16
votes
Accepted
Would it be possible to sequence human DNA from wastewater treatment plants?
As it turns out, you are not the first to have this idea. Prior research claims that it is, at least in principle, possible to conduct epidemiology of cancer by sequencing on wastewater DNA for ...
- 6,977
9
votes
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Why are large amounts of DNA required for analysis?
Firstly, A DNA sample obtained from a cell or whatever is never going to contain just the DNA sequence you want but will instead contain the entire genomic DNA, plasmids, RNA sequences and whatnot. By ...
- 827
5
votes
What are the roles of guanidine-HCl and ethanol in binding of DNA to silica?
Guanidine HCL is a chaotropic salt. Chaotropic salts are critical for cell lysis and binding to the silica resin. Specifically, Chaotropes have two important roles in nucleic acid extraction
...
- 29.7k
5
votes
Would it be possible to sequence human DNA from wastewater treatment plants?
As already hinted in the answer by @jakebeal, the low concentration (high dilution) of human DNA in waste water would mean that we need huge sequencing depth in order to detect something. This is not ...
- 3,832
4
votes
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Can I pellet DNA back from dissolved state?
No, you cannot pellet dissolved DNA with ultracentrifugation.
Yes, you can recover a pellet with additional treatments, similarly to how you got it in the first place; only instead of your input ...
- 6,192
3
votes
Accepted
State of extracted DNA
Yes, normal DNA extraction protocols fragment genomic DNA. In my experience, extracted DNA tends to have a size distribution on the order of 10 - 20 kilobase pairs (kbp), independent of the protocol ...
- 8,256
3
votes
Origin of the 260/280 ratio?
Here's one explanation: It's not the base composition that determines UV absorbance (260 nm), but whether the nucleic acid is in a single- or double stranded state.
Promega cites Griffiths biochemical ...
- 1,769
3
votes
Detecting nuclear DNA in suspension of mitochondria
Centrifuge the suspension in Cesium Chloride solution at a particular g value which causes the mitochondria to settle to the bottom of the centrifuge tube but leaves nuclear DNA forming a layer near ...
- 506
3
votes
During the process of plasmid isolation, how can we be sure that only plasmid DNA has been isolated and there is no chromosomal DNA?
It comes down to the size of genomic DNA (relatively huge) compared to that of plasmid DNA (rather small).
Cell lysis for plasmid extraction involves an alkaline buffer that includes sodium ...
- 1,879
3
votes
Accepted
How long can one leave sample in lysis buffer for DNA extraction?
It should be fine. Unless they have been contaminated with DNase, none of the components will damage or denature DNA. I've left purified plasmid DNA on the bench for weeks with no apparent degradation,...
- 15.2k
3
votes
Purifying large amounts of PCR product
We had to do this frequently. What I would first recognize is that all of your current methods only work for at the small scale and that for you to purify mg quantities of DNA, you need to work with ...
- 7,867
2
votes
0.1 M sodium citrate in 10% ethanol and DNA solubility
The sodium ions will bind to and neutralize the (-) charge on the phospho backbone of DNA. This reduces hydrogen bonding sites for water, which then results in less solubility.
Edited for clarity and ...
- 1,309
2
votes
What evidence is there that common PCR DNA purification kits can isolate DNA from pathogens engulfed in macrophages?
For this problem, I would generate the evidence myself taking the following approach:
Apply the DNA extraction kit to the macrophages with pathogens engulfed. As controls, also use the DNA extraction ...
2
votes
Accepted
DNA extraction from plants and algae don't use phenol. Why?
CTAB is for removing polyphenols and polysaccharides which are found in plant tissues. Animal cells/bacteria don't have these. You can do an additional phenol-chloroform extraction if you want.
See ...
- 35.2k
2
votes
Separation of smaller DNA fragments and larger fragments without using gel electrophoresis?
One option is to use SPRI beads, like those sold by Ampure (Ampure XP beads) to separate DNA fragments by size. By adjusting the ratio of beads to sample, you can selectively bind fragments of certain ...
