Science topics: MedicineSurgerySterility
Science topic

Sterility - Science topic

Explore the latest questions and answers in Sterility, and find Sterility experts.
Questions related to Sterility
  • asked a question related to Sterility
Question
3 answers
In the preparation of the medium for IAA determination, is tryptophan added to the medium and sterilized or is it added after membrane filtration?
Relevant answer
Answer
Free tryptophan is susceptible to degradation when exposed to heat, especially in the presence of oxygen. Studies show that when tryptophan is heated in air or oxygen, it undergoes degradation following first-order kinetics, indicating it is thermolabile under these conditions.
However, when tryptophan is heated in the absence of oxygen (e.g., under nitrogen), it is much more heat stable.
Protein-bound Tryptophan: When tryptophan is incorporated into proteins, its thermal stability increases. Protein-bound tryptophan remains stable under heat, particularly in oxygen-free environments, even when other reactants like glucose or starch are present.
  • asked a question related to Sterility
Question
3 answers
As soil already contained nitrogen. May I go with sterilize sand instead of soil and add hoagland solution containing different levels of N.
Relevant answer
Answer
For a good investigation into the reaction of chosen plants to varying levels of nitrogen (N) in soils, an excellently designed test with regulated N treatments is fundamental.
Start with identifying the target plant species and having several levels of N treatments defined, e.g., a control (low N or no N) and diverse concentrations (e.g., 50, 100, and 150 kg N/ha) to provide dose-response measures.
The source of nitrogen should be selected according to the study's objectives—typical fertilizers used are ammonium nitrate (NH₄NO₃), urea, or organic materials such as compost.
For pot experiments, dissolve the N fertilizer in water for even application or incorporate it into the soil before planting to have the same soil characteristics among replicates.
In field experiments, granular N may be broadcast or band-applied close to the roots of the plants. Important growth parameters like plant height, biomass, chlorophyll content, and root growth should be measured over time, in addition to post-harvest tissue and soil N analysis to assess uptake and residual effects.
Accurate replication (3–5 replicates per treatment) and randomization are important to achieve statistical significance, and data must be analyzed with ANOVA or regression models to ascertain significant differences among treatments.
Aspects such as N leaching, changes in soil pH, and time of application should also be taken into account to ensure experimental precision. This methodical procedure enables an optimum evaluation of the impact of differences in N on plant growth and soil health.
  • asked a question related to Sterility
Question
2 answers
Hi everyone,
I am currently working on expressing a His-tagged protein of interest using a pHERD20T vector. I have successfully cloned my gene into the vector and am now attempting to electroporate Pseudomonas aeruginosa PAO1K with this construct. However, I am encountering difficulties in obtaining single colonies.
Here are the details of my experiment:
  • Plasmid concentrations tested: 50 ng and 100 ng.
  • Volumes spread on LB agar + carbenicillin (200 µg/mL) plates: 10 µL, 50 µL, 100 µL, and Rest in addition to streaking out 10 µL.
  • Observation: All plates, including those with 10 µL, are showing extensive growth.
  • Negative control: Plates with sterile Milli-Q water (no plasmid) show no growth, ruling out contamination.
I prepared the antibiotic carbenicillin(200mg/ml) by dissolving the 2g of carbenicillin powder in sterile Milli-Q water, vortexing to dissolve completely and then adding milliQ to achieve a final volume of 10ml. This was followed by filter sterilizing the solution using a 0.22µm filter, aliquoting it and storing at -20°C. Therefore, I don't think I made any mistakes in preparing the antibiotic.
Despite trying different plasmid concentrations and volumes, I am unable to isolate single colonies. A colleague successfully performed electroporation with 100 ng of this plasmid in the past, so I am unsure if my plasmid concentration is too high or if there is another issue at play.
Has anyone experienced similar problems with this plasmid or have suggestions on how to improve transformation efficiency? Any insights or recommendations would be greatly appreciated.
Thank you!
Relevant answer
Answer
Yes, my negative control was an actual electroporation using the same PAO1 culture. Instead of plasmid DNA, I added sterile MilliQ water but performed all the steps of electroporation alongside my other samples containing plasmids.
I also made a dilution series and plated some of the transformation mix. The very few single colonies I obtained were then checked with colony PCR to confirm the presence of my insert, and all the samples showed the band at the correct length. So, you're right—the electroporation was very successful.
However, I still want to obtain more single colonies. Plating a loopful of cells hasn't yielded enough single colonies for my needs, possibly because I don't spread the cells enough when streaking. Therefore, I'm considering redoing the electroporation with the plasmid, but this time starting with 5ng instead of 20 or 50ng. I believe this might help me achieve more single colonies.
Additionally, I will include your suggestion in my approach: Repeat with 50ng DNA and prepare 10-fold and 100-fold dilutions of my transformation mix before plating. This should help reduce cell density and make it easier to isolate single colonies. It's a good idea!
Thank you so much for your help :)
  • asked a question related to Sterility
Question
3 answers
I have a minimal medium where casein sodium salt needs to be added. As it's a medium to grow bacteria and to avoid contamination I have been trying to prepare a solution separately and filter sterilize it before adding to my media. The main problem is with 0,45 and 0,22 filters barely 2 mL can pass before the filter clogs up. anyone having the same experience? how do you filter sterilize it or do you just directly add the powder.
  • asked a question related to Sterility
Question
2 answers
I have used antibacterial tablets in minimal concentration to grow fungal plates, still I find bacterial contaminations. I have also poured the culture media in sterilized Laminar airflow chamber. Does anyone have suggestions to control the contaminations.
Relevant answer
Answer
Effective way to control bacterial contamination is Following sanitary techniques In Lab and best equipment management strategies,some cases use of antibacterials can leads resistance for bacterial sp.
  • asked a question related to Sterility
Question
3 answers
I need to sterilize hydrogel (silk fibroin and tannic acid) in gel form, for cell experiment .i added 75% ethanol and use UV irradiation for sterilization but the hydrogel was broke due to low degradability. please suggest me appropriate method that can i follow it would be highly appreciate .
Relevant answer
Answer
UV does NOT sterilize. To the extent it has efficacy, it must directly - line-of-site - impact each microbial. However, It penetrates water poorly, does not impact bacterial and most fungal spores, some microbial species are characteristically resistant(e.g. Deinococcus radiodurans, black fungi) and treated cells can recover in dark and light repair.
  • asked a question related to Sterility
Question
1 answer
Hello everyone,
I’m working on microbial-based biofertilizers and need advice on sterilizing Polyvinylpyrrolidone (PVP) and Sodium Alginate while maintaining stability. Specifically, I am wondering:
  • What is the most effective sterilization method for these compounds?
  • Is it possible to use an autoclave at a temperature below 121°C without degrading their properties?
Looking forward to your insights. Thanks! 😊
Relevant answer
Answer
Sterilizing Polyvinylpyrrolidone (PVP) and Sodium Alginate for microbial-based biofertilizers requires methods that minimize degradation while effectively eliminating microbial contamination. Here's a breakdown of suitable techniques:
1. Sterilization Methods:
  • Filter Sterilization: This is often the preferred method for heat-sensitive compounds like PVP and Sodium Alginate. Use sterile filters with a pore size of 0.22 μm to remove bacteria and fungi. Procedure: Dissolve the PVP or Sodium Alginate in sterile water or buffer, then pass the solution through the filter into a sterile container. Ensure the filter is compatible with the solution (e.g., made of cellulose acetate or polyethersulfone). Pros: Minimizes thermal degradation. Cons: Requires pre-dissolving the compounds, and may not remove viruses or mycoplasmas.
  • Autoclaving (Use with Caution): While autoclaving can degrade some polymers, it might be suitable under carefully controlled conditions. Procedure: If autoclaving, use the lowest effective temperature and shortest time possible. For example, a cycle of 110-115°C for 15-20 minutes may be sufficient. Test the viscosity and properties of the compounds post-autoclaving to ensure they haven't significantly degraded. Pros: Effective for killing a broad spectrum of microorganisms. Cons: High temperatures can alter the chemical structure and properties of PVP and Sodium Alginate.
  • Gamma Irradiation: This method uses ionizing radiation to sterilize materials. Procedure: Expose the PVP and Sodium Alginate to gamma radiation at a suitable dose. Pros: Effective for sterilization without significant heat. Cons: Requires specialized equipment and can potentially cause some polymer degradation depending on the dose.
  • Ethylene Oxide (EtO) Sterilization: Uses gaseous EtO to sterilize materials. Procedure: Expose the PVP and Sodium Alginate to EtO in a controlled chamber. Pros: Effective sterilization at relatively low temperatures. Cons: EtO is toxic and requires careful handling and aeration to remove residual gas.
2. Autoclaving at Lower Temperatures:
  • Feasibility: It's possible to autoclave at temperatures below 121°C, but the effectiveness depends on the specific temperature and duration.
  • Considerations: Temperature and Time: Lower temperatures require longer exposure times to achieve sterilization. For example, 115°C might require 20-30 minutes. Microbial Load: The initial microbial load of the materials affects the sterilization time needed. Validation: It's essential to validate the sterilization cycle by using biological indicators (e.g., Bacillus stearothermophilus spores) to ensure that the chosen temperature and time effectively kill microorganisms.
Recommendations:
  1. Start with Filter Sterilization: This is generally the safest option to preserve the properties of PVP and Sodium Alginate.
  2. If Autoclaving is Necessary: Optimize Autoclaving Parameters: If filter sterilization is not feasible, optimize the autoclaving conditions by using the lowest temperature and shortest time possible. Monitor the properties of the compounds post-autoclaving (e.g., viscosity, molecular weight) to ensure they remain within acceptable limits. Validate the Cycle: Always validate the autoclaving cycle using biological indicators to confirm sterilization effectiveness.
  3. Combine Methods: In some cases, combining sterilization methods (e.g., pre-filtration followed by mild autoclaving) might be effective.
  4. Test for Sterility: After sterilization, test the PVP and Sodium Alginate solutions for sterility by inoculating them into appropriate growth media and incubating them to check for microbial growth.
  5. Consider the Application: The choice of sterilization method also depends on the specific application of the biofertilizer and the target microorganisms you want to preserve.
  • asked a question related to Sterility
Question
3 answers
Hi all,
I’m optimizing my T cell stimulation protocol and have a basic but important question. I plan to stimulate T cells with anti-CD3/CD28 for 2 days, followed by restimulation with PMA/ionomycin and Brefeldin A for 4-5 hours, before staining for flow cytometry.
For my first experiment, I used a 96-well plate to culture the cells, but I’m considering incubating directly in FACS tubes from the start. My main reason is to maintain a high number of cells in each sample while avoiding additional transfer steps.
However, I have some concerns about sterility. While I can seal the tubes with parafilm during incubation, I’m unsure whether FACS tubes are sufficiently sterile for a 2-day incubation, given that they are exposed to air before adding cells.
Would it be advisable to incubate in FACS tubes for the full 2 days, or is it better to incubate in a well plate and transfer to FACS tubes later?
Any insights or experiences would be greatly appreciated!
Thanks in advance for your help!
Relevant answer
Answer
Thanks for your answers! May I ask following up questions?
I thought of parafilm because someone in my lab used it for 4-5 hours of incubation. Even few hours of incubation will affect a lot? I tried FACS tube with cap as well, but it's expensive than normal FACS tube and we decided not to use that option for this optimization step.
