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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15
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1answer
214 views

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 ...
6
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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 ...
6
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1answer
323 views

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.
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 ...
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 ...
5
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1answer
745 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 ...
5
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1answer
77 views

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 ...
4
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1answer
175 views

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 ...
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 ...
4
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1answer
1k views

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 ...
4
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2answers
421 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 ...
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,...
4
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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 ...
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. ...
4
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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 ...
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 ...
3
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2answers
896 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 ...
3
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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 ...
3
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1answer
93 views

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? ...
3
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3answers
1k views

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 ...
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. <...
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 ...
3
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1answer
48 views

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.
3
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0answers
291 views

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 ...
3
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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 ...
2
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2answers
265 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 ...
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
321 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 ...
2
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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 ...
2
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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 ...
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 ...
2
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1answer
137 views

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 ...
2
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1answer
180 views

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 ...
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 ...
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?
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 ...
2
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0answers
39 views

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 ...
2
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1answer
2k views

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 ...
1
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2answers
33k views

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 ...
1
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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
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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 ...
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
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1answer
213 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 ...
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. ...
1
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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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1answer
713 views

How to improve DNA extraction

I am using the following protocol to extract chromosomal DNA from bananas: Cut up one banana into small pieces, approximately (1 cm3) Add ½ a cup of warm salt water and the banana pieces into the ...
1
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1answer
50 views

How to incorporate intraspecific variation in discrete characters in comparative analyzes?

I'd like to run a multivariate analysis (Pavoine et al. 2011) that aims to disentagle the effect of environmental gradients on traits, considering its autocorrelation with phylogeny and space. It uses ...
1
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1answer
67 views

What are known methods of non-surgically disabling neural tracts/pathways (esp. Corpus Callosum)?

I think I've read something about usage of TTX and optogenetics, but I cannot find the papers for either anymore. Any reference would be much appreciated, especially those concerning mice and the ...
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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 ...
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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) ...