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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24
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3answers
2k views

Is it necessary to conduct a power analysis before beginning an experiment?

I know that power analysis is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power ...
17
votes
3answers
322 views

What is the reason behind choosing the reporter gene when experimenting on your gene of interest?

I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you ...
13
votes
3answers
652 views

Is Behe's experiment (evolving the bacterial flagellum) plausible in the lab?

[Warning: this question is motivated by a prominent proponent of "intelligent design": Prof. Michael Behe. I'm not interested in debating creationism.] According to Wikipedia[1]: In Darwin’s ...
13
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1answer
162 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 ...
9
votes
3answers
406 views

Do biological phenomena follow Gaussian statistics?

I have recently entered the life sciences (from physics). I am concerned about the use of p values in the life sciences literature. For example, in this article, they test 9 - 12 rats in a control ...
7
votes
1answer
166 views

How much does a biological experiment to validate a gene function cost?

I am computer scientist working on machine learning methods applied to predicting missing Gene Ontology annotations. In many papers, I wrote that my computational methods are very useful to suggest ...
7
votes
4answers
354 views

Is there a comprehensive life science techniques/methods database?

There are so many techniques/methodologies in the life sciences that we can use to interrogate interesting questions. The thing is, most of us are completely unaware of the available methods we can ...
7
votes
1answer
637 views

How to Design an siRNA Experiment?

I'm going to undertake an siRNA experiment soon, but I have only read about them. I want to address the role an enzyme plays in processing a protein. From what I understand, I will need to pick two ...
7
votes
1answer
78 views

Experimental Analysis: What are possible reasons for this increase in N₂O production?

My professor wanted us to each conduct an experiment for class on something we thought would interesting. My experiment was very simple, but I'm not sure how to interpret my results. (Please note that ...
6
votes
4answers
225 views

How to measure bacterial content

I´m using water container placed on a radiator to humidify room air. Someone might argue that it is a perfect nest for bacteria. I have to put copper coins into the water to kill the bacteria. I ...
6
votes
1answer
190 views

Brain + ethanol experiment suggestions needed

I need to demonstrate the effects of ethanol on a human brain (or other brain with developed telencephalon) in vitro; ideally the effects on vigilance and/or memory. Could you please suggest such an ...
6
votes
2answers
932 views

GWAS: why is replication in another cohort so crucial?

Almost all the landmark GWAS (Genome-Wide Association Studies) reviews agree that, for a GWAS finding to be valid, it needs to be replicated in an independent cohort. What exactly is the rationale ...
6
votes
1answer
3k views

Why extract DNA from certain white blood cells instead of whole blood?

In my lab, human DNA is extracted from whole-blood samples. I don't actually do the extractions and I am not familiar with the specific protocol but I understand that platelets and red blood cells ...
6
votes
1answer
106 views

How does the frequency of a visual stimulus affect the steady-state visually evoked potential?

I want to design a project for EEG signal processing. In my research I found the concept of SSVEP. SSVEPs represent the electrical activity of the brain as measured via EEG, and are evoked by visual ...
5
votes
3answers
190 views

Measuring reverse transcriptase activity in E. coli

Goal: To quantify the HIV-1 reverse transcriptase (RT) activity for a number of mutated RTs. Idea: Put RT into a vector in E.coli. Deliver GFP mRNA to E.coli. RT will process the mRNA. The ...
5
votes
2answers
218 views

How to identify genes required for biofilm formation

