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

2
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0answers
47 views

Why do Petri dish lids not fit?

I understand that they are generally "vented", but why such a poor fit? For the batch I bought, the lid and container don't even recognizably go together (like 1/2" difference in diameter). The wind ...
1
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0answers
18 views

What kind of sieve does one use to extract meiofauna?

Suppose I have a core of sediment, and I want to extract the meiofauna from it, in order to study these organisms. According to the sources I could find, this involves using a very fine (e.g. 45 μm) ...
2
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0answers
30 views

DNA preservation at room temperature

I am considering preserving the DNA of a family member who passed away. The funeral home offers a service called DNA Memories from a Canadian company (CG Labs). They have two options: Store the DNA in ...
1
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0answers
34 views

Why Cerebrospinal fluid is not heated for VDRL?

For performing VDRL of serum , we heat serum to inactivate complement proteins which may otherwise interfere , but why don't we do same for CSF even though it too has complement proteins in it? Is it ...
0
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0answers
10 views

Does The Storage Temperature have any Effect on Blood Samples Using QuantiFERON-TB Gold Plus (QFT-Plus) Tubes?

There are two blood draw options using QFT-Plus tubes: 1) When collecting blood directly into 4 QFT-Plus tubes, samples could be stored at room temperature for up to 16 hours. 2) When collecting ...
0
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0answers
45 views

How is the role of ethylene in ripening demonstrated in biology (or agriculture) education?

I want to know what are some typical experiments performed in the course of biology education (or possibly in applied biology education e.g. agricutlure education) to prove to the students (or have ...
2
votes
1answer
39 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
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0answers
12 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
63 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
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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
14 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 ...
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0answers
35 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
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0answers
35 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
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0answers
32 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
15 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
89 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....
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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
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0answers
32 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
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0answers
64 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
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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
135 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
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2answers
20 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 ...
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0answers
61 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
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1answer
38 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
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0answers
17 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
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0answers
33 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
71 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
105 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
80 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
105 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
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0answers
16 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 ...
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0answers
23 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
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0answers
19 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
103 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
598 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
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0answers
63 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
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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
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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
132 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
116 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
530 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
63 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
1k 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
151 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
630 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
31 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 ...