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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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I am working on the strain Penicillium chrysogenum, but I have a problem with cultivation in a liquid medium and it doesn't grow or its growth is not properly. As we have a general incubator (33c and 162rpm) I use this incubator for the project. we have also an incubator that has not shaker but I can change its temperature. I prepare the culture medium that is attached under this question and I pour it into a flask and autoclave it at 121 c (all of the materials in one flask). I use solid culture as inoculum (one loop). 33c and 162rpm.
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First of all you should optimize the conditions i.e, temperature (not more than 30C and the RPM.
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What are the names of strains of Saccharomyces Cerevisiae which are generally used in production of nutritional yeast?
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The tablet contains a single strain and it has been compressed at an average weight of 500mg.
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CFU/g(Colony_forming units per gram for solids can be calculated using miles and misra methods.
No. Of colonies ×Total dilution factor
_____________________________________
Volume of culture plated in ml
The attached illustrate procedure of dilutions in detailed.
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I would like to know how I can get a standardized suspension of Aspergillus brasiliensis. I used a paper Whatman No. 4 to separate hyphae and spores when I check in plate count at various dilutions get inconsistent results after incubating at 20 ° C to 25 ° C in three days.
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This is routine practice for this fungus
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Question 1: For example, if 70 bps of complete homology exist between a fragment and host chromosome (in let's say E. coli), will all 70 bp's be exchanged between the two DNA molecules?
Question 2: Will each strand go through recombination as in holiday junction etc...?
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Dear Chris,
Your question depends on whether or not the second homologous fragment is part of a circular piece of DNA (e.g. a plasmid) or not.
If you have homologous recombination between two circular DNA's then all of the DNA is conserved, and the outcome of this will be a single, larger DNA circle containing two 'copies' of the homologous recombination site. These may be slightly different to one another if the two original sites were not perfect copies of one another, and the final sites are in fact hybrids with the first part of the first site linked the second part of the second site, and the second part of the first site linked to the first part of the second site (!). This recombination can occur between homologous sequences that are very short (10 - 20 bp) though generally it is accepted that homologous recombination requires at least 100 bp of homologous sequence. The recombination produces a single Holliday Junction, which if resolved properly results in a single larger circular DNA, and if resolved in the other way, merely recreates the two original DNA circles.
If you have recombination between a circular and linear piece of DNA, then the resolution of the Holliday Junction will produce a larger linear DNA that contains all of the original sequences (or if resolved in the other way, reconstitute both original molecules).
The recombination between a circular DNA and a linear fragment can get more complex if the homologous sequences are large (i.e. if the linear fragment is a copy of a section in the circular DNA). In this case, you can have cross-overs at either end of the linear fragment, in which case the outer-halves of the two crossover sites in the linear fragment are lost, and the product is a circular DNA in which the original, larger homologous sequence has been replaced by the linear fragment. This is a very useful out come, as you can replace the middle section of the linear piece with a section of DNA of interest (e.g., a gene for antibiotic resistance), and then use double-crossovers to insert that gene into the circular DNA (this is how you could make a gene knockout in a bacterial chromosome). All you have to do is to make sure that the two ends of the linear fragment each have a homologous sequence in the target circular DNA (they could be adjacent to one another, or separate).You could select for the appropriate outcome by growing transformed (or mated) cells on the appropriate antibiotic plate and confirm by PCR or sequencing.
Regards, Andrew.
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Anybody knows about Pride conference, does it is authentic, please let me know because I have received invitation as one of the speaker in the conference. Details regarding conference and contact person are given bellow,
“International Conference on Microbiology & Infectious Diseases" which is scheduled at Hilton Rome Airport , Rome, Italy from November 08 - 10,2021.
Isabelle Smith
Program Manager | Microbiology & Infectious Diseases
Pride Conferences
4 Lombard Street, London, EC3V 9HD, UK
T:  +44 - 2392160593
eFax Number:442081816247
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Dear Joana Lima ,
I think you are right that this is a predatory business. There are more red flags:
-They are mentioned in the list of questionable conferences https://libguides.caltech.edu/c.php?g=512665&p=3503029
-The address is suspect and most likely misleadingly suggesting UK origin https://www.abcn.com/offices-london-city--lombard-street-2533
-Even if the address is legit it loos like they are not registered here https://suite.endole.co.uk/explorer/postcode/ec3v-9hd
Best regards.
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Do you think the COVID-19 pandemic will significantly impact on water systems? With respect to recreational, surface and groundwater quality and supply?
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Before answering your valuable question, let me ask the following two questions:
  • Is there a lack of interpretability and transparency related to this virus?
  • Did we reach a state with this pandemic that is hard to control and monitor?
It's a matter of regret that COVID-19 is a "One Thousand and One Nights" story. It seems that we are at the beginning!
Most hope from Allah (Subhanahu Wa Ta'ala) to come back to our normal life as it was before!
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I want strong, constitutive expression of my protein in m. smegmatis.
I have a strong, constitutive promoter. However, the RBS is very weak.
I want to exchange the RBS for a new one that is better.
However, I worry that I will "break" the promoter when I try to add the new RBS.
How do I determine the important parts of the promoter, so I can replace the RBS without destroying the promoter?
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Theoretically, you could perform experimental mapping of the promoter start site, but his is likely not necessary because promoters usually don't overlap with the 5-6 bp of the RBS, so if you just change these, there is little chance that you will affect the promoter. There is also no guarantee on how much the expression of your gene will be improved, but you won't know until you try.
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can I use the spectrophotometer to get the OD for my bacterial suspension before doing a disk diffusion antibacterial test to have a 0.5 McFarland turbidity , and if yes at what wavelength and what value should I get at said wavelength ?
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At 600 OD
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Does the same group of bacteria always produce the same type of secondary metabolites or does the product depend on different factors (like the substract, for example)?
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It depends on the growth conditions and metabolic machinery of a given microorganism.
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I have listeria selective agar (oxford formulation) and listeria selective supplement.
I need to know what is the best diluent for enrichment of listeria.
is it possible to use Maximum recovery diluent or Buffered peptone water in enrichment step?
please support
thanks in advance.
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If I want to transport the sterilized laboratory glassware and bacterial culture in petridshes from one lab to another lab of a short distance then what will be the complete best strategy to avoid the contamination??
