Team:Sorbonne U Paris/Experiments
Experiments
Cloning Protocole
The goal is to clone the insert we ordered into a level 0 plasmid. Once this plasmid is obtained, the insert is cloned with a promoter and a terminator to form a [...]
Transformation
This operation consists in introducing an exogenous DNA sequence into the host organism that we want to genetically modify. In the Onishi protocol, we used [...]
RNA Extraction
The aim of the step is simply to extract RNA coming from transformed colonies before reverse-transcription. Here we have chosen [...]
Proof of concept
Here, the objective is to try and see whether the addition of our peptide can reduce mortality among Chlamydomonas reinhardtii in presence of [...]
Trasnformed cells
The aim of this experiment is to assess whether the expression of our antioxidant peptide has a protective effect over cells in contact with [...]
In vitro test
This step aims to assess the capacity of our antioxidant peptide to protect one protein from reactive oxygen species. We want to put together one enzyme [...]
Irradiation
The aim is to submit our transformed cells that are expressing the antioxidant peptide to γ-radiations mimicking some of the space radiations. Three strains of [...]
Notebook
Week 1 = from the 12th to the 16th of july
- Reception of the antiox sequence.
- Assembly of plasmide pL0-294, containing our antioxidant insert, with GoldenGate method and transformation of the assembled plasmid into NEB 10-beta Competent Escherichia coli (High Efficiency), that are plated on LB-agar+Spec+Xgal plates.
Week 2 = from the 19th to the 23th of july
- Selection of white transformed bacteria on spectinomycin plates and growth in liquid culture of LB of our selected clones.
- Extraction and purification of plasmid DNA.
- Digestion with restriction enzyme BsaI and migration on agarose gel to confirm the presence of our insert : amplification by PCR on transformed colonies and migration on agarose gel.
- Third attempt to identify if the antiox sequence is present in the plasmid : digestion by BsteII and HindIII.
- The plasmid is sent to sequencing.
- Assembly of the p1 plasmid, transformation into E. Coli and selection on ampicillin.
- PCR reaction and agarose gel electrophoresis on selected bacterial clones.
- Extraction and purification of plasmid level 1 with Nucleospin kit.
- Assembly of the pM plasmid, transformation into E. Coli and selection on spectinomycin plates.
Week 3 = from the 26th to the 30 of july
- Assembly of the pM plasmid, transformation into E. Coli and selection on spectinomycin plates.
- Range of toxicity essay with 3 oxidant molecules (H2O2, Rose Bengale and Methyl Viologen) at different concentrations on non transformed Chlamydomonas reinhardtii.
- Revelation of dead cells by incubation with Evans Blue.
- Extraction of plasmidic DNA to recover final pM and verification by agarose gel electrophoresis after digestion with BbsI.
- Digestion of pM-156
- Linearization of pM-156 with EcoR
- First transformation of Chlamydomonas reinhardtii strain 45-33 using glass marbles with the plasmide pM-156.
Week 4 = from the 2nd to the 6th of August
- Prepared TAP broth.
- Count of dead and alive cells within the oxidant range on non transformed Chlamydomonas strain determination of the survival rate.
- Second oxidant range on non transformed Chlamydomonas reinhardtii, dead cells are colored with Evans blue. We used doses of oxidants to try to obtain survival rates between 20 and 50%.
- Count of dead and alive cells within the second oxidant range on non transformed Chlamydomonas strain determination of the survival rate.
- Second attempt of transformation of Chlamydomonas reinhardtii strain 45-33, using Onishi protocol.
Week 5 = from the 9th to the 13the of August
- Dilution of dry peptides we had ordered.
- Several Bradford and BCA (bicinchoninic acid) dosages were made to determine the decapeptide concentration. (LOL)
- First antioxidant test with H2O2 and Rose Bengale on non transformed Chlamydomonas reinhardtii in the presence of our 2 peptides.
