive index, UV/Vis, light scattering and viscosity detectors.

I have used the OMNISEC system to analyze the aggregation state of several biological samples (eg. recombinant antibody/protein preparations) in standard Phospate, MES or Tris buffers (pH range 5.5-8).

I found amazing the performances of the OMNISEC RESOLVE module, that thanks to the presence of a temperature controlled Autosampler (4oC – 60oC), allow to load in reproducible way an high number of samples and guarantee a very good throughput.

One of the main drawbacks (which i'm not sure if is it is common or not to other light scattering systems) that i found is the high tendency of the LALS detector to get dirty after the passage of some biological samples.

In this post i would like to share with you my experience about the cleaning procedure to use when you  see a strong increase of the LALS baseline signal after the passage of biological samples.

For example in the following video yoo can see the baseline LALS signal that was detected some months ago after the run of about 20 mab samples in a SEC coloumn (all the mabs were expressed from ExpiCHO cells, purified with MAbselect resin and buffer exchanged in PBS by desalting) :

If the RALS signal is not much higher than the optimal (aobut 80mV), the LALS signal was very high (optimal range is 200-300mV) and a cleaning procedure was required.

Since we do not observe any improvement (data not shown) from the passage of any routine cleaning solutions (methanol 10%, acetonitrile 10%, sodium azide 0,02%) suggested on pag106 OMNISEC SYSYEM Basic Guide manual provided with the instrument, we then decided to proceed with Deep cleaning (pag.105) using a 5% HNO3 solution:

        BUT UNFORTUNATELLY WE OBSERVE ONLY A WEAK REDUCTION IN THE LALS BASELINES SIGNAL

we than tested SDS (1% solution) which may be able to resuspend and remove protein aggregates/precipitate:

BUT UNFORTUNATELLY  ALSO IN THIS CASE WE DO NOT OBSERVE A REDUCTION IN THE LALS BASELINES SIGNAL

Finally we tested NAOH 0,1M solution, which is routinelly used for the cleaning of  several chromatographic resins  used for biologic purification  (e,g proteinA, proteinG, sepharose)


NAOH 0,1M works very well 
and restore the LALS BASELINES SIGNAL in the optimal range

 Thanks a lot to 

 Mirco Toccafondi 



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



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...