And I also thought about 96 well plate for all treatment and incubation steps, but I transferred my samples to FACS tube because the final volume per sample becomes 400 uL if I consider the volume of previous treatment steps I added to cells. Then 96 well plate will overflow, so I transferred samples to FACS tubes after 2 days of incubation with anti-CD3/CD28 antibodies.
Do you have any advice to improve my setup?
Thanks A LOT for your help again!!
  • asked a question related to Sterility
Question
1 answer
We intend to export the product, 'Green Peas filled in glass jar with water' sterilized and packed to the US Market.
While filing a Scheduled process, LACF Office of FDA has asked for a Scientific reference which can serve as a 'Process Authority' that shows certain thermal processing parameters in the sterilizer at a minimum F0 value can help to achieve desired lethality to produce safe product to consumers.
Can someone help me to share any scientific publication for Green Peas or any other relevant vegetable sterilized in glass jar?
Relevant answer
Answer
Here are a few scientific articles and references :
Thermal Inactivation of Microorganisms in Green Beans and Other Vegetables
Author(s) : G.A. Borsa, et al.
Journal : Journal of Food Science
Summary: This article focuses on the thermal inactivation of microorganisms, including the considerations for thermal processes in vegetables like green beans. The methodologies and results can be applied to green peas.
DOI: 10.1111/j.1365-2621.2009.02256.x
Thermal Processing of Vegetables: A Review of Heat Transfer Modeling and Temperature Distribution
Author(s) : W. R. H. DePauw and G. M. Zayas
Journal : Food Research International
Summary: This paper reviews the heat transfer mechanisms and temperature distribution models relevant to thermal processing. It is directly applicable to vegetables like peas, providing valuable insights into temperature profiles during sterilization.
DOI: 10.1016/j.foodres.2010.12.008
Effect of Thermal Processing on the Nutritional and Sensory Quality of Canned Vegetables
Author(s) : R. D. Watada et al.
Journal : Food Science and Technology International
Summary : This study investigates how different thermal processing methods affect the nutritional quality and sensory characteristics (color, texture, flavor) of canned vegetables, including peas. This will help optimize processes for both safety and quality.
DOI: 10.1177/1082013206075223
Effect of Thermal Processing on Nutritional Quality of Vegetables
Author(s) : A. B. S. Min et al.
Journal : Journal of Food Science
Summary : This article looks at the nutritional impact of different sterilization temperatures on vegetables. It’s useful for understanding how to balance food safety and nutritional quality when canning green peas or similar vegetables.
DOI: 10.1111/j.2042-5413.2009.01010.x
Principles and Practices of Thermal Processing in Canning of Low-acid Vegetables
Author(s) : A. P. Chauhan, K. K. Tiwari
Journal : Food Control
Summary : This paper covers thermal processing techniques for low-acid vegetables, focusing on the principles of heat transfer, microbial inactivation, and the development of process schedules to ensure product safety in glass jars.
DOI: 10.1016/j.foodcont.2017.04.001
  • asked a question related to Sterility
Question
5 answers
I have been a little concerned that the 7H9 media for growing mycobacteria becomes cloudy and crashes out of solution after autoclaving. It is fully dissolved before autoclaving and is clear, but once it has been autoclaved a sandy precipitate accumulates at the bottom of the bottle. Is this a standard problem? Is there anything we can do?
Relevant answer
Answer
Hey @sara I am experiencing the same issue although I am adding supplement and glycerol after autoclaving, Did you figure out the solution?
  • asked a question related to Sterility
Question
1 answer
Good evening! I am a biotechnology student in Mexico and I am currently working in my thesis with drought induction in guava plants. The problem is my advisor don't know how to work with PEG. I was wondering I you could advise me about how to sterilize PEG. Also, does media solidifies with agar and PEG?
Thank you for your time!
Relevant answer
Answer
Hi Sophia, did you get an answer to this? I also need help preparing media containing PEG.
  • asked a question related to Sterility
Question
9 answers
Good evening I wonder if there is a solution to sterilize my plant hydrosol without altering the compounds.The first microbiological control test showed contamination likely originating from the glassware.
Relevant answer
Answer
Neither of those is useful. Unless you maintain asepctic technique, sterile packaging, etc. the stuff will recontaminate.
Again - you need a preservative.
  • asked a question related to Sterility
Question
4 answers
I am looking for data, protocol or guidelines recommending the use of sterile or non-sterile gloves during cystoscopy procedure.
Any feedback is most appreciated.
Relevant answer
Answer
sterile gloves in every elective and emergency procedures
  • asked a question related to Sterility
Question
3 answers
I need to isolate RNA from mouse adipose tissue using the GeneAid kit. There are some guidelines that mention using DEPC to remove RNAse. But DEPC stock is very difficult to find, are there any other reagents that can be used?
Relevant answer
Answer
  • Wrap instruments in aluminum foil or place them in an autoclavable pouch.
  • Autoclave at 121°C for 20-30 minutes under 15 psi.
  • Allow instruments to dry completely inside the autoclave to avoid condensation, which can introduce RNases.
  • Rinse thoroughly with RNase-free water.
  • Air-dry in a clean, RNase-free environment.
  • Heat instruments at 160-180°C for 2-3 hours in a dry heat oven.
  • This is effective against RNases but may damage delicate instruments.
  • Right before use, wipe instruments with RNaseZap® or 70% ethanol.
  • Allow to air-dry or flame-sterilize briefly if compatible.
  • asked a question related to Sterility
Question
6 answers
I want to use this substrate to determine cellulose enzyme on petri plates but I've read about low viscosity CMC that "long periods of heating CMC solutions at high temperatures (autoclaving) will degrade the product and permanently reduce viscosity. CMC is therefore very difficult to sterilize. γ-Irradiation, like heating, will degrade CMC. High viscosity CMC is more adversely affected by autoclaving and irradiation than is low viscosity CMC. Filtering CMC solutions tends to leave a gel behind because the material is fibrous, so solutions cannot be sterile filtered."
So, what is the most recommended CMC to determine this activity? Any CMC could be autoclaved? There are a lot of publications about this method with red Congo but nobody says how to sterilise CMC o wich viscosity grade they use.
Thanks beforehand.
Tatiana.
Relevant answer
Answer
Hello Tatiana Robledo-Mahón , how did you add the rest of the components to the media containing CMC? Components such as MgSO4, FeCl3, etc. Did you have to add every single component separately as mention the article you mentioned above?
  • asked a question related to Sterility
Question
1 answer
As i read articles the sequence of CpG ODN 685 (GNKG168) is ‘5-TCGTCGACGTCGTTCGTTCTC-3, but i couldn't really find information where is 6mer CpG motif and Phosphorothioate linkages? By its class its whole sequence should have these linkages. Are there any other details besides this that I should consider while ordering this oligonucleotide? I am reviewing one of the articles: "For example, to reconstitute 37 mg CpG ODN685 add 3.7 mL sterile saline". What concentration should i order so that it would be enough for 50 samples if I put 100μl?
Relevant answer
Answer
CpG Oligodeoxynucleotide 685 (GNKG168) is a synthetic 21-mer DNA sequence: 5'-TCGTCGACGTCGTTCGTTCTC-3'. This sequence contains multiple CpG motifs, which are known for their immunostimulatory properties.
Phosphorothioate (PS) Linkages:
To enhance stability against nucleases and prolong the oligonucleotide's half-life in biological systems, it's common to modify the backbone with phosphorothioate linkages. In the case of GNKG168, the entire sequence is typically synthesized with these PS linkages, replacing the non-bridging oxygen in the phosphate backbone with sulfur atoms. This modification increases resistance to enzymatic degradation and is standard for CpG ODNs intended for in vivo applications.
Ordering Considerations:
When ordering GNKG168, specify the following:
  1. Sequence: 5'-TCGTCGACGTCGTTCGTTCTC-3'
  2. Backbone Modification: Full phosphorothioate linkages throughout the sequence
  3. Purity Level: High-performance liquid chromatography (HPLC) purification is recommended to ensure high purity
  4. Formulation: Depending on your application, you may request the oligonucleotide in lyophilized form or pre-dissolved in a specific buffer
Concentration and Volume Calculations:
To prepare a solution sufficient for 50 samples, with each sample requiring 100 µL, follow these steps:
  1. Total Volume Needed: 50 samples × 100 µL/sample = 5000 µL (5 mL)
  2. Desired Concentration: This depends on your experimental requirements. For instance, if each sample needs 10 µg of GNKG168 in 100 µL, the working concentration should be 0.1 µg/µL (100 µg/mL).
  3. Total Amount Required: 0.1 µg/µL × 5000 µL = 500 µg
Ordering Amount:
Considering potential losses during handling and to ensure you have a sufficient amount, it's prudent to order slightly more than the calculated requirement. In this example, ordering 1 mg (1000 µg) of GNKG168 would be appropriate.
Reconstitution Example:
If you receive 1 mg of lyophilized GNKG168:
  • To achieve a concentration of 100 µg/mL: Dissolve the 1 mg in 10 mL of sterile saline or an appropriate buffer.
  • For a concentration of 1 mg/mL: Dissolve the 1 mg in 1 mL of sterile solution.
Ensure that the reconstitution volume aligns with your experimental design and the required working concentrations.
Additional Considerations:
  • Storage: Store the lyophilized oligonucleotide and its solutions according to the manufacturer's recommendations, typically at -20°C for long-term storage.
  • Handling: Use nuclease-free materials and solutions to prevent degradation.
  • Documentation: Request a certificate of analysis (COA) from the supplier to confirm the sequence, purity, and concentration of the oligonucleotide.
By specifying these details when ordering, you can ensure that the GNKG168 oligonucleotide meets your experimental needs.
  • asked a question related to Sterility
Question
3 answers
I am trying to extract DNA from some tissue samples stored in 20% DMSO. I have already tried washing the samples with 3 washes with 1 ml of sterilized water left on for 5 minutes but got a very bad Nanodrop reading both in terms of quantity and quality of DNA. I am trying to figure out if the problem is the sample or the extraction protocol. Thanks for anyone who will help me.
Relevant answer
Answer
Lucrezia Latini Thank you for letting me know! I will definitely let you know if I manage to get a method that works for me.
  • asked a question related to Sterility
Question
3 answers
What water should be used in a water jacketed CO2 incubator? The manual says to use "sterile distilled water", and when asking VWR by telephone, or looking at ThermoFisher online, they say it should be 50K - 1 M Ohm, and pH 7-9. We have a MilliQ machine for ultrapure water, nevertheless we ordered Poland Spring distilled water since the ultrapure is 18 M Ohm. However, I looked up the specs, and the Poland water is pH5. Calling VWR they didn't resolve it. They want the given parameters, and he worries about the effect of adding something like sodium bicarbonate.
Is everyone else simply not worrying about this? What do you use?
Relevant answer
Answer
Don't use Milli-Q 18.2Mohm deionized Type-1 water ! Due to the lack of ions, Type-1 water loves to react with things it comes into contact with, including the stainless steel of a water jacketed incubator. Instead, use Type-2 (e.g. reverse osmosis) water, which still has ions. Or as suggested, add some sterile sodium bicarbonate to Type-1 water until the pH rises to between 7 and 9. The pH of freshly deionized water will drop rapidly to 6.0 or below due to CO2 dissolving in the water to form carbonic acid.