Week 6 = from the 16th to the 20th of August
- Revelation of dead cells by incubation with Evans Blue.
- Manganese toxicity range of wild-type Chlamydomonas reinhardtii.
- Transformation of Chlamydomonas reinhardtii strain 45-33 attempt 3 with Onishi protocol.
- Toxicity and characterisation assay of our 2 peptides to assess whether it’s toxic and understand why it provokes agglomeration.
- Plates patch of strain 45-33 on different conditions check its antibiotic resistance : we came to the conclusion that strain 45-33 was resistant to hygromycin, so we couldn’t use it to select our transformed algae.
- Highlight of the interaction between Evans Blue and our peptides -which forms wide aggregates
- under the microscope.
Week 7 = from the 23th to the 27th of August
- Linearization of pM-156
- First transformation of Chlamydomonas reinhardtii strain UVM4 with Onishi protocol and spreading on hygromycin plates. Cells seemed to have not survived the electroporation process, so we had to throw them out and try again.
- Second transformation of UVM4 with Onishi protocol on hygromycin plates.
Week 8 = from the 30th of August to the 3rd of September
- Prepared PBS buffer.
- Prepared TAP broth.
- Third transformation attempt of Chlamydomonas reinhardtii UVM4 with plasmid pM156 containing the antioxidant gene, with glass marbles.
Week 9 = from the 6th to the 9th of of September
- First try of LDH test : we tried to characterize the activity of LDH enzyme after flowing through the Amicon tube. We wanted to use Amicon to get rid of H2O2 before putting the substrates (NADH and pyruvate) and reading the absorbance. The absorbance was too important so we modified the NADH concentration.
- Second try of LDH test : this time the absorbance was right but the enzymatic activity detected was about 0,0297 ΔAbs/min, which is quite low. We thought we had lost a lot of enzymes through the Amicon tube.
- Third try of the LDH test : we characterize the activity of LDH without Amicon tube and without any ROS to assess how the reaction takes place without any perturbation. The enzymatic activity was around 0,097 ΔAbs/min.
- Fourth try of the LDH test : we don’t need the Amicon tube because H2O2 will be diluted in the final volume of tampon and pyruvate. Incubation of LDH with H2O2 10mM reduces the activity of the enzyme just enough for us to work with.
Week 10 = from the 13th to the 17th of September
- Selection of 10 clones that grew on hygromycin after transformation with plasmid pM-156.
- Extraction of RNAs from the transformed strain of Chlamydomonas reinhardtii UVM4.
- Electrophoresis of the total extracted RNAs on an agarose gel.
Week 11 = from the 20th to the 24th of September
- Reverse-transcription of total RNAs extracted.
- Multiple PCR tests with primers RT-08 and RT-09 to amplify our insert and CBLP primers (housekeeping gene), with different annealing temperature and revelation with agarose gel electrophoresis.
- In vivo test on 10 clones of transformed cells UVM4 with H2O2 to see if the expression of the peptides has a protective effect.
Week 12 = from the 27th of September to the 1st of October
- PCR of the cDNA with 2 new primers pairs : RT10/RT11 and RT12/RT13.
- Shipment of 5x10^6 cells of the clones expressing the antioxidant peptide : 2, 5, 7 and the untransformed UVM4 strain (each sample in triplicate).
Week 13 = 4th to 8th of October
- Irradiation of Chlamydomonas reinhardtii shipped at the Belgian nuclear research center
- Preparation of 16 TAP-agar 6 wells plates.
- Collect of irradiated strain, serial dilution, spread in previously made plates and growth under light.
Let's set the context…
The main proof we had to provide is that the undecapeptide has the same radioprotective effect as the decapeptide mentioned in our main source article, as our transformed cells will express the undecapeptide. The only difference between those two is the presence of the amino acid methionine at the beginning of the sequence.
Did we succeed?