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When transporting glassware from one place to another, I do not think that you can avoid contamination 100%, but as much as possible it can be reduced by wrapping these utensils with sterile cellophane and transporting them with the dishes in a sterilized container, knowing that it is better to transfer bacteria through transport media. In general, if you use special selective culture media, you do not need to worry, because such media will prevent the growth of any species other than the one you are investigating.
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I am Performing the pomegranate juice evaluation, So Please help me with the process of microbiological assay of vitamin or provide the link of related paper or website
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Kindly check the following link that may be useful:
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Hi,
I and working on a project for extraterrestrial life, and i need few work on the titled topic. If is there any data, recommend it or please discuss the evaluation mechanism.
Thank you,
Muhammad Furqan Ali
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You can search for the following articles: National Environmental and Natural Resources Information System Environment and Temperature Report, light, atmosphere, wind
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We have isolated several strains of an organism from cultures of canine and human blood and subcutaneous nodules (using sterile techniques of course). These isolates have been subcultured on PDA and/or PD nutrient broth and found to be similar in appearance, both the macroscopic colonies, and the microscopic swabs viewed in wet-mount preparations. The organism stains positive with calcoflur white (contains chitin or cellulose) and seems capable of forming a variety of tertiary structures, depending on environmental conditions (ie, hyphae/pseudohyphae, sporocyst-like structures etc..). One universal property is that the small cells/spores etc... become motile within about 15 minutes after addition of sterile water or sterile saline to the smear. The “swimming” pattern appears eukaryotic rather than prokaryotic. I’ve attached a video showing time-lapse of about 25 minutes, during which a drop of stained liquid containing these possible “zoospores” undergoes several morphological changes. We think this represents the process of “zoospore induction” and eventual zoospore settling (maybe with release of stored mucilage etc... causing the white “fluid” appearance that develops upon the termination of “zoospore” motility?). We are awaiting WGS results on the cultured samples, and hopefully those sequencing studies will clarify the identity of these organisms, but in the meantime, we are trying to better understand the “behavior” we are seeing here, and figure out how it might relate to the apparent ability of this organism to infect and cause illness in, mammalian hosts. As far as we know, pythium and lagendium are the only zoospore-forming pathogens currently recognized as mammalian oomycete pathogens. We do not think this organism to be either of those, but we would appreciate help from anyone familiar with the movement patterns of zoospores from those (or other) pathogens to let us know if the movement seems similar to what would be seen in standardly done zoospore induction protocols and/or if there is an explanation for the “bleaching” effect that occurs after the motility ceases. Thank you!
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By experiments, It was noticed that the tap water induces zoospores production.
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I'm trialing a method of culturing the plant microbiome and I'd like to know if a majority of the microbial cells will still be viable for culturing if I store the whole plant sample in a -80 degree freezer. Will I only be selecting for and ultimately culturing micro-organisms that can withstand -80 degrees, or will the microbiome still be as viable for culturing had I processed the samples before freezing.
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It is more likely the former: you will perhaps be only selecting for those that can withstand -80 degC (likely those who can form spores[?], among others). A literature review is perhaps in order to give you an idea of what storage strategy to implement that will properly maintain microbiome diversity/strain representation in the sample.
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I am a graduated student.
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I think that colleagues specializing in food can suggest names of topics
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N/A
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prodigiosin is naturally occuring in Serratia macrcescens the pigment extracted by adding large volume of organic solvents,while the use of waste and un conventional bioresources for effectiveness of production using oil_extraction leftover wastes might help in commercial coast effect.
Ref:https:ncbi. nlm.nih.gov
Journal Genetic engineering&Biotechnology
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I need to do antimicrobial testing of a sample with gram-negative and gram-positive but I can only do BSL 1 in my lab. S.aureus is often used in the literature of similar experiments but it is BSL 2. What would be another gram-positive BSL 1 organism I can use instead?
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Thank you Mariana Emilia Cozzolino , Dr.Michael J. Benedik , and Dr.Roger Bayston for your input and advice! I will take this into consideration and given the current application of interest I'll pursue S.epidermis ATCC 12228 and consider B.subtilis as an alternative with your comment about spores in mind.
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Anaerobic microorganisms are very common in periodontal diseases especially periodontitis. My concern is how to isolate those organisms and transport it to the microbiological lab in a easy way.
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You need transport media, samples should be placed in fluid thioglycollate medium in a test tube and transport to the laboratory, and processed immediately.
Kindly check the following RG link:
In it, it has been explaind in detail how to transfer and deal with samples and how to deal with aerobic and anaerobic bacteria.
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We use malt extract agar with addition of 5 % tartaric acid to adjust the pH more acidic for yeast &mold counts (suppress the growth of the bacterial flora). The colonies formed in this medium were as in the image. What can we think about the white non-uniform growth in this medium? We would be very happy if you could share your experience.
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Atiye Degirmenci
thanks- can you elaborate?
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Hello,
I am trying to establish a growth curve for E.coli k-12 strain. I picked a colony from a fresh overnight plate and inoculated in 20 ml of fresh TSB in a 50 ml flask for 18 hours at 37 degrees Celsius at 220 rpm. Then I transferred 100 micro-liters of this culture into 250 ml of fresh TSB in a 500 ml flask at 37 degrees at 220 rpm. I took 5-ml aliquots immediately at time 0 and then every hour for up to 8 hours. I took optical density measurements of the aliquots and also did plate counts to get cfu/ml data. My calculated generation time was about 1 hour which seems to be a bit slow for E.coli and I was expecting to only get a lag phase of about a couple of hours. Does the outcome I obtained reasonable for E.coli? My plot has the typical shape of E.coli growth curve but the time I obtained for generation time and lag phase seem off to me.
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(I would say its fine, but I would like someone to agree)
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I am aware of a study that has compared the use of citrated and defibrinated sheep's blood in microbiological media ( ), but can anyone tell me if sheep blood prepared in Alsever solution interferes with any microbiological diagnostic tests?
Thank you for your input.
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I recently got indications of beta-hemolysis on blood agar made with sheep's blood in Alsever's solution with bacteria that should be gamma-hemolytic. The plates were fresh, as was the blood.
Unfortunately, I won't have fresh blood again for a few months, so I may not be able to verify these results for a while.
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Hello, I have a few hundred trimmed 16S metagenomic sequences from the Human Microbiome Project online database that I would like to search for the presence of several strains of bacteria via pairwise sequence similarity. Does anyone have any recommendations for software that can achieve this?
