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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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2
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1answer
49 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
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3answers
326 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
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1answer
34 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
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1answer
41 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
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1answer
36 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 ...
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0answers
12 views

Insect collection question: Where to find anchor pins for specimen vials

Where can I purchase anchor pins for insect specimen vials for an insect collection. They look like they are in an 'M' shape,sort of, and stainless? will hopefully hold better than staight pins.
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0answers
22 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 ...
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0answers
19 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 ...
4
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2answers
423 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
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1answer
1k 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
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1answer
15 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 ...
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0answers
13 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
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3answers
130 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
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0answers
27 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. ...
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0answers
49 views

How to find papers about voltage imaging (with GEVI) for human brain research?

I would like to follow the Nature article https://www.nature.com/articles/d41586-018-06694-6 about voltage imaging of brains, about use of GEVI - Genetically Encoded Voltage Indicators. But I am ...
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20 views

How can I approach this data that has a different total number of results between samples?

I was not sure whether I should post this in Biology Stack Exchange or Math Stack Exchange so I posted it in both. I was planning on doing a small research for my math class (a final project for the ...
0
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1answer
48 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,...
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0answers
52 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) ...
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0answers
17 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
1answer
4k 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
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1answer
65 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
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1answer
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
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1answer
34 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
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1answer
27 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
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1answer
114 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
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1answer
83 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
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0answers
59 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
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2answers
267 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
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2answers
897 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
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2answers
353 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
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1answer
165 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 ...
2
votes
1answer
133 views

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 ...
1
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1answer
85 views

Why must gene entrapping constructs be integrated into introns and not exons?

Homework Question: In enhancer trapping, reporter transgenes are integrated randomly into the fly genome and their expression identifies enhancers and thereby genes expressed in particular patterns. ...
2
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0answers
35 views

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?
6
votes
2answers
173 views

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 ...
2
votes
1answer
150 views

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 ...
1
vote
1answer
397 views

Positive control for microorganisms

I'm planning to test the antimicrobial activity of endophytic fungi (their secondary metabolites) against Gram-positive bacteria, Gram-negative bacteria, and one fungus (Candida). I was wondering ...
1
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0answers
38 views

Where can I get fungal extracts?

Does anyone know how I can get fungal extracts from fungal isolates? I have isolates in PDA slants and I'm gonna need to get their respective extracts to impregnate in sterile discs. I'm a novice in ...
3
votes
1answer
114 views

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 ...
1
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0answers
47 views

Spectroscopy on plant leafs

I'm trying to do spectroscopy readings on plants where I shoot electromagnetic waves and look at their signature/profile. I want to be able to do this at a distance, in the field and on live plants ...
5
votes
1answer
748 views

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 ...
1
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1answer
392 views

Well Plate Method VS Kirby Bauer Method

Any pros and cons? One puts the test substance in sterile discs, while the other one puts it directly into wholes in the agar. Any thoughts?
1
vote
1answer
377 views

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

"The fermentation broth (600 mL) of each endophyte was filtered, and the filtrate was extracted three times with ethyl acetate at room temperature and further concentrated in vacuo to give dried ...
1
vote
1answer
214 views

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

In our experiment we use a fly to determine the flicker fusion frequency, i.e., that frequency where the fly starts perceiving a pulsating light as a constant light source. The human eye also has a ...
4
votes
0answers
51 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 ...
2
votes
1answer
131 views

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 ...
1
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0answers
141 views

What is/are the effect(s) of altering the Tris concentration on polyacrylamide gels?

Why do we use two different concentrations of Tris (i.e. 1.5M Tris in resolving gel and 1.0M Tris in stacking gel)? For the gel to run properly there needs to be a different pH, but that can be done ...
3
votes
1answer
218 views

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 ...
4
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2answers
104 views

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,...
2
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0answers
68 views

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 ...