Stack Exchange Network

Stack Exchange network consists of 174 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange
Join us in building a kind, collaborative learning community via our updated Code of Conduct.

Questions relating to protocols, procedures, and good practice when using laboratory equipment.

2
votes
1answer
34 views

When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and ...
1
vote
0answers
9 views

Using distilled water on sterile swab for collecting microbes on solid surfaces

I was wondering if it is acceptable to use distilled water on a sterile swab for the collection of microbes on a solid surface. - in this case, Salmonella and Shigella.
2
votes
1answer
61 views

How can enzymes be immobilised on glass?

I’m studying a hypothetical model for urease activity, which involves fluorescence measurement, hence the need for an optical window to which the enzyme urease is immobilised. From my previous ...
0
votes
0answers
6 views

Why is it more difficult to measure a decrease in fluorescence in FRET assays?

In the slides, the professor mentions that it is better to use a substrate double labelled with donor-acceptor molecules because we start with FRET quenching and measure increase in fluorescence if ...
1
vote
1answer
12 views

Can experiments in ELISA kits be monitored via both fluorometry and photometry?

In my bioanalytics course slides, the professor has written at one point that in a heterogenous immunoassay such as ELISA, we use fluorimetry to measure concentration of an analyte. In another slide ...
1
vote
0answers
26 views

What are the safety precautions I should take if I want to experiment with C. elegans (at home)?

Caenorhabditis elegans (C. elegans) is a nematode (roundworm), and many nematodes do infect humans and cause diseases. How much is C. elegans safe (or unsafe) in this respect? C.elegans is a popular ...
0
votes
0answers
34 views

Why is plasma glucose concentration not double that of whole blood?

It is known that the concentration of plasma glucose is 12% higher than that of whole blood. But since 45-50% of whole blood is red blood cells, shouldn't the plasma glucose be almost double — since ...
1
vote
0answers
31 views

Control for Bisulfite sequencing

I am wondering how can I control my converted DNA! I converted my DNA with bisulfite then I amplified the converted DNA with specific primers of BSP and purified my product and finally sequenced the ...
2
votes
0answers
10 views

Minimum number of cycles for effective qPCR quantification?

I have been having an apparent problem with gDNA contamination in my no-reverse transcriptase (NRT) controls by the appearance of fluorescence peaks in my qPCR data. I have/am trying multiple DNase ...
2
votes
1answer
56 views

Why shouldn't I clean microscope slides with a paper towel?

I've recently bought a microscope and been looking at a lot of bacteria and such, and have quickly run out of clean slides. I've seen videos and articles saying how you shouldn't clean microscope ...
3
votes
1answer
177 views

How do you keep track of past/new lab protocols?

Does there exist a list grouped my subject (e.g. 'microscopy') for keeping track of what protocols have been designed and used? Closest I could find is http://www.protocol-online.org/ but it's fairly ...
2
votes
1answer
25 views

What do the column labels in this table mean?

This table shows the effect of sound (song and tones) on female birds. However, I'm not sure what the labels (F1 22, P and η2) mean. I've seen the labels on other tables too. (from https://www.ncbi....
0
votes
0answers
12 views

How can I measure the efficacy of RNAi with high sensitivity?

I'm expressing RNAi against some candidate gene using the Gal4/UAS system in Drosophila. I know protein is expressed from the gene in the targeted cell types based on immunostainings, and the good ...
0
votes
0answers
27 views

Yeast transformation: is it necessary to remove template plasmid from PCR?

I'm frequently transforming budding yeast with PCR fragments. Normally, after PCR I digest with DpnI to remove the template plasmid. DpnI is a restriction enzyme which cuts methylated DNA, i.e. the ...
2
votes
0answers
62 views

Would I expect salt precipitate on fibres of DNA in a NaCl water solution?

I just recently conducted an experiment in my biochemistry class where we had to add DNA to distilled water, isotonic saline and 2.5M NaCl. I noticed different physical aspects depending on the ...
0
votes
0answers
5 views

Does removing water from sample affect chemical composition test results?

I have a sample of a (deceased) fungus and I want to measure its nitrate/phosphate composition. The sample is about 30% water by weight, and I'm going to test it by soaking it in diluted water and ...
3
votes
1answer
92 views

How is the gradient in density gradient centrifugation made?