I am not a bioinformatician by any means, so something that has a user-friendly UI and can run on Windows would be much appreciated (although I can make my way around a command-line interface if need-be)!
As an aside, can I make a reasonable claim for species-level identity solely using 16S sequence identity? If so, is the >97% threshold generally accepted or is there another metric (e.g., score-based) that is more reliable?
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Hi Abhijeet!Thank you very much for the important question. Very difficult question to answer. You know metagenomic data can be of two different types i.e. Targeted/amplicon (16S rRNA) metagenomic data and shotgun whole metagenome sequencing (WMS) data. For the first one, you can analyse your data using QIIME, MOTHUR, MetaMLST, PanPhlAn, IDSeq, Pathoscope and MG-RAST (http://www.metagenomics.wiki/tools/pathogen-screening).
For WMS, you have limited database options, and includes only PathoScope (https://doi.org/10.1186/2049-2618-2-33) and IDSeq (https://idseq.net/) and MG-RAST (https://www.mg-rast.org/) (see our latest articles: https://doi.org/10.1038/s41598-019-49468-4; https://doi.org/10.1016/j.ygeno.2020.09.039)[email protected]
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I am currently researching the impact of different antimicrobials on the amount of endotoxin released from two different gram-negative bacteria types. I am using nutrient broth as the growth medium and it will end up being transferred into my samples for endotoxin analysis. I am using the ToxinSensor ™ Chromogenic LAL Endotoxin Assay Kit and a spectrophotometer for my analysis. The instructions state not to use a colored sample as it will interfere with the color change when detecting the presence of endotoxins. Is there a way to account for the color of the nutrient broth as the "standard" like I would for the water-blank step or do I need to remove the color completely? How could I remove the color without using something that will damage my sample?
If needed for reference, the instructions for the kit are listed at this link: https://www.genscript.com/product/documents?cat_no=L00350&catalogtype=Document-PROTOCOL
Thanks!
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use a defined medium with trace metals and micronutrients?
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RNA vaccines follow a different strategy, without using any "real" component of the virus at all. Instead, researchers aim to trick the human body into producing a specific virus component on its own. Since only this specific component is built, no complete virus can assemble itself. Nevertheless, the immune system learns to recognize the non-human components and trigger a defense reaction. So May I ask, What are your opinions about the safety and efficacy of the BNT162b2 mRNA Covid-19 Vaccine?
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I am preparing a metagenomics experiment from the soil sample. I will use Oxford Nanopore technology, which has only limited throughput (approx. 8 GB), so I need to discard all eukaryotic cells before the sequencing (because their genomes are really large, and would saturate the device quickly). So I am interested in the simple and reliable method, how to obtain only the prokaryotic and viral species. Is it a good idea to use some syringe filters? E.g. with the pore size 1 micron? So the eukaryotic cells will be stuck on the filter surface, and bacteria, archaea, and viruses will go through?
Thanks for all suggestions,
Martin
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For details of the possible methods to use, the article suggested hereunder refers.
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Hello everyone, I'm a biologist who is interested in the astrobiology and microbiology. I want to study master degree in microbiology and emphasize the thesis project in astrobiology. However I have never worked in something related with that, I lack of experience in that fields. On the other hand, a preview of the project is a requisite to apply for scholarships and study the postgraduate course in any university in the world.Recently I finished the latest book of microbiology of brock, also i have read books of astroiology, and papers, with them i got many ideas to research. However most of them require special devices which are able to simulate extraterrestrial enviroments such as venus, mars, etc. I'm living in Australia and apparently none of the universities in the country has this kind of machine. In addition to this, the development of one of this devices are too expensive and needs specialized personal to be constructed. So I had to read more about anothers possibilities and I got more ideas. But searching for papers, I noticed that always someone has already do the same (sometimes with differents kind of methods that I tought ). Am I being too exigent with me trying to do something unique, new and original? what can I do? it doesnt matter how much I try getting new ideas of research, always looks that someone already do the same. I'm stuck and out of ideas and time.
Thank you for read, I'll appreciate any advice.
Kind regards
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Astrobiology need prerequest courses about space microbiology,microbiology in general both theory and practical to facilitate your research which fillfull the request of MS.C thesis.
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I`ve been attempting to extract RNA from M. tb grown in lipid media using the Trizol method and the Direct-zol kit from Zymo Research. The growth of these strains in this media is minimal (reaches OD 0.6 - 0.9), so after extraction I`ve been getting low concentrations and low absorbance ratios for A260/230. The 260/280 ratios could also be better. Any idea on how I can improve these purities?
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Kindly refer to the above book mentioned by Negar.
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I streaked e.coli from the glycerol stock on an agar plate, and after 48 hrs, I only got three single colonies on the plate. The colonies look fine. However, since the only thing that grew on the plate is these three colonies, I'm a little worried about contamination.
This is my only stock, and I've been trying to revive the same bacteria and prepare some new glycerol stocks for a couple of weeks. But this is the only time that I managed to get results.
Do you think it's a good idea to use these colonies to make new stocks? Or should I continue trying until I get proper colonies on my plate?
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What agar did you streak the glycerol stock of E. coli on, please. Perhaps the preservation method was not good for the strain. How was the glycerol stock preserved? If you had three single colonies, you could propagate even a single colony of E. coli. Please confirm that it is E. coli and propagate the single colony in tryptic soy broth and re-stock using three different preservation methods. Read up culture maintenance carefully.
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Hi expert out there!
I'm using crystal violet staining to determine gram +ve and -ve bacteria, which is a very traditional method, but at the same time, I noticed that crystal violet also can use for cell viability tests. It seems that the sample that I'm going to use involves cells too, so my question is how can I minimize the chance for the cell to get stained but instead only the bacteria (ie increase the decolorization time will help?)?
Thanks in advance!
Cheers.
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You perform Gram reaction with crystal violet on pure cultures and not mixed cultures. So, please purify your cultures and apply the crystal violet to what you want. The cell culture techniques is a different protocol entirely.
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Hello everybody,
my name is Riccardo and I work as a microbiological analyst in a pharmaceutical company.
It's been a while since I started looking for alternatives to the huge amount of plastic we waste everyday with petri dishes, but I can't find anything.
I'm looking for alternatives both to stop using petri dishes or using biodegradable ones.
Glass is quite hard since we perform a lot of analyses and could be a complex solution.
