Questions tagged [methods]
The methods tag can be used for questions on experimental hardware; experimental set up; experimental procedures; surgical techniques etc.
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Pipetting: do human experimenters need liquid class information?
I've been working on a protocol standardization project where, among other things, we want protocols to be able to be run equivalently by both humans and robots.
Something that I've noticed in doing ...
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1
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Doing a medical study on yourself?
What research guidelines is a person legally mandated to follow if they want to do medical experimentation on themselves?
There is a large amount of variation in the types of medical experiments so I ...
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1
answer
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What's happening in the "C" and "T" stripes of a covid test kit?
I have a COVID home test kit which produces C and T (control and test) stripes when the solution is applied to the strip. Something similar happens in pregnancy test kits.
I understand the purpose of ...
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1
answer
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How do non-ionic polymers help precipitate proteins?
Some non-ionic polymers (e.g. chitosan and polyethylene glycol) are also commonly used as protein precipitating agents. What is the principle of protein precipitation resulting from the addition of ...
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Is there a term for a procedure in which the chromatography column is washed with 20% alcohol
From a method description in a Russian document:
After the chromatographic analysis is complete, the column is flushed with at least 2-3 volumes of water at a rate of 0.4 ml/min. The column is then ...
- 1,309
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How can I convert plate reader measurements of Pichia pastoris OD to cells per ml?
I am performing experiments with the yeast Pichia pastoris where it will be beneficial to calculate product yield per cell. I plan to use a plate reader to measure OD600 of my cultures and then ...
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1
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What are the units of Phylogenetic Independent Contrasts (PICs)
PICs are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.
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How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?
No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds ...
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Double Digestion with Restriction Enzymes Using Different Buffers
I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site ...
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1
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Are vacuum centrifuges the same as normal centrifuges?
I came across a method that used a vacuum centrifuge:
Carvalho et al. 2012. The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant ...
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votes
1
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How are the physiological properties of mitochondria measured?
this is my first question on BiologySE. I am a Physics and Mathematics student currently doing a project on cell growth simulation. I am doing literature survey and I have a question about cellular ...
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Alternative to distilled water for pH test
I am looking to test soil pH in a remote location. The test results don't need to be perfectly precise, and a pH test strip should provide sufficient accuracy. However generally this kind of testing ...
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5
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2
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Does food really give our bodies the energies that we have determined by burning them in the lab?
You are likely to have come across numbers like sugars 17kJ/g (4kcal/g) as the energy supposedly available to our bodies after eating. Yet these values have been determined using very artificial means,...
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Methods for getting clean C. difficile spore preps without spores clumping together
I'm a microbiologist recently who recently started working on an ongoing C. difficile project for the first time. One of the things I need to do is verify the lower detection limit of my qPCR ...
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4
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1
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How can I reduce the background gradient in phase contrast microscopy?
I'm looking for ways to set up a phase contrast microscope to reduce the brightness gradient that appears across the background of my images.
I use phase contrast to find the outlines of cells in my ...
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1
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Using catalase-test to determine if Staphylo- or Streptococcus
If the microscope clearly shows bacteria of cocci morphology but it is difficult to determine if they are Staphylo- or Streptococcus, are catalase tests a good way to differentiate between the two ...
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Measuring body size in flies/insects
"Mesothorax length (the distance from the tip of the scutellum to the
most anterior part of the mesothorax)"
From Bergland et al 2008.
Would that be this distance (green line)?
If not, how would ...
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4
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1
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What is the role of potassium acetate in plasmid extraction?
What is the role of potassium acetate in the alkaline lysis method of plasmid extraction?
Earlier I was thinking its role is to shield plasmid DNA (the same as sodium acetate in genomic DNA ...
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0
answers
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How do scientists determine the nature of ions passing through a channel/carrier/pump?
The NCE (Sodium Calcium Exchanger) transports 3 Na+ inside the cell for 1 Ca2+ outside.
How did we figure this out, and other mechanisms of this sort?
If it were a protein, we could tag it with GFP. ...
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4
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0
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How to anaesthetise mosquitoes during a mass-trapping field study?
Do any of you have experience in anaesthetising mosquitoes during a mass-trapping field study?
Normally, mosquito traps have a little net in which you catch the mosquitoes. The nets can, after ...
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1
answer
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The information carried by nerve signals
Action potentials carry nerve signals in individual neurons and somehow encode information. My question is if it is possible to read that information carried by the nerve signal and feed it into a ...
3
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2
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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 ...
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3
votes
1
answer
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NMR spectroscopy detection methods for proteins
I've stumbled upon a table comparing the sensitivities of different detection methods in NMR spectroscopy: "Direct", "DEPT" and "Inverse", where "Inverse" seems to be the most sensitive.
What exactly ...
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1
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How to best conserve a beetle inside a jar?
Few days ago a giant beetle appeared on my house. Well, it's dead now. Since it attracted some attention from my little girl, I'd like to preserve it inside some jar. What's the best way to do it? ...
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3
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LCMS/MS versus Western Blot
I have a general question regarding which method would you recommend me to use if I would like to investigate the difference in the level of several proteins in tissue samples and compare different ...