To achieve that evidence, we tested the two peptides in both in vitro and in vivo assays. Unfortunately, our results weren’t conclusives. We did not have time to test the antioxidant capacity of both peptides in vivo with FDA, as we lost a lot of time working with Evans blue. In vitro, we did not succeed in characterizing the activity in LDH in the presence of the MDP or MUP complexe (manganese - peptide - pyrophosphate), as the enzymatic activity wasn’t repeatable between experiments.
Conclusion & what could be improved !
Furthermore In “MDP: A Deinococcus radiodurans Mn2+-Decapeptide Complex Protects Mice from Ionizing Radiation”, the article that we relied on to design our project, researchers tried several peptides sequences, that were less successful but still had a protective effect. With that in mind, we believe that the peptide potentializes the effect of Mn2+, so we strongly feel that the addition of only one Methionine to the sequence won’t change this effect much.
Despite the inconclusive results we remain convinced that the design of the experiments was relevant; a better preparation of the reagents and the use of a machine allowing us to carry out our experiments in one day would have made it possible to prove the effectiveness or ineffectiveness of the undecapeptide.
Cloning results
Construction level 0 : pL0-294 (BBa_K3836000)
The insert we ordered from Eurofins is cloned into a recipient plasmid pAMG9121 by GoldenGate reaction. To select the plasmids that received the insert, the reaction products were transformed into Escherichia Coli NEB10b bacteria by heat shock and plated on LB plates containing X-gal and the antibiotic spectinomycin. The results can be seen in figure 1, after 24h of incubation at 37°C. A majority of white colonies confirms that most of the recipient plasmids received the insert coding for the antioxidant peptide.
By observing the two plates, we notice that the control plate has a higher blue/white ratio than the plate with the bacteria transformed with the GoldenGate reaction product. This observation is coherent: the insert is present and the GoldenGate reaction replaces the LacZ sequence with the insert in the recipient plasmid, making the colonie white.
Three white clones and one blue clone were amplified by placing them in liquid culture in LB medium at 37°C for 24h. The plasmid DNA was then extracted and digested with the restriction enzymes BsteII and HindIII in order to confirm the obtention of our plasmid pL0-296. The digestion product is runned on a 1% agarose gel. The profile of the migrated products, visible on figure 2, is confirmed by comparing it to the expected profile for two of our clones.
We can therefore conclude that we have obtained the level 0 plasmid pL0-294. A second verification was performed by sequencing at Eurofins using a primer binding upstream of the insertion site of our undecapeptide coding sequence (see figure 3).
This screenshot shows that the sequenced plasmid has the same sequence as expected from the in silico model. So we continued by assembling level 1.
Construction level 1 : pL1-226 (BBa_K3836001)
We then assembled our level 1 plasmid: pL1-226. It contains the transcriptional unit allowing the constitutive expression of the undecapeptide. The GoldenGate reaction is performed with the recipient plasmid and the plasmids providing the PSAD (Photosystem I reaction center subunit II) promoter, the PSAD terminator and the undecapeptide CDS. The enzyme used to assemble the level 1 plasmid is BbsI. Cloning products are then used to transform Escherichia Coli NEB10b again. The culture results can be seen in figure 4.
Again, three white colonies and one blue colony are grown in liquid LB medium. After 24 hours, the plasmids are extracted and characterized by PCR, with primers placed on either side of the transcriptional unit insertion site. Non-recombinant plasmid will carry the LacZ insert. Success of the transformation will be determined thanks to the size of the amplicons : expected amplicons are 717 bp for the plasmid containing LacZ, and 1520 bp if the plasmid has integrated the inserts.
By comparing to the expected migration profile, this electrophoresis confirms that we have obtained our level 1 plasmid: pL1-226.