Thanks everybody for anyone who reads this or gives some suggestion!
Kindly
Riccardo
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Great initiative here. There are several articles on this subject. Check insights from: https://mosaicscience.com/story/scientists-labs-sustainable-plastic-recycling-research/
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Dear all,
Hope everyone fine.
I'm having a doubt regarding that I'm going to do several in-vitro assays in subsequent days with the bacterial cells. In this regard, Shall I Culture a particular concentration of bacterial cells and store it in the refrigerator and reuse it? Will that be advisable? Will the live cells behave as normal as before?
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My doctor stored bacteria from 2017, within nutrient slants with added Glycerol 20 ml and kept within freezer.then she wanted to throw them away by scientific way.
BUT WE NEED IT FOR PRACTICAL MICROBIOLOGY LECTURE,
I subcultured them 70 Percents of them growths very well with all their characters.
This picture is just after first its subculture Pseudomonas aeruginosa.
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Could you please share with us your latest scientific achievements (i.e. papers, books, etc) regarding anaerobic digestion technology? Your worthwhile findings would definitely respond to the need for "Engineers without borders" worldwide for tackling the energy crisis, especially in the Global South.
Plaese discuss about your achivements.
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Mohammad Javad Bardi Latest achievements when you are asking about is on personal basis>?
well being in the industry for more than 20 years now i can say i must have done many researches and recent development is i have tried using different types of paddy straw from different parts of our country (INDIA) and tested the feedstocks for monodigestion as well as combined multifeed digestion designing a reactor for the same at mono scale and also tried bagasse and pressmud in combination with rice straw at individual levels and mixing all together and the results are wonderfull and it might change the industry look all together when one looks at the gas price hikes
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I was wondering which databases would be best for a scoping review on how drugs effect the microbiome. Not sure if this falls into pharmacology, microbiology or metagenomics, but I would probably want to search a database that contains all of them!
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If you know the name or sequence of your target gene or protein, submit it in the database to know effective drug against it.
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Dear Friends and Colleagues,
To date very few journals are available to accept video articles for submission/publication in our field, although these types of articles are of paramount importance in microbial ecology in order to share new techniques and approaches.
For this reason, I decided to open a Collection titled “Multi-targeted approaches to evaluate microbial interactions and ecosystem assemblages in diverse environments” on the Journal of Visualized Experiments (JoVE): https://www.jove.com/methods-collections/919.
The purpose of the Collection is to offer a comprehensive overview of wet- and dry-labs perspectives in the field of microbial ecology.
The most recent Impact Factor for JoVE (ISSN 1940-087X) is 1.163, according to the 2019 Journal Citation Reports released by Clarivate Analytics in 2020, and the Journal is currently indexed in the major databases, including PubMed, EMBASE, Scopus and Web of Science.
After submission, each manuscript will be editorially and peer reviewed, which is typically a 1-2 month process. Once a text article passes review, a script will be generated. Generally, a filming date will be scheduled within 4-8 weeks after acceptance. A videographer will be sent to the authors’ site to film the procedure.
If you are interested, either message me or submit an abstract here:(https://www.jove.com/methods-collections/submit-an-abstract?collection_id=919).
Best Regards,
Prof. Elaine CP De Martinis, Ph.D – Full Professor, University of São Paulo, Brazil
Otávio GG Almeida, B.Sc. – Ph.D. candidate, University of São Paulo, Brazil
Guest editors.
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Thanks for sharing!
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I would like to know what is the best dose of levan to use in vivo and the treatment period. I am using mice and I would like to gavage them with levans.
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We have lost many flasks due to contamination to B. cepacia. We have added Pen-Strep to no avail.
What are other antibiotics that could be used in culture media that does not belong to b-lactam or aminoglycosides class of antibiotics?
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It appears that your Bacillus cepacia contaminant is a resistant one. However, you could try Meropenem, ceftazidime, minocycline, temocillin, and piperacillin/tazobactam separately or in combination. Preparation of the antibiotic and introduction protocols could be sources of concern. Please follow the protocols carefully to achieve the final exposure concentration suitable for the contaminant concentration.
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I want to know about the different media used to check the growth and characterization of cadmium resistant bacteria to know the best media for its growth and also to aid identification of the bacterial species, what are the most commonly checked media for that?
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You should be able to check for Cadmium resistance using any media you wish to use. The choice of media should be dictated by the bacterial species you think you are going to get or you wish to grow.
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Hello,
We are also doing an experiment about siderophore. Can anyone please inform us why the color change occurs in the CAS media? I mean what chemical reaction is going on there?
Thank you very much in advance.
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The chrome azurol S (CAS) assay is a universal colourimetric method that detects siderophores. The competitive exchange of iron(111) from the indicator dye, CAS by the siderophore forming bacterium occurs. In this assay, siderophores scavenge iron from a Fe-CAS-hexadecyltrimethylammonium bromide complex and subsequently release the CAS dye which results in a colour change from blue to orange. The following link will lead you to the original paper of the assay. I hope you will find more knowledge about this by reading the following paper.
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I tried to transform the pET32a plasmid in dh5 alpha cells a couple of times. The first time I got no colonies after spreading the bacteria on the ampicillin plate, and the second time I only got 3 single colonies.
I also transformed another plasmid which contained an ampicillin resistance gene in the same dh5 cells, to make sure my cells are competent, and got a plate full of colonies.
Is it normal to get only three single colonies after transformation?
Are these single colonies reliable enough to use for plasmid extraction?
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Hi there, With the view of plasmid amplification, one transformant is enough. Are you sure about the amount of plasmid you engage in the transformation? If you get very few clones for one plasmid and loads with the other it might be due to the amount of circular plasmid in the transformation mix. If you want to make sure that the few clones you get are relevant you have to run the control experiment without plasmid to check the behaviour of the recipient strain on selective media.
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I am performing wastewater treatment thought different microorganisms such as microalgae and afterwards determining the lipid content in the biomass though Bligh and dyer method. Due to the COVID restriction, we are allowed to have limited time in the laboratory and therefore, a lot of samples should be stored and tested later.
I have to store my sample for cell counting and lipid determination?
For cell counting, Can I store my sample in ethanol to persevere it and count it later?
(0.3 ml sample and 0.7 ml ethanol)
For lipid: Can I store my liquid sample at -20C. and perform the lipid determination by Bligh and Dyer method later?
