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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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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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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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3answers
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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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23 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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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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18 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 ...
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1answer
45 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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43 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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2answers
173 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 ...
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16 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 ...
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11 views

Is there a way to image or monitor subcellular trafficking in vivo?

In my field, it's recently been demonstrated that there is very little correlation between in vivo and in vitro outcomes. I'd like to investigate where these discrepancies occur, and part of that ...
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60 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 ...
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3k 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 ...
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1answer
33 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. ...
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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 ...
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2answers
292 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 ...
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1answer
74 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 ...
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55 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 ...
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2answers
205 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 ...
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2answers
718 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 ...
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2answers
235 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 ...
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1answer
136 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 ...
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1answer
83 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. ...
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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?
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1answer
133 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 ...
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1answer
309 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 ...
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1answer
584 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 ...
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1answer
322 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?
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1answer
317 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 ...
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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 ...
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1answer
187 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 ...
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1answer
904 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 ...
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0answers
47 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 ...
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41 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 ...
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171 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 ...
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135 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 ...
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1answer
109 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 ...
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2answers
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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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117 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 ...
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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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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.
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38 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 ...
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1answer
647 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 ...
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1answer
199 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 ...
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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. <...
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1answer
127 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 ...
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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 ...
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1answer
47 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 ...
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809 views

How to calculate the LOB, LOD and LOQ of an enzyme assay

I understand how to calculate limit of blank (LOB), limit of detection (LOD), and limit of quantitation (LOQ) in the traditional way i.e., average and SD of raw analytical signal of blanks and low ...
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1answer
83 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? ...