Construction level M : pLM-156 (BBa_K3836003)
The transcriptional unit of pL1-226 as well as the sequence for constitutive expression of the hygromycin resistance gene are integrated into the M-level recipient plasmid by GoldenGate reaction (using the enzyme BbsI). The bacteria were transformed with this reaction product and 24 hours later we again obtained white and blue colonies The transcriptional unit allowing the expression of the AphVII gene (conferring hygromycin resistance) is composed of the synthetic and constitutive promoteur pAR, the AphVII CDS and the terminator of the Rbcs2 gene. The name of this part is BBa_K3836002.
A white and a blue colony are cultured to amplify the plasmids they contain. After pDNA extraction, the plasmids are digested with BbsI (blue colony) and BsaI (white colony). And the digestion product is run on a 1% agarose gel. The digestion profiles show that we have obtained the expected bands. This confirms that we have obtained our M-level plasmid.
Now that we obtained the final level M plasmid (pM-156) we can insert it into our host organism : Chlamydomonas reinhardtii.
Transformation results
After the Onishi protocol, UVM4 Chlamydomonas reinhardtii were spread on TAP-agar dishes containing the antibiotic : hygromycin. As you can see on figure 8, no colonies were found on the negative control. Three little colonies, that have grown afterwards (figure 9), were spotted on the positive control, and assess that the transformation was a success. More importantly, 42 colonies were able to grow on hygromycin : among them, some may have inserted the sequence coding for the antioxidant peptide. The colony PCR should answer this question.
RT-PCR results
To evaluate the expression of the antioxidant undecapeptide, we performed PCR product run on agarose gel electrophoresis. Several primers were tried to amplify the antioxidant sequence. The first pair of primers we used were only amplifying 14 pb, and no amplification was observed, whereas RT10/RT11 and RT12/RT13 allow the amplification of 19pb and 20pb respectively.
The result for the housekeeping gene CBLP is letting us think that the same amount of genetic material was put into each well (Figure 10).
According to figures 11 and 12, we can see that several strains showed a specific amplification of the antioxidant sequence, with more or less expression. Finally, we retain as successfully transformed the strain numbered 2, 5 and 7 (corresponding at wells 3, 6 and 8 in below pictures).
We could not confirm the presence of the undecapeptide as we do not have specific antibodies that can recognize it. We thought about doing steric exclusion chromatography after protein extraction and try to see, in the low molecular mass products, a band showing up by comparison with a non transformed strain.
Proof-of-concept : In vivo tests results
First, the effects of three antioxidant molecules were evaluated with a concentration range toxicity test (figure 13) : H2O2, Rose Bengal (which you can clearly see in the center of figure 13) and methyl viologen. The aim was to find the correct amount of molecules to kill around 60% of the cells. Each condition was made in triplicate. An equivalent number of wild-type Chlamydomonas reinhardtii were put in each well. The concentrations tested were the following :
Cells were cultivated 24h in the presence of oxidant molecules. We collected 50µL of cells and added 10µL of Evans blue, an exclusion dye for which dead cells are permeable to. The observation under an optic microscope allowed us to count alive cells, dead cells and the total number of cells. With all this information, we were able to calculate a survival rate displayed on figure 14.
A second toxicity range was done with what we thought were more accurate concentrations (figures 15 and 16). The protocol was the same.
From this point on, we chose to use Rose Bengal as the oxidative-stress inducer, as the results were more consistent.
The next step was to try out the antioxidant effect of the peptide on these non transformed cells, with manganese, when put in the presence of oxidant molecules. An equivalent number C. reinhardtii was put in each well, all conditions were done in triplicate (figure 17). For the antioxidant effect to happen, Mn2+, the peptide and pyrophosphate must form a complex, that’s why the experiment is held in a phosphate-enriched medium (TAP+Pi). It was important to review the effect of both decapeptide and undecapeptide, which have the same sequence except for a methionine at the beginning of the undecapeptide.
