Science topic

Microbiology - Science topic

Microbiology is a broad term which includes virology, mycology, parasitology, bacteriology, immunology and other branches.
Questions related to Microbiology
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Dear All,
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Eligibility: M.Sc. Chemistry/Biochemistry/Biotechnology/Microbiology/Bioinformatics with first class of 60%.
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RS 25,000 per month for full three years will be given.
For further details, contact me on: +919182864256. Call or what's app me for further details.
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I apologize and excuse the owner of the post. I would like to invite you to read my ebook and discover why microorganisms are so fantastic. https://www.amazon.com.br/dp/B0CF1VKKK8
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Hi all,
I am currently planning an experiment that involves viewing E. coli cells tagged with gold-conjugated secondary antibodies using a scanning electron microscope, and I am running into the issue of cost for primary antibodies. I might have the option of using primary antibodies previously purchased for Western blots, but I am unsure if these antibodies can also be used for SEM imaging. I do not yet know enough about the chemistry and reactivity of antibodies to answer this question, thus I find myself here!
On a related note, if anyone has any recommendations of good websites to purchase primary antibodies for E. coli that work with SEM, I would love some! I have found a few websites, but each of them only has 2 or 3 antibodies for this purpose.
Thanks,
Joel
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Agree with Yannick. However, some antibodies work for both WB and imaging applications. A relatively easy way to test a primary ab for imaging is usually by light (fluorescence) microscopy, using applicable secondary ab (fluorophor conjugated). Also keep in mind that most ab do not bind after fixation with standard glutaraldehyde concentrations used for EM.
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I am currently optimizing a RPA-based protocol. As everyone knows, this nucleic acid amplification technique is based on isothermal amplification (around 37-42˚C) in combination with recombinases and single-stranded DNA binding (SSB) proteins.
I have designed several candidate primers to optimize my RPA. All of them were searched in literature and designed considering the criteria to be used in an RPA reaction.
These same primers were verified by conventional PCR (At different Tm: 55-65ºC), obtaining a successful result.
The problem started when I used the RPA master mix (lyo version from Twistdx) and performed the RPA reaction with the same primers and samples used in the conventional PCR. ALL THE RESULTS BECAME NEGATIVE?!
Primer concentrations used in RPA reaction was 400nm (recommended by twistdx) and the reaction time was 30 minutes at 39 °C (conditions recommended for the set of primers tested). Visualization of the amplification was done on agarose gel (1.5%) and doing a posterior melting curve assay. In all cases, no amplification was detected.
Does any one have a clue on what is happening???
I don´t know which other variables I can change to obtain good results
Suggestions?
Thank you
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It will be classic but you mentioned using a 30-minute reaction time, consider extending it slightly, as sometimes longer incubation times can improve RPA results, especially when using DNA extracted from complex samples. While 400 nM is a typical primer concentration for RPA, you can try titrating the primer concentration to optimize the reaction. Sometimes, higher or lower concentrations may work better depending on your specific setup. While the primers worked well in PCR, they might not be optimized for RPA. You could consider redesigning the primers specifically for RPA conditions. RPA primers may have different requirements, such as longer lengths (usually 30-35 bases) and specific GC content. First things that come to my mind. Good luck.
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Hello everyone! I am looking for Q1 journals in which it is free to publish in the area of ​​microbiology or pharmacology and I wanted to know if you know of any.
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Revered Dr.Andrea Celeste Arismendi Sosa,
Hope you are from developed countries of Europe.
I came across these top ranked Scopus Indexed Journals are mostly waive off for third world countries stakeholders than others.
I have some list of free Scopus Indexed Journals that I will attach to your email ID.
Since you are from Microbiology that I will find some free Journals in your field of study.
Be in touch with my email ID drsenapathy@gmail.com
I will send in the returning mail reply.
Regards
Senapathy
Ethiopia
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We are using Bio-Rad RAPID'Salmonella agar (prepared from powder media) for Salmonella spp confirmation. We recently switched over from pre-poured plates directly from the manufacturer to making our own in house. Lately we have had extremely poor recovery on the positive control plates, with little to no growth (it should result in defined purple lines in the quadrants but we see barely light lavender colonies and <5 per plate). We are following manufacturer's preparation instructions exactly and the same as a sister lab who has no QC issues, but we're still seeing failures about 50% of the time.
Wondering if anyone else has experience with this particular issue and if you could share your preparation or any other ideas to try and rule out factors. Thus far we've tried with new lots, slightly altering the heat step, and multiple parallel preparations/incubations with unpredictable and inconsistent results. This media and it's preparation info are easily available with a quick google search of Rapid'Salmonella agar Bio-Rad.
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This is a recall be Remel based on failure of their microbiological medium to achieve excepted results. Again - Bio-Rad's produict is also a medical device used to diagnose disease. Your results indicate a problem and they're blowing it off. Suggest you file a complaint the FDA. They can detyermine if this is serious.
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Hi everyone!
I'm currently working in a microbiology lab at a hospital, and there's a lot of antimicrobial susceptibility testing (disk diffusion). We're following Ecucast's recommendations, included this 15-15-15 rule. I can understand why it's important to respect the first and the last "15", but I'm having a hard time seeing the meaning of the second "15"... Anyone who can help?
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According to the European Committee on Antimicrobial Susceptibility Testing, inoculation agar plates, should be at room temperature before inoculation. The first 15 minutes is about the usage of adjusted inoculum suspension within 15 minutes of preparation. The second 15 minutes state that the disks should be applied within 15 minutes of inoculation because if it is left at room temperature for a long period before disks are applied, the organism might begin to grow which will result in an erroneous reduction in sizes of inhibition zone diameters. With that being stated, according to Anna King and Derek F.J. Brown in their journal entitled Quality Assurance of Antimicrobial Susceptibility Testing by Disc Diffusion, if the problem includes too large or too small zone diameters with all antimicrobials, the following should be observed:
1. Depth of agar should be checked, if it is incorrect, the amount of agar should be adjusted.
2. Inoculum size should be checked.
3. Ensure that the discs are applied to the inoculated plates within 15 minutes and that the plates are incubated within 15 minutes of the application of the discs.
The inclusion of the 15-15-15 rule in the troubleshooting controls proves that it is done to reduce errors in susceptibility testing in disc diffusion.
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I have a few substances that resemble curcumin, and I need to conduct antimicrobial tests, especially MIC experiments in a 96-well plate, with these substances. However, these substances are highly colored, making it difficult to determine if there is inhibition or turbidity. I've checked the literature, and some studies have used growth indicators like MTT.
Despite this, it remains unclear in which one growth has completely stopped.
Do you have any advice on assessing the antimicrobial effect of such highly colored substances?
Do you think agar dilution is the only solution? If you recommend agar dilution, should I initiate the experiment in a manner similar to MIC testing in a 96-well plate and then, after 24 hours, spread each 100 µL solution onto agar plates? Alternatively, should I conduct this study initially in a 24-well plate or Eppendorf tubes and then proceed to agar dilution?
Thank you in advance for your responses.