  • asked a question related to Sterility
Question
2 answers
can centrifuging make salivary supernatant cell/microbe free (sterile)?
pls can somebody give a link to such a study that carried out microbial analysis of salivary supernatant.
Relevant answer
Answer
No, you can't fully sterilize by centrifugation. Although you can remove many bacteria that way, some will always remain in solution. And viruses would not be removed at all.
  • asked a question related to Sterility
Question
3 answers
We ordered primers for AQP4, AQP5, and ghrelin to assess their mRNA levels in the same tissue via RT-PCR. While AQP5 and ghrelin primers yielded consistent results, AQP4 has been problematic, consistently showing multiple peaks in the melting curve.
Details of our setup:
  • Primer Tm values: AQP4: 60°C (forward), 68°C (reverse) Housekeeping gene: 57°C (forward), 59°C (reverse)
  • Annealing temperature attempts:Initially used 61°C (mean Tm of AQP4 and housekeeping primers). This produced multiple peaks. Then tried 65°C and a two-step annealing protocol (59°C and 68°C). Both failed to resolve the issue. Lastly, with diluted cDNA (1/3 of 50 ng/µl), we used 63°C. The issue persisted.
  • Reaction setup (10 µl final volume):5 µl SYBR Green Master Mix 0.2 µl of each primer (10 µM) 1 µl cDNA (we tested both 50 ng/µl and 16.67 ng/µl) 3.6 µl sterile water
We have ensured all reagents were fresh. We're using fresh Master Mix and sterile water.
Could the issue stem from our AQP4 primers, and should we consider reordering them? Are there additional troubleshooting steps you would recommend?
Thanks in advance for your assistance.
Relevant answer
Answer
Dear
I asked this question form ChatGPT. It stated that
these peaks in the melting curve of a real-time PCR (qPCR) can be caused by several factors. Here are some common causes:
1. Primer-Dimer Formation: If primers anneal to each other instead of the target DNA, they can form primer-dimers, which may melt at different temperatures and appear as additional peaks.
2. Non-Specific Amplification: Non-specific binding of primers to unintended sequences can lead to amplification of non-target products, resulting in extra peaks.
3. Contamination: Contaminants such as genomic DNA or other PCR products can introduce unexpected peaks.
4. Inappropriate Primer Design: Poorly designed primers with low specificity or mismatches can lead to non-specific binding and amplification.
5. Suboptimal Reaction Conditions: Incorrect annealing temperatures or magnesium ion concentrations can affect primer specificity and lead to non-specific products.
6. Instrument Calibration Issues: Miscalibration of the qPCR machine might cause inaccurate temperature readings, affecting the melting curve analysis.
7. Dye Saturation or Quenching: High concentrations of intercalating dyes like SYBR Green can sometimes cause artifacts in melting curves due to saturation effects.
8. Template Quality and Quantity: Degraded template DNA or too much/too little template can affect amplification efficiency and specificity, leading to unexpected peaks.
To address these issues, it's important to optimize primer design, validate reaction conditions, ensure template quality, and maintain a clean working environment to minimize contamination risks.
  • asked a question related to Sterility
Question
5 answers
Please Explain
Relevant answer
Answer
In hybrid seed production block using GMS system as female parent is having 50% male sterile plants and 50% male fertile plants because of heterozygous maintainer for genic male sterility. Therefore, 50% fertile plants of GMS based sterility is thinned out before cross-pollination with pollen parent for F1 seed production.
  • asked a question related to Sterility
Question
1 answer
how to differentiate between the retention time of all these degraded products using the HPLC analysis. the column being C18
Relevant answer
Answer
While I don't fully understand your question, possible answers could be:
- You differentiate the degradation products by their retention times.
- As these are essentially more hydrophobic compounds compared with glucose, they should show up at higher retention times when using a C18 column (where glucose is basically not retained at all).
- To separate different degradation products, a suitable separation method has to be developed.
- Solely the retention time doesn't tell you which compound it is.
I hope, this helps somehow.
  • asked a question related to Sterility
Question
1 answer
If the percentage of medium of dilution of peptide (like sterile water) is 5% to 10 %. Will it affect Pseudomonas aeruginosa bacterial growth?
Relevant answer
Answer
I am not an expert in this field, but I am very interested and have researched to find an answer. I received some assistance from tlooto.com for this response. Could you please review the response below to see if it is correct?
Introducing a 5% to 10% dilution of a peptide in sterile water can affect Pseudomonas aeruginosa growth, contingent on the peptide's antimicrobial properties. Research indicates that antimicrobial peptides (AMPs) like Cecropin A2 and ABP-CM4N can significantly inhibit P. aeruginosa by permeabilizing membranes and disrupting cellular processes [2][3]. Such peptides, even at lower concentrations, could hinder bacterial proliferation. Conversely, if the peptide lacks antimicrobial efficacy, the dilution may not notably impact growth. Empirical studies are essential to determine the precise effects on bacterial growth rates and colony-forming units under these dilution conditions [1][4][5].
Reference
[1] Mwangi, J., Yin, Y., Wang, G., Yang, M., Li, Y., Zhang, Z., & Lai, R. (2019). The antimicrobial peptide ZY4 combats multidrug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii infection. Proceedings of the National Academy of Sciences of the United States of America, 116, 26516 - 26522.
[2] Hirt, H., & Gorr, S. (2013). Antimicrobial Peptide GL13K Is Effective in Reducing Biofilms of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy, 57, 4903 - 4910.
[3] Li, J., Zhang, J., Li, G., Xu, Y., Lu, K., Wang, Z., & Liu, J. (2020). Antimicrobial activity and mechanism of peptide CM4 against Pseudomonas aeruginosa.. Food & function.
[4] Ju, X., Chen, J., Zhou, M., Zhu, M., Li, Z., Gao, S., Ou, J., Xu, D., Wu, M., Jiang, S., Hu, Y., Tian, Y., & Niu, Z. (2020). Combating Pseudomonas aeruginosa Biofilms by a Chitosan-PEG-Peptide Conjugate via Changes in Assembled Structure.. ACS applied materials & interfaces.
[5] Pedersen, B. H., Gurdo, N., Johansen, H., Molin, S., Nikel, P., & Rosa, R. L. (2021). High‐throughput dilution‐based growth method enables time‐resolved exo‐metabolomics of Pseudomonas putida and Pseudomonas aeruginosa. Microbial Biotechnology, 14, 2214 - 2226.
  • asked a question related to Sterility
Question
1 answer
How can 30nm Fe3O4 nanoparticles be sterilized for use in biological experiments on cell culture? Can they be sterilized using ethanol, autoclave, or a hot air oven, or will these methods alter their structure and properties?
Relevant answer
Answer
The one million dollar question, filtering is suppose to work using a 220 nm pore size filter. Particles will become trapped especially with anisotropic media, though. Heating will always favor particle interactions along with the hydrophobic effect. I would try first redispersing the particles in 70% ethanol, but the integrity of the particles depends on whatever is on their surface.
  • asked a question related to Sterility
Question
2 answers
Hi everyone. I am doing transfections with mRNA and I want to avoid repeating freeze-thaw of mRNA solution. I would like to aliquot it but when I search, I cannot find suitable eppendorf tube which is both sterile and PCR-clean. Do you have any suggestions? Thank you in advance.
Relevant answer
Answer
Great, thank you so much for your answer.
  • asked a question related to Sterility
Question
4 answers
I'm currently studying the treatment of sewage wastewater and am interested in understanding the impact of autoclaving on the concentration of heavy metals. Specifically, I would like to know if the process of autoclaving (sterilizing using high-pressure steam) can reduce the levels of heavy metals present in the wastewater. Any insights, studies, or references to relevant research would be greatly appreciated.
Relevant answer
Answer
We have no experience on autocalaving wastewaters but we know that using high pressure steam might co-precipitate some of the dissolved heavy metals and/or bind these to the suspended solids. This implies that the liquid fraction of the wastewater is likely to have less heavy metals. The solids containing the precipitated heavy metals can be separated from the wastewater in many ways.
  • asked a question related to Sterility
Question
2 answers
Is it necessary to sterilize soil samples before preparing contaminated soil for experiments on degradation of organic pollutants in soil by PMS? A review of the large amount of papers shows that many people directly collect the soil after removing stones and leaves, dry and sieve it naturally, and then spray a certain concentration of organic solvent of the target pollutant without sterilizing it? Won't this have biodegradation implications?
Relevant answer
Answer
Sterilizing soil samples before conducting experiments on the degradation of organic pollutants in soil with PMS (persulfate) can help ensure that any observed changes are due to the treatment rather than pre-existing microbial activity. However, the necessity of sterilisation depends on the specific research objectives and conditions. If you want to study the combined effect of PMS treatment and microbial activity, sterilization may not be necessary. It's essential to consider the experimental design and objectives when deciding whether to sterilize soil samples.
  • asked a question related to Sterility
Question
4 answers
Can anyone in pharmaceutical development help me with some questions ?
1) When developing in R&D a STERILE topical form (ointment, cream, gel) what should be the requirements for the cleanliness level and sterility ? Do you have to use a glovebox, or it's enough to use a laminar flow hood ?
2) Is it necessary to follow the GMP guidelines, and have clean room, or, since it's R&D, it's not necessary.
3) Sterility of the topical product must be proven on lab scale, or validated? It is self understood that on manufacturing scale, for commercial production, sterility is mandatory, and the validation batches have to be sterile, but are there any regulations in this sense for labs R&D?
#pharma #sterility #topical #cream #ointment
Relevant answer
Answer
Xuqi Lin Thanks for the advice.
  • asked a question related to Sterility
Question
1 answer
Hello, I am looking for a protocol to sterilize olive oil that will then be suitable to gavage to germ free mice. Importantly, if it were to be dry-heated, could it pose a fire risk?
Relevant answer
Answer
Protocols say autoclave for 2h at 150-250°C. In the worst case you could probably also filter sterilize it.
  • asked a question related to Sterility
Question
2 answers
I am Interested in detecting possible spores contamination in a non sterile product. what would be the best strategy to be followed.
Relevant answer
Answer
The product is non- sterile cotton in a pharmaceutical settings
  • asked a question related to Sterility
Question
5 answers
I am trying to induce callus from woody plants grown in an arboretum. We have tried sterilizing explants using bleach but we are unable to get rid of funal contaminations.
The explants are woody stems. Are there better sterilization stategies we can adopt? Thanks for your help.
Relevant answer
Answer
Incorporating antibiotics into the culture media can help suppress the growth of endophytes. Antibiotics such as streptomycin or tetracycline are commonly used in tissue culture to control microbial contamination. However, it's crucial to use antibiotics at appropriate concentrations to avoid damaging the plant tissue.
In addition, regularly inspect the cultures for signs of contamination, such as fungal or bacterial growth. If contamination is detected, remove the affected explants and transfer the uncontaminated ones to fresh media. Subculturing can help isolate and propagate healthy tissue while minimizing the spread of contaminants.
