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23 votes
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Pipetting: do human experimenters need liquid class information?

In my experience it is very rare to see a protocol for humans that describes how to pipette a certain liquid, but I don't have as many years pipetting as others do. In general, it is left to the ...
Noah Sprent's user avatar
23 votes

Pipetting: do human experimenters need liquid class information?

I work on software that controls one model of robotic pipetter. There are a few reasons why we use complex liquid class definitions: One of the selling points of using a robot is high speed. You ...
Dan Bryant's user avatar
11 votes
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What's happening in the "C" and "T" stripes of a covid test kit?

This is a lateral flow assay. [image source] A sample is applied at one end of the strip and flows across to the other side by capillary action. It first encounters antibodies against the target ...
canadianer's user avatar
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7 votes

Pipetting: do human experimenters need liquid class information?

Just to be clear, it has been many years since I have done real lab work, so I am certainly not an expert on the specific question. However, I have a fair amount of experience writing clear ...
apc's user avatar
  • 71
6 votes

Are vacuum centrifuges the same as normal centrifuges?

A "normal" centrifuge = piece of laboratory equipment, driven by a motor, which spins liquid samples at high speed to allow centripetal acceleration to separate substances of greater and lesser ...
theforestecologist's user avatar
6 votes
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How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?

From a technical perspective, for the FlopR package you mention (and I believe also for Jacob Beal's protocol) you can simply change the bead size and perform a new calibration. The only information ...
ajhfedorec's user avatar
5 votes
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The information carried by nerve signals

Neural info is contained in spike trains, mainly in terms of spike frequency and related parameters. These spike trains in individual neurons can be measured by techniques like patch clamp and Ca2+ ...
AliceD's user avatar
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5 votes
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Do all plants grow roots when separated from parent?

Dear respected person, I am not a professional botanist, but I adore gardening, and would like to help you as much as I can from my humble garden experience. As far as I have experienced, not all ...
Taimur's user avatar
  • 506
5 votes
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Is there a term for a procedure in which the chromatography column is washed with 20% alcohol

Prepared or conditioned for storage would probably be perfectly acceptable. If you're looking for a single-word equivalent, in this case, I would translate as stabilized. From dictionary.com: ...
hBy2Py's user avatar
  • 166
5 votes

Why choose strawberries for DNA extraction?

There's more than one reason behind the use of strawberries: They are octoploid (8n), so they have eight copies of each chromosome per cell, i.e., there is a lot of DNA to isolate per unit of volume; ...
AliceD's user avatar
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5 votes

Why are IMAC and gel filtration combined?

Without knowing your specific protocol, it is common to use more than one purification method for a single protein. Given the broad similarities that all proteins and even most biomolecules share, it ...
canadianer's user avatar
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4 votes
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How does one experimentally obtain a hemoglobin-oxygen dissociation curve?

There are existing instruments commercially available to measure hemoglobin-oxygen saturation curves. Whole blood or lysed blood can be used; I would expect the instrumentation to come with specific ...
Bryan Krause's user avatar
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4 votes

How do bull semen companies get the semen out of the bulls?

Colorado State University has two helpful pages that explain the main procedures (h/t Tom). Semen Collection goes through the 3 ways that are used to collect semen from animals. Semen Collection from ...
Denis de Bernardy's user avatar
4 votes
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Change of DNA concentration due to restriction digest?

Summary The poster wishes to know why spectrophotometric readings (presumably absorbance at 260 nm) on a sample of genomic DNA from an unspecified organism appear “slightly” greater after incubation ...
David's user avatar
  • 26k
3 votes

Agarose gel Ladder smear

Are you sure that your TBE is at the right dilution? And that you're using TBE to make the gel and also as the buffer for running? That sort of wavy line looks like what you might get if you'd made ...
mykinz's user avatar
  • 41
3 votes

How do you test soil for the nutrients present in it?

