Applied Microbiology - Science topic

Hello to all my fellow Biologists.

I have resorted to posting this question as my last desperate attempt to find a place for myself in the world of biotechnology.

I am a first class student with relatively good grades (GPA 3.77/4.00) in BSc. of Biotechnology (Hons), excellent extra-curriculars and competitions under my belt, 6 months of work as a Field/Research Assistant and 4 years of previous work experience in events management. I have experience in the microbiology, molecular biology, antivirals, nutraceuticals and cell culture disciplines. I have also taken a great liking to scientific communication and create visual content to make biology simpler for the Layman, both bother and in my own time.

Despite all this, I haven't had a single postgraduate application succeed for the last 2 years. And though I do understand there is high competition for available spots, I also wonder what I may be lacking despite some telling me I have an "impressive CV" and can do a direct PhD.

It is unfortunate however that my family is not doing financially well, therefore I can only afford opportunities with a scholarship or that are work/salary-based. Perhaps this narrows available opportunities but regardless, studentship scholarships have very evidently not opted for me, simply because "there were too many applicants this time around". Perhaps lacking funds is not enough of a criteria? (Hint of sarcasm).

Additionally, I was born and raised in the UAE (I do not get citizenship), therefore I am also looking for a potential country to eventually settle down in while doing the work I love.

I would greatly appreciate if anyone would know of opportunities I may be able to apply for like fully funded PhDs, or skilled/summer programs and workshops/internships, or even Research or Lab assistant positions you or someone you know may be looking for, because unfortunately, I'm 2 rejections away from being completely out of options.

I would greatly appreciate any input you may have or can share with me! I have also added my CV for your reference.

I don't want my impression of the field I love to be tainted with nothing but rejections, and to settle for a job outside our field simply because I had no other choice.

I look forward to hearing from you all.

Sincerely,

Zahraa Ozeer

biofilm and quorum sensing genes of E.coli, not used drug but chemical material (Thiophene)

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?

I had test the killer effect of the yeast and I found some colonies seem to have an misty inhibition zone rather than a clear inhibition zone on plate as you can see in the picture. Is there any academic definition of this phenomenon? Can I say it is inhibited or resistant? I didn't see any paper discuss about this or I use wrong key words.

I understand the extreme pH can kill the normal skin microflora bacteria. But how. can someone explain the process?

Hello, I am isolating PBMCs to obtain Endothelial Progenitor Cells, but during the culture, I discovered that both of my plates included "unknown creatures" 3 days after the isolation; may I know what these are?

In our diagnostic lab, we extract pure viral RNA (Qiagen viral RNA extraction kit).

Therefore, no 28S and 18S rRNA can be traced in agarose gel for total RNA integrity assesment. However, very small bands appear on gel (as seen in picture), are those 5S rRNA or other small RNA moleculea? If so, may they be correlated to total RNA integrity?

Is there any other way to asses the pure viral RNA integrity (besides Bioanalyzer)?

Thanks

I understand every protein is different regarding induction and solubility. I'm just wondering if there is a rule of thumb regarding a molecular weight limit. I'm thinking about trying to express a ~165 kDa cytosolic protein. Thanks!

I am writing a review article in biotechnology and as you know graphic images are so important in these papers. I would appreciate it if you suggest the best options. Thank you

I am learning about predatory bacteria.

Could you give me a recommendation for researcher & research group that focuses on predatory bacteria? Especially the predatory bacteria from animal samples, not just environmental samples. Hopefully, this can be a list for someone interested in this topic.

Thank you in advance.

Sometimes all of scientific articles are not available in google search even in another search engine. But when I intended to do a new work, so how can I know that this is first time. Even though, it may be that the work has been done before but it did not appear in my search engine. So, what could basis that we can say this is first time work or research.

Hello, help me! I did selective isolation for actinomycetes on selective media like ISP 2, Bennett's agar, Starch M protein and more from soil sample but turned out my colonies looks like this. almost all media turned out this way.. they look almost the same. I'm not sure if bacteria can look like this (even it is not actinomycetes i just need to count the CFU) or is it the effect from the antibiotic supplemented in the media? How do i count the CFU if they turned out like this. Totally appreciate any suggestions and help. Take a look at these pictures and thank you so much in advance.

What is the lowest known detection limit of microplate testing for identifying antifouling agents?

