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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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4 votes
1 answer
555 views

Why choose strawberries for DNA extraction?

The NileRed video What is DNA and what does it taste like? | Edible Chem shows the extraction of a surprisingly large amount of DNA from some strawberries. At 02:22 ...
3 votes
2 answers
142 views

Change of DNA concentration due to restriction digest?

Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about ...
1 vote
2 answers
76 views

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 ...
1 vote
1 answer
57 views

Method to detect Protein aggregation

I have a specific human protein that was purified from E. coli. This protein was tagged with MBP and diluted in an elution buffer. This protein has a tendency to aggregate, and when it does, it can ...
0 votes
1 answer
56 views

Why can SPRITE measure many simultaneous interactions?

Why is the SPRITE method not limited to a number of simultaneous interactions that can be measured, while microscopy and proximity ligation are limited to 2-3 interactions?
1 vote
2 answers
47 views

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?
4 votes
0 answers
63 views

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 ...
8 votes
1 answer
314 views

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 ...
3 votes
1 answer
104 views

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 ...
2 votes
1 answer
108 views

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? ...
1 vote
1 answer
98 views

RNA sequencing and taxonomic analysis of gut microbiome

I've been searching for methods of RNA sequencing, and I always find that the step of rRNA removal is emphasized. However, in my research, I need to analyze both functional and taxonomic data from the ...
0 votes
3 answers
311 views

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

In articles like this one, I often read that several "genes variants are associated to a given trait". It is often added: "genetic factors explain (say) 20% of the trait variance." ...
12 votes
1 answer
382 views

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 ...
5 votes
0 answers
56 views

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 ...
3 votes
1 answer
85 views

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 ...
6 votes
1 answer
818 views

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 ...
2 votes
1 answer
47 views

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 ...
21 votes
4 answers
2k views

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 ...
0 votes
0 answers
40 views

cell proliferation assays for research proposal

I'm an undergrad Biology student and I'm working on a research proposal for a certain course. I need help or guide on cell proliferation assays. I have a target gene , recent papers show that this ...
1 vote
1 answer
13 views

Meaning of the word "targeted" in a description of chromatin immunoprecipitation

From a research paper: The ChIP assay demonstrated that CIC physically binds to the promoter region of FOLR1, PCFT and RFC1. Compared with IgG control antibody, CIC antibody enriched 4.1-fold more ...
1 vote
0 answers
95 views

How to fit simulated with measured data having systematic errors?

Consider a given time series of measured data, i.e. the number of persons tested positive for COVID-19. And consider a simulation - consisting of a model, possibly fed with some parameters estimated a ...
1 vote
0 answers
29 views

How to Identify Astragalus Species

I have several photos of a plant I believe to be in the genus Astragalus. I would like to determine the particular species in my area, the foot hills of San Diego County. Do I need a microscope to ...
2 votes
1 answer
9k views

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 votes
3 answers
1k views

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 ...
1 vote
1 answer
44 views

Is there a system biology approach to compare pathways or famillies of proteins from an evolutionary point of view for the same organism?

I would be interested to know if there is a method/analysis or a set of methods to compare two groups of pathways or families of proteins. I would specifically be interested by a system biology ...
2 votes
1 answer
46 views

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 ...
3 votes
1 answer
472 views

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 ...
0 votes
0 answers
30 views

Why don't materials and methods describe culture media in volume?

After reading several materials and methods sections of cell culture experiments, I have not seen the recipe for culture media ever described in terms of volume. Human adipose tissue was obtained ...
0 votes
0 answers
20 views

How do I homogenise a small pellet of 10 to 50 cells within less than 50 µL?

I have a problem with declumping/ homogenising bacterial cells in small volumes (10 to 50 µL). I know that I can get all of my cells out of the tube, but they are still stuck together and won't form ...
5 votes
2 answers
1k views

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 ...
3 votes
1 answer
2k views

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. ...
0 votes
1 answer
18 views

When is really necessary to visit field to observe sample collection process?

I know this could be a bit generic question, but for the sake of providing context this applies to a Transcriptomics Thesis. Yesterday I've seen two researchers discussing about if it was really ...
1 vote
0 answers
18 views

Does the preservation fluid (ethanol or formaldehyde) leach heavy metals from mollusc tissue?

In a thread on researchgate, the concern was raised that long term exposure to unbuffered preservation fluids such as ethanol or formaldehyde may leach heavy metals from biological samples due to a ...
5 votes
3 answers
1k views

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 ...
4 votes
0 answers
42 views

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. ...
0 votes
1 answer
67 views

Proof of mechanisms and causal relationships in biology [closed]

Statistical methods in biology are strongly encouraged: they are quantifiable, unbiased, and usually the only ones that are accepted as evidence. However, it doesn't seem like the whole picture. Say,...
1 vote
0 answers
64 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) ...
1 vote
0 answers
50 views

Determine planar phyllotaxis characteristics

Is there any method to fast and precise count the number of spiral and the divergence angle on a planar phyllotaxis pattern? The example of spiral phyllotactic arrangement of emerging flowers on ...
4 votes
1 answer
8k views

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 ...
3 votes
1 answer
87 views

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 ...
4 votes
1 answer
1k views

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 ...
0 votes
1 answer
43 views

Re-Plumping Dried Insects

I have begun to display some of my soft bodied insects and as I am trying to rehydrate some of them that were plump in the abdomen, they appear to have shrunk and the bodies have sunk into themselves. ...
0 votes
1 answer
56 views

Inexpensive way to determine mass of tiny seeds?

My niece is doing a science project and she wants to weigh various seeds, determine their volume and density. She tried using my kitchen scale, but it is not sensitive enough. I've suggested ...
6 votes
1 answer
138 views

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 ...
0 votes
1 answer
96 views

Methods for phage separation

How can a mixture of unspecified phages be separated (into singular phage strains)? I.e, what are the main methods? My research shows it can be done using CsCl centrifugation and affinity ...
1 vote
0 answers
68 views

Protein expression in K. lactis system

I am trying to express a protein in K. lactis Protein Expression Kit (E1000S - NEB) in the way that the protein is secreted into the medium. I know that I can get some protein but it is not active. As ...
2 votes
2 answers
667 views

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 ...
3 votes
2 answers
2k 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 ...
0 votes
2 answers
943 views

Biology experiment with algae method help

I'm planning a biology experiment I need to complete. I was planning on measuring the affect of pH on algae growth. I chose chlorella to be the test algae I use (are there any algae that would be ...
0 votes
1 answer
400 views

Phylogenetic Independent Contrasts with discrete traits

I understand that PICs are normally only used for continuous traits. However, on this how-to site (https://www.r-phylo.org/wiki/HowTo/Phylogenetic_Independent_Contrasts) there is mention of "Discrete ...