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I don't think it matters whether you do your assays in 96 well plates, 24 well plates or tubes. But if you can not measure optical density or turbidity, then the easiest thing may be to measure surviving CFUs. You can plate out a sample of the culture after treating, but you might need to also do a dilution series. You can just do a series of 10 fold dilutions and spot 5 ul of each onto your plates (you can usually get a number of spots per plate). Otherwise plating directly after 24 hours is likely to have too high a cell density to count directly, unless the compound is highly inhibitory.
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How many grams of K2Cr2O7 to dissolve it in 1 liter Distilled water to obtain 50 ppm of Chromium? to become aqueous solution, Is there a specific equation to apply? Thanks
Ali
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Why are so many methods and no answers the same? Other papers also mention the different results. What is actually the correct answer?
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Hi I have a question, I was reading some articles about different conditions for storing aliquots of antibiotics for use in culture media. But I would like to ask you, according to your personal experiences, have you had problems storing antibiotics at -70 or -80 ºC? I am specifically interested in penicillin, streptomycin, blasticidin S, ampicillin and amphotericin B. Would you recommend storing them at -80 ºC to better preserve their properties and even extend their shelf life?
Thank you in advance!
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It all comes down to chemistry. The colder it is the slower chemical reactions happen (especially endothermic reactions). So yes storing your aliquots at -80ºC will prolong their shelf life compared to -20ºC but you will also need to factor in cost since colder freezers chew more power so are more expensive to run. This means you need to offset the cost of just buying in a new batch of antibiotics over the cost of keeping them colder.
Another factor you should consider is how the antibiotics degrade. Usually this is by oxidation so you can prolong the shelf life further by purging the atmosphere in the aliquot with argon or nitrogen. Note this would then need screw top vials since regular Eppendorfs are not great at preventing gas exchange.
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Please submit your abstract on or before 15th September 2023. There will be no publication fees.
Preface of the Book:
The field of microbiology is undergoing a revolutionary change due to the emergence of Artificial Intelligence (AI). AI is being used to analyze massive data in a predictable form, about the behavior of microorganisms, to solve microbial classification-related problems, exploring the interaction between microorganisms and the surrounding environment. It also helps to extract novel microbial metabolites which have been used in various fields like medical, food and agricultural industries. As the pace of innovation in Microbiology is accelerating, the use of AI in these industries will be beneficial.  It would be challenging to search out specific features and discuss future research on AI in Microbiology.
The proposed book will be focused on:
  • Identification of micro-organisms including genus and species through AI.
  • Development of novel drug targets through AI and use of AI techniques in the diagnosis of infectious diseases.
  • Efficient and cost-effective production of viral vaccines via AI.
  • Enhancement of bioactive microbial metabolite production using artificial neural networks.
  • Disadvantages or challenges for using and selecting appropriate AI tools.
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Dear Dr Hasi,
Hope you're in good health.
After adding the name of the author in TOC, Elsevier will send the link directly to the author.
And then he or she is able to login in EMSS.
Please let me know if you have any questions
Thanks for your time and support
With warm regards
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I am a researcher in Microbiology. I am trying to prepare a nano material from hydroxy appetite. Can anyone give me a brief on how to do that?
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DEAR DR EVIEN
Certainly, preparing hydroxyapatite (HA) nanoparticles involves several steps, and it's important to have a clear understanding of the process to ensure successful synthesis. Hydroxyapatite is a biocompatible material often used in various biomedical and dental applications. Here's a general outline of the synthesis process:
1. Chemical Precursors:You'll need calcium and phosphate sources as your main precursors. Common choices are calcium nitrate or calcium chloride for the calcium source, and diammonium hydrogen phosphate or ammonium dihydrogen phosphate for the phosphate source.
2. Mixing:Dissolve the calcium and phosphate precursors in deionized water separately to create two solutions. Then, add the phosphate solution dropwise into the calcium solution under constant stirring. This will lead to the precipitation of hydroxyapatite.
3. pH Adjustment:The pH of the mixture is critical for obtaining pure hydroxyapatite. Adjust the pH to around 9-10 using a base (like ammonium hydroxide or sodium hydroxide) to promote HA formation.
4. Aging:Allow the mixture to age for a certain period, typically several hours to overnight. During aging, the nanoparticles will grow and form stable structures.
5. Filtration and Washing:After aging, the precipitate is usually separated by filtration and washed with deionized water to remove any residual chemicals and impurities.
6. Drying:Dry the obtained precipitate in an oven at a temperature around 60-80°C. This will result in the formation of hydroxyapatite nanoparticles.
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Please, help asap.
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In addition to Phil Geis question, in what subspecialty. There are hundreds or perhaps even thousands of microbiology journals but many are specialized, for example in pathogenesis or clinical microbiology, environmental, industrial, molecular genetics, etc
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compatibility of bacillus subtillis whit others quimicals pesticides;
idem trychoderma sp;
idem amyloliquefaciens and
idem liqueniformes
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By culturing in bacterial culture media
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I am in need of individuals knowledgeable about pharmacopeia. Could someone please explain the distinction between 'Non-aqueous preparations for oral use' and 'Aqueous preparations for oral use' in terms of the microbiological control of non-sterile pharmaceutical products according to the European Pharmacopeia 10th edition, page 659? Moreover, if I have a tablet or capsule, how should I conduct its microbiological control and determine its classification based on Table 5.1.4.-1. – Acceptance criteria for microbiological quality of non-sterile dosage forms in the European Pharmacopeia 10th edition, page 659? Lastly, if I possess an antibiotic in dry form that will be reconstituted into a syrup with water, how should it be categorized, under 'Non-aqueous preparations for oral use' or 'Aqueous preparations for oral use?
THANK YOU
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The microbiolgical quality in the pharmocopia kept a modern apothecary " natural body care"
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The question is: Atopic patient, with 78% of body surface Affected. IgA=98.00mg/dL, IgE=>2000.00KU/L, with serologies (-). Leukocytosis =13000mm³, Segmented=-8840mm³, Eosinophiles=130mm³, Monocytes=390mm³, Microbiological skin culture=Aspergillus spp (+). 20 days after the leukogram, the following was presented: Leukocytes=11030mm³, Eosinophils=1831mm³, Neutrophils=6309mm³
Current symptoms: Insomnia, pruritus, Intense Atopic Triad Crisis.
In general: We will use
Itraconazole 300mg, for how long to use in cutaneous aspergillosis? and can I combine it with methotrexate 7.5mg /week?
HOW DO I MAKE THE BEST DRUG MANAGEMENT OF THIS SITUATION?
# DERMATOLOGY
P.S.: filaggrin and profilaggrin tests are not available in the region, bewm with serum interleukin dosage..
to be clear I know the evolution of AD and its immunopathology, the question itself is this UNCOMMON EVENT OF CUTANEOUS ASPERGILOSIS AND HOW I MANAGE ITRACONAZOLE EFFICIENTLY BECAUSE THE PATIENT HAS HAD VERY RECURRENT PRURIGINOUS CRISES THAT TAKE HIM TO THE EMERGENCY SERVICE HOSDPITALAR.