See : "A marine bacterial adhesion microplate test using the fluorescent DAPI dye: a new method to screen antifouling agents" C. Leroy et al. Letters in Applied Microbiology ISSN 0266-8254

Our method allows the quantification of adhered marine bacteria in well from about 2 · 10⁷to 2 · 10⁸ bacteria per cm2

Thanks in advance

Hello,

I'm going to be attempting to perform a bacteria killing assay using E. coli ATCC #8739. I have performed a bacteria killing assay using this bacteria before, however the previous protocol I used it for started with E. coli in a dehydrated powder and I can't seem to find them in that form anymore (in Australia). However, I can find E. coli ATCC #8739 in capsules where the bacteria is stored on the lid and just needs to be rehydrated (https://www.thermofisher.com/order/catalog/product/R4717050?SID=srch-srp-R4717050).

Having not used this product before I'm curious if anyone else has used them, and could explain in a bit more detail how they work.

For my previous protocol, from what I remember (was 5 years ago), I rehydrated the powder form of E. coli ATCC #8739, plated it on agar overnight, and then used an inoculating loop to take a sample and make a stock solution of desired concentration. Does anyone know in what way these capsules work differently? or do they essentially work the same?

Any further information would be appreciated,

Thank you,

Elliott

i got mann whitney test value U=1402, i am confused about this so large value. this value is right? i mean if value comes in thousands then no need to worry or there is any problem??? please

I am culturing N. europaea ATCC25978 in minimal media with phenol red pH indicator, wrapped in foil at 30degC. I supplement the media with more sodium carbonate when the media turns yellow/acidifies. I usually sub culture once every two weeks (or when the culture stops turning yellow within 2 days after adding more carbonate), or start a new culture from a frozen stock (stored at -80degC in 5% DMSO). This was working just fine for about a year, and then suddenly, the cultures became non-viable. Even the frozen stocks would not grow again. I waited 9 weeks for a sign of viability - nada.

I had re-ordered the strain from the culture collection, and it looks like I may have lost viability after only two sub-cultures. I assess viability by the media acidifying, and confirm by measuring nitrite production. Are these cultures dead? Inactive? What could I do to revive/reactivate these cultures? And what could have happened that suddenly killed them off?

Chitosan is a natural biopolymer with antibacterial properties and the solution of chitosan is prepared in acetic acid. So, has acetic acid any effect in contributing towards the antibacterial behavior of chitosan?

Government laws require occupational biohazard management. However, they do not present guidelines on which methodology to apply. I guess it's because of the particularities of each occupation and organization. Do you know any methodology for the evaluation of biological risk, in which the calculation of the level of risk can be obtained?

I am going to optimize the medium composition for enzyme production. there are many optimisation method such as RSM, Taguchi Orthogonal array etc... Which method is best for medium optimisation?

Hello, For my industrial microbiology courses assay, I would like to Ask if anyone knows or have an idea about the the manufacturing procedures of Antimicrobial Discs? how to make them from scratch? The quality control procedure? how to put the discs on the Cartridges?

Any help would be muchly appreciated.

Thank you.

Hello everyone!

Recently, I was confused by E.coli electroproration. My goal is to transform the recombinant fragments and pGRB-SgRNA plasmids into competent cells containing pRED-Cas9 by electrotransformation to achieve knockout of related genes.

I made competent cells according to the instructions above of https://barricklab.org/twiki/bin/view/Lab/ProtocolsElectrocompetentCells (100ul 1m IPTG was added to 100mL medium to express Cas9 protein when the cells grew to OD₆₀₀ was 0.4-0.6). Usually, the concentration of the fragment I added to the tube was about 200 ng, and the concentration of plasmid was about 100 ng. The pulse was released twice by BIO-RAD electrotometer in EcI mode, and then resuscitated at 800ul LB 30 ℃ for 2 hours, then coated on the double-resistant plate. The above process was proceeded on the ice.

However, after transformation, it grows very slowly on the screening plate (usually 18-24 hours, and it often takes 24-48 hours recently), and the final colonies are all wrong by PCR identification.

Researchers are welcomed to discuss the causes of this phenomenon.

Few year ago, a friend publish an article in a journal that was not quoted as 'prédator'. Rencently the same journal was found in the list of 'prédator journal'

1-Which are the Criteria to Identify a Journal as predator?

2-In which circonstances a scientific journal can move from 'non predator' to 'predator'?

3-Which agencies (structures) are qualified to classify a journal as predator or not?

I sent my bacteria for identification by FAME analysis but the service provider only provided me the fatty acid profile of the bacteria. now how to identify the bacteria with only fatty acid profile information.

Please someone help me.

I need to sequence an entire bacterial gene (6.1 kb). Is there a way to do it other than amplifying several smaller overlapping fragments for Sanger sequencing? Can I Sanger sequence the whole amplified gene using "walking primers", and if so, how is it techincally performed?

