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

9
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3answers
431 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 ...
0
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0answers
9 views

making tissues grow in vitro

I heard during a class on morphogenesis that it is not possible to make any tissue grow in vitro. The example that was given was about epithelium, for which people are using cancerous cells. Why is ...
0
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1answer
26 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 ...
1
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1answer
22 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 ...
2
votes
1answer
62 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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0answers
12 views

How to dissociate a viral particle into constituent proteins?

Is it possible to take purified a virus particle and dissociate it into a mixture of its constituent proteins (and nucleic acids)? I am wondering if it would be possible to disassemble the particle ...
0
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0answers
12 views

How are siRNAs introduced to cells for RNAi experiments?

Specifically, can somebody explain how in-vitro transcription can synthesize siRNAs to conduct RNAi? I have been reading a number of research papers that discuss how to use siRNA and shRNA to conduct ...
1
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1answer
45 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, ...
0
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0answers
21 views

In a factorial design, if the effects of drug A and B are independent, how would the A+B treatment compare to A/B only?

The sample is divided into four groups, taking A and B, taking A, taking B, taking neither. I want to know what the theoretical outcome table would look like if the effects of drug A and B are ...
3
votes
1answer
133 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, ...
2
votes
1answer
340 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 ...
0
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0answers
45 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 ...
2
votes
1answer
56 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 ...
0
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0answers
25 views

What is a control in an enzyme question.

If Im conducting an investigation to test how pH (2,5,7,9,11) affects the effect of catalase on hydrogen peroxide, what would the control(s) be in the investigation
2
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0answers
55 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 ...
1
vote
1answer
49 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 ...
0
votes
1answer
52 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 ...
4
votes
2answers
872 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 ...
5
votes
1answer
228 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 ...
1
vote
0answers
29 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 ...
1
vote
1answer
79 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" ...
3
votes
0answers
61 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 ...
3
votes
0answers
499 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 ...
3
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0answers
109 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 ...
3
votes
1answer
161 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 ...
5
votes
2answers
956 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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0answers
47 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 ...
4
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0answers
45 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, ...
2
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0answers
74 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.
2
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0answers
81 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 ...
1
vote
1answer
162 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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0answers
450 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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0answers
30 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 ...
0
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1answer
34 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 ...
0
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1answer
26 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 ...
1
vote
3answers
126 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 ...
3
votes
1answer
46 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 ...
7
votes
1answer
97 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 ...
2
votes
1answer
517 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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0answers
32 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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0answers
49 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 ...
0
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0answers
61 views

Potential Thermometer Error

This question may be better placed in another subject but I'll start here since our project is looking at mammal populations. I'm working for a researcher right now studying small alpine mammals. ...
2
votes
0answers
75 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 ...
1
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0answers
369 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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0answers
120 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....
1
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1answer
194 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 ...
0
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2answers
333 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 ...
0
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1answer
35 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 ...
4
votes
1answer
30 views

How would one determine whether a chemical will upregulate a certain class of proteins?

I'm trying to determine whether certain organic chemicals will upregulate classes of proteins that possess deacylase activity.  How would I go about this experiment? I'm assuming I would use some ...
6
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2answers
116 views

Books about famous experiments in biology - 'methods of investigation'

I'll explain briefly what I need (hoping to find something) : I wanted to know if someone knew about a book that in a way or another talked about the greatest experiments in biology (Griffith, Avery-...