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Dear doctor
Go To
Association between atopic dermatitis and serious cutaneous, multiorgan and systemic infections in US adults
Shanthi Narla, and Jonathan I. Silverberg,
Ann Allergy Asthma Immunol. 2018 Jan; 120(1): 66–72.e11.
doi: 10.1016/j.anai.2017.10.019
"Introduction
Atopic dermatitis (AD) is a chronic inflammatory skin disease affecting 13% of children1 and 7–10% of adults across the United States. It is well established that AD is associated with a higher incidence of certain cutaneous infections, including Staphylococcus aureus colonization, molluscum contagiosum and eczema herpeticum (EH), and possibly cutaneous warts. In fact, predisposition toward cutaneous infection is one of the Hanifin and Rajka minor diagnostic criterion for AD8. The mechanism of such predisposition is thought to be multifactorial, including impaired epidermal barrier function9, decreased expression of antimicrobial peptides, and abnormal innate immune response in skin.
Recent US population-based studies showed that AD is also associated with higher rates of extra-cutaneous infection in both children and adults, such as infections of the upper and lower respiratory tracts, ears and urinary tract. Those studies utilized surveys with questions about self- or caregiver-reported AD and infections. In the present study, we sought to determine whether there is an association between healthcare diagnosed AD and serious infections in adults. We hypothesized that adults with AD have significantly higher prevalences of cutaneous, respiratory, multi-organ and systemic infections.
In conclusion, adults with AD had significantly higher odds of cutaneous, respiratory, multi-organ and systemic infections. Serious infections were associated with a substantial financial-burden in patients with AD."
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If you are interested in collaborating project on Biotechnology, Bionanotechnology, Microbiology, Plant Tissue Culture etc., Please let us know.
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I am interested in initiating a bilateral project, here are some general steps you can follow:
  1. Identify Partner Organizations: Look for organizations, institutions, or companies in the target country that share similar interests and expertise. Reach out to potential partners to explore their interest in collaboration.
  2. Define Project Objectives: Clearly define the objectives, scope, and expected outcomes of the bilateral project. Ensure that the project aligns with the goals and missions of both collaborating parties.
  3. Establish Communication Channels: Set up effective communication channels between the project teams in both countries. Regular communication is crucial for successful collaboration.
  4. Secure Funding: Identify potential funding sources for the project. This could include government grants, international organizations, or private sponsors. Both parties may contribute resources to the project as well.
  5. Draft a Memorandum of Understanding (MoU): Develop a formal MoU that outlines the terms of the collaboration, including roles and responsibilities, intellectual property rights, budget allocation, and project timeline.
  6. Obtain Necessary Approvals: If the project requires regulatory approvals or permits, ensure that you obtain them before commencing the collaboration.
  7. Implement and Monitor the Project: Start implementing the project according to the agreed-upon plan. Monitor progress, track milestones, and address any challenges that arise during the collaboration.
  8. Share Knowledge and Resources: Foster knowledge exchange and resource sharing between the collaborating parties to maximize the benefits of the project.
  9. Evaluate and Report: Regularly evaluate the project's progress and outcomes. Prepare periodic reports to update stakeholders on the project's achievements.
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I am looking for a PhD Position in Microbiology, Virology, and Molecular Biology.
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Bonjour,
Pour le moment tous nos projets sont pris par les doctorants.
Cordialement. M. SIDQUI
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Hello, I'm trying to find pre labelled 90mm petri dishes to be included in an automation workflow for a new biotech lab. Does anyone know a brand? I can't find one! THX
Nidia
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Binyamin Kerman very kind for your answer, thanks. Exploring all your suggestions!
N
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I need recommendations for a digital microscope for microbiology, primarily for molds observation
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Certainly! When it comes to digital microscopes for microbiology, there are several options available. Here are a few recommendations that are commonly used for observing molds:
1. Celestron 44341 LCD Digital Microscope: This microscope features a built-in LCD screen and a 2-megapixel camera. It provides magnifications of up to 200x and has built-in LED illumination. It's portable and easy to use, making it suitable for mold observation.
2. Dino-Lite AM4113T Digital Microscope: This microscope offers a higher resolution with a 1.3-megapixel camera and magnifications up to 200x. It also includes built-in LED lights for illumination. The Dino-Lite series is well-regarded for its quality and versatility.
3. OMAX 40X-2000X Digital Binocular Microscope: If you're looking for higher magnifications, this binocular microscope from OMAX is a good option. It comes with a built-in 1.3-megapixel camera and includes multiple objectives for magnifications ranging from 40x to 2000x. It also has a mechanical stage for precise specimen positioning.
4. Levenhuk DTX 500 Mobi Digital Microscope: This portable microscope offers magnifications of up to 500x and includes a 1.3-megapixel camera. It has eight built-in LED lights for illumination and can be connected to a computer or smartphone for image capture and analysis.
Remember to consider your specific requirements, such as budget, desired magnification range, portability, and connectivity options, when choosing a digital microscope for your microbiology needs. It's also a good idea to read customer reviews and compare features before making a purchase to ensure it meets your expectations.
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I am trying to design a primer for a specific gene and the Tm is coming near to 60 degrees when I select a minimum of 30-35 bp, for forward as well as for reverse primer. As the template is too long I think it might lead to non-specific binding, what are the possible solutions for this problem? I am using Snapgene to design primers for cloning
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1. Adjust primer length: Increase or decrease primer length slightly.
2. Evaluate Tm prediction methods: Use different algorithms or tools for Tm calculation.
3. Adjust primer sequence: Make small modifications to fine-tune Tm.
4. Check for secondary structures: Identify and minimize hairpins or self-complementarity.
5. Consider primer placement: Avoid repetitive or variable regions.
6. Follow primer design guidelines: Adhere to established recommendations.
7. Validate and test primers experimentally.
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I want to submit my work on "International Journal of Microbiology" (Hindawi)?
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Dear Sudeep Poudel The impact factor as indicated by Phil Geis is legit. Since June 2023 Clarivate assigned journals indexed in their ESCI an impact factor, as announced for example here https://clarivate.com/blog/mapping-the-path-to-future-changes-in-the-journal-citation-reports/
The journal is as indicated in their own indexing info https://www.hindawi.com/journals/ijmicro/ai/ still indexed in Clarivate’s Emerging Sources Citation Index (ESCI) and has an impact factor of 3.4
Best regards.
PS. Unfortunately nobody here on RG seems to have the JCR report list with the IF of all ESCI titles (yet).
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The smaller white colonies are Rhodococcus, however the yellow ones I am not sure! I collected some of the isolated yellow looking colonies? and streaked them on a separate agar plate and what I got looked like Rhodococcus. Could it be mutant colonies or just bacterial lysis? Thank you!!
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yes it looks contaminant
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I have manufactured a product (pharmaceutical product) by spray drying. Batch size is 120 kg. The product passes microbiological limit test (MLT).
When I run a 6 kg batch size, my product is failing in microbiologcal test (MLT). With 120 kg batch size, product passes microbiology test.
Before running every batch, I take microbiology clearance of the spray dryer, but empty spray dryer gives high count, inspite of thorough washing and sterilization (heating at 120 deg C).
Why am I getting high count when I run a 6kg batch and NIL count with 120 kg batch size in a spray dryer, keeping all other conditions same? Can someone help me to understand?