Send soil samples to a soil lab (e.g., here). They will likely use the Mehlich III extractant method to extract and quantify the nutrients (most importantly the bases such as Ca, Mg, K, and Na). ...
theforestecologist's user avatar
3 votes
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How do you determine the length of an annelid?

Leeches: According to Taube (1966)$^1$: The adults of American leeches range from about 1/4 inch to 12 inches in contracted length. Because leeches can bloat to more than 10x their "normal"...
theforestecologist's user avatar
3 votes
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Using catalase-test to determine if Staphylo- or Streptococcus

Generally yes: streptococci are catalase negative while staphylococci are catalase positive. The catalase test is important in distinguishing streptococci (catalase-negative) [from] staphylococci ...
canadianer's user avatar
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3 votes

What does it mean when you "extract the filtrate with ethyl acetate three times?"

This procedure is referring to chemical extraction, which is a separation process used in chemistry (and biochemistry) to isolate compounds of interest by using two immiscible phases in which the ...
Bryan Krause's user avatar
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3 votes

Double Digestion with Restriction Enzymes Using Different Buffers

NEB double digest planner is suggesting to use 2.1 buffer for your combination of restriction enzymes (XmaI 50% and KpnI 75% activity). I would be more worried about the star activity of KpnI in ...
BagiM's user avatar
  • 583
3 votes

Double Digestion with Restriction Enzymes Using Different Buffers

If you haven’t already ordered your enzyme, you could get high fidelity KpnI, which has been engineered for use in CutSmart. You could also consider doing a sequential digest rather than a double ...
canadianer's user avatar
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3 votes
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Double Digestion with Restriction Enzymes Using Different Buffers

In my experience, a double digestion in CutSmart buffer will work perfectly well. The reaction may proceed slower, but incubate it a little longer and run a gel after the digestion - you'll see ...
S Pr's user avatar
  • 6,262
3 votes
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Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)

The term appears to be in use as a synonym. PLOS ONE is a good journal, and in it Okubo, 2016 write "The protocol for ISHH was described in detail previously [22]." Where [22] is Yamanaka, ...
Mike Serfas's user avatar
  • 2,475
3 votes
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T-vector creation

Personally I would use Taq DNA polymerase to A overhang my inserts, especially if you are PCR amplifying the insert. It leaves an A overhang on the end of all amplicons natively. All you have to do ...
bob1's user avatar
  • 12.4k
3 votes

How do we know if a trait is genetic rather than via rearing environment?

It's purely and simply that there is no single answer - as in the linked paper, there's no "gay gene", there is a group of identified genes that contribute, but not all the variance in the ...
bob1's user avatar
  • 12.4k
3 votes

RNA sequencing and taxonomic analysis of gut microbiome

The article that you link to clarifies in the methods section that there are two different extraction protocols employed, one for 16S information (probably DNA extraction) and one for total RNA. In ...
Maximilian Press's user avatar
3 votes

Change of DNA concentration due to restriction digest?

As you did a clean up, then you lost some DNA in this process. There are always losses from clean up steps. Note also that spectrophotometry is notoriously unreliable for DNA quantitation; it's more ...
bob1's user avatar
  • 12.4k
2 votes
Accepted

How is the flicker fusion rate interpreted as an on-off rate?

Short answer A light flashing at 50 Hz means there are 50 flashes of light per second. The unit hertz means cycles per second. 1 cycle is the time it takes for the light to be ON and OFF. 50 Hz cycle ...
AliceD's user avatar
  • 52.5k
2 votes

Is there a term for a procedure in which the chromatography column is washed with 20% alcohol

This is a routine procedure in FPLC to prepare columns for storage. 20% ethanol is used to prevent microbial growth. See this technical note: All SEC columns are delivered in 20% ethanol to prevent ...
canadianer's user avatar
  • 17.8k
2 votes
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Well Plate Method VS Kirby Bauer Method

I came across a nice Master's thesis that investigated precisely that. The conclusion reads as follows: Automated microbroth dilution-based testing methods are increasingly used by many clinical ...
Johnny's user avatar
  • 1,509

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