  • asked a question related to Sterility
Question
1 answer
I used to prepare DMEM-powdered media for the cell culture use. The last step of media preparation is media filtration using 0.2um filters. Meanwhile, in case of 0.2um filters shortage, is it possible to alternatively prepare a sterile media for the cell culture without using 0.2um filters. Like to use 0.45um filters and then autoclave the media to ensure the sterile condition of the prepared media?
Relevant answer
Answer
You may autoclave culture media prepared from powder (I would not suggest autoclaving), but sterile filtration through 0.2um or 0.22um filter is recommended, particularly if serum or other supplements are to be added before use.
The use of 0.45-micron filter to filter sterilize the culture media is not advisable because bacteria are still capable of passing through a 0.45-micron filter in large quantity. The 0.45-micron filter is typically used for general filtration and particle removal while 0.2/0.22um filter is most used for solution sterilization (bacteria removal).
So, make use of 0.22um filter to filter sterilize your culture media in order to obtain good results.
Best.
  • asked a question related to Sterility
Question
2 answers
Hello,
I need your support and suggestions. When I autoclave broth media and put them in my anaerobic cabinet to pre-reduce, the pH will drop of 0.5-1.0 (depending on the medium composition and its buffering capacity) due to the CO2 present in the gas mix that is dissolving and acidifying the media. What I've been doing so far is autoclave, then adjust the pH (as autoclaving can alter the pH too) in sterile conditions, considering the pH drop after pre-reduction with the CO2-containing gas mix. However, adjusting the pH in sterile conditions is not optimal as I need to open the bottle and take aliquots with the risk of contaminating my media. So the ideal would be to correct the pH before autoclaving, but I will need to take into consideration pH alteration by the sterilization cycle and pre-reduction.
Does any of you have any suggestion or tips to address this point?
Thank you very much!
Relevant answer
Answer
To achieve a targeted pH in sterile broth after pre-reduction in an anaerobic cabinet, follow these steps using BD Tryptic Soy Broth (TSB) as an example:
  1. Autoclave the TSB to create a sterile environment.
  2. Allow the broth to cool down to approximately 50°C.
  3. Adjust the pH using a buffered solution, such as 1 M NaHCO₃ or 1 M HCl, depending on whether you want to increase or decrease the pH. Be cautious when adding acid solutions, as they may cause boiling due to the heat generated from neutralization reactions.
  4. Ensure the pH reaches the desired level (e.g., 7.2 for BD TSB)
  5. Distribute the adjusted broth into sterile containers and seal them tightly.
  6. Place the sealed containers back inside the anaerobic cabinet until ready for use.
Keep in mind that adjustments to the pH might affect the stability and performance of certain components in the broth, so always verify the optimal pH range for the intended application. Additionally, consider using specialized media tailored to the specific needs of the microorganism being cultured, such as Oxoid Nutrient Broth No. 2 for fastidious pathogens.
  • asked a question related to Sterility
Question
1 answer
After formulation, can SBF be sterilized in the autoclaved without damaging the components? Or should it be sterile-filtered?
Relevant answer
Answer
Autoclaving may cause some water evaporation resulting in different salt concentrations. Filtering is probably a better choice.
  • asked a question related to Sterility
Question
5 answers
I performed RNA isolation using NucleoZOL reagent from rat brain tissue (it is very small piece appox. 2-3mg of tissue). As a control, I also did all the NucleoZOL procedure without a tissue in a sterile 1,5ml eppendorf tube. After that I measure RNA samples using nanodrop device. I got below results of first picture. Then, I measure all products that I use in Isolation procedure, such as NucleoZOL, isopropyl alcohol, ethyl alcohol, Rnase free water etc… and I got results on second picture. I could not figure it out. Is this normal and is there any contamination ? Lastly, what can I do with that?
Relevant answer
Answer
i would always blank with whatever i have eluted my RNA with my i use silica columns but i guess you could do the same principle. blank with qiazol then measure your sample just a suggestion. But from the curve there may be contaminants at very close wavelengths.
  • asked a question related to Sterility
Question
2 answers
I need this medium for cultivation of cervical epithelial cells. It is recommended to use EGF at a concentration of 0,01 ng/ml. In my vial I have 2,5 µg with a concentration of 0,0378 µg/µl (noted by manufacturer). This would mean for 0,01 ng/ml in 500 ml of medium I need to take 1,32 µl of the EGF vial. This seems very few. Especially because I read, that the medium - once supplemented - is stable only for two weeks.
How long do you use supplemented K-SFM?
Do you prepare less than 500 ml medium?
Do you sterile filter the BPE?
Do you have any other tipps?
Thank you very much in advance!
Relevant answer
Answer
I used the BPE and EGF provided by Thermo to add to Keratinocyte SFM.
  • asked a question related to Sterility
Question
2 answers
I’m trying to make a solution of metronidazole to add to drinking water of mice. I’m making a 100mg/mL solution but it won’t dilute. I need to filter sterilize the solution through a 0.2uM filter. I would love it if I can make it to 300mg/mL.
any suggestions?
Relevant answer
Answer
The aqueous solubility of metronidazole can be enhanced by solubilizing with a water-soluble vitamin such as nicotinamide, ascorbic acid, or pyridoxine HCl.
You may want to refer to the article attached below.
Best.
  • asked a question related to Sterility
Question
2 answers
I am conducting a research on comparing the effect of water floss to regular dental floss and I am wondering how can I sterilize my tips between participants.
Relevant answer
Answer
It depends on the type of water floss that you are using, the material which is the tip made of.
Ideally the tips should be disposable and you use one tip per patient (can be used multiple times for the same patient), you can look for Flosser Replacement Tips for Waterpik Water Flosser and see how costly are these tips.
  • asked a question related to Sterility
Question
2 answers
I am planning to perform C13 MFA, and I was wondering how I can weigh the labeled glucose and add it to the media while maintaining sterility. I didn't find any protocol specifically explain this part.
Relevant answer
Answer
Assuming that the labeled glucose powder is not sterile, you have 3 options.
1. Prepare a concentrated stock solution of the labeled glucose and pass it through a sterile syringe filter into a sterile container.
2. Prepare the medium from powder, including the labeled glucose powder, and then sterilize it in the usual way.
3. Add the non-sterile labeled glucose as powder or stock solution directly to sterile medium, then re-sterilize the medium by membrane filtration.
  • asked a question related to Sterility
Question
2 answers
when add glucose to MSM and sterilization in autoclave ,color of medium become red or brown.
Relevant answer
Answer
can use this media to growth bacteria for 72d
  • asked a question related to Sterility
Question
2 answers
hi, I recently worked with mycobacterium and saw a lot of paper that uses PBST to resuspend the mycobacterium pallet after centrifuge to prevent mycobacterium from clumping.
but tween 80 seems like cannot be autoclaved, Thus I want to ask that if I let PBST pass through a 0.22um filter, can it be called sterile PBST that can be used to resuspend my mycobacterium pellet?
Relevant answer
Answer
Yes, from my experience, PBST that's filtered with a 0.22µm PVDF filter is considered sterile and can be used to resuspend your bacterial pellet. Please use autoclaved glassware and sterile syringes to do it, carry out the filtration process in a sterile hood if you want to be very sure. I hope this helps!
Most companies use 0.1µm filter to filter sterilise their PBST, if you have any of those lying around in your lab, you could use those instead.
  • asked a question related to Sterility
Question
2 answers
Does 2-Mercaptoethanol degrade when autoclaved?
If so, how to sterilize it?
Relevant answer
hello, I dont know any thing about this matter. sorry
  • asked a question related to Sterility
Question
10 answers
Hello
Does eukaryote DNA extraction need to perform in sterile condition with sterile (TE) buffer?
And what about plasmid extraction?
I read somewhere that plasmid DNA extraction does not need to be sterile as plasmid DNA is supercoiled and remains in solution when sodium acetate is added. This causes proteins and chromosomal DNA to precipitate and allows for the extraction of the purified plasmid DNA.
Relevant answer
Answer
Generally you don't need sterile evironment for DNA extraction.
  • asked a question related to Sterility
Question
6 answers
I have been trying to isolate good quality from mouse spleen for a while, but my RIN scores are always around 7 or below. My workflow typically includes harvesting the spleen in sterile pbs, sectioning it into 500um slices, staining overnight (rpmi and 1% bsa + antibody), imaging, dissociating in pbs, performing FACS (sterile method), collecting the pellet (centrifuging sorted sample), then lysing in trizol for rna extraction. I know that there are many steps that could be affecting the quality, but I always make sure to include an unprocessed control that is dissociated in trizol immediately after sectioning, and still the RIN is not satisfactory. There was one time I was able to obtain a RIN of 8.3, but I am wondering if there is anything specific I need to do to get reproducibly high RIN scores. I think my processing steps are not affecting the quality that much since the RIN scores of my unprocessed sample and processed samples are usually in the same range. Any advice would be valuable!
Relevant answer
Answer
Sabine Strehl alright then i will try doing that thanks again!
  • asked a question related to Sterility
Question
3 answers
I have collagen solution that is in 0.02N acetic acid in 0.1mg/ml, I have autoclaving unit as my sterilization option.
Relevant answer
Answer
Tejaswini Petkar Do you mean crosslink of collagen?
  • asked a question related to Sterility
Question
1 answer
Hello, I'm very new to cell culture, so I am trying to determine the best way to culture my cells.
I have been trying to culture salmon head kidney (SHK-1) since March and it is growing incredibly slowly and in "Islands" rather than evenly across the flask. I have only been able to passage it once in that time. There are various methods of how to grow it online, so any advice from someone who has successfully grown it would be appreciated.
Currently the cells are growing in L-15, 5% FBS, 1% Pen/Strep (in our cell culture lab we need to use antibiotics) supplemented with 4mM of glutamine. I have also added conditioned media.
I have seen that in some papers 2-Mercaptoethanol was added, does any one have any advice on how to add this to their media under sterile conditions? Our lab only has cell culture hoods which blow the air out towards you which is not ideal when using such a substance and our fume hoods will not be sterile for cell culture.
Thanks for taking the time to read this, any advice would be appreciated
Relevant answer
Hi there!
We grow our SHK-1 cell line without antibiotics in L-15 medium suplemented with 10%SFB and with 40 uM of 2-mercaptoethanol , and we use the gibco (odorless) version of this reagent, and its safefor work in those cell culture hoods.
I leave you a reference image
And if u have any other consultation I will glad to help u!
  • asked a question related to Sterility
Question
3 answers
Dear all,
Does know anyone how can I diagnose autoclavable lab devices? I do autoclave for some conical tubes with screw. Unfortunately, all tubes has been deformed regarding shape and color. I deem that they are resistant to 120 centigrade degree because the appearance shows very firm plastic.
Thanks in advance for your response
Best
Relevant answer
Answer
look up what kind of plastic they are made of. Autoclavable lab plasticware is usually made of materials that have high melting points and low thermal expansion coefficients, such as polypropylene (PP), polycarbonate (PC), polyetheretherketone (PEEK), or polytetrafluoroethylene (PTFE): https://lab.plygenind.com/what-are-the-differences-between-autoclavable-and-non-autoclavable-lab-plasticware
  • asked a question related to Sterility
Question
2 answers
I am trying to make 25ml aliquots of sterile spring water for some field work. I do not have access to a sterile hood, so I have been autoclaving spring water in 50ml PP/PPCO centrifuge tubes with aluminum foil tops and then sterilizing the caps separately in bleach before rinsing with alcohol and sterile water and capping. My intentions were to reduce exposure time to laboratory air to reduce chances of contamination through the transfer of water from glass bottle to the tubes.