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For spray dryer -after heat treatment - does water remain and what are the microbes recovered?
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Is there any selective media available commercially for isolation of Nitrosomonas europaea from water? I need to introduce AOB's into my experimental setup and later count/detect them in water samples. I am unable to find any selective media or any other appropriate method to follow. Suggestions needed.
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Could you please share with us how you isolated the Nitrosomonas bacteria?
tank you
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Please i need the contact of the Algerian Society of Microbiology
Thanks.
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Do you mean The Algerian society of clinical microbiology (société algérienne de la microbiologie clinique SAMiC) ?https://www.samic.dz/site/index.php
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Hello,
I want to grow bacteria on glass coverslips by immersing them in a liquid bacterial culture. I would like to fix them to the bottom of petri plates or well plates , because otherwise they float in the medium. I've tried double sided adhesive tape, but when I try to remove the cover glass slip for fixation, they often shatter since they're strongly adhered to the tape. I would like to remove them from the original container because after fixing I need to adhere them to substrates with carbon tape for SEM visualization.
Are there any recommended techniques for fixing the cover slips in place during inoculation and then easy removal afterwards?
Thanks in advance.
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Don't know either. Just an idea.
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I was wondering why in developed countries even though the medical facilities and education is better , however, the presence of MDR multi durg resistance and XDR is higher in developed countries compared to some other developing countries?
My second question is why betalactams do not work on Chlamydophyla pneumonia? What makes it special ? And why betalactam is bacteriostatic against Enterococcus?
#antibiotic #Microbiology #resistance #betalactams
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As Phil Geis mentions it might be due to the level of use of antibiotics in those regions. However another possibility might be that screening for MDR and XDR is not as prevalent in developing regions so we don't know the actual levels due to insufficient screening for it.
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I realize that depending on the sample used in the microbiological assay, the same strain of p. aeruginosa produces a bluer or greener color. Is there any mechanism that explains this difference?
A photograph is attached.
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The fluorescence is caused by pyoverdines which are iron scavenging siderophores. The difference in colour can be caused by differences in ion binding and structure of the compounds at either a synthesis (https://microbialcell.com/researcharticles/the-biosynthesis-of-pyoverdines/) or degradation ( ) level. Potentially one of your antibiotics is inhibiting a step in the synthesis pathway or is changing the pH of the cell.
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For a Microbiologist interested in the work in Vaccine Development and Clinical Research, and wants to study Microbiology, Epidemiology, Immunology, Public health, and Infectious Diseases, is it better to make a master in Vaccinology or Microbiology and Infectious Diseases ?
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Vaccinology is a broad term of sciences dealing manufacuring vaccine which licenced after sucessful expermental researches on efficacy, safety and economic consedartions.
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Hello everybody, I'm a master degree student. I'm working with 16S data on some environmental samples. After all the cleaning, denoising ecc... now I have an object that stores my sequences, their taxonomic classification, and a table of counts of ASV per sample linked to their taxonomic classification.
The question is, what should I do with the counts for assessing Diversity metrics? Should I transform them prior to the calculation of indexes, or i should transform them according to the index/distance i want to assess? Where can I find some resources linked to these problems and related other for study that out?
I know that these questions may be very simple ones, but I'm lost.
As far as I know there is no consensus on the statistical operation of transforming the data, but i cannot leave raw because of the compositionality of the datum.
Please help
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Assessing diversity metrics in 16S data is an important step in analyzing microbial communities. Handling count data in this context can be challenging due to the compositional nature of the data, as you mentioned. While there is no one-size-fits-all approach, there are several techniques and considerations you can explore. Here are some suggestions:
  1. Transformations for diversity metrics: The choice of transformation depends on the diversity metric you want to assess. Common transformations include rarefaction, normalization (e.g., by library size or cumulative sum scaling), or transformations that aim to address compositionality, such as log-ratio transformations (e.g., centered log-ratio, clr transformation) or Hellinger transformation. Different transformations may be more suitable for specific diversity metrics, so it's essential to consider the metric's assumptions and properties.
  2. Compositional data analysis (CoDA): Compositional data analysis provides a statistical framework to analyze and interpret compositional data. It accounts for the constrained nature of relative abundance data by working on transformed data. CoDA methods, such as ALDEx2 or ANCOM, can help identify differentially abundant features between groups while considering the compositional structure.
  3. Multivariate analyses: If you want to explore the overall community structure and relationships, multivariate techniques like principal component analysis (PCA), correspondence analysis (CA), or non-metric multidimensional scaling (NMDS) can be employed. It's advisable to perform these analyses on transformed data to mitigate the effects of compositionality.
  4. Research articles and resources: To delve deeper into the subject, you can refer to scientific articles and resources that discuss the statistical analysis of 16S data. Some useful references include: "Microbiome Analysis Methods" by Paul J. McMurdie and Susan Holmes. "A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses" by Egoitz Martínez-Costa et al. "Statistical analysis of microbiome data with R" by Yinglin Xia et al. "MicrobiomeSeq: An R package for analysis of microbial communities in an environmental context" by Paul McMurdie and Susan Holmes. These resources provide insights into various statistical approaches, transformations, and analysis techniques for 16S data.
Remember that there is ongoing research in the field, and best practices continue to evolve. It's important to critically evaluate the methods, consider the specific characteristics of your data, and consult with your advisor or peers with expertise in microbiome analysis to make informed decisions about data transformations and diversity metric assessment.
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In some cases the -10 of the promoter is known, while in others it is not.
In that case how do we predict the transcription start site (TSS)?
I have tried using the popular tools available. They give inconsistent results compared to some of the characterized promoters and transcription start site.
The bacteria I am using is Lactococcus lactis NZ9000.
Thank you in advance.
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Don't forget that the transcription start site might be very far away from the ORF, especially if the ORF is part of an operon. So don't just look immediately upstream from the ORF.
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We are working on Biofilm and Quorum sensing genes of E.coli, we suggest some of reasons maybe:- Contamination, Annealing Temperature, Melting Temperature, DNA Extraction mistakes in the Techniques, we identified them by biochemical tests to be sure the isolates are E.coli, but now we are collecting samples from the beginning and doing the procedure again
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There could be several possible reasons why no bands are observed in the PCR amplification of 16S rRNA of E.coli genes:
  1. Contamination: Contamination with other organisms, DNA, or PCR reagents can lead to false-negative results. Make sure that your reagents are free from contamination and that you use appropriate precautions to avoid contamination during the entire PCR process.
  2. Annealing temperature: The annealing temperature of the primers may be too high or too low, which can lead to poor amplification or no amplification. You can try adjusting the annealing temperature to optimize the PCR conditions.
  3. Melting temperature: The melting temperature (Tm) of the primers may be too low or too high. If the Tm is too low, the primers may anneal nonspecifically to other regions of the DNA, resulting in no amplification or non-specific amplification. If the Tm is too high, the primers may not anneal to the template DNA, resulting in no amplification. You can try adjusting the Tm to optimize the PCR conditions.