After 24h of incubation, we could not draw any conclusions. First, the concentration of manganese was too high (10mM) and most of the cells were aggregated because of the induced stress. As we learned by doing some research, we realized that manganese, in the concentration with which we wanted to use it, could become a stress for phototrophic organisms. Secondly, in the presence of 6µM of Rose Bengal, all of Chlamydomonas reinhardtii seemed dead. But, more importantly, every condition with the decapeptide or the undecapeptide showed some unusual blue aggregates that none of our Chlamydomonas reinhardtii experts were able to identify and that made cell count impossible (see figure 18).
.jpg)
.jpg)
.jpg)
.jpg)
.jpg)
In order to specify the adequate concentration of manganese to allow our experiment, we then realized a range allowing to establish a toxicity threshold (figure 19). A toxicity range assay was made to quantify the effect of manganese. In each well, we put 200µL of C. reinhardtii liquid culture and different concentrations of MnCl2. Doses of manganese went from 0,25mM up to 10mM.
Again, cells were incubating 24h in the presence of manganese and Evans blue was used to color dead cells. The proportion of dead cells accumulates with manganese concentration, but starting from 5mM of Mn2+, we could witness the development of brown aggregates, that Chlamydomonas reinhardtii is known for when under a lot of metabolic stress (figure 20). So we choose to keep the concentration of manganese at 1mM for the following experiences.
To understand where the blue aggregates were coming from, the effect of the peptides, alone and with Evans blue, were reviewed under the microscope (figure 21).
From this experiment, we were able to conclude that Evans blue and both the decapeptide and undecapeptide were interacting and forming aggregates, preventing us from counting dead or alive cells. At this step, we had to find another way to numerate cells that did not involve Evans blue.
In vivo tests results on transformed cells
The aim of in vivo tests was to see how transformed Chlamydomonas reinhardtii would react in presence of an oxidant, as they should express the undecapeptide. To count cells, we had the idea of adding FDA (fluorescein diacetate), which produces fluorescein when hydrolysed by esterase : FDA only colores living cells.
A range of survival ratios was measured with different concentrations of H2O2 : we have selected the dose of 2,5mM, for a survival rate of 37%. Transformed colonies were incubated 24 hours in presence of Mn2+, H2O2 or both. The experiment is again done in triplicate and, as we can see in figure X, we analyzed the mean number of cells of each triplicate. Numbers of living cells are coming from a cell counter after the addition of FDA. The final number of cells were calculated under the form of a percentage in relation to the number of cells without any treatment. After analysis, we retain the strain that showed a greater number of cells in the condition Mn2+ & H2O2 than in the condition H2O2 only. The number should also be superior to the Mn2+ & H2O2 control strain.
In conclusion, according to this analysis, only strains 1 and 9 could present an antioxidant effect. However, from the PCR outcomes, only strain 2, 5 and 7 expressed the RNA corresponding to the antioxidant peptide.
Nevertheless, multiple biais were found in this experiment. The manganese concentration was still too important and killed 61% of cells on average. We may not have homogenized the cultures enough before taking the sample to the cell counter. But most importantly, the cell counter wasn’t precise enough and we observed some irregularities. Without any cells in the sample, it was identifying about 4,89 * 105 as background noise.
Eventually, we gave more credit to the PCR results than to the in vivo tests to choose which strains to send for irradiation.
In vitro test results
In the first attempt, we tried to characterize the activity of the lactate dehydrogenase (LDH) enzyme after flowing through the amicon tube. The amicon tube was supposed to get rid of H2O2 before putting the substrates (NADH and pyruvate) and reading the absorbance. The activity of LDH is reflected by the decrease in absorbance at 360 nm due to the consumption of NADH during catalysis. The absorbance was too high during the whole experiment so we had to decrease NADH concentration.
In the second attempt, the absorbance was in the wanted range but the enzymatic activity was too low, around 0,0297ΔAbs/min (see figure X). We thought we had lost a great amount of enzymes through the Amicon tube.