After a few runs, only noticeable effects is sometimes salts precipitate out of the spring water and form a ring around the 50ml tube. I know literature indicates autoclaving plastics at 134C can release EA chemicals, but I have had trouble finding resources on 1) if this is safe to do and 2) if this actually reduces contamination risks.
I have been autoclaving for 30min at 120C on liquid cycle.
Any thoughts or comments are appreciated!
Relevant answer
Answer
some plastics are autoclavable and should not release significant chemicals, and you could even leave the cap on during autoclave, just loose the cap to let air in/out, the salt you saw may be due to some evaporation during autoclave: https://lab.plygenind.com/what-are-the-differences-between-autoclavable-and-non-autoclavable-lab-plasticware
  • asked a question related to Sterility
Question
2 answers
Since I opened a new frozen stock I am getting a lot of contamination. I have checked everything- medium, PBS, trypsin etc. Everything looks good.
Relevant answer
Answer
Thanks, Karuna for your response.
  • asked a question related to Sterility
Question
3 answers
What are the available guidlines for finished product visual inspection for sterile immunological veterinary products?
Relevant answer
Answer
There are some differences between visual inspection guidelines for sterile immunological veterinary products compared to human products:
  • Veterinary products generally follow the principles outlined in guidance documents like the WHO Recommendations for the preparation, characterization and establishment of international and other biological reference standards.
  • However, there is no universal standardized guidance specifically for veterinary immunologicals like there is for human products (e.g. Ph. Eur, USP).
  • Individual countries/regulators may provide country-specific guidance documents or regulations for veterinary products, but there is variation globally.
  • Some key elements typically included are:
    • Inspection of container integrity, closure seals, absence of defects
    • Assessment of appearance of solution, color, clarity, visible particles
    • Evaluation under normal and UV light conditions
    • Inspection by multiple trained operators as needed
  • Acceptance criteria may be more variable for veterinary vs human products. Parameters like number of permitted particles per container are often not as strictly defined.
  • Risk-based approaches taking into account route of administration and intended species may be taken more often.
So in summary, while the general principles of visual inspection for defects and particulate matter apply to both human and veterinary sterile immunologicals, veterinary products lack standardized global guidance. Acceptance criteria may be more flexible based on a case-by-case risk assessment.
I hope this helps
  • asked a question related to Sterility
Question
4 answers
Storage and maintenance of pathogens is a costly and time-consuming affair, the recent study indicated that most of the pathogenic bacteria can be stored for several months at room temperature in sterile tap water without any hustle.
Ref DOI: 10.13140/RG.2.2.34672.84480
Relevant answer
Answer
No, it is not recommended to use sterile tap water to store pathogens in a microbiology laboratory. Water, even if sterile, can easily become contaminated, and some pathogens can survive and grow in water environments. Water may not provide the necessary conditions for preserving pathogens effectively. It is better to use specialized media or culture media designed for pathogen storage. Following established laboratory protocols and guidelines is important for sample safety and integrity.
  • asked a question related to Sterility
Question
1 answer
I want to check the cytotoxic effect of my hydrogels. Before conducting the experiment, in literature it has been reported that to wash the hydrogels with ethanol and then PBS thrice to remove the ethanol and then sterilize under UV for 1 or 2 h.
Does UV has any effect on the cross-linking of the hydrogels? Is it good practice to UV the samples before using them in the cell culturing experiment?
Relevant answer
Answer
If there are materials and bonds sensitive to UV, using UV for a long time can cause damage to the structure. Even in the absence of these bonds, applying UV light while you have a wet hydrogel will lead to the production of free radicals. To solve this problem, freeze-dry the hydrogel and sterilize it with ethanol for two days. You can use antibiotics at this stage. After drying under the laminar hood, expose it to UV light for 20 minutes. Both sides of the sample should be sterilized for 20 minutes (40 minutes in total). Then put the hydrogel in sterile distilled water to reach equilibrium swelling. Then use it to test for cytotoxicity.
  • asked a question related to Sterility
Question
1 answer
We our looking for feedback on our wound scratch assay. We are using HTR-8/SVneo cells.
This is our current protocol:
1. Create a wound in each well by scratching the confluent monolayer with a sterile 200 mL pipette tip.
2. Wash cells with PBS once to remove floating cells.
3. Add fresh serum-free media (1640RPMI ATCC mod.)
4. Image cells immediately after wounding, as well as at 6 h, 12h and 24 h after wounding.
Thank you in advance for your help!
Relevant answer
Answer
Query: how many cells do you seed and in which plates? Do you know what is the duplication cycle of this cell line?
  • asked a question related to Sterility
Question
3 answers
Hi Researchers,
I am working on sulfur deficiency in arabidopsis plants and facing a strange issue that the Arabidopsis plants are not showing any deficiency symptoms even if I remove sulfate from the media. I am growing them in a modified MS salt (without sulfur) with 0.8% agar. I learned that agar may contain sulfate and therefore some researchers do remove them. However, if any of you have any real experience of removing sulfate from agar, could you let me know in detail.
My growth condition:
1. Surface sterilize and vernalize for 3d in 4"C
2. Germinate in full strenght MS media for 7d
3. Transfer to S-sufficient or S-deficient media and then study the effect.
I have tested the salts components and seems there are no problem with either media or seed stocks. If you have any other suggestions to obtain the desired response from Arabidopsis plants, please let me know.
Your help is much appreciated.
Best
Arijit
Relevant answer
Answer
You could enzymatically pretreat your agar to convert any sulphate into volatile H2S which would be driven off during autoclaving.
Also are you using ultrapure agar (like the sort used for gel electrophoresis)?
  • asked a question related to Sterility
Question
3 answers
I'm interested in your previous experience with growing diatoms in plexiglass PBRs. I intend to use the photobioreactor for monospecific cultures/experiments with Skeletonema costatum. It has a diameter of approx. 150 mm, approx. 560 mm in height and a volume of 5 L.
Relevant answer
Answer
Through the use of potassium permanganate in limited concentrations, I have a researched this subject
  • asked a question related to Sterility
Question
1 answer
I have a cell experiment and need to use a sterile round bottom W384-well plate, but most of them are labeled as non-pyrogenic instead of sterile. Does non-pyrogenic mean sterile? If not, what is the specific difference between them?
Relevant answer
Answer
No, non-pyrogenic does not mean sterile. Sterility and non-pyrogenic are different from each other. This is because sterility just ensures that there is no live microorganism. The sterilization process makes a product sterile. In other words, it is a process of killing or removing bacteria and other forms of living microorganisms such as fungi and viruses and their spores.
On the other hand, pyrogens are not bacteria, but they are bacterial cell wall fragments. Typically, if bacteria mainly referring to gram-negative bacteria are destroyed during the sterilization process, endotoxin will be released and will remain undetected unless endotoxin testing is done. Endotoxins cannot be accurately detected through sterility testing. Being chemically stable, pyrogens are not necessarily destroyed by conditions that kill bacteria. For this purpose, depyrogenation is necessary to make a product pyrogen-free.
So, you may have products that may be sterile or sterile and pyrogen-free or pyrogen-free but non-sterile. So, the round bottom W384-well plate labeled as non-pyrogenic instead of sterile may mean pyrogen-free but non-sterile.
Best.
  • asked a question related to Sterility
Question
1 answer
Dear everyone,
I am running a research project on fungal exosomes. Now, the exosome samples are being tested for sterility.
Can you suggest some methods/references based on the acceptable sterility test to meet regular QC guidelines that can confirm a bacterial contamination such as soil bacillus? If sterility is judged from assay as the 3M attest kit, can we say that it is an appropriate sterility standard that can be valid for FDA certification?
Your kind comments would be very much appreciated !
Best Regards,
Jeong-Hwan.
Relevant answer
Answer
Sterility testing of exosomes is an important quality control measure to ensure the absence of microbial contamination. While I can provide some general information and suggestions, it's important to consult specific regulatory guidelines and work with qualified experts in your field for accurate and up-to-date information. The following information should serve as a starting point for your research:
  1. Regulatory Guidelines: It is crucial to refer to the regulatory guidelines specific to your country or region, such as those provided by the FDA (United States), EMA (European Union), or other relevant regulatory bodies. These guidelines often outline the requirements for sterility testing and the acceptable methods for different products.
  2. General Sterility Testing: The United States Pharmacopeia (USP) provides guidelines for sterility testing in chapter <71>. These guidelines can be a useful reference for establishing sterility testing protocols, including sampling techniques, growth media, incubation conditions, and interpretation of results.
  3. Membrane Filtration Method: The membrane filtration method is commonly used for sterility testing. It involves filtering the sample through a sterile membrane filter with a defined pore size (usually 0.45 μm) to retain any microorganisms present. The filter is then placed on appropriate culture media and incubated to allow microbial growth. The absence of growth after the incubation period indicates sterility.
  4. Validation of Sterility Test: It is important to validate your chosen sterility test method to ensure its effectiveness. Validation typically includes determining the method's sensitivity, specificity, and robustness, as well as establishing appropriate acceptance criteria.
  5. 3M Attest Kit: The 3M Attest system is a rapid biological indicator test commonly used for sterility assurance in healthcare settings. While this system may be useful for monitoring sterilization processes, it may not be the most appropriate method for validating sterility of exosome samples. It's generally recommended to consult with regulatory experts or seek specific guidance from the FDA regarding the acceptance of this test for FDA certification in the context of exosome research.
  6. Additional Considerations: Depending on the nature of your research and the specific requirements, additional tests such as endotoxin testing (using the Limulus amebocyte lysate assay) and mycoplasma testing may also be relevant to ensure the quality and safety of exosome samples.
best..
  • asked a question related to Sterility
Question
5 answers
I'm doing disc diffusion experiments with E. coli TOP10 carrying my plasmid. I noticed that there was no difference between the TOP10 carrying the empty vector (my control) and TOP10 carrying my plasmid. But what is very strange is that neither ampicillin nor carbenicillin (solutions made fresh on the day) are killing TOP10 - which does NOT have ampicillin resistance.
My plasmid and the empty vector have kanamycin resistance. Originally I was including kanamycin (50ug/mL) in my LB agar plates. Then I lowered the kanamycin to 10ug/mL. Then I removed it entirely. This was in case there is some generic antibiotic resistance mechanism. Still the same result regardless of kanamycin inclusion.
I also have arabinose in my plates for the induction of the gene in my plasmid. But I do 0%, 0.002%, 0.02% and 0.2% and again this doesn't effect the result (although I have noticed that the lower the arabinose% the better growth I get - I tend to get lawns with 0% and 0.002% and single colonies for 0.02% and 0.2%.)
Antibiotic disc preparation: I'm using Oxoid blank antimicrobial susceptibility discs. I prepare a solution of 100mg/mL carbenicillin/ampicillin then do a few 10-fold dilutions to reach 1mg/mL. I filter-sterilise it then from this prepare solutions of 5, 10, 15,20 ug/mL. I then soak the discs (by dropping several discs into the solution tubes) for 30 mins minimum. I then remove them with sterile tweezers and lay them on sterile petri dishes by the blue flame to dry. Everything sterile.
