Questions tagged [experimental-design]

Questions on how to plan an experiment to gain the best results. Also suitable for questions on why other researchers followed a certain procedure.

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Why didn't these scientists restore electrical activity in this pig's brain?

This experiment was published in Nature Magazine: Pig brains kept alive outside body for hours after death. The researchers used a system called BrainEx to revive certain metabolic and physiological ...
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20 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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24 views

Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?

Let's assume that I am searching for gene editing candidates for curing human adiposis. Are there computational frameworks that can allow me to select the best candidate-genes for editing via some ...
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26 views

How can I estimate the total number of yeast cell in a medium?

So I want to run an experiment with yeast. I want to monitor the population as close as possibly in regards to its size. I am aware I could use a colorimeter or such, but I can only get a microscope. ...
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19 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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52 views

What would “N” and “V” stand for in DNA barcoding?

I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:...
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219 views

How can I measure the population growth of yeast?

So I will soon have to carry out an experiment. I thought about estimating the rate of growth of a populaiton of yeast, although I do not know if it is possible to at least estimate the number of ...
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66 views

How does the OD correlate with the number of algae cells?

My research team and I are using a spectrometer to measure the OD of an algae sample. We are trying to answer the question "Is there a correlation between OD and the number of algae cells?" What ...
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739 views

Why did scientists think humans had 100,000 genes (before the Human Genome Project)?

One of the major results of the Human Genome Project (HGP) was that humans have far fewer separate genes than previously thought. From a 2004 article about the HGP: Francis S. Collins, director of ...
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36 views

Are there situations where in vivo results work better than in vitro results would have shown?

Basically, if I have poor in vitro cell line results but decided to test them in vivo in a mouse anyway what are the possibilities of having better results in the in vivo live mouse model that I would ...
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25 views

What does $g_0$ mean for a centrifuge?

I'm about to make some Graphene Oxide and in the paper for Tour's Method it uses a centrifuge to isolate the solution. However it requires $319g_0$. What does this mean, and will a centrifuge with ...
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69 views

How can enzymes be immobilised on glass?

I’m studying a hypothetical model for urease activity, which involves fluorescence measurement, hence the need for an optical window to which the enzyme urease is immobilised. From my previous ...
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73 views

Is this experiment to check enzyme reaction rate according to substrate concentration correct?

We just had an experiment to check enzyme reaction rate according to it's substrate concentration. In the experiment, we used a varying amount of substrate and the same amount of enzyme: (1.5mm enz, ...
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375 views

How is the gradient in density gradient centrifugation made?

From the literature I read, I came to understand the following. Please correct me if wrong. In CsCl gradient centrifugation, the gradient is achieved by centrifuging the CsCl solution at high rpm, ...
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929 views

Growing bacterial culture on gelatin

I'm very new to experimental biology and don't know much about it. So, i was looking to grow some bacteria in petri dishes and looked up how to do it. Unfortunately, I'm finding it difficult to get my ...
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72 views

Electrical field stimulation of neurons: what are commonly used stimulation protocols and which are physiological?

I am doing a labproject with primary mouse nerve cultures (hippocampus and midbrain) and part of the experiments involve performing electrical field stimulation on these neurons. For now we have ...
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1answer
77 views

How does radiolabeling work?

Protein turnover can be measured by calculating the "decay" or loss of radio-labeled proteins in the blood, for example, but I am confused at how this calculation works. Wouldn't the radioactive ...
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64 views

Criticism of the significance of fMRI studies [closed]

On the german Wikipedia page on fMRI I read the following "There is some critisism of the basic assumptions and possible insights gained from fMRI studies which is based on a constructive ...
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54 views

How are fMRI responses to auditory stimuli measured?

How can fMRI experiments be conducted which measure the response to auditory stimuli (e.g. music) when the apparatus makes such loud, nasty, and distracting noises? Are there quieter MRI tomographs in ...
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56 views

Is my RNA-seq experimental design correct to use it for SNP calling?

I am a newbie here and would highly appreciate your advice about one particular experimental design. We have data from RNAseq experiment which was originally designed to assess differential ...
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2answers
1k views

Measuring the Rate of Photosynthesis

Update: I have just received a grant to pursue this research. However, I must still perform the preliminary experiment described below before dipping into my very limited funds. Thank you for any ...
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1answer
312 views

Quantifying DNA in a band on gel electrophoresis

I am a first year science undergraduate and I am just asking this as a more theoretical question rather than for carrying out a protocol, so I would appreciate if answers do not involve lots of ...
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34 views

Does vegetable oil allow methane to pass through? [closed]

I'm doing an experiment investigating how temperature affects the rate of methanogenesis. I'm using a peat sample that will be kept in a conical flask connected to a gas syringe with a layer of Janus ...
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1answer
141 views

What is sequential passaging?

I have read a journal that describes sequential passaging with the purpose of measuring resistance development in bacteria. I would like to know more about how the method works ie. what does "passage" ...
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78 views

Webtool to design guide RNA (gRNA) for use with CRISPR-AsCpf1?

My goals are to use a free webtool to: Identify guide RNAs (direct-repeat sequence followed by the targeting sequence) appropriate for use with AsCpf1 in order to target a specific segment of genomic ...
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800 views

What is preliminary work in a biological investigation?