In the third try, we characterized the activity of LDH without Amicon tube as we realized the final volume was enough to dilute ROS without disturbing the oxidation of NADH. This time, we wanted to see how the reaction was taking place without any ROS. This experience was repeated three times, results were repeatable and the enzymatic activity was around 0,097 ΔAbs/min.
In the fourth try, we could finally define the effect of H2O2 on the enzyme. Incubation of LDH for 1h with 10mM H2O2 reduces the activity of the enzyme to 17% (figure X).
| Conditions | Incubation volumes | Reaction volumes | Average enzyme activity (ΔAbs/min) |
|---|---|---|---|
| LDH only | 3,12µL LDH 0,4µM → 1,246pmol 46,88µL Tris-HCl 250mM |
338µL pyruvate 16mM → 5,4mM 597µL Tris-HCl 250mM 15µL NADH 12,4mM |
0,0995 |
| LDH+H2O2 | 3,12µL LDH 0,4µM → 1,246pmol 5,1µL H2O2 98mM → 10mM 41,78 Tris-HCl 250mM |
338µL pyruvate 16mM 597µL Tris-HCl 250mM 15µL NADH 12,4mM |
0,0017 |
On the fifth attempt, we followed the whole protocol to evaluate the protective effect of both decapeptide and undecapeptide on the enzyme, alone or in complexe with Mn2+. Unfortunately, no enzyme activity could be detected, even with the enzyme only. We made the assumption that the pyruvate had deteriorated, as it hadn't been made de novo the same day.
Finally, we made a sixth try in which we took the time to review again the effect of oxidation on LDH when it is incubated 1h with H2O2. Results were different this time, there was no difference, in average, of enzymatic activity with or without H2O2.
Sadly, we did not have enough time to repeat these experiments all over again.
Irradiation results
After an irradiation of 50 or 100Gy, transformed Chlamydomonas reinhardtii returned to our lab. We performed a serial dilution and spread cultures onto TAP-agar plates with the aim of diluting enough to count and compare cell concentration. The results of the cultures under the different conditions are shown in figure X.
Results of this experiment weren’t conclusive. Three of the replicates were uninterpretable, most likely due to an oversight by the experimenter : strain 2 dose 1 triplicate 3 - strain dose 2 triplicate 1 - strain 5 dose 1 triplicate 3. Otherwise, replicates seemed consistent. Unfortunately, non irradiated cells weren’t in greater numbers than the irradiated ones. We couldn’t even tell which of the two doses was the strongest one.
We tried to quantify every condition by counting the number of colonies in the last well, with the biggest dilution factor, to help interpreting (figure X). At dose of irradiation 1, we could say that transformed cells were more resistant to γ-radiations than the control strain, but this conclusion is not true for dose 2.
To conclude, the RT-PCR results showed that the transformation was a success on some of the colonies, but we can’t confirm that the expression of the undecapeptide has a significant impact on resistance to γ-radiations yet. With all that we learned, we wanted to do some more experiments to evaluate the power of the undecapeptide, but time was running out.
Safety
Safety is fundamental in the development of genetically modified organisms (GMOs). To reduce the risks, it is important to experiment safely and responsibly by following laboratory safety rules.
Moreover, the handling of GMOs and micro-organisms in the context of laboratory research is highly regulated in France[1]. In this perspective, we were able to develop our experimental tasks thanks to the Laboratory of Quantitative and Computational Biology (LCQB), which benefits from a convention for the use of GMOs given by the Ministry of Higher Education and Research.
Biosafety and biosecurity
Although we have been authorized to handle GMOs, our main concern was to ensure that the modified organisms did not pose any risk to humans or the environment.
In our project, we introduced a gene from a prokaryotic organism into a eukaryotic photosynthetic organism. We chose to use a eukaryotic organism because they are non-pathogenic to humans, better controllable to avoid environmental and contamination risks.