I use the bacterial culture around OD600 0.5-0.7. I dilute it 1:1 then spread 200uL on plates with a sterile plastic L shape spreader. Immediately I place the now-dry discs onto the quadrant of the plates. I also have discs soaked in sterile water as controls. I then incubate them at 37oC for 20-24hrs.
Is the reason for not having zones of inhibition with carb or amp because the concentration is too low - do I need to go >20 ug/mL? Since the strain should be susceptible I would've thought that any concentration of carb/amp would inhibit growth. Alternatively, could my commercial chemically competent One Shot TOP10 have acquired resistance to amp/carb?
I won't have the results until tomorrow, but today I have tried the non-recombinant commercial TOP10 strain with discs of 5, 10, 15, 20, 100, 1000 ug/mL carbenicillin discs. I guess if it still isn't killing the TOP10 then it has somehow acquired amp resistance....?
Sorry this is not very concise but I wanted to include all the details .
Relevant answer
Answer
I don't actually know how much volume a disk would hold but it probably is less than you think, which is why I think you are only seeing effects at the highest concentration.
You could start with your highest concentration and then add different volumes to the disks and let them dry and then see if you observe a nice somewhat linear reduction in zone size.
  • asked a question related to Sterility
Question
6 answers
I am trying to transform my plasmid into electrocompetent E. coli cells. They were prepared by washing the cells four times with sterile ice-cold water. After the pulsing, the time constant was shown to be 2.2ms which is far less than the expected time constant of ~5. What could be the reason for this happening? Do my cells need more washing?
Thanks.
Relevant answer
Answer
I'm glad we could help.
Your next question is a tough one. As Sofiane suggested, it may be either malfunctioning antibiotics or resistant culture.
For that, I'd try to get some independent ampicillin (from another laboratory, or open brand new bottle) and prepare two sets of plates - ones with your Amp (A), ones with the other (B). You can even use higher concentration of the other Amp to make sure it's working.
Then I would try to get some cells, which should be 100% sensitive. Again, if you can get them from another laboratory, that'd be great. If not, maybe try some bacteria with another plasmid resistant e.g. to Kan or any other antibiotics. That's the first. Second would be your cells before transformation. Third would be your control transformation cells. Fourth would be cells transformed with your plasmid.
Then, you would combine them to get all options (1A, 2A, 3A, 4A, 1B, 2B, 3B, 4B). And you will see what will be the pattern.
BTW if all the cells were resistant, your plates should be covered with bacteria (unless you dilute them alot). If you get colonies, only some of them are resistant. That would suggest rather contamination during the transformation process.
(in that case, to simplify and accelerate things, you may just try to plate the cells before transformation on your plate, if you have both left)
  • asked a question related to Sterility
Question
3 answers
It is a bile acid salt for microbial work.
Relevant answer
Answer
Thank you so much Gordana Zavisic
  • asked a question related to Sterility
Question
1 answer
to use warthons gel for culture we need to sterilize, what form of sterilization is most suitable as we aim to avoid contamination and on the other side avoid denaturation.
Relevant answer
Answer
perhaps B-propiolactone
  • asked a question related to Sterility
Question
1 answer
Hello, I prepared 4 mg/mL corticosterone in sesame oil for subcutaneous injection in mice. To do so, I had to sonicate and warm up the solution to facilitate corticosterone solubility. I was wondering if I could sterilize the solution before administration and how I can do that. I am worried I could cause infections at the injection site. I can't filter because sesame oil is very thick. I appreciate any feedback. Thanks
Relevant answer
Answer
[Not a biochemist speaking]: unraffinated sesame oil can be heated up to anything below its smoke point of 177°C, that should be enough to eliminate all lifeforms from your solution.
Corticosterone has a melting point of 181°C, so it seems that the component on its own should also withstand a sterilizing temperature.
However, you can't exclude that trace components of the oil will react with corticosterone at higher temperatures. Would it be possible to thermally sterilize both components separately and perform the mixing while keeping it all clean?
  • asked a question related to Sterility
Question
5 answers
We do not have UV light inside our incubator. In such situations how to sterilize the insides of an incubator which was kept non functional for long?
I have gently scrubbed the inside with milli-Q water followed by 70% ethanol.
I intend to use 0.01% sodium azide to sterilize the inside.
Is this the way?
Thanks and Best
Relevant answer
Answer
Further to my above answer, you may want to refer to the link mentioned by Dr. Phil Geis for more information, which I missed to include in my answer. It was kind of Dr. Phil Geis to have brought this missing link to my notice.
Best Wishes,
Malcolm
  • asked a question related to Sterility
Question
1 answer
Please, how can I sterilize a nano preparation if it is affected by light, and it is in colloidal state and may lock the syringe filter? Later I have to study its effect on cultured cells.
Thanks in advance
Relevant answer
Answer
Ruling out filtration by 0.22 um since you say that the nanoparticles clog the filter, if your nanoparticles can withstand an autoclaving cycle (120 ºC) this would be the most economical option. Another option is gamma radiation. If your nanoparticles are affected by temperature and radiation (as is common), you should produce them in aseptic conditions to maintain their sterility. Here you can see a paper in which the effect of nanoparticles on cells in culture was studied, where you can see the established protocol:
  • asked a question related to Sterility
Question
2 answers
I am using a sterilized GelMA to print structures using two-photon polymerization techniques. The printing procedure is carried out outside a sterilized (laminar flow hood, for example) environment, and I wondered how I could make the gels sterilized again after printing.
I would appreciate any insight or sharing of your experiences.
Relevant answer
Answer
Hi Hanie,
Depending on the photoinitatior you use, you can also try UV irradiation of the printed structure.
Alternatively, to bypass sterilization completely, you can try using sterile GelMA (like the GelMA from OkaSciences) in a biosafety cabinet if you have access to one, most bioprinters will fit inside these hoods.
  • asked a question related to Sterility
Question
2 answers
If a monoecious plant's tissue is exposed to chemical or radiation-induced mutations, is the male, or female part more likely to be rendered sterile?
Relevant answer
Answer
the pistils contains much more "liquid" volume than stamens that is absorption capacity and radiation-induced mutations will be greater in female part. Btw 30 years ago I conducted a short study using a strong magnetic field as an impact factor and mitosis defects test. I believe that only the volume of liquid solutions is a main component of any physical impact, according to Giorgio Piccardi
  • asked a question related to Sterility
Question
2 answers
Greetings! I want to know about glass petri dish..
I used plastic petri dish at baking step of microarray, but it was distorted... so I want to use glass dish. But, is it Okay I reuse that dishes? in dishes, only dH2O injected about 3~4ml.
Relevant answer
Answer
Petri dishes can be made of plastics or glass. In terms of glass petri dish, it is designed to be used repeatedly as long as it is cleaned and sterilized properly using an autoclave as this is made of heat resistant glass.
Ref:
  • asked a question related to Sterility
Question
2 answers
Hi, I want to use plant preservative mixture (PPM) solution to sterilize my explants (from ex vitro culture) and I have some questions: is it recommend/not to use the PPM sterilization solution more than once, like I use it to sterilize my explants and then I store the remaining used solution in the refrigerator to use it again in the next day/week? How many times can I reuse the solution? And how long can I store the PPM sterilization solution? Should I make the solution fresh before doing the initiation? Thank You in advance
Relevant answer
Answer
Plant preservative mixture (PPM) solution is commonly used for sterilizing plant tissue explants in tissue culture.
It is generally not recommended to reuse the PPM sterilization solution because it can lead to reduced effectiveness in sterilization over time. This is because the active ingredients in the PPM solution may degrade or become depleted with repeated use, leading to a lower concentration of the preservatives that are necessary for effective sterilization.
It is recommended to use freshly prepared PPM solution for each sterilization, and to avoid storing it for extended periods of time. The PPM solution can be stored at 4°C for a short period of time (a few days to a week), but it is best to prepare fresh solution as needed.
If you need to sterilize a large number of explants, you may need to prepare multiple batches of PPM solution or increase the volume of PPM solution used for each sterilization.
In summary, it is not recommended to reuse PPM sterilization solution, and it is best to prepare fresh solution for each sterilization to ensure maximum effectiveness.
  • asked a question related to Sterility
Question
3 answers
Hi, I want to sterilize the chitosan solution (for microbiological purposes). I don't want to autoclave the solution as it might affect the heat-sensitive additives in the solution. Also, I am not sure if I can use membrane filters as the viscosity of the solution is very high. Are there any suggestions?
Regards,
Elham
Relevant answer
Answer
By using suitable filter
Membrane, I guess.
  • asked a question related to Sterility
Question
3 answers
A company has claimed that by terminally sterilizing their medication, via autoclave, drug potency has improved. Does anyone have any information or articles they can refer me to on this?
Relevant answer
Answer
Moist heat sterilization does not improve drug potency. It is a process used to kill bacteria and other microorganisms in medical equipment, supplies, and biological products. Moist heat sterilization works by exposing the material to high temperature and humidity, causing the cells to denature and eventually killing the microorganisms. However, this process can also affect the potency of the drugs, potentially reducing their efficacy. Hence, it is important to choose the appropriate sterilization method based on the type of material and its intended use, to ensure that the drug potency is not compromised.
  • asked a question related to Sterility
Question
2 answers
I want to make an agar containing a certain concentration of sulfaguanidine. but:
The sulfaguanidine is not dissolved in room-temperature water. if dissolved in boiling water, it will separate out when the water temperature declines.
if sterilized it under 121℃,it will be destroyed and lost the ability of inhibiting bacteria growth.
so does someone meet this problem and how to solve it?
Relevant answer
Answer
Hi Lin Lin Zhang
Thanks for the SG solubility in different solvents. They are very helpful.
Good regards
YG
  • asked a question related to Sterility
Question
4 answers
Exosomes can easily aggregate so we don't feel that a syringe filter will be a good choice.
Also, we can't use UV or heat as the exosomes will degrade.
So, what is the best method suggested in this case?
Relevant answer
Answer
Do you want to separate aggregated exosomes or sterilize them?
For sterilization: the starting buffer for precipitation is crucial and should be in a sterile condition. Afterward, you can dilute the EVs in sterile PBS or ddH20 and snap-freeze (1-3s) in liquid nitrogen to inactivate any contaminant/bacteria. However, there has been a point of contention as to using fresh EVs or thawed EVs from -80 for functional assays. if you want to just perform cytotoxic tests, then either might be ok but for cargo delivery assays, then fresh EVs might work well.
For separating aggregated EVs: I think this may depend on the downstream application that you want to use them for, for characterization studies you may need not worry about the aggregation as that itself can be a point in your data. However, for single EV analysis- after diluting the EVs in your choice of buffer (you might see some precipitate at the base of the tube, this should in itself give a vague idea of how condensed the exosomes are), carefully passage the EVs either with 20ul tip of syringe for about 10-20 times and then you might want to sonicate them briefly as well.
hope this helps Nourhan S. Elkholy
  • asked a question related to Sterility
Question
2 answers
Hi, i wonder if i can sterillize guanidine thiocyanate 2M solution for qPCR purposes (to remove RNase and DNase), does anyone knows how the high temp impacts the solution? thanks
Relevant answer
Answer
Hey,
the whole purpose of guanidine thiocyanate is to inactivate nucleases. There is no need further sterilization.