  4. DNA extraction: Mistakes in the DNA extraction process can lead to poor DNA quality, low DNA concentration, or PCR inhibitors in the DNA samples, which can affect PCR amplification. Make sure that you follow a standardized DNA extraction protocol and use appropriate controls to monitor the quality and quantity of DNA samples.
  5. Genetic variation: There is genetic variation among different strains of E.coli, and the 16S rRNA gene sequences may vary among different isolates. Make sure that the primers you are using are appropriate for the E.coli strains you are working with.
  6. PCR conditions: Other PCR conditions, such as the extension time, cycle number, or buffer components, may also affect the PCR amplification. You can try optimizing the PCR conditions to improve the amplification efficiency.
These video playlists might be helpful to you:
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Dear colleagues,
I am trying to standardize bacterial reduction after UV treatments. UV doses and log reductions for each dose are known, but log reductions in food are often non-linear because food matrices are complex and the inactivation of microorganisms is attenuated in higher doses. One example of this can be the next paper, in which some bacteria are disinfected in a J pattern and others in a reverse-S shape:
How can I calculate the decimal reduction dose in these cases?
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The decimal reduction dose (D-value) is a measure of the effectiveness of a non-linear logarithmic reduction treatment, which is typically used in microbiology to determine the amount of radiation, heat, or chemical treatment needed to reduce the number of microorganisms by 90%. The D-value is calculated using the following formula:
D = (log N0 - log N1) / k
Where:
- D is the decimal reduction dose (in the unit of the treatment)
- N0 is the initial number of microorganisms
- N1 is the number of surviving microorganisms after treatment
- k is the slope of the logarithmic reduction curve (also known as the "death rate constant")
To calculate the D-value, you will need to perform a series of experiments where you expose a known number of microorganisms to different doses of the non-linear logarithmic reduction treatment, and then count the number of surviving microorganisms at each dose. You can then plot the data on a logarithmic scale, and determine the slope of the curve using linear regression analysis.
Once you have the slope (k) of the logarithmic reduction curve, you can use the above formula to calculate the D-value for a given treatment. For example, if you have determined that the D-value for a particular radiation treatment is 10 kGy, then you would need to apply a dose of 10 kGy to achieve a 90% reduction in the number of microorganisms.
Note that the calculation of the D-value assumes that the reduction in microorganisms is a stochastic process that follows a logarithmic distribution. The actual reduction may be affected by other factors, such as the age and physiological state of the microorganisms, the presence of protective materials, and the environmental conditions during treatment.
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biofilm and quorum sensing genes of E.coli, not used drug but chemical material (Thiophene)
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Lack of aseptic techniques
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1-The conditions of the relationship between the pigment (Pyocyanin) with Gold (Au Nanoparticles)?
2-Dose the pigment (Pyocyanin) work as Reducing agent or not?
3-Dose the pigment (Pyocyanin) endures high temperatures or not?
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1.Pyocyanin can be adsorbed on the surface of gold nanoparticles. It does not oxidize or reduce gold. Gold is oxidized with potassium cyanide or aqua regia.
2. When interacting with gold ions, Pyocyanin (quinone) acts as an oxidizing agent.
3. Pyocyanin melting point 133 0С.
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In the latest edition (2016) of the Basic Practical Microbiology Manual from the Microbiology Society, all the aseptic procedures are carried on near a Bunsen burner. This is the common practice I've seen for yeast cultures.
However, while working with HEK cells, I've used a laminar flow hood to avoid contamination of cultures.
In the case of yeast cultures, would it be advisable to work with a laminar flow hood, or is it always best to work near a Bunsen burner?
The first drawback I'd claim about using a laminar flow hood while working with yeast is that you can't use a Bunsen burner inside the hood, so it would make flaming difficult.
Could you give me your opinion/experience about this? Thank you!
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Dear Diana,
I think that all of the answers above are reasonable but none have mentioned directly another factor – what is the air quality like in your laboratory? I have worked in university labs in warm and humid places, where mould was always a problem, in which case a laminar flow cabinet with a good filter would be very useful, and in colder drier places where we never seem to have problems with air-born spores, and where a bunsen that can be moved around to suit may be a better option.
Andrew
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What methods reduce microbiological pollution and effective method used in removing water borne micro organisms from bottled water?
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As far as I know, to ensure the safety of water, we need a combination between filtration and chemical treatments, first with ozone as a very strong oxidizing agent, then filtration using biological activated carbon to get rid of oxidation residues, which may constitute good nutrients for the remaining bacteria, causing rapid growth and thus water pollution. ... Then chlorination to eliminate the remaining harmful microorganisms...My sincere gratitude to everyone.
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For instance what roles does emergence play in inorganic chemistry, in the earth sciences, in organic chemistry, the molecular biology of the cell, physiology, psychology, sociology, in ecology, economics, or in astrophysics?
I am studying the development of emergence up through the levels of the hierarchic organization of material reality, from elementary particles to the emergence of galactic clusters.
Another goal is to reveal the isomorphic aspects of the stages of emergence as they occur throughout that development.
I am interested in the following:
1. What are the initial components of the process of emergence in cases of emergence in your field of research?
2. What are the major stages of the process of emergence in those cases?
3. How does the list of components change with the changing stages of your processes of emergence?
4. What then are the components that constitute the final emergent product, whether it be a quality, an object, or a pattern-of-organization of material structure or process?
An Emergence Primer
Ø In its simplest form, emergence is the coming into existence of newly occurring patterns-of-organization of material structure and process due to the motion of units of matter.
Ø Emergence is a creative process, and is the source of the organized complexity of the material universe.
Ø There are two basic stages of emergence—first there is the process of emergence, and second there is the event of emergence that occurs as the consequence of the prior process.
Ø Emergence develops. It occurs in simple forms in simple situations in which few other factors are playing roles, and in progressively more complex forms in progressively more complex situations where increasing numbers of other factors are playing roles.
Ø Emergence is isomorphic because the simplest form of emergence also occurs within the core of all developed forms, giving them their intrinsic-identity as cases of emergence. An isomorphy is a pattern-of-material-organization that occurs in two to many different situations or systems. What is known about an isomorphy and the role it plays in one situation can be used to enhance the understanding of a different situation in which that isomorphy also occurs and plays a role. Thus what is known about emergence and its role in one situation can be used to enhance the understanding of a different situation where emergence also occurs and plays a role.
The Intrinsic Nature of Emergence—With Illustrations.
Vesterby, Vincent. 2011. The Intrinsic Nature of Emergence—With Illustrations. Proceedings of the 55th Annual Meeting of the ISSS, Hull, U.K.
Emergence Is an Isomorphy
Vesterby, Vincent. 2017. Emergence Is an Isomorphy.
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Emergence has become the front and center of my research in the couple of last years. To be capable to understand its working in depth, I had developed several open-source Python programs (ranging from the simplest one to the most advanced one) that enables everyone first to understand the cellular automata programming, and later apply them to studies of emergence that is occurring in so-called 'Game of Life'.
Quite a few videos depicting animated emergent structures are accessible in my profile at sections about data and software: e.g., logic-gates AND, OR, NOT, and quite a few emergent structures emerging in generalized neighborhoods of the original GoL. The latest paper is describing another interesting area, the design of error-resilient emergents, which can withstand the of 1% of errors into their evaluation process.