The organisms are classified into risk groups [2] according to the danger they cause to humans and the environment (Table 1).
| Risk group | Pathogenic for humans | Hazard to workers | Spreading | Effective prophylaxis or treatment | Safety equipment |
|---|---|---|---|---|---|
| 1 | No | Unlikely | Unlikely | Available | Open bench work |
| 2 | Can cause human disease | Likely | Unlukily | Available | Open bench work - BSC* for potential aerosols |
| 3 | Can cause severe human disease | Serious | possible | Usually available | BSC for aerosols - Other primary devices |
| 4 | Can cause deadly human disease | Very serious | Likely | Usually non available | Class III BSC - Positive pressure suit |
As we only used organisms belonging to risk group 1, there was no risk to the people working at the WetLab.
For cloning, we used the Escherichia coli DH5α strain. This strain is non-pathogenic and its impact on the environment is minimal. The potential risks associated with this bacterium are related to contact with the skin. We therefore handled this organism wearing gloves and a protective lab coat.
The UVM4 strain of Chlamydomonas reinhardtii is also non-pathogenic. Indeed, this microalga is a GRAS organism (Generally Recognized As Safe according to the FDA) and is therefore considered safe[3]. We still handled it while wearing gloves and a protective lab coat. However, we performed the algal cultures under a fume hood, not because of the risks involved but to protect our samples from contamination. Thanks to the laminar flow incorporated in the hood, we were able to protect our manipulations from any potential contaminants.
Safe project design
Our project was designed so that our modified C. reinhardtii is confined in a bioregenerative life support system (BLSS), so a closed system. However, there is a risk that our alga could end up outside this closed system. If this were the case, it would end up on the International Space Station (ISS) or on Mars, so there would be no risk of environmental contamination.
As for the risk to humans, a study has shown that the peptide we use is not toxic in mice and even provides protection against radiation. Although these results have been demonstrated in human cells they have yet to be confirmed in humans. Nevertheless, these results pave the way for potential protection[4].
Safe lab work
General laboratory safety rules
For a laboratory to function correctly, it is necessary to respect the common spaces (tidy up and leave clean the common work stations and living spaces), to respect the common work tools, and to know how to manage one's needs in work materials (small materials, consumables, culture media, sterilized materials).
The good practices in the laboratory are as follows :
- Respect security instructions
- Know the procedures to follow in case of fire or accident
- Locate fire extinguishers and alarm buttons
- Keep corridors, stairways and halls clear
- Do not obstruct the closing of fire doors
- Leave free access to the isolation valves (gas and water) and to the electrical cut-off devices
- Close doors and windows when leaving your workplace. The last one to leave checks that the doors are closed
- Wear the individual protection equipments (IPE)
- Identify the risks – respect the labeling rules
- Work in the right place (workstation adapted to specific risks)
- Respect the procedures of the isolated worker
In case of professional risk (biological, chemical, radioactive), it is recommended to contact the professional risk prevention department by phone or by email. The Faculty of Science and Engineering also has an infirmary open every day.
Workspace
To work in the laboratory, we had to wear appropriate clothing (long trousers, closed shoes and tied up hair) and a lab coat. To avoid contamination of our samples, we changed our gloves regularly. Then, after each experiment, the samples were disposed of in the appropriate bins and we disinfected our bench to avoid any contamination.
We worked in different spaces with specific equipment. For each room, eating and drinking is forbidden. Certain protections may be necessary depending on the danger to which the experimenter is exposed in the room.
Laundry and preparation area: Ice machine, washing machine, MilliQ water, autoclaves, scales.
The hazards associated with this room are the presence of a pressure vessel (autoclave), the risk of burns, the electromagnetic field (microwave) and corrosive chemicals. In addition, this is a noisy area. In this room, wearing a lab coat is mandatory.
Machine and storage area: Liquid nitrogen tank, centrifuges, culture chamber, cold room, -80°C freezers, plate reader, qPCR machine, PFGE (Pulse-Field Gel Electrophoresis), pipetting robot.