Best
Soner
  • asked a question related to Sterility
Question
10 answers
Hello,
I have band of my negative control. I am sure there is no contamination. I used new everything, sterile and change my gloves 5 times. I did negative control mix separately my samples. My PCR product should be 214 bp and my samples are not important, I know reason why there are two bands. What is negative control band? Really I don't know. It's look like picture there is no smear or something else.
Relevant answer
Answer
This is clearly pcr contamination and it can be hard to get rid of. I would clean up my working area and pcr machine. Dismantle and clean all pipettes and change to new plasticware. Move temporarily to another persons working area and using their pipettes dilute new primer stocks and either borrow or make up new NTPs Taq and use their water.Run a pcr with one positive and 3 no template controls. When you can get a negative NTC then move back to your pipettes and working area. Often contamination comes from aerosol spreading when opening pcr plates or tubes or transfer of used buffer from the gel tanks on gloves to your working area. If you cannot solve this problem then redesigning one primer to be outside the amplimer that causes the contamination will always work
  • asked a question related to Sterility
Question
3 answers
I am afraid that I will kill the seeds by crutial concentration of EtOH and NACIO. May I get some good protocol or information?
Relevant answer
Answer
You can treat the seeds with hydrogen peroxide (20%). However, for the germination of Orchid seeds, fungal spores are needed, with which the plant is in symbiosis. Consequently, any sterilization can kill the spores of the fungus and seed germination will become impossible. I think it would will better if you put the seeds in the substrate in which the mother plant grows Habenaria dentata.
  • asked a question related to Sterility
Question
2 answers
Good evening,
How to avoid evaporation to drying in the wells of cell culture plates in a CO2 incubator (parameters shown in the attached photo)?
The medium evaporated and even some wells dried out in the middle of the plate while we put medium or sterile water in the border wells.
PS: we put a container with distilled water inside.
Could you help us to overcome this problem?
we would be very grateful, thank you.
Relevant answer
Answer
Sometimes you just have to change the medium more often, too.
  • asked a question related to Sterility
Question
2 answers
I need to sterilize it in a way that doesn't alter the compound and can later be used for cell growth.
Relevant answer
Answer
hello,
I think filtration using 0.45um filter membrane can work.
  • asked a question related to Sterility
Question
3 answers
how to sterilize dextrose or glucose???
Relevant answer
Answer
An easy option is filter sterilization with 0.2 micron sterile filter in the hood.
  • asked a question related to Sterility
Question
2 answers
Hi,
I am going to do lipofectamine transfection of my plasmid with GOI into HEK 293 and ShSY5Y cell lines. However, I have a question at the colony picking stage. How can this be done, especially if I do not have a microscope like the EVOS inside my hood? Our microscope is big and outside the hood, but I will not be able to pick colonies outside of the BSC because of sterility issues. Has anyone found a workaround to this?
Thanks and Regards,
Mathangi
Relevant answer
Answer
Aaron Dhanda Yes, I was thinking exactly of that! Thank you:)
  • asked a question related to Sterility
Question
4 answers
Hi all ,
I am performing root exudates collection for Arabidopsis using Hydroponics based system. However, I am unable to find any protocol where people have colleceted exudates in liquid MS media and performed LC-MS analysis based on that. Whereas most protocols say, they collect exudates in sterile MQ water. Can we perform root exudates analysis using the exudates collected in liquid MS in hydroponics system?
Appreciate any lead on this angle, thanks.
Relevant answer
The salts will not interfere in the metabolites but may be used up by the roots as well. For LC/MS you can have a plain MS run to eliminate the media components.
And if you are working with the exudates, drying will not help you I think.
  • asked a question related to Sterility
Question
11 answers
How to sterile plastic instruments in microbiology lab effectively in an easy way? Plastic materials which can't be autoclaved?
Relevant answer
Radiation can be done to sterilize materials that can not be autoclaved. X-rays and Gamma rays can be of help in sterilization of plastic items. They rays are rendered more dangerous due to increased penetration compared to UV rays but it is effective for large scale sterilization of plastic items such as plastic syringes during manufacturing.
Oswald, N. (Mar. 9, 2021). 6 Laboratory Sterilization Methods. Retrieved from https://bitesizebio.com/853/5-laboratory-sterilisation-methods/.
  • asked a question related to Sterility
Question
1 answer
I have to prepare MRS broth and add 0.4% phenol to that media . How can I sterilize this media containing phenol?
Relevant answer
Answer
Did you try UV sterilisation or radiation sterilization (i.e. gamma rays or electron beams). Radiation could be aggressive in aqueous medium, but performing irradiation on frozen state could help.
SIncerely,
Nicolas
  • asked a question related to Sterility
Question
4 answers
I used a maxiprep kit to obtain the plasmid pUC18-k2 from E.coli LB cell culture. In the end i tried to dissolve the DNA pellet with sterile water but it seems the pellet doesn't dissolve completly? I also quantify with Qubit and have a very low yield compared to what the kit says it should isolate per column? I dont know how to proceed
Relevant answer
Answer
If you could tell the Abs 260/280 and 260/230 ratio it will be a bit easy to understand what sort of contamination might be there.
As of now you can vacuum concentrate your DNA sample and try dissolving in warm 10mM TE buffer pH8 and check on Qubit. Not very sure it will improve the concentration, but you can try.
Subham.
  • asked a question related to Sterility
Question
3 answers
I am sharing an incubator and I am used to using sterile water and regular cleaning program to keep my water sterile. However, the copper sulfate keeps being added to the incubator. I have heard this is common practice for other types of cell culture but I am wondering if this is something that could affect a more fussy type of cell such as stem cells.
Relevant answer
Answer
Yes, many laboratories do successfully use a number of chemical additives in their incubator humidity trays including copper sulfate (1.0 g per litre). In 10 L of pure water, you may add 10 g copper sulfate and 0.2 g EDTA. Fill your water tray to the mark. Once you see a blue deposit in the tray, it’s time to change the solution, but once a week will be the right way.
Use the correct concentration of copper sulfate as using copper sulfate in water at high concentration or for long term may harm cells and incubator components over time because of the warm, humid and slightly acidic atmosphere (due to the CO2 gas + humidity making weak carbonic acid) in a CO2 incubator.
If you do not have a copper lined CO2 incubator, copper sulfate may corrode your stainless-steel interiors. So, double check what you’ve got before you try using copper sulfate to keep water sterile in the incubator.
Best.
  • asked a question related to Sterility
Question
5 answers
I am trying to test whether certain compounds we have formulated exhibit antimicrobial activity and I am using Whatman 6mm assay discs. I want to sterilize them in the autoclave but after wrapping them in aluminum foil and sterilizing them on a dry cycle the discs came out slightly wet. Would this impact the disc's ability to take up solutions? Is there a way to sterilize them without the discs taking up moisture in the autoclave?
Relevant answer
Answer
They can be autoclaved to sterilize them and then put in dryer for few hours to remove the moisture.
  • asked a question related to Sterility
Question
19 answers
tldr; we're having massive contamination in our bacterial agar plates, and cannot figure out where it's coming from, even with testing. It doesn't appear to be coming from our autoclave, the Petri dishes, the agar media, the room, etc. I need to pour 1500 more plates by the end of the month but can't keep having 50-100% contamination when I pour.
I work as the lab manager for the biology teaching labs at my university, and pour over 10,000 agar plates every year (almost 20 different kinds) for the students. We didn't have any issues until November of 2021, when we started seeing massive contamination issues on our bacterial plates, and we've yet to figure out where it's coming from. I would love to hear some perspective from others to see if there's anything obvious I'm missing or something we should try differently.
Our plate pouring background:
We pour all of our plates by hand. Typically, we'll make 3 x 3L of media at a time, autoclave the media (45 minutes), let them cool to ~55-65C, and then pour. We do our pouring in a UV room, where we disinfect the bench top with lysol and then ethanol, and then leave the UV light on for at least 15 minutes. I often will come back after the 15 minutes, lay ~50 Petri dishes, and then turn the UV light back on for another 15 minutes. To pour, we use a Bunsen burner to thoroughly flame the neck of the 6L erlenmeyer of media, then we pour some of it into a sterile 500 mL erlenmeyer (which was also flamed). We again flame the neck of the 500 mL erlenmeyer, and then pour. If any media drips down the side, we wipe with a paper towel, flame again, and continue. After we fill all of the plates on the bench, we'll put a second layer of plates down and continue. 9L of media gets us 275-325 plates. After about 30 minutes, we flip them. We normally would let them sit out for 1-3 days, then put them back in their sleeves, and store in our cold room until needed. Most of the plates are used within six months, but we can sometimes use them a year or 18 months later with no issues. Normally we see less than 10% of plates becoming contaminated. This is how things have been done for years (decades) by many people before me.
The problem:
Last fall, we pulled out some bacterial plates (LB, lambda, and TKC) to use for the students, and found that they were contaminated. In November, I decided to pour more to make sure that we had enough. 100% of these were contaminated. We tried pouring again. More than two-thirds were contaminated. And we tried again. Same result. We've poured over 40 batches of plates since then (over 6000 plates), and our results are all over the place. We'll go through periods where 100% of the plates are contaminated, and then we'll get a couple batches that are okay. There's no rhyme or reason that we can find.
In the beginning of May 2022, we poured 12 batches (close to 1000 plates), and most of them had negligible amounts of contamination. But then halfway through May, we started seeing contamination again. We've now started seeing contamination again out of the blue. We're at a complete loss for where it's coming from.
The contamination itself is these tiny white/yellow/pinkish specks floating in the agar (not just on top). It looks like snow from a snowglobe, scattered throughout the plate. It takes about 3-5 days at room temperature for us to see it start growing. And it smells terrible if we leave it too long. With our bacterial plates, we now leave them out for 5 days before packaging, just so that if there is contamination, we'll be able to see it and discard those plates.
Since we typically do three large flasks at a time, we try to keep track of which plates were from which flask. Sometimes, an entire flask-worth of plates will be contaminated. Other times, it's random plates in the batch, with non-contaminated plates in between contaminated ones.
Oh, an an important thing - we do not see any contamination whenever ampicillin or kanamycin are added to the agar media for the plates. So whatever it is, it's killed off by those antibiotics.
Things we've tested:
The autoclave:
- First thing to note is that none of our liquid media has ever been contaminated during this whole ordeal. We make a bunch of liquid media and keep it for a while (months), and we have had zero bottles of media show contamination.
- There was a period of three or so months where our autoclave was the only operable one in the building, and I had about 20 other people using it. No one else ever had contamination or sterilization issues while using our autoclave. (Our contamination issues started a couple months before this)
- Our autoclave is serviced every 3 months. It passes their inspection every time.
- Originally, we used foam stoppers in the necks of the erlenmeyer under the foil. We tried getting rid of the foam stoppers and just using foil, but aren't seeing a difference.
The agar media:
- As stated above, the liquid media has had no contamination.
- I have tried autoclaving the agar media and then just leaving it in the flasks to see if anything grew, but we didn't get any contamination.
- We have tried reserving small amounts of agar media in the flasks when we're done pouring, so that we can see if contamination grew in the flasks if we saw it in the plates. However, whenever we've done this are of course the times that we don't see contamination in the plates, so it's not super helpful information. It's hard for us to do this all the time, because we need to use the flasks and not let them sit around for five days while we wait.