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For cell counting you can just add 1-2 drops of lugol solution to a 10 ml sample and store it.
For lipid determination, I recommend you to store your Microalgae pellet in the own extraction solvent with an antioxidant (BHT is commonly used) and inert (N gas) atmosphere in the freezer (-20-40ºC is OK)
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Hello Everyone,
The past few years have seen a lot of new cyanobacterial taxa being described using a polyphasic approach. It will be interesting to know that what are the various good things about using this approach and importantly, are there some particular taxonomic groups/clusters that are still unresolved where the polyphasic approach is still to give any proper answer?
What further developments do we anticipate in the coming years? What are the new techniques/methods that can be further incorporated for a better understanding of cyanobacterial taxonomy?
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Although it is not my specialty, I advise you to read the following paper:
A polyphasic approach for the taxonomy of cyanobacteria: principles and applications, by Jiří Komárek (2016).
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Hi everyone,
I am a new PhD student with very little microbiology experience and I have a few questions regarding the growth of Lactobacillus Reuteri which I hope you can help me with.
I want to grow L. Reuteri so that I can use it to create a standard curve for quantifying my bacterial qPCR data. I know lactobacilli are facultative anaerobes that grow best in anaerobic/microaerobic conditions. However, I do not have access to any anaerobic equipment in my lab.
I am planning to purchase the following Lactobacillus reuteri Kandler et al. (ATCC® 23272™) strain from ATCC which says it is aerobic on the product webpage so I am assuming I can grow it aerobically? (https://www.lgcstandards-atcc.org/products/all/23272.aspx#generalinformation).
Questions:
1. Could you please provide me with a step-by-step protocol with the best way to grow this ATCC® 23272™ strain in the lab without anaeorobic equipment?
Since I am not interested in the fermentation products, I only need to make a standard curve so surely aerobic growth should be fine?
2. If not, could someone provide me with a step by step protocol for microaerobic growth without specialist equipment?
3. From your experience, which lactobacillus species grow best in oxygen?
I have a general idea on how to grow it but I am really struggling without access to any protocols or any Microbiologist contacts... The research papers I have found are too vague. I would really appreciate your advice.
Best wishes
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I have earlier worked with lactobacillus species where I used to grow them with traditional method as my lab had no equipments for growing anaerobes. I used to use candle and jar method, jar was a typical bell jar (pictures attached). The steps are as follows:
i) First streak or spread the bacteria in your desired agar or broth (I used MRS agar/broth)
ii) Stack them in a plain surface
iii) Light a candle
iv) Cover it with the bell jar
v) Wait until the candle goes off
vii) You will observe your bacteria growing after 24-48 hours
This method creates a microaerophilic condition. However, the conditions are not 100% anaerobic. All the best with your work.
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Good afternoon,
I recently used OmniLog from BIOLOG for my experimentations : I tested the metabolism of different strains on 2 types of plates. I have 16 strains of 3 different groups (treatments) and when I analyse the data on OmniLog I don't know when and how to normalise the raw data : before or after calculating the parameters ? I would like to know if there's a significant difference on the metabolisation of a substrate between different groups but I don't know how to procede with this package.
Would you have any advice on how to treat this kind of data ?
Thanks !
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Hi Inês
I would recommend to normalize the data beforehand (using the extract function) because that enables you to recognise biological differences more easily.
Maybe this paper will help you:
opm: An R package for analysing OmniLog Phenotype Microarray Data (r-project.org)
... especially section 2.8
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Hello everyone,
For part of my PhD project, I'm hoping to grow some lactobacillus species in the lab so that I can create standard curves for a qPCR quantification of a faecal sample. However, I have only ever grown E.coli before so I'm not confident with the lactobacillus growth conditions.
Can you please provide me with some information about growing different lactobacillus species? Preferably aerobically as it will be more difficult for me to access an anaerobic chamber...
I was thinking of ordering some cells from ATCC (https://www.lgcstandards-atcc.org/products/all/23272.aspx#generalinformation). Is it possible to use the same agar and LB broth recipe as I'd use for e.coli or does it need to be altered for lactobacilli?
Any advice would be much appreciated. (As detailed as possible).
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We use MRS for a general Lactobacillus growth.
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That vaccines have been produced in such a short time, makes me doubt if they will help fight this pandemic and if they will not do us more harm.
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Yes, the preliminary results coming from mass vaccination drive in Israel are very encouraging.
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Hi everyone,
Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each primer. I understand then that have to mix them equimolarly, am I right? Has anyone used them?
Thx!
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The coronavirus pandemic has brought the world to a grinding halt and no doubt has altered the lives of each one of us. I think COVID-19 also has an impact on our normal research (i.e. related to our relevant field) and diverted us to work on various aspects of coronavirus to help combat the virus.
What's your opinion in this regard?
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I agree. My routine research into the environmental epidemiology of waterborne disease, and my preferred research into alcohol policy and climate policy, have been largely pushed aside in favour of research into the geospatial epidemiology of covid-19.
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We know that bamboo shoots are highly nutritious, low in fat and calorie. Did you ever tasted bamboo shoots recipe? If yes in what form.
What is the name of the recipe in your native place or language?
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Yes, I can confirm that bamboo sprouts are tasty. I ate bamboo sprouts as a side dish in various dishes, most recently in broth with soy noodles.
Regards,
Dariusz Prokopowicz
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Due to their ubiquitous nature, there is a tendency of the presence of microbes in a given mineral(s). For instance, if microorganisms that love the of pH less than 6 in the pH value, is isolated from a soil sample, we assume the soil is acidic. Is this also applicable to the type of mineral microbes love? How would this microbes tell the presence of such mineral?
Your contribution would mean so much for me
Thank you.
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recommend
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I will be using the lowered pH broth for MIC test of some disinfectants, and I do not want the acid to have any interfernece with MIC results.
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Assume you'll perform with appropriate controls. Why the low pH ?
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How can I know the stationary phase of growth of several bacteria?
We are aiming to collect exoproteome of several bacteria. We know that the ideal time to collect exoproteome is during the stationary phase of a particular bacteria. Perhaps we have many bacteria and there is very limited literature on few bacterial stationary phase. Further the information is not available for many bacteria. Could someone suggest us any manual or a paper which describes stationary phase of these bacteria.
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In stationary phase living cells number are equal to dead cells and there are many secondary products
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Hi all,
How would you use qPCR to quantify the amount of a particular bacterial species in a sample experimentally?