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3
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1
answer
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T-vector creation
I'm working on TA cloning for the first time and I need to turn some existing plasmid backbones into T-vectors. I'm using a Klenow fragment (3' -> 5' exo-) to dA-tail my inserts. Is there any ...
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1
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What are wave frequencies in the EEG?
Here is a typical EEG reading:
(source: frontalcortex.com)
I understand that each row corresponds to the signal read between two sensors on a standard 10-20 (or 10-5) distribution setup (e.g. ...
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3
votes
1
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Difference between LIGR-seq and PARIS methods
I would like to reuse a dataset produced by LIGR-seq for ncRNA secondary structure prediction in the style of PARIS method.
At ...
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votes
1
answer
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What buffer should I choose for IEX chromatography for purifying IgY
I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
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1
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Can fireflies species be identified with their wavelength?
I was wondering if we could ID male fireflies using their wavelength? A bit like how we use UV light to ID species of scorpions.
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Is there a standard formula/calculation for sexual dimorphism?
Is there a standard, or most accepted, way to present a value for sexual dimorphism? For example, one could use
$$\frac{\text{Female value}}{\text{Male value}} -1$$
This would give negative values ...
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What is an extinction test?
In Stolerman & Olufsen (2001) I read the sentence:
After drug-appropriate responding with the training mixtures reached
85%, generalisation to ethanol was examined in extinction tests.
Here is ...
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2
answers
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Do all plants grow roots when separated from parent?
Recently I bought my very first plant.
I thought it was doing well because it remained green, sometimes a yellow leave but all of my acquaintances which do know about plants told me not to worry, and ...
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Why are IMAC and gel filtration combined?
In a practical course I used an Biorad Profina system to purify a protein with a histidine tag.
The device uses a column for IMAC and one for gel filtration. Why are these two devices combined in one? ...
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How do bull semen companies get the semen out of the bulls?
Prompted by this article, which discusses the low number of bulls who sire US dairy cows.
How do semen companies extract semen from bulls?
The procedure to extract semen from humans is simple enough,...
2
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3
answers
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What is Modulation Power Spectrum?
I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4562283/ , but I cannot make sense of what MPS nor how should I read the pictures that make use of this method.
The authors say
...
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How does one experimentally obtain a hemoglobin-oxygen dissociation curve?
I've always wanted to do comparative eco-physiology studies looking at Hemoglobin-Oxygen affinity of populations in different environments, but I can't find a protocol to experimentally measure the ...
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Is there a difference between ISH and ISHH? (In Situ Hybridization, In Situ Hybridization Histochemistry)
I came across the term ISHH in my document and discovered that it stands for In Situ Hybridization Histochemistry. I's translating to Russian a document that uses this abbreviation.
Example from the ...
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1
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How do you determine the length of an annelid?
I'm currently studying a horse-leech, and would like to know if it is fully grown or not. When I read about different annelid species a maximum length is often given, so I wonder if there is some ...
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How do you test soil for the nutrients present in it? [closed]
I recently noticed that my rose garden has been in a very terrible state. The roses keep dying. I tested the soil for its pH and that was fine.
Now I'm wondering how would I carry out a test to see ...
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2
votes
1
answer
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Efficacy of the 10-20 montage for EEG
I am trying to better understand the relationship between the placement of EEG electrodes and the quality of the "brainwave" signals they produce.
There is the standard 10-20 system which has me ...
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2
votes
1
answer
183
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Genomic DNA isolation from wheat
Can I use dry seed, wheat for example, in place of young leaves for isolation and purification of genomic DNA for PCR amplification?
The goal of my experiment is to validate a novel gene which is ...
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votes
1
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How is magnet based bead capture used for indexing-first ChIP-seq?
The context for this question can be found in this paper by Lara-Astiaso et al. Here, to study H3K4 trimethylation in various cell types, they
sort cells
sonicate chromatin
immobilize chromatin on ...
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0
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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?
2
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0
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PCR limits of detection calculate method
Is any standard method for use to gain PCR sensivity or limit of detection? my mean is not for RT-PCR or Real-Time or any other kind and just simple PCR. After making PCR product free of dNTP and ...
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0
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Stable isotope sample preparation: Bone Collagen
I am performing research in which I need to extract bone collagen from the foot bones of American Beaver (Castor canadensis). I have read through the literature fairly thoroughly on both the ...
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1
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What are the highest and lowest amplitude values in ECG for humans?
I'm currently trying to parse the records captured from an ECG device and display them on a mobile application. I am wondering what the highest and lowest possible amplitude values for ECGs are in ...
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2
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What is the effect of the wavelength on the spectrophotometric measurements of protein?
Does the wavelength setting affect the absorbance reading of a spectrophotometer? For example, if I am using a spectrophotometer at 550 nm to determine the protein concentration of my samples, would ...
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2
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Methods to obtain the mass distribution of an ensemble of bacteria?
Are there any mainstream methods to obtain the mass distribution of a bacterial population?
What kind of assumptions to they make?
Could anyone point me to some references?
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2
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Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability
I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like ...
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