From the literature I read, I came to understand the following. Please correct me if wrong. In CsCl gradient centrifugation, the gradient is achieved by centrifuging the CsCl solution at high rpm, ...
0
votes
2answers
19 views

Do PC-12 cells have to be stored in nitrogen?

My lab has been storing their PC 12 cells in the -80 freezer... upon arriving here and investigating a new project I see that it specifically stated to be stored in nitrogen vapor? Is this the ...
1
vote
0answers
44 views

What are the optimal conditions for storing frozen glycerol stocks of bacteria?

The common method of storing bacteria long-term is to collect saturated liquid culture, such as LB, and mix it with sterile glycerol so as to obtain 10-30% final glycerol concentration. The resulting ...
0
votes
1answer
37 views

How to choose right volume of DNA and SYBR Green

I'm testing fluorescence level of a sample having dsDNA, SYBR Green and milli q water but I'm facing difficulty in choosing right volume of dsDNA and cons level of SYBR Green. Details of sample: ...
0
votes
0answers
16 views

Hybridization based technique to detect SNP.

What should be done in order to avoid non-specific hybridization when trying to detect an SNP with hybridization between a probe and sample? Since there is only a single base pair difference, how ...
1
vote
0answers
26 views

What are these colonies on my Bacillus pumilus lawn?

I am growing Bacillus pumilus and I have plated some on agar plates. Now I can see some colonies on top of the lawn. Does anybody know what they could be? A contaminant? Bacillus pumilus? I have ...
3
votes
2answers
65 views

Using nanodrop for analysing biological samples other than nucleotides

I am a 3rd timer postdoctoral fellow with some experience in molecular biology and biochemistry, but major skills in Zoology and Natural History. I am studying some natural extracts, and isolating ...
2
votes
0answers
95 views

At what g force do bacteria start to pellet down a tube?

I am working with C. elegans and bacteria and I want to get rid of the bacteria they eat by centrifuging the worms without centrifuging the bacteria. I am using a g-force of 600 and the bacteria ...
4
votes
1answer
70 views

Test of antibiotic A for sensitivity as surrogate of antibiotic B

I am reading the WHO Global Antimicrobial Resistance Surveillance System (GLASS) - Manual for Early Implementation. it mentioned some of the drug-bug combination that will be put under surveillance in ...
1
vote
1answer
68 views

Should I use RNAseZAP on my bench and pipettes before RNA extraction?

Should I spray RNAseZAP on my bench and pipettes before working with RNA? I am regularly using RNase at my bench and would like to work with RNA as well. Could traces of RNase on my equipment degrade ...
1
vote
0answers
15 views

How to convert a test tube assay to microplate assay?

I am trying to measure Ascorbic acid levels in tissue using Omaye et al protocol (Methods in Enzymology, Volume 62, 1979, Pages 3-11). This method is based on reduction of ferric chloride and ...
1
vote
0answers
18 views

What is known and what can be measured of biofilms?

Context for the question I am a mathematics researcher working on the mathematics of imaging and parameter estimation (inverse problems). I found an interesting diffusion equation that models the ...
0
votes
0answers
18 views

Reference article to typical Proteins in E.coli (identify bands in SDS-PAGE)

I am curious to know if there are any reference articles that sum up typical protein bands that you get from protein expression in E.Coli. I know that you can do some lab work and experimentally find ...
4
votes
1answer
101 views

DNA quantification in a high school bio lab

I'm working on a project in a high school bio lab (so limited resources), and I need a way to quantify the concentration of DNA in a PCR product. I can't use spectrophotometry (cheap ...
0
votes
1answer
32 views

Why marker and control are loaded in the beginning or ending lane of the gel?

I have seen gel images in several literature. Almost in all, markers and controls are loaded in the extreme lanes (before 1st sample or after last sample) of the gel. I am just curious, is there any ...
9
votes
2answers
461 views

Is working with (nitrile) gloves around a bunsen burner safe?

Recently I have started in a new microbiology lab, and with a new lab come new habits. When I was working with my bacterial (liquid) culture next to the flame (Bunsen burner) wearing nitrile gloves, ...
0
votes
0answers
59 views

How to increase the yield of cfdna extraction?