I understand you could use specific primers for the 16s V region of a bacterial species e.g. Lactobacillus Reuteri but how would you then quantify the CT values generated from your sample?
For instance, would you include a standard curve of Lactobacillus reuteri on the plate? If so, how is this possible if you cannot culture the bacterial species?
Instead of culturing, is it possible to order in bacterial samples to use on a qPCR plate for quantification? e.g. Bacterioides?
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You can PCR amplify and clone the 16S region of your bacteria of interest. Use the purified & digested plasmid to create a standard curve. If you calculate the exact copy number of your plasmid in the standard curve, then you can use it to determine exact copy numbers of your bacteria in your environmental sample (e.g. # bacteria genomes per 1 g of soil).
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I have tried to use TTC agar overlay method for a few times to identify respiratory-deficient yeast which were affected by EthBr. The problem is that cells which should have stayed white also have turned red or pink.
Evaluation of the overlayed colonies was done after 1 h, 2 h, 3h and 6 h. I tried different TTC concentrations: 0,1%, 0,05%, 0,03% and 0,01%.
I have attached photos of the colonies which were affected by EthBr and which were not.
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I used the same method to identify mutants defective in surface Fe3+ reduction so it might be that that is what you see and not respiration. As controls I always included a heat-inactivated (not too hot or your agar is melting, rather incubate longer) or UV inactivated plate, where cfus remain white. Also, antimycin A works as an respiration inhibitor. So if you still get a signal with cfus grown on that it's probably Fe3+ reduction you see...
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Need to check quorum sensing activity of Vibrio campbellii.
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I think that this medium is used for antibiotics method.
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What is the best method for prebiotic delivery to mice? dose of prebiotics? and treatment period?
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The prebiotic I use is added to the composition of the feed that the animals feed on. I use a 10% prebiotic diet.
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I read an article and actually met someone who suggested that human breast milk contains microorganisms and could be a source of novel bacteria
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I am working on the production of exoploysacchardes from Psychrophilic bacteria. I need deproteinization of the sample before precipitating EPS. Any alternative method will be appreciated. 
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What if, if I dont conduct dialysis step for my EPS? I do not have dialysis bag for now.
I wanna conduct NMR analysis, do you think there will be any drawbacks?
Thanks
Best
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The common method for phosphorus solubilization efficiency measurement of soil microbes is zone formation in agar media (generally Pikovskaya media) but this is a qualitative study. However, there is also a liquid culture method with insoluble phosphorus in liquid media. The estimation of available phosphorus by ICP-OES is quite promising and precise.
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But ICP-OES is a costly instrument and therefore available in a few research laboratories of third world countries.
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I need to know effect of heat treatments that are made when making camel milk powder on chemical , microbiological properties and shelf life of camel milk powder compared to cow milk powder. Thanks
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Congratulations!
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I received several strains of bacteria from another lab far away. However, one of the samples appears to have high fungal contamination. When I grow it in broth, I see lots of fungal contamination. It would be difficult and time consuming to have them send it again, and I worry a new sample would still be contaminated. I am confident it's not my reagents that are contaminated (uninoculated media showed no growth, and other strains they sent were fine).
Is there a good way to recover my bacteria from the fungus?
0.45 um filters? Addition of cyclohexamide?
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Antifungal agents are best to use
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To assess the air microflora in indoor air of laboratories
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We had conducted the Petri dish method to assess the fungal flora in our Zoonoses Laboratory.We used Sabouraud dextrose agar and Pal sunflower seed medium.The culture plates were exposed inside the laboratory for 5 to 10 minutes and then incubated for the growth of airborne fungi.
We have described this technique in the book entitled" Veterinary and Medical Mycology" authored by Mahendra Pal and published by the Indian Council of Agricultural Research New Delhi in 2007.
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What is the best way to preserve non-sporulating bacteria for further study?
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here's an oldie but goldie that could help you out:
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I have a culture of heterogeneous bacteria that will NOT form endospores.
This bacteria was originally isolated in nature and is a complex culture of multiple species.
I want to be able to preserve samples of these cultures for future study, but I cannot get them to last more than a few weeks in a refrigerator.
I CANNOT freeze this bacteria.
Is there a way I can put this bacteria in a quiescent state that will preserve it for a few months in a refrigerator?
Thanks!
Chuck
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Lyophilisation but with the use of a cryoprotectant (such as (DMSO) / glycerol) , although not recommended to all. Being heterogenic, it will be quite a challenge
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I am working with this strain but I do not have the formula for spore counting. please just suggest a spectrophotometric method.
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I made a new bacterial strain with an unmarked deletion using 2 step homologous recombination (with sacB counterselection). The full protocol is given in the link at the bottom.
The protocol worked well and I thought I got my desired knockout strain. However, I have now found that I cannot electroporate plasmids into my new knockout strain successfully.
I don't think it's something unique about the gene I deleted, as I have another strain with the same gene interrupted by a transposon and it's fine (electroporations normal).
I've tried electroporations repeatedly with new reagents and another strain as a positive control. Every time, my old strains work (I get lots of electroporated colonies), but my new knockout strain gives no colonies. All the reagents and protocols work fine for my old strains.
Why could this be? I picked a second clone of the knockout and it behaves the same: No colonies from electroporations.
The KO strains seem to grow pretty normally in broth. I don't see a growth defect.
I used hygromycin selection to make the KO and hygromycin to select for electroporation transformants. Could that cause problems? The deletion mutant should have completely lost the resistance cassette, and, indeed, when I put my KO strain in hygromyicin selection it does not survive -- consistent with successful unmarked deletion.
Protocol:
Fig 2 shows the genetics and Fig 3 shows the workflow. Section 3.5 shows the steps.
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One possibility is that you have a contaminant strain and what you think is your KO is actually something else.
I would suggest designing PCR primers that will serve to diagnostically verify your final genotype construct is what you presume it is and also show that the material lost after homologous recombination is actually gone.
Are you electroplating a new replicating plasmid or are you relying on homologous recombination to see transformants? If the latter, it might be you have a deletion or rearrangement of the target region so the problem is the recombination event.
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Discussions could be in any area e.g. medicine, engineering, biomedical engineering, microbiology, etc.
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Качество образования зависит от индивидуальных особенностей учеников. Однако, самым главным является вербальное общение. Оно помогает развиваться ученику. Нехватка вербального общения приводит к понижению уровня развития сознания человека.