Is there any other method to sequence a single gene?

Thanks

Respected researchers or professors,

I am Kumar Sharp, currently a third year MBBS student from India. I will be graduating medical school in 2024.

I have a very keen interest in Pharmacology, drug development, infectious diseases, microbiology and immunology. I have done my best to develop my interests in research and development, public speaking and leadership, publishing work in COVID-19 as well.,which you can see from my profile.

I would like to pursue my future career in these fields and teaching. I belong to a middle class family and do not have adequate resources to apply for international exams.

Can you all suggest if there are any ways to apply for these specialization in countries other than India.?

I am having bacterial strains in the agar plate. I want to extract these strains and store them in glycerol for long-term use. Is there any stepwise procedure for this process?

Hi.

I have prepared hetero-atom-doped carbon dots (Nitrogen with sulfur, boron, phosphorous) for the eradication of biofilm of drug-resistant bacteria. But, I did not see any bacterial death at low concentrations when I am using doped carbon dots. Should I change any parameters or something else?

I was wondering if LB broth would be harmful if ingested. The ingredients don't seem particularly toxic, but many safety sheet warn against drinking it. If anyone could help me with my query I would be very thankful.

Greetings,

I have more than 100 bacterial isolates, and I want to identify them. Would you like to suggest to be the best way for their 16s rRNA identification (most probably by 27F and 1492R universal primers), concerning; 1) reliability, 2)time taken, 3)cost/price, and 4)service provider from KSA.

Thanks.

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?

In all labs I saw, I found that ethanol is used for sterilization of hands etc. in experiments with microorganisms. Why is isopropyl alcohol not used while it is relatively cheaper? Is it harmful for skin upon frequent use?

I am working on an iron inducible promoter screen and would like to perform it on solid media. However, using agar may contaminate my control media with iron and I would like to use some method to deplete the usable iron to the bacteria. I have seen a few papers that use 2,2'-dipyridyl to do so, but I am skeptical because I have never heard of this method and am having trouble finding literature pertaining to this topic. If anyone has experience or can steer me to an article discussing the use of the substance in this way I would appreciate it.

THANKS!

I have listeria selective agar (oxford formulation) and listeria selective supplement.

is it possible to use Maximum recovery diluent or Buffered peptone water in enrichment step?

please support

thanks in advance.

I want to do a fermentation test for my yeast. I want to know if i can do it using YPD broth supplemented with phenol red as pH indicator. If can, how much phenol red would it needed, and how to formulate the broth as a whole. It would be very helpful if you attach some literature. Thankyou.

I want to do a fermentation test for my yeast to know if they can ferment glucose or not. After some study i found that phenol red broth might be the media for it. But the example that using that broth is commonly for bacteria. So i want to know whether it can be used for yeast and how to formulate one. It would be very helpful if you give the literature for the formula. Thankyou

After a positive Ziehl NeeIsen coloration (M. paratuberculosis suspected), I want to recover and concentrate Mycobacteria from stools (cow dung) for further investigations. Is there any abbreviated protocol?

A bacteria grew on macconkey, they were white and round colonies, oxidase negative, catalase positive, nonlactose fermenter but when I did gram staining it appeared as gram negative cocci sometimes in chains and others as a diplococci. It was isolated from xanthan gum powder used to manufacture drugs. Any idea what ir could be or what I can do to identify it?

Oh it also grew on Oxoids Brillance Salmonella agar forming pink colonies which also rules out salmonella the thing is that that agar has novobiocine and cefsulodine as antibiotics so that bacteria must be resistant to both at least at the concentrations in the agar, and the and gram staining gave the same result as the macconkey. Also before plating in both agars 10g of the xanthan gum were enriched on triptic soy broth for 24h at 37C

The very interesting Hypothesis about Fungi on Mars was considered in the preprint "Fungi on Mars? Evidence of Growth and Behavior From Sequential Images" :

What is your opinion regarding this? I think that use AI/ML image recognition can be the next step of study this hypothesis until NASA will check this idea with help rovers on Mars. As input data for ML need use similar images of similar Fungi on Eart.

Could you please tell about the opportunities available at various Universities and Institutes which offers Post Doctoral Fellowship for Doctoral students of life science stream (Especially Ph. D's of Biotechnology, Microbiology and Biochemistry) from India.