Here is an example of preliminary work that confuses me (from an A level Biology exam question). Please help me by providing an explanation of preliminary work in the generic sense, then use the ...
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223 views

Need help to determine the parameters of an experiment [closed]

I need to conduct an experiment where I compare 5 drugs. For the trial I am supposed to use 30 animals subjects. Each drug will be injected to 6 randomly picked animals. After a period of time, 2 ...
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270 views

Why is EcoRI supplied with a unique buffer when it is allegedly 100% active in universal buffers?

Thermo packages a unique buffer with EcoRI: 50 mM Tris-HCl (pH 7.5) 10 mM MgCl2 100 mM NaCl 0.02% Triton X-100 0.1 mg/mL BSA However, they also list their EcoRI enzyme as 100% active ...
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1k views

What are “primary amino acids and secondary amino acids”? Context: analysis of amino acid content using reversed-phase HPLC

In a Russian document I'm translating, an HPLC system is used to analyse the amino acid content of a substance. The detector wavelength is set at 262 nm for "secondary amino acids" and 338 nm ...
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63 views

Plasmid transformation yields only empty vectors

I have to electroporate pMAD cloned with an insert of 7.4 kb in my S. aureus isolate. When I electroporated in RN4220 I had no problems but when I put it in my isolate I just recover few colonies and ...
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46 views

How to send many samples to a lab for testing mosquito-transmitted diseases?

I am doing a project for the science fair in my school on mosquito-borne diseases in Panama. We want to collect mosquitoes from three different areas in the country to document what diseases they had, ...
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142 views

Can LSD in very small amounts increase mental ability?

Can one take a small amount of LSD(acid) and not trip but still benefit from the intended purpose? It was said the military invented it for extra sensory abilities. It has also been said it could ...
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98 views

How would you identify the independent variable in an experiment where it isn't specified? [closed]

I know that the above question is broad, but I specifically want an answer in terms of the following investigation - all of question 3 (ONLY) of this paper. The independent variable, according to ...
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200 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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684 views

When is it unacceptable to measure dry mass in an experiment to measure growth of plants?

I'm an A level student (British high school final year) and I was doing an exam question which asked for the design of an experiment to test the effect of light intensity on the growth of a certain ...
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41 views

How should the interval between serial dilutions be expressed?

The interval between simple dilutions is a constant value added to the preceding dilution to get the next. How should a factor for serial dilutions be mentioned? As there is no common difference ...
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36 views

What are some effective strategies for testing whether a trait is an adaptation?

Although signs of evolution are to be found everywhere across taxa, it sometimes seems difficult to discern whether a trait is a retained accident or an adaptation. It also seems like there is a ...
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1answer
27 views

RNA seq: Should non-infected units be used for RNA-seq?

I am designing a RNA-seq experiment to study transcriptomic profile changes upon parasite exposure. Some papers I read, mostly extract RNA from the entire treatment group (organisms exposed to ...
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3answers
157 views

Does cell phone radiation promote longevity?

This preprint presents results from a 2-year National Toxicology Program study on the effects of cell-phone radiation in rats. On page 8 of the PDF, survival results are presented. The presentation of ...
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47 views

Why use embryonic neurons to study protein knockouts/mutants in long term potentiation?

Just wondering if anyone had some ideas about the question in the title. I'm just wondering why some papers use embryonic cultures of specific brain regions for neurones to test the effects of ...
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113 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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1answer
741 views

What bacteria results in a Gram +ve cocci and catalase +ve? What test comes next?

Results so far. We are trying to determine unknown microorganisms in intro to microbiology course. I first did gram stain and they were all cocci morphology, purple color and clumped together (...
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35 views

Is it possible to both extract DNA sequences from plasmids and fuse them using primers for Gibson assembly?

Maybe I'm overcomplicating this, but I'm having some issues with a construct. So, I have three plasmids containing a total of eight DNA sequences that I need to fuse into one linear sequence. I plan ...
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52 views

RNA-Seq library normalization and experimental setup

I'm working on an RNA-Seq project and I am trying to figure out library normalization. I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization. However, I was ...
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92 views

Decoding animal language (dolphins etc)

I have this idea about how we perhaps could decode animal vocabularies that I would like to have some input on. The idea is to design an experiment/challenge where we could predict roughly what has ...
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472 views

Wet weight measurements: Setting up cultures for measuring growth rate via wet weight

I have some isolates which I am trying to grow in some toxic leachate in order to measure their growth rate I also want to measure the growth rates of certain combinations of these bacteria. I've ...
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166 views

The most reliable way of identifying deer antler measurements?

I am creating a (theoretical) study on how males use antlers to assess fellow males' abilities. I thus would need to have accurate measurements of antlers, including length, width, number of tines etc....
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298 views

What does the phrase 'background level' mean?

I was reading BIOS Biochemistry and stumbled upon a phrase 'background level' in the following excerpt $-$ The lac operon contain lacZ,lacY and lacA genes encoding $beta$-galactosidase, galactoside ...
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411 views

What is the best way to analyze non-quantitative mass spec hits from an immunoprecipitation pull down?

I am studying a nuclear protein and want to come up with a list of potential proteins that it interacts with. From the nuclear fraction of 293T cells, I did an IP (immunoprecipitation) to pull down my ...
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37 views

How would one determine if an up regulation of one protein leads to an over expression of another?

Again, I'm new to biology and have a bunch of questions. Does it depend on the proteins involved? OR are there basic co expression procedures one could implement to determine exactly how much one ...