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Stable extracellular enzyme activities are associated with soil colloids and persist even in harsh environments that would limit intracellular microbiological activity. Thus, only strictly intracellular enzyme activities can truly reflect microbial activity because the contribution of free extracellular enzyme released by active microbial cells is negligible; indeed, these enzymes are shortlived because they are degraded by proteases unless they are adsorbed by clays.
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Внеклеточная ферментная активность сохраняется только при благоприятных условиях среды, при которой микроорганизмы непрерывно выделяют их в окружающую среду для получения питательных элементов для своего роста и развития. При наступлении неблагоприятных условий, микроорганизмы теряют активность и перестают выделять ферменты.
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Virology, microbiology, immunology, vaccine
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Please take a look at this useful link.
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Hi,
I want to predict operons on entire bacterial genomes (already annotated). I used to use operon-mapper ( https://academic.oup.com/bioinformatics/article/34/23/4118/5040321), which is great but it has been "under maintenance" for weeks now and I really need one now.
MicrobesOnline doesn't support private genome hosting anymore and I think that the DOOR website is now down.
If you know any other tool, online or not, that would allow the genome-wide prediction of operons in complete, annotated bacterial genomes, that would be of great help to me.
Thanks
Julian
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You can try annotating your genome with tools like PROKKA, PGAP or RAST. And look at the predicted genes and other features
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I have a heterogeneous culture of nitrifying bacteria that was originally isolated from the field.
It has been kept alive for several months in a bioreactor.
I want to pull some of this bacteria out of the bioreactor and put it in a fridge for several months to examine later and possibly use it to re-seed a different bioreactor.
What would be the best way to preserve a heterogeneous culture of nitrifying bacteria?
(As a note, this culture contains ammonia oxidizing, nitrite oxidizing, AND heterotrophic bacteria)
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Lin Jyh-Yan Thankyou
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Dear All,
I need your help on how to calculate CFU/g soil. I would greatly appreciate if you could check if my calculation is correct.
5 g of soil was placed into 50 mL water. The solution was serial diluted 10x (1/10). 0.1 mL of the dilution was spread onto the agar plate.
30 bacterial colonies were obtained. 
My calculation:
5 g of soil was placed in 50 mL water so I have 100 mg soil in 1 mL of water.
With a dilution of 1/10, I have 10 mg of soil in 1mL of water
Next, I spread 0.1 mL of this dilution -> 1 mg of soil
I have obtained 30 CFU so I have 30 CFU on 1 mg of soil. Consequently, I have 30 000 CFU on 1 g of soil
Is this correct?
Thanks in advance.
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I agree with J. C. Tarafdar added an answe
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Vertigo is a condition that can make it feel like you or your surroundings are spinning, sometimes leading to a loss of balance, according to the U.S. National Library of Medicine.
Coronavirus 2019 or COVID-19 is a novel entity which had led to many challenges among physicians due to its rapidly evolving nature. Vertigo or dizziness has recently been described as a clinical manifestation of COVID-19.
So, Are dizziness and vertigo COVID-19 Symptoms? and why?
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Because covid_19 virus attack different organs and system after viremia the virus localised inCNS and cause both dizzeness and vertigo.
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Please note that the data is excel sheet is not my real data and my intention behind attaching the excel file is only to give our feedback community a clearer idea of how my data is expressed. This is the reason I have not run a two way ANOVA for this hypothetical data values. However, I have run a two-way ANOVA for my actual dataset.
Description:
Let's suppose I have a dataset for 'three types of vehicles (let's call them A,B,C), three types of tires (let's call them P,Q,R), and I measure the speed of each vehicle for each type of the tire. I record total 6 values for speed for each combination of vehicle and tire (Please view the excel file so as to get a clearer idea of how my data is expressed). I run a two-way ANOVA and I realize that my data does not follow homogeneity of variance. However, it is normally distributed and there are no outliers.
Then, I transform my data to log values however, I encounter the same issue (i.e. homogeneity of variance violated, data is however, normally distributed and no outliers).
So, my question is, do we have a non-parametric test that I can run instead of two-way ANOVA to analyze my data and obtain similar parameters in the output as a two-way ANOVA (such as mainly telling me the significant differences if there are any between "tires P for vehicle B" and "tire Q for vehicle C")?
Software I use: Excel, SPSS.
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the study of microorganisms is called microbiology
Microbiology is the study of microscopic organisms, such as bacteria, viruses, archaea, fungi and protozoa. This discipline includes fundamental research on the biochemistry, physiology, cell biology, ecology, evolution and clinical aspects of microorganisms, including the host response to these agents.
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Questions regarding biotechnology and microbiological and bio chemistry DEPARTMENT practically project working my contacts number is 8248413604
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What exactly you need? Frame a valid querry.
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Hi friends,
In the attached picture, you can see the primary RPE cells contaminated with small motile rode shape bacteria in 40 magnification microscope image. i cultured the extracted cells in Miller medium included 2%pen-strep and 10%pig serum. the bacterial contamination can be removed(not always) if i change medium every day . If not, under microscope i can see these bacteria which are motile and are moving in the living cells and in the space between them and after some day the cells all will be dead .
I think they are not mycoplasma. because I see them individually under 40 magnification microscope, how is your opinion?
can some body help me
1)which antibiotics can remove them?
2)what kind of microbes are there?
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Hi, Elmira and to all the experts out there:)
I'm replying to this post here hoping that whoever who is facing the same problem can get a solution and also to get help myself.
I'm using Retinal pigment epithelium cell too for my enzyme work, human in particular. However, I'm facing a serious contamination problem during the process. I had tried using 2% and even 3% penicillin-streptomycin to clear the bacteria but the media doesn't get any clearer, still cloudy. At the same time, I'm seeing these long &short rod bacteria swimming around actively( as attached in the video below). At this point, I'm not sure is it still bacteria or it's some parasite contamination cause they were swimming very actively.
Does anyone know
1) What type of bacteria is this?
2) Any antibiotic to successfully kill it?
and also to Elmira Keramatfar, if you have successfully cleared the bacteria contamination, how did you do it? What did you use?
Have a nice day everyone.
Regards,
Eunice Cheah
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We want to screen halotolerant protease producing bacteria. Since Skim milk (HiMedia) is available in our lab, therefore, we want to screen extracellular protease by this compound/ supplement. We have followed four papers to make agar medium with skim milk (with 5% NaCl). But every time the media got clotted after autoclave.