I wanted to isolate osmotolerant yeast from natural resource, i want to know the minimum concentration i'll make in the media to make it a high osmotic environment for yeast

I want to screen osmotolerant yeast in PGY Agar using some different glucose concentration to make a high osmotic pressure in media (like grow it in 10%, 12%, 15%, and 20% Glucose concentration) I want to know how to determine the suitable sets of glucose concentration for screening the yeast. Thankyou, it would be very helpful if there is any paper that use or explain this method

I want to study the interactions between some putative fungal endophytes and model plants related to valuable crops. As far as I know nothing is known about their possible interactions with plants. I was thinking of using either Lotus Japonicus or Medicago truncatula.

What model plant would you recommend and why?

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!

Dear colleagues!

I am trying to figure out how to do an extraction for soil microorganisms for further metabolomic analyses. I am only interested in the microbiota part, so I would like to discard any organic matter present in the samples.

Do you know any useful method for that? Any suggestions that could help me?

Thanks for your help!

Hello,

If I want to clone a gene of interest in a plasmid containing ORF, how should I do that, and which criteria I should follow?

Thanks,

Ramanjaneyulu

I have a 200 mg/ml ampiciline solution, how much should i add to 300 ml of LB medium to get the final concentration of 40 ug/ml?? How much bacteria (in ml) should i add to 75 ml of medium to dilute the culture 50 times??

Can anyone please suggest some related topic or area in microbiology and immunology except COVID/SAARS?

I'm determining bioburden of textile materials by filtering on a membrane the diluent used to extract the microorganisms. As it's textiles I'm working with they naturally lose a lot of lint in the liquid making it easy to clog my membrane. I was thinking of pre-filtering the solution on Whatman Paper 4 but I think 25 um can still retain some fungal spores. Is there any other method or filter paper you recommend?

In the pulp and paper company that I work in, samples from paper, water and pulp from the paper machine gave information about existing spores of Presumptive Bacillus cereus.

Our paper is used for food packaging manufacture, so the presence of spores in it is unacceptable.

Can you give me an advice on how to deal with this problem? Is there a way to remove spores from the machine?

Is it better to use kanamycin aesculin azide agar or bile aesculin agar when selecting for enterococci? Are there advantages of one media over the other? Thanks

Looking for tools with proved accuracy to detect ploidy levels in microbial whole-genomes.

Dear all,

I am looking for recommendations for an efficient protocol for the extraction of Genomic DNA from several fungal cultures.

I have most of the chemicals and equipment used in the process, but I am not getting a complete procedure (Starting from Cell disruption) to purification and quantification of DNA.

Any kind of help will be appreciated.

Best Regards

Arush

While maintaining cancer cell lines originated from cattle squamous cell carcinoma we are troubleshooting an unusual problem as we are getting some spheroid like structures in our flasks maintained in DMEM-F12 with antibiotics. To exempt the probability of contamination we performed gram staining, Leishman's staining, and inoculation in both blood & SDA agar, and there was supposed to be no contamination. Then we performed immunostaining with oct-4 & TRA-1 which was available in our lab as a canine ADSC marker. We performed rt-qpcr with cattle specific primers for cancer stem cells, and it yielded that there is positive fold expression in these tumor spheres of oct-4, sox-2, lin28 & klf4. Then parent cancer cells and very high expression of CD24 did not match the product size when run on gel to confirm, but oct4, sox2, lin28 & klf4 matched their size. Then we tried to perform karyotyping from these Embryoid bodies (?) and got not exact spread but something like bundles of long chromosomes united at their centers and heavily condensed. We have done the soft agar colony forming assay, but still we are facing the problem that its growth is very fast and media color is towards yellow when kept in differentiation medium & HESC medium for a day. As our lab doesn't have a lab animal facility is there any way to know exactly what it is? RNA content is also low (9ug) and showing 200 bp difference in both 18s & 28s RNA size when run on bio-analyzer. Attached is a picture of what we are getting.

Hi,

I constructed a network with igraph showing the connections between bacterial groups in three different systems (suppose A, B and C). Each node represented an OTU/ASV and edge represented connections between them. Each system formed a hub and showed their respective connections. Now I am interested in knowing the number of nodes, edges in each hub and also connectivity degree, cohesion and modularity. I want to know whether the degree of connections between two systems are larger than the other. Like whether A and B are connected strongly than A and C.I am not sure how can I do that. Any help will be appreciated. I will be happy to share more information if needed.

Best,

Sandipan

I am inviting researchers for collaboration on a research project, which includes the testing of some nanotechnology based disinfectants (surface disinfectants) efficacy testing for different microbes and viruses. I will try to provide concerned developed product samples for different experimental procedures.

Isolation and screening of bacteria for cellulase production. 