- 1,879
2
votes
Accepted
Lysis step during DNA purification
You want to isolate the cfDNA, and leave anything else in the plasma out of your analysis — essentially, the lysis step is part of the purification.
(See here)
(I'll elaborate with edits shortly)
Edit:...
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2
votes
Is there any possible way to take a DNA test without using blood in humans?
Yes, we don't have to use blood to extract DNA for testing.
There are many resource we can use include: hair, buccal swabs and urine. And it seems hair can provide good quality of genome DNA.
Here is ...
- 218
2
votes
Why pellet and resuspend E. coli for plasmid prep
The reason this centrifugation/resuspension step is done has a simple reason: It concentrates the bacteria in a much smaller volume which is much easier to handle afterwards.
For a maxiprep you ...
- 51.5k
2
votes
How were the first genes isolated from genomic or cDNA libraries without already knowing a hybridization probe?
The following is based on a chapter on Cloning DNA in the 10th edition of The Biochemistry of the Nucleic Acids (RLP Adams et al.) published by Chapman & Hall in 1986. (This is probably more ...
- 24.3k
2
votes
DNA extraction kit for microbial mats, rocks, and soil in a remote area
Those are some pretty tough samples to get high-quality DNA from, even in a lab. Your best option is probably to place samples in a nucleic acid preservation buffer and carry them out for extraction ...
- 4,671
2
votes
What options are available for high-throughput isolation and identification of microbes from soil?
Hard to know what you would consider "high-throughput", but it might be worth checking out the work by Kim Lewis at Northeastern University — see for example his 2020 Perspective in Cell1.
...
- 5,577
2
votes
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A DNA extraction protocol that is equipment-less for bacterial metagenomes?
You'd be far far better off waiting until you can get them to a lab. Given the sensitivity of the technique and the unknown abundances and likelihood of getting samples, giving them the best ...
- 11.2k
1
vote
Would it be possible to sequence human DNA from wastewater treatment plants?
Reputedly Osama bin Laden was tracked this way
... according to Water and Wastes Digest citing Time Magazine, but few of the details are known. Given that 10 milligrams of feces is sufficient to ...
- 2,455
1
vote
Blood and hair follicles from 25 people put on the Moon; enough to regenerate a human population?
If we assume for a moment that the samples could be successfully cloned, 25 individuals is probably not enough to maintain a stable human population for more than a few hundred year without ...
- 4,671
1
vote
Microsatellites and Minisatellites: Which of these form the basis of DNA fingerprinting?
1) I'm told that VNTRs are used in DNA profiling. Does this refer to both minisatellites and microsatellites...or just minisatellites?
Actually, it refers mostly to STRs. I worked a bit in forensic ...
- 707
1
vote
Why does DNA need to be pure for restriction enzymes to act on it?
Some other macromolecules or other solutes may be present that could interfere with the affinity of the restriction enzyme. For example, there could be salts that denature or modify the conformation ...
- 11
1
vote
How were the first genes isolated from genomic or cDNA libraries without already knowing a hybridization probe?
Specific to the insulin gene, the following paper is, as far as I can tell, the first to isolate it:
Ullrich A, Shine J, Chirgwin J, Pictet R, Tischer E, Rutter WJ, Goodman HM. 1977. Rat insulin ...
- 17.6k
1
vote
Why are large amounts of DNA required for analysis?
Many of the methods used to visualize the presence of DNA, such as gel electrophoresis, rely on visual analysis whether by human eye or machine. A significant amount of DNA beyond what might be ...
- 1,351
1
vote
DNA extraction from plants and algae don't use phenol. Why?
I have used phenol:chloroform many times for algal DNA and RNA extractions. These protocols needed only minor tweaks to adapt it to a particular species (some cell walls can be extremely though). The ...
- 1,415
1
vote
Separation of smaller DNA fragments and larger fragments without using gel electrophoresis?
In my mind, gel separation (using a fairly high percentage gel to separate the bands as much as possible) and manual excision is by far the best option. The problem with molecular weight cutoff ...
- 15.2k
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