This room presents a biological risk, a risk of asphyxiation, and a low temperature due to the presence of dry ice and liquid nitrogen. Protection of the body, face, eyesight, hands and feet is mandatory in this room. This space is air-conditioned, so the door must remain closed.
BET area : ADN/ARN electrophoresis, gel documentation system.
The hazards associated with this room are ethidium bromide (BET), UV radiation, and the electromagnetic field (microwave). Access to this room is restricted to laboratory staff and requires the wearing of a lab coat, gloves, and face protection when using the portable UV lamp.
The safety officers left us a summary of common sense practices to have in the BET room:
- Always wear your lab coat and gloves when working in this room
- Close the BET dropper bottle well and clean if necessary. Use 1 drop/100 mL TBE/TAE liquid, not more
- Clean the UV gel box when finished with water or ethanol and put your gel in the BET dry waste bin
- After staining your gel, put staining/destaining liquids into the BET liquid waste bin
- After running a gel, cover and label the gel box you are using, noting how many times the same buffer has been reused
- Use a support tray and tissue to remove your gel to take a photo. Do not leave TBE/BET drops on the floor. Clean up spills
- Turn off the UV gel box when finished
- Respect our co-workers by keeping this room clean
For the preparation of the electrophoresis gels, we used ethidium bromide. This fluorescent marker is a DNA intercalator and allows the visualization of DNA on the gel. This product is toxic and mutagenic, which is why we only used it in a dedicated room, wearing a protective lab coat and gloves to avoid carcinogenic risks. We received explanations from the laboratory's safety officers who showed us the specific bin in which to dispose of objects contaminated with the BET. Excess and non-recyclable solutions are then disposed of by a licensed waste disposal company. We also took care not to contaminate surfaces outside this room by changing our gloves before going into another room.
Evacuation
We have received safety instructions in case of evacuation. As soon as we hear the alarm signal :
- Exit and follow the signs
- Head to the gathering point or the secure waiting area (reserved for people with reduced mobility)
- Do not go back
- If there is smoke, get down
- Before leaving, the person in charge makes sure that the windows and doors are closed
COVID-19 protocols
Due to the pandemic, we had to respect certain rules in order to work in a safe environment. The number of people in the lab being restricted, we limited our iGEM team members to 2 people to perform the manipulations. In order to respect this, we had set up a schedule to make sure that each day, 1 or 2 people would be present in order to make the experiments progress. We also had to sign authorisations for each member to work in the lab.
According to government guidelines, we applied the following barrier gestures:
- Wearing a mask is mandatory (except for eating and drinking)
- Wear one lab coat per person
- Wash your hands very regularly
- Cough or sneeze into your elbow
- Use single-use tissues
- Greeting without shaking hands
- Keep physical distance (1.50 m)
- Follow the directions of traffic
- Maximum 1 person in the elevator cabin
As for the work outside the laboratory, we favored remote working sessions, or in the boxes at the university library, wearing masks. We also divided the tasks into small working groups to avoid being in a confined area with all the team members.
References
- [1] O.G.M. en milieu confiné. Ministère de l’Enseignement supérieur, de la Recherche et de l’Innovation //www.enseignementsup-recherche.gouv.fr/pid28968/o.g.m.-en-milieu-confine.html.
- [2] Use of Micro-organisms or Derivatives. https://www.esrf.fr/Infrastructure/Safety/Experiments/Biology_Experiments/use-of-micro-organisms-or-derivatives.
- [3] Arias, C. A. D. et al. Semicontinuous system for the production of recombinant mCherry protein in Chlamydomonas reinhardtii. Biotechnol Prog 37, e3101 (2021).
- [4] Gupta, P. et al. MDP: A Deinococcus Mn2+sup>-Decapeptide Complex Protects Mice from Ionizing Radiation. PLOS ONE 11, e0160575 (2016).