With respect to the questions provided in this answer. I highly recommend watching said videos and even run the open-source GoL-N24 Python software and try to play with emergence on your own. The personal experience with those simulations is always the best way to start to understand that we do not understand the theory of emergence!
Everyone is welcomed to play with emergence. One thing is sure, there are hiding huge treasures both experimental and theoretical in such 'playing' with the concept of emergence. Hopefully, this year will be published a paper that is going to address, at least, some root questions about emergence and its very principles (stay tuned).
References:
There are all three logic-gates avaiable
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Does DMSO can have cytotoxic effects on microorganisms and may interfere with the results of microbiological assays?
What is the concentration that is used to secerning the antimicrobial activity of plant extracts?
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Yes, it could be cytotoxic depending on its concentration and less than 1% is mainly recommended in a working solution.
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I’m doing a cartwheel assay to see if a bacterial strain I’ve deemed resistant from an MIC has efflux pumps. Would it be possible to use Nile red instead of EtBr for the cartwheel assays instead? the concentration is .5mg/L in the plates. I’ve tried using broth to perform the assays but only a few of the bacteria actually fluoresce.
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Yes, it is possible to use Nile Red instead of EtBr for the cartwheel assay to detect efflux pumps. Nile Red is a lipophilic dye that can be used to monitor changes in the hydrophobicity of bacterial membranes, which is associated with efflux pump activity.
The concentration of Nile Red in the plates should be optimized for the particular bacterial strain being tested. A concentration of 0.5 mg/L may be appropriate for some strains, but others may require a higher or lower concentration. You may need to perform a dose-response experiment to determine the optimal concentration for your bacterial strain.
Using broth for the assay may not be the most suitable approach for all bacterial strains. The composition of the growth medium can affect the expression and activity of efflux pumps. You may want to try using solid media instead, such as Mueller-Hinton agar, which is commonly used for MIC assays. The bacterial cells can be inoculated onto the agar surface and then incubated with the Nile Red-containing media.
Additionally, you may want to consider using a positive control strain that is known to express efflux pumps, to ensure that the assay is working properly. Finally, it is important to interpret the results of the assay carefully, as there may be other factors that can affect the fluorescence of the cells, such as changes in membrane potential or alterations in membrane composition.
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"Dynamin-related proteins such as DynA are common in bacteria, and the only three dynamin-like protein encoding genes found in archaea are of bacterial origin." https://www.cell.com/trends/microbiology/fulltext/S0966-842X(16)00074-3?code=cell-site
What are these three genes? Can't find.
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The three domains are the archaea, the bacteria and the eukarya. prokaryotic organism belong either to the domain archaea or the domain bacteria,organism with eukaryotic cells belong to the domain eukarya.
The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. The current state of research regarding the structure function relationships of several archaeal chromatin proteins histones, Alba, cren7 and Sul7d.
Microorganism transfer genes to other organisms through horizontal gene transfer -the transfer of rRNA or tRNA or DNA to an organism that is not its offspring.
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Hello,
I have performed some recombineering protocols and realised that the chances of my plasmid being in a multimeric state are quite high.
I previously designed 7 primer pairs that will produce alternating amplicons of 500 and 700 bp around my recombineered plasmid (which is 35kb) just so that I could get an idea that no weird recombination events occurred when looking at it in a gel.
Anyways, I did the 7 PCR reactions on a control with the original plasmid, and they produced the expected pattern, but when performing it on my miniprep-purified plasmid I was obtaining a lot of bands of all sorts of sizes (larger and shorter than expected amplicon). Funny thing is that these multiple bands seemed to follow the same pattern in all my replicates (different pattern for each primer of course, but same throughout the different colonies tested) which makes me rule out the possibility of salt contaminants affecting primer binding etc. I thought it might be bacterial genomic contamination that was being amplified, so I performed a CsCl-ethidium bromide density gradient to purify it and sent it off for sequencing.
But now Im wondering, would a multimeric plasmid yield multiple bands if amplified with a single pair of primers?
By the way, I can't run it on a gel to assess if it's multimeric because of its large size 35kb, although I am going to ask if anyone at my lab has a pulse field gel electrophoresis just in case.
Thanks!
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Hi all,
Thank you for your answers,
I did a restriction digest with enzymes that cut multiple times and indeed, this plasmid has recombined in all sorts of ways except the one I was planning on...
I don't know if any of you have practiced recombineering before, but if you have I would really appreciate your advice regarding how to reduce unwanted recombination events in this type of cloning.
I am using an L-arabinose inducible plasmid for the λRed system. Are NEB10betas good cells for these protocols or maybe Stabl3 would be a better option? Also, would co-electroporating my plasmid at very low concentrations and the linear dsDNA into E. coli (which contains the induced λRed system-plasmid) help in avoiding these undesired recombinations?
Any other thoughts or help on how to avoid this?
Thanks!
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I have few sets of questions related to CHO cells (CHO-S cell line) :-
1) Can somebody tell me what effect physical factors like light (other than UV or radiation) have on CHO cell growth, viability, morphology, and quality profile?
2) Can anybody with a microbiology or algal background provide a set of light intensity or LUX ranges for observing any difference in the profile of CHO cells? Though this physical agent appears to be ineffective, as light has no influence on the growth profile of the CHO cells but for an observation and to monitor the growth profile I wanted to setup this experiment.
3)Can someone provide some strategies for installing a tube lamp or a light source inside a CO2 incubator such that the shaking flask with CHO cells is constantly exposed to light and the effect can be easily monitored?
4) Is there any research paper or review paper on effect of light on cells specifically CHO cells, or any other cells which shows a remarkable impact on the overall profile?
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I'm not sure if you are only interested in physical factors related to light.
However, another important physical factor in the cultivation of CHO cells in a shake flask / stirred tank reactors is the generated shear force. If you want to investigate this further - test different rpm and flasks with/without chicanes.
As far as light itself is concerned - keep in mind that light can also influence the culture medium and this could then indirectly influence the cells.
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We are doing a research on Biofilm formation of Bacteria, for knowing each isolate strong, moderate or weak, by calculations tables of Standard deviation, Variance and Cutoff (Ct) etc… and with the help of Microsoft Excel but the results in the program differ from the hand written and don’t know the best way to calculate and compare the results, any help will be very appreciated, Thank you
Ali
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Dear Ali,
There are probably many ways you can differentiate bacterial biofilm formation and I'd suggest either following the procedure described in a research paper working on the species or strains you are interested in, or by using your own criteria. We characterise our air-liquid interface biofilms using a combined biofilm assay measuring biofilm strength, attachment levels and total growth - which means we can describe 'biofilms' using one or all three quantitative measurements. We tend not to use 'no biofilm' control strains, as many biofilm-formers produce such weak and poorly attached structures it is not clear when a 'no biofilm' becomes a measurable one (though we can use a sterile microcosm/culture as the negative control if appropriate).