By asking the question I wanna know whether gene present in one genera of bacteria coding for particular antibiotic resistance will also be present in another genera of bacteria. For eg whether qnr gene coding for fluroquinolone resistance will be same for Staphylococcus spp and E.coli or not.

The Corona Virus Epidemic poses an important challenge to practical hygiene on a mass level. Recent research has shown that in places where a great number of persons convene, toilets and wash rooms might be critical for reducing or enhancing spread.The effectiveness of various types of eletcric hand dryers hasbeen at the origin of heated discussions, but to show evidence the the presence or absence of microbes on the hands is just one factor. Other factots, such as the risk of contamination of surfaces surrounding the hand drying device or of the release of contaminated aerosol into the atmosphere surrounding the device. Who knows of more recent studies which have taken into account these elements?

hi,i have lyophilized legionella and I don't know what broth media I can use. Please, help me to know what media is good for growing them

Hi dears

Anybody know the percentage of MRSA and MSSA of S.aureus in the differen population? or totally in the world?

Dear expertise,

1) I have some trouble to get reproducible results of phosphorylated protein from western blot. Please give me some ideas and suggestions to get the perfect/reproducible results from the blot.

2.) How different is the western blot protocol for phosphorylated protein from regular western blot?

Thank you in advance for your help.

I need a transport media to hold swabs potentially containing E. coli strains for latter lab processing. It must be viable for at least 36 hours. Have you guys got any advice on the matter?

I want to isolate fungi from sea water. Which medium do you recommend to do so?

I was thinking about PDA modified with sea water but I am not sure if I should use either 100% sea water or a mixture distilled or deionized water/sea water? I do not know either if it is better to use natural filtered sea water or to prepare artificial sea water.

Thank you in advance

Hello,

I want to isolate the brightest bioluminescent mutants of photobacterium phosphoreum from my culture, but all colonies look equally as bright. Any ideas, how I could isolate brighter mutants??

If yes, then how to preserve it economically instead of making its glycerol stock? Cryopreservation in liquid nitrogen becomes costlier.

What about oil preservation? but, there is still a concern over preservation of oil degrading bacteria/microbe.

Please discuss your views.

i want to grow rhizosphere bacteria on nutrient broth and subsequently check their growth through OD. I need a robust protocol that can tell me all the details about conducting this experiment.

I'm not sure how to achieve this in a microtitre plate or petri dish, I did think by electrophoresis, but is there anything else I can use and voltage?

Is it possible to separate (distinguish) different AMF morphotypes which may possibly represent different taxa just by looking spores under a stereo microscope of say, 60x?

I have a cryo stock of a gram negative bacteria, which came with the instructions to grow in a highly nutritive media NBRC 802 for activation. However it has been contaminated with a gram positive Bacillus sp. that seems to be outgrowing it in all conditions. Using an M9 has proved unfruitful as either bacteria are too slow growing in it, and as soon as higher nutrition is introduced, the Bacillus completely overgrows the target bacteria. Does anybody have any suggestion of classical or molecular techniques to resolve this issue?

I used falcon tubes instead of cryovials for the preservation of microbial cultures.

As cryovials were expensive for me to buy So, instead I used falcon tubes.

But I'm looking for the scientific reason or say difference between cryovials and falcon tube preservation materials.

What are pros and cons of cryovials and flacon tubes?

What If someone asked me about these preserving materials I used especially falcon tubes,

How should I justify that I used cryovials or falcon tubes because of blah blah.....?

Cellulose from acetic acid bacteria through fermentation method, but give me steps about this procedure.

At the current moment I've come across 2 studies: Castelino et al. 2017 and Parnell et al. 2017 who compared different regions regarding amplification of low biomass samples and the comparison with negative controls (Parnell). Perhaps anyone could suggest any other study covering this topic?

Hi, I was testing for Siderophore producing bacteria but I found in one culture plate only a portion of my culture plate become pink in colour. What is the reason behind that ?

We are going to innoculate fungal spores to biochar but not able to get a higher amount of fungal spores. So, if anyone has some idea about the concentration of fungal spores which is suitable for good growth in biochar, please inform.

Dear researchers,

I am doing some experiments on poultry samples. I found difficulties to prepare my samples for artificial contamination in the lab. My purpose is to completely decontaminate the samples to avoid any synergies with the strains that I will be using meanwhile keeping the meat in the fresh state (no thermal treatment).

Do you have any publications or protocols that may help me with that?

Thank you.

For developing good portable sterilizer for field use (maybe for forest, desert) which source can work with smaller battery source, with less energy, in a smaller box without producing hazards to the personnel?