I use Qiagen circulating nucleic acid kit for extraction of cfdna. Many times I got low concentration of cfdna or sometimes I got nothing. Can I add extra amount of carrier RNA to get high yield cfdna?...
0
votes
0answers
29 views

What does having no consensus symbols in a ClustalX2 alignment mean?

I have completed a full sequence alignment of 30 tyrosinase sequences using ClustalX2, yet there are no consesus symbols above the data like there normally is. I think it has run correctly, but am not ...
3
votes
0answers
39 views

Can anyone expolain this? Cell culture vials have strange hair-like condensation patterns

What is the hair-like polymer that condenses on the caps of the plastic cell vial? Inside vial are cells in a mixture of FBS and DMSO. The vials were frozen slowly in a special isopropanol-filled ...
1
vote
1answer
31 views

HELP hepes preparation [closed]

I need help: I would like to prepare an HEPES solution, without using the powder. It is possible? I remember that I did it once, but maybe I'm wrong...does someone know a protocol for HEPES ...
5
votes
1answer
130 views

Optimization of Signal Peptides

We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line. The cell line already expresses an unusually high amount of the protein, but much of it is not ...
1
vote
0answers
103 views

How to keep Paraffin Sections from falling apart?

I've been trying to make 5 uM sections of injured mouse spinal cords and stain the tissue with Luxol Fast Blue and H&E. At first I was removing the bones from around the spinal cord, but the ...
3
votes
2answers
470 views

Agarose gel Ladder smear

We are having trouble with agarose gel electrophoresis. It used to work a couple of months ago but now the ladder always look smeared. We switched the components (1x TBE, 100bp ladder, different type ...
2
votes
0answers
60 views

What happens during fixation of Nucleic acids on nylon membrane

In Southern blotting technique, fixation of DNA to nylon membrane is a step prior to hybridisation with probe. It is done by baking at 80ºC and according to this cross linking between DNA and nylon ...
8
votes
1answer
960 views

What is the role of glucose in plasmid isolation?

My understanding is that glucose is used in the resuspension solution to prevent cells from bursting by maintaining the appropriate osmotic pressure. Why do we even bother doing this? The cells are ...
1
vote
1answer
145 views

How can the melting temperature of PCR primers be so far below the extension temperature?

Since our primer TM is lower than the extension temperature by design, (and often by a significant amount) shouldn't the primers be released from the template at extension temperatures? Now, I have ...
3
votes
2answers
547 views

Why does high EDTA concentration cause swelling of platelets?

According to this textbook, high ( >2mg/ml of blood) EDTA concentration causes swelling of platelets which lead to their fragmentation. I know that high concentration of EDTA increases plasma ...
2
votes
0answers
29 views

How urination prior to blood test may give error?

Source: Textbook of Practical Physiology, 4th Edition according to it urination within 30 minutes is a precollection factor that may alter the results of blood test. I am unable to comprehend how ...
0
votes
1answer
62 views

How to watch a Zebrafish embryo in detail?

How much microscope zoom would I need to watch the development of a Zebrafish embryo in certain detail? Thanks guys!
3
votes
0answers
12 views

Propagating errors for percentage reduction

Need a bit of help for this particular problem. I have three averages collected from three genotypes (A, B, and C) and their associated SD (a, b, and c). A is my control. I have been asked to ...
2
votes
0answers
34 views

Nucleic acid extractions

Is it fine to leave pulverized plant tissue in CTAB buffer at -80 degrees over night? will the buffer remain effective to generate good quality nucleic acids?
1
vote
0answers
27 views

What are preparation mistakes that could make red blood cells appear crenate in isotonic solution?

Thank you for your time. I separated red blood cells from a whole blood sample purchased from a blood bank. In isotonic solution, the red cells appear crenate. I would like to know if there is ...
2
votes
1answer
100 views

Help with preparing Congo Red TSA

So I want to make Congo Red TSA. My instructor gave some hints but I still have some questions: I start by making two stock solutions: 20 mg/ml of congo red and coomassie in two different falcon ...
1
vote
1answer
62 views

Is it possible to produce a tangible mass of DNA/RNA using a PCR reaction?

A Polymerase Chain Reaction (PCR) is a method of amplification which enables one to produce many copies of a certain DNA/RNA strand for many applications (as described in the link above). I have ...