- We already use Millipore DI water to make our agar, but we decided to change out the tubing on the end of the system and also we autoclaved our water carboys in case that could be a cause of contamination (although it all gets autoclaved again with the media, so it shouldn't matter, but we are desperate and will try anything).
Pouring method:
- We've had four different people pouring, all of which seem to have the same issues.
- We decided to try using a pump to pour for the first time last week. The test batch (2L) looked good. The second batch (3 x 3L) has issues - at least a third of the plates were contaminated, and we're waiting to see if any more have issues. What's extra confusing is that the contaminated plates were from the flask that was poured first, and my coworker did not change the pump's outlet tubing, so we can't figure out how the second and third flasks of plates don't have contamination since they were using the same output tubing as the contaminated flask!
- We tried flaming the top of the plates after pouring (which we do to get rid of bubbles, but we started doing it to all the plates in case it helped). This did not have an effect. The contamination is in the agar anyways, so I didn't expect it to help.
- We've also been using plates from all different manufacturers due to supply chain issues (Fisher, VWR, Corning, etc), and there's no difference, so the contamination isn't from the Petri dishes themselves.
Location:
- When this started happening, I disinfected EVERYTHING in our pouring room - the walls, the ceiling, the floor, everything. I used disinfectant spray and ethanol. I changed the UV bulbs to new ones. We left the UV light on for a couple hours. This did not help.
- I tried leaving some bacterial plates open in our pouring room. 30 minutes of being open did not show contamination (I closed them then let them sit out). When I left them open for 24 hours, I did see some contamination. But when we pour plates, the Petri dishes are open for just seconds, so I don't know how the 24 hour window would correlate.
- We started pouring in different places. We've poured in three other lab spaces, and the contamination seems just as random. We've tried pouring in UV hoods. Still no difference.
- One thing I will note is that we had some summer programs, and some students swabbed the bench top in our plate-pouring room, grew out the bacteria, and sent it for sequencing. It came back as Staphylococcus hominis. Now I will say that we had not done our normal sterilizing procedures (disinfectant, ethanol, then UV light) before they swabbed, and if that is indeed the contamination, I'm not sure why the disinfection methods don't kill it. Also, I'm not sure how that bacteria would get from the tabletop into the plates, and be spread so thoroughly throughout the agar. We constantly ethanol our gloves (and we always wear our gloves when pouring), so it seems unlikely that we're transferring it. And why would it happen now, after years and years of not being an issue?
I need to pour 1500 more lambda plates before the end of the month for students, but I can't keep pouring batches of 300 plates where I throw out 250 of them! If you have any ideas of what I can try or where the problem might be coming from, I'd greatly appreciate any insight!
Relevant answer
Answer
From your description, it appears that the contamination isn't due to airborne microorganisms settling on top of the agar, but that it is present in the liquid agar at the time of pouring the plates. You mention that you autoclave the agar in rather large batches (3x3 L); could it be that with such large batches, 45 min autoclaving isn't sufficient time for the liquid to reach a high enough temperature to kill the contaminants, especially if theu are spore formers that could be more heat resistant ? I realize that this might be inconvenient to prepare large batches for a lab course, but what about trying to pour a small batch of plates, e.g 500 ml, to see if the problem still occurs ? If not, I would suggest to subdivide the agar medium to be sterilized into more smaller aliquots for autoclaving to allow more efficient heat transfer.
  • asked a question related to Sterility
Question
3 answers
In the protocol, they sterilized the agarose by passing it through a 0.2 mm filter. but this was not possible. it freezes directly. Will it be sterile enough if I autoclave it? Also, do you think it will be toxic in cell culture? Does the type of agarose matter?
Relevant answer
Answer
Oh I see. Anyway autoclave will be just fine even if you use agarose in the cell culture!
Have a nice day too!
  • asked a question related to Sterility
Question
2 answers
Our experiment aims to examine biofilm formation and structure on tomato plant roots by conducting a soil drenching experiment using transformed B.subtilis with RFP/BFP, and will be visualized through confocal microscopy. This will be conducted by purchasing a nearly mature tomato plant from a nursery that have been grown in soil. Would washing the roots with sterile water be enough to get the soil off and not disrupt the biofilm structure, or would there be any recommended methods of root washing?
Thank you!
Relevant answer
I would use isotonic water, which is less likely to disrupt cell membranes :)
  • asked a question related to Sterility
Question
3 answers
Can In sterilize agar medium in a flask first and then dispense them into broths/slants/deep tubes under aseptic conditions? Or else should I dispense the agar medium first into broths/slants/deep tubes and then sterilize? Which way is acceptable and what is the reason? Kindly let me know.
Relevant answer
Answer
Obviously the first option is the best as it will give you a homogenized media in whole batch. In second option, sometimes it happens that agar does not dissolve properly during preheating and will not give you a homogenized media.
Good luck.
  • asked a question related to Sterility
Question
1 answer
Can we fumigate a bio-safety cabinet to sterilize its HEPA filters.
Relevant answer
Answer
yes
  • asked a question related to Sterility
Question
1 answer
Hi,
We perform in vitro retinal cell cultures in our lab. We have a bunch of packaged sterile equipment (syringes, pipette tips, filters, etc.) that are past their expiration dates by a couple of months. Their packaging is intact and they've been restored in dry dark drawers in a room with minimal personnel access. How high is the risk of contamination if we use them in new in vitro experiments?
Relevant answer
Answer
Hi. If it´s only for a few months and stored as you wrote, I would use them without fear. If infections appear, rather re-sterilize everything what you will need and use.
  • asked a question related to Sterility
Question
2 answers
Im gonna add veratryl alcohole to my culture medium. I think the autoclave destroys its structure. can every body propose me a method for its sterilization
Relevant answer
Answer
Hello, Filteration by Cutoff 0.2 can work too,
Good Luck!
  • asked a question related to Sterility
Question
4 answers
I'm cultivating intestinal organoids from Adults rats...but even using antibiotics, the cell culture always contaminates.
Relevant answer
Answer
Did you figure out a way to resolve this? If yes, could you kindly share what you did?
Best,
Shruti
  • asked a question related to Sterility
Question
3 answers
As we have started molecular biology programme in UG, we want to make it low cost
Relevant answer
Answer
DNA stored in water for 16 years at –20ºC remained intact, but showed varying degrees of degradation when stored at 2–8ºC. Please see Fig 1 & 2 in the link below.
Good Luck!
  • asked a question related to Sterility
Question
2 answers
Hi Everyone,
Our lab utilizes amber stop codon suppression to express proteins and peptides in E. coli. We grow our cultures in M9 media supplemented with 0.5% yeast extract. As of recent, we have been observing cell death in our cultures. We transform into BL21(DE3) cells and the cells grow normally when plated on LB agar plates and in an overnight culture containing 5 mL of LB media. However, when we transfer the overnight cultures to larger cultures (i.e. 200-500 mL in M9 media) for protein expression, we observe normal cell growth up to around OD600 = 0.3-0.4, but when we return about 0.5 - 1 hour later too induce expression, the culture has gone clear and the cells have died. It seemed to happen randomly at first with a few cultures perishing here and there. As of recent, all of my cultures seem to die the same way. In addition, if i do get normal cell growth, the protein yields are lower than normal.
Another note is that other member of our lab do normal protein expression (i.e., no amber stop codon suppression) in LB or TB media. Their cultures do not die as frequently as mine do in M9 media. However, they have noted a reduction in protein yields. Does anyone have any advice at what could be causing this issue? Could it be a phage contamination issue and cell death is more predominant in cultures expressed in minimal media? We have tried treating our flasks with virkon, sterilizing pipettes, wiping down the incubators, but the issue seems to persist. Any insight will be greatly appreciated. Thank you!
Relevant answer
Answer
A way to try to determine if the problem is phage contamination would be to preform a plaque assay and look for plaque formation. If you make plates with M9 and then when moving the cultures to the larger volume for expression take out 100uL for plating. Add the bacteria to 0.7% M9 agar melted and cooled to around 50c and quickly pour onto plate after mixing gently. After incubation overnight you should get a lawn and if phage are present you would presumably see plaques.
Do you use different temperatures for the overnight grow up and the protein expression? The phage may be lysogenic in the first conditions and then triggered into lytic cycle when you move them.
  • asked a question related to Sterility
Question
11 answers
Hello all.
We are facing an issue with endotoxin contamination in our purified protein which is intended to be used as a drug, hence the endotoxin limit is very stringent i.e. lesser than 0.2 EU/mg of protein.
The protein is over-expressed in E. coli host and purified in a two step process involving affinity and ion exchange chromatography. Furthermore, we employ another poly lysine based resin which is supposed to have affinity to endotoxin and we obtain our protein as flow-through. Right now we are stuck with a level of around 1 EU/mg and struggling to reduce it further.
PS: Colorimetric LAL assay is being used to determine the endotoxin conc. and the assay itself has a limitation that it could produce a variation of 50 - 200%.
Relevant answer
Diego Sosa The conductivity before passing into the ET trap resin is ~6mS/cm and the buffer has 50mM NaCl (which is as per the recommendation of the resin manufacturer). This resin acts as a weak anion exchanger too.
  • asked a question related to Sterility
Question
2 answers
1. People gets odd chromosome no. crossing with their native resources
2. I want to cross using my own resources
3. People gets from 2 way crossing & I will get from 3 way crossing
Relevant answer
Answer
Quite a few interspecies hybrids are fertile and produce offspring. This is true for both plants and animals. A number of these are farmed. If the two species have different ploidy numbers there's a good chance the offspring will be sterile, but some are not.
  • asked a question related to Sterility
Question
2 answers
Hi All,
Our lab dissects brain tissue for culture under a stereomicroscope that is set up outside of a hood. We don't have too many problems with contamination, but I recently ran across some small UV cabinets to sterilize personal medical equipment (CPAP) or household objects. Some of these boxes are quite affordable, and I thought they might make a good addition to the lab for a way of sterilizing tools prior to dissection, without having to autoclave them. I must not be the 1st person to see a "lab use" for these devices, and I am wondering if anybody else has tried them out. If you have, what was your experience?
Thanks!
Relevant answer
Answer
Thanks Phil. Yes, I am aware of the line of sight. This is for simple dissection tools, that can be easily treated by line of sight. Autoclaving between dissections is not feasible if we are dissecting 6 animals in one day, which we often due for tc. This would be as an add on to autoclaving prior to use, and then using ethanol between animals.
  • asked a question related to Sterility
Question
2 answers
Hi everybody,
I want to test the sunscreen protection on cultured keratinocyte cells, but I don't know if it's possible and how could be the procedure. I mean is it weird to just add sunscreen mixed in the medium ? it is really sterile ? Did someone already test the efficiency of this procedure in vitro ?
Thanks
Relevant answer
Answer
Adding sunscreen to the medium would be challenging as you would need to produce a sterile emulsion. The paper Malcolm mentions uses skin equivalent models so the sunscreen can be directly applied to a "dry" surface. If you need to use monolayer cultures (is this an appropriate model?) you could consider applying the sunscreen as an even film (at whatever density you required) to a UV-transmissible plastic lid that would cover your culture plate. This way the sunscreen would not need to be sterile and would better mimic sunscreen use. Just a thought...