I can't comment on your problems with Excel, but one simple way is to graph the mean results from your experimental replicates, and divide these into quartiles about the median (i.e., from the minimum values to Q1, from Q1 to the median, from the median to Q3, and from Q3 to the maximum value). You could then simply state that no or poor biofilm formers are min - Q1, biofilm formers are Q1 ≤ Q3, and good biofilm-formers are Q3 - max (if you liked, you could divide your bacteria into no biofilm, poor biofilms, good biofilms and very good biofilms – the number of categories is up to you, but you can't have lots when you have relatively few bacteria to distribute across these categories).
There are statistical tests you could use, and assuming that data (or residuals) are Normally distributed, you could say that no or poor biofilms are not significantly different to a no-biofilm control, etc., but this gets messy because it is hard to know when a very poor biofilm is effectively no biofilm, etc.
Andrew
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Soil scientists, root biologists, (soil) microbiologists, can anyone point us towards reliable literature / measurements about soil oxygen dynamics? I.e. oxygen gradients across soil depth / type / compaction / water content? Many thanks in advance!
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@ Sjon, the attached file may be useful to you.
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Beef extract provide many nutrients to the culture media thus is an important element of it. But the use of beef extract is not ethical enough to be accepted as the only source for it.
Is there any other substitute which is ethical and can be used in place of beef extract?
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We have been using an anaerobic jar with an active catalyst and a microaerophilic gas generator pack to culture the H. pylori strain (NCTC 11639) from ATCC on ATCC Medium 260, which is Tryptic Soy Medium with 5% Defibrinated Sheep Blood agar. Unfortunately, our bacterial strain has not grown, even after waiting for 4 to 7 days at 37°C. Could you please suggest any other culture media or potential issues that could be hindering growth?
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Hello, most studies have used Brucella agar or Columbia agar as the agar base. An amount of 7 to 10% blood improves the growth of H. pylori. Horse blood may also improve the growth of H. pylori as compared to sheep blood.
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Probiotics are working of life (living organisms, esp. bacteria) for life, by life and in life's suitable niche. They favour friends and ward off enemies, boosts immunity, maintain balance of the microbiome in gut. We can find its wide applications in the field of aquaculture.
You all please present probiotics' application in diverse fields of environmental management in tackling pollutants and toxicants. Discuss in detail and share relevant resources about how they act to fulfill the goal
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In fact the major mechanisms of action of probiotics is the regulation of host immune response. Thus, the immune system is divided into the innate and adaptive systems. The adaptive immune response depends on B and T lymphocytes, which bind to specific antigens. Some of the beneficial effects of probiotic consumption include improvement of intestinal health by the regulation of microbiota, and stimulation and development of the immune system, synthesizing and enhancing the bioavailability of nutrients, reducing symptoms of lactose intolerance. Probiotics Modulate Both Innate and Adaptive Immune System. One of the most powerful effects of probiotics is to modulate the immune system. Probiotics strengthen both innate and adaptive immune responses through bacterial-epithelial-immune cell crosstalk. By the provision of energy sources for gut microbiota, prebiotics are able to modulate the composition and the function of these microorganisms. Distant bacterial species in phylogeny share their skills to consume a specific prebiotic regularly. Prebiotics are specialized plant fibers. They act like fertilizers that stimulate the growth of healthy bacteria in the gut. Prebiotics are found in many fruits and vegetables, especially those that contain complex carbohydrates, such as fiber and resistant starch. The prebiotic atmosphere is the second atmosphere present on Earth before today's biotic, oxygen-rich third atmosphere, and after the first atmosphere of Earth's formation. The formation of the Earth, roughly 4.5 billion years ago, involved multiple collisions and coalescence of planetary embryos.
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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
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By using suitable filter
Membrane, I guess.
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Hi, this is my first time making a bacterial growth curve
Should I use 10% v/v 10^6 CFU/mL as an inoculum in my working flask (so there will be a final 10^5 CFU/mL inoculum in my working flask)? It's enough or too low?
and then if 10^6 CFU/mL is fine, can I use my standard curve equation to predict what OD is equal to 10^6 CFU/mL?
(the standard curve is made using the spread plate method)
Thank you
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Generally I like to use 100-1000 fold dilution of the inoculum for the final culture volume. It is ok to go more dilute, really the main criteria should be how long you want to grow the final culture for.
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We have a Flask that contains broth, and we want to inoculate it with Bacteria inoculum, Can we simply take a touch by the loop or by micropipette?
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Kseniya Kondrasheva Nikhita Madhav Chambhare Thank you very much, The Goal is Pyocyanin production, we tried 1:100 and yes by micropipette because the loop carry small volume
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It would be preferred if the book covers all aspects of biological wastewater treatment including but not limited to chemistry, microbiology, resources recovery, and characteristics of bioreactors.
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Book titled “Wastewater Engineering Treatment and Reuse” by MetCalf & Eddy is considered the Holy Bible for Wastewater treatment.
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Dear Experts,
I was wondering if you could kindly provide some insight on how may I confirm a certain bacteria strain is BL21 strain whether biochemically or by molecular methods.
Your attention is highly appreciated.
Thanks,
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You are totally right, it is mentioned in the guidelines of FDA and other agencies that the production strain must be validated through WGS and supplier's documents. However, unfortunately, both are unavailable at the moment. If the regulators do not accept this method, there is no option but to perform WGS.
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I am starting to use phage T4 for some experiments with students. Last summer I tried to titrate a sample and it was ok. Some times it didn't work (I don't know why) but others it worked correctly.
The problem is now I am trying again and I can not obtain any phage plaques. I am trying different T4 samples (one from the microbiology lab upstairs my own lab) with E. coli B at different growing states but I can not see any plaques.
Any idea of what can be wrong?
Thanks all in advance
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What do your plates look like? Sometimes if you have a contaminant somewhere you get an unusual lawn and this hides the appearance of plaques. So is your lawn really nice and even and opaque over the entire plate?
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is there a specific ratio to follow during the addition?
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Add Chloroform to a total of 50% total volume and vortex vigorously for a min or half. Let the sample settle for 10 minutes
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Right now, I am doing a project to characterize yeasts that I isolated from honey.
I found that the yeasts can grow even at 40% sucrose medium. is this yeast can be considered osmotolerant yeast, if yes I needed some reference to prove that this yeast are may or in fact osmotolerant.
Thanks.
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The yeast Zygosaccharomyces rouxii is known for its high tolerance to osmotic stress, which is thought to be caused by sets of specific genes.
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Dear researchers we write and publish research articles in the Discipline of Microbiology, molecular biology and Pharmacology. If someone wants work in collaboration with us please let us know. Thank you
Whatsapp: 00923145099045
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Yes @Daniil you can do email me
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Hello,
I would like to come up with the fermentation volume required for an enzyme manufacturing project.
I have the volume/concentration necessary and I have the fermentation activity of the strains.
Ex. If the fermentation activity of the strain is 5000 u/ml and if I need to produce 20000 Kgs of enzyme with an activity of 50000 U/g then what would be my fermentation volume?
TIA for all the help
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One thing I would add to Adam B Shapiro response is the % recovery during processing and fermentation. The final yield of enzyme is often a small fraction of the initial yield.