What is the reason and solution for this problem? Can anyone suggest anything?
Thank you.
We have followed these papers:
1. Babavalian, H., Amoozegar, M.A., Pourbabaee, A.A. et al. Isolation and identification of moderately halophilic bacteria producing hydrolytic enzymes from the largest hypersaline playa in Iran. Microbiology 82, 466–474 (2013). https://doi.org/10.1134/S0026261713040176
2. Adinarayana, K., Ellaiah, P. & Prasad, D.S. Purification and partial characterization of thermostable serine alkaline protease from a newly isolated Bacillus subtilis PE-11. AAPS PharmSciTech 4, 440–448 (2003). https://doi.org/10.1208/pt040456
3. Wery, N., Gerike, U., Sharman, A., Chaudhuri, J. B., Hough, D. W., & Danson, M. J. (2003). Use of a packed-column bioreactor for isolation of diverse protease-producing bacteria from antarctic soil. Applied and environmental microbiology, 69(3), 1457–1464. https://doi.org/10.1128/aem.69.3.1457-1464.2003
4. Rydén, A. C., Lindberg, M., & Philipson, L. (1973). Isolation and characterization of two protease-producing mutants from Staphylococcus aureus. Journal of bacteriology, 116(1), 25–32. https://doi.org/10.1128/JB.116.1.25-32.1973
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casein colloid, calcium ions, pH, temperature, and other casein components precipitate, all are forming the milk coagulum.
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Microbiologist’s opinion needed
Hello everyone,
Short version: We want to study microbiologically influenced corrosion in simulated seawater. How do we cultivate marine bacteria in the laboratory?
my mentor and I have been studying electrochemical behavior of metals and alloys in simulated acid rain. Since we came across alloys (steel and bronze) used in the shipbuilding industry we thought about changing the media for seawater. If we do so, we are obliged to take into consideration microorganisms living in the seawater and participating in direct corrosion processes through the formation of complex bioflms.
We were wondering, is there any “easy” way, or to say beginner cultures to start with? We’re aware of a hustle it may be to get the experiment and the conditions right or take care not to contaminate the working station. What interests us the most are bacteria or algae from Central or Southern Adriatic. We may also order a MIC culture from abroad (sulfate-reducing bacteria is the most popular one atm). Either way, we don’t have confidence in growing them in the laboratory or the right knowledge to set up conditions for the experiment. Thought someone would share some insights and help us plan ahead. Should we try getting pure culture from natural seawater sample or just make an online purchase?
We’re only interested in examining corrosion parameters on the metal surface, but if anyone finds it interesting and would like to contribute with their knowledge more, we’d be more than happy to broaden our horizons and collaborate. I have a Master’s degree in Biology and Chemistry and would love to explore the dynamics of processes and interactions between microorganisms and metal surfaces more.
Lastly, is bacterial culturing even worth trying if we don’t have a Microbiology expert by our side?
Looking forward to the answers,
please feel free to message me if you want to discuss more.
Thank you for your time,
best wishes,
Gloria
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Mrs Dana Ulanova , Mr. Ciamak Ghazaei and Mr. Andrew Macrae thank you so much for answering! Your answers help us aim for the right research approach and certainly raise a lot more questions. We don't have specific microbiological equipment you're mentioning, but some of the equipment that we use in electrochemistry measurements might do the job since the methods are sensitive and require to be controlled. Need to research more on that. Also, there's a clinical microbiology lab at University Clinical Hospital, we'll make sure to know if they are available or can contribute.
Thank you for your time,
Best wishes
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How long is it possible to store the bacterial culture at 4C?
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Some bacterial strains can be stored for up to 1 year at 4°C in agar stab cultures, which are especially useful for transporting samples to other research facilities.
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Hello all,
I am trying to create a graph on excel to express -log10 reduction of treatment groups and CFU spores using the equation -log10(final concentration/initial). However, one of my groups does not have a control to compare to.
How do i overcome this? Analysing data given to me
Thankyou (:
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Sadly, I think the best advice for you is to drop that particular group.
You can still mention it in text/graph and comment that the control is missing if it's a very important sample. This makes more sense if, for example, all other groups have very similar starting conditions.
The technical solution might be to use the average of all starting conditions (again, assuming they are similar). If they are not similar - there is no good technical alternative
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I've been trying to recover some bacterial cells by streaking them on agar plates, without success.
The stock has been kept in good conditions. But, there is a white pellet at the end of the glycerol tube, which I'm not actually sure whether it's the bacterial cells or not.
Do bacterial cells form pellets at the end of the glycerol stock tube?
Is there any way to recover them from the glycerol stock?
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You should inoculate the bacteria in eneichment broth medium, like lauria medium, brain heart infusion broth with double- concentration, then transfer growth on suitable agar medium and conferming its identification.
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I am having trouble figuring out where to obtain Streptomyces lividans strains that are commonly used for enzyme production. Specifically I am searching for the following strains: S. lividans TK24, 1326 and/or GSAL1 . They don't seem to be available from ATCC. Does anyone have any suggestions? Thanks in advance!
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Follow
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I want to know how to make probiotic in different concentration. I am planning to probiotic experiment with different concentration. I also want to know how to make the freeze dry probiotic powder with a definite concentration.
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Dear researcher,
Using McFarland standard we can workout for the turbidity matching for a particular number of cells per ml by performing TVC and use that concentration for the desired experimentation. The same can be use for freeze dry powder preparation by the method of choice.
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If i have silicones, alcohol and gas in my hair spray do i still need to test it for microbes?
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Agreed - but only for ethanolic products.
It might be worth finding out if there is a maximum ethanol concentration (if water is present, too) at which microorganisms will grow. Yeasts spring to mind.
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Hi
I am calculating intraparticle diffusion for adsorption studies . For calculating diffusion co efficient we need to know the radius of the adsorbent material .My material after activating i sieved and found its below 500 micrometre . I need to know if this is the radius or we have to calculate with any other methods.
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I'm working with cheese whey as an alternative culture medium. So far, the sterilization method that I use involves the precipitation of insoluble compounds (including proteins) by lowering the pH and heating for an extended period of time. Autoclave conditions are too extreme for the media and results in a slightly burnt color and smell.
I am wondering if there is an existing protocol that would allow sterilization of the media without precipitating the proteins.
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