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I have been looking to expand our virology department here for a year since joining my current institution. I have only ever purchased viruses from Carolina Biosciences (bacteriophage) and ATCC (most of our cell lines and viruses). Now I'm looking to buy HCoV‑NL63 and -HKU1 after working with 229E and TGEV for the last few years between my last employer and current, to give our microbiologists (and myself) some more room to develop. Does anyone have any helpful insight?
Sincerely,
A green microbiologist (>5 years working in the field)
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This is a scientefic and commercial subject ,so the only mean is coordination between your institute and intenational organizations like WHO,CDC ,FAO so ....on for scientfic side while commercial side follow an agreements of manufactury prducing
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Hello!!!
I would like you to help me with information about full predoctoral or doctoral fellowships in areas such as bioinformatics, computational biology, microbiology or related fields to which I can apply.
I would be very grateful if you could recommend some of them.
Fausto Cabezas-Mera
Greetings from Ecuador
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HI,
where are you from? Are you willing to travel?
This web site is filled with opportunities regarding what you are looking for:
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There are many complicated and detailed steps, devices like cold centrifuge, O.D measurement, silica gel, columns, HPLC, If possible please i need a short recap of the procedure and advices with Many Thanks to you
Ali
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A simple method:
Obtain a pure culture broth of P. aeruginosa.
Centrifuge the broth.
Separate the supernatant.
Add chloroform to the supernatant.
Keep it for settlement.
Add HCl. It will turns into pink/red. Again keep for settlement.
Add NaOH, it will turns blue.
Pigment isolated.
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I do recognise Penicillium, but it looks like there are a number of other genera growing on my plates - perhaps Cladosporium or Aspergillus?
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Plate No 4 contains Penicillium (blueish colony, Aspergillus paraciticus (dark green colonies), Fusarium (whitish colony), and Alternaira blackish colony)
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Right now Im working with a modified LB media. Like usual i melt the agar before plating it. The modified agar contain yeast extract, Lb, glycerol, KH2PO4, K2HPO4, agar. Thank you
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Dear Harry,
We regularly make up King's B medium – Proteose peptone, glycerol, KH2PO4 and K2HPO4. To avoid precipitates, I always add the KH2PO4 and K2HPO4 to the deionised water and wait until that is dissolved, before adding the glycerol and peptone (and agar).
Andrew
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I work for a cosmetics lab in the microbiology department. Our lab is not accredited, but we do follow the International Standards (ISO).
One of the steps in these standards is to contaminate a cosmetic sample with a known strain (S. aureus, P. aeruginosa, and/or E. coli) in a known concentration and then plate the suspension. The media used is a non-selective media (TSA) and the plates after solidifying are incubated inverted. The entire procedure is done in a laminar airflow chamber. The strains used were purchased and then cryopreserved.
The issue is with the P. aeruginosa strain, regardless of the incorporation technique used it will form an aggregate of colonies. Furthermore, the stock strain (kept refrigerated at -5ºC) is changing color after 3 weeks and won't grow after streaking to new non-selective agar media, when most of our strains last at least 6 weeks.
What should we do to avoid the colonies from merging on the plate and is it normal for a strain to become invalid after that short of a period?
The first photo is of the colony aggregation issue and the second is the aspect of the stock strain after 3 weeks.
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Hello.
You should identify grown colonies on the MALDI-spectrometer. If it is the target microorganism, then the dilution should be rechecked.
No, it is not normal that after 3 weeks of freezing, the culture dies. Typically, long-term storage of P. aeruginosa stock cultures is carried out at -80ºC.
Sincerely yours,
Artem Trofimenko
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Hi!
I would like you to help me with information about full predoctoral or PhD fellowships in bioinformatics, if possible in the area of microbiology.
Thanks
Fausto Cabezas-Mera
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You might consider the well-renowned Max Planck Institute, see for example: https://www.age.mpg.de/science/core-facilities/bioinformatics
Best regards.
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Hello
I would like you to help me with information on doctoral or predoctoral fellowships in bioinformatics, if possible in the area of microbiology.
Thank you
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Hi, In Brazil, you can apply to these programs of Bioinformatics. We have so many other bioinformatics programs and other microbiology programs.
http://www.pgbioinfo.icb.ufmg.br (Registration starts on December 2022)
Good luck.
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Hi everyone,
I am trying to grow marine cyanobacteria from my samples using BG11 and L1 as nutrient and agar as gelling agent. I found agarolytic bacteria thrives in my plates, liquifying my agar. So, I tried using gellan gum as an alternative to agar. In my trials, I keep getting wobbly unstable gellan gels even though I used magnesium sulphate as cations. After overnight upside-down, I got dome-shaped gellan gel surface. When I tried using cell spreader, the gelling broke. Has anyone encounter this problem?
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Kristova Yubilius Indrataruna I have two suggestions for you: 1) Use ASNIII medium for marine CB: BG-11 was elaborated for freshwater CB; 2) Use very purified agarose (like Kim Sea) instead of either agar or gellan gum because very purified agarose does not support the proliferation of heterotrophs. Good luck. Igor Brown
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I have an extract that is more effective at lower concentrations against tested strains of bacteria. I have done some research and some says it might be to do thickness of the extract that doesn't allow it to diffuse into the plate equally. but to the naked eye it doest seem that way.
Any suggestions would be greatly appreciate it.
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You may also consider precipitation/crashing of compound at higher concentration also.....which will make it unavailable to cells, if that is case.
Hope that helps!
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we have a microbiology reader (LOGPHASE 600, BioTek), but unfortunately, we can not draw a growth curve for SC and SCEG BUT it works for YPD and YPEG. If you had a similar experience, kindly let me know and provide your solution in writing.
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The question does not have enough details. Is the problem that the strain does not grow at all in SC and SCEG? Or that the data is not reproducible, or the curves don't look correct? Those are all very different sorts of problems.
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Anyone knows Microbiology test specification for Cosmetics?
need for TAMC, TYMC, Pathogens specifications
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Simplifying
Cosmetic micro specs include two elements;
1) Total count. Some reg's recognize two of these - one for kids and eyes (to to 500/ml or g) and another for general products (up to 1000 cfu/ml or g. Major industry works at 100 cfu/ml or g.
2) Objectionable microbes. For health concerns, no detection of Staphylococcus aureus, Pseudomonas aeruginosa or Candida albicans is universal. Some reg's add Enterococcus. Many add Burkholderia cepacia complex. Major cosmetic companies specify no staph or candida as above and no detected Gram negative bacteria.
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The total mesophilic plate count is widely used as a broad indication of Microbiological quality, although it is unsuitable for this purpose in fermented foods sample, why is that?
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Hi Twana,
The total mesophilic plant count will be unsuitable in case of fermented food as there are chances of mesophilic contaminants active in the fermented food if kept in exposure to contamination or the result of poor quality control while the packaging David Sturm has answered nearly the exact same answer. It can also be understood by a condition that while the food sample has been a fermented product and the time the other mesophilic contaminant was inactive due to certain reason and with due course of time after a certain time limit the microbe dominating the fermented food might start producing metabolites that other contaminant can consume. Although microbe in the food sample present in its packaging it can be slow but while being the mesophilic and getting the nutrient from the plate itself it has a good chances of experiencing a better growth then in the food itself.
Hope this might clear your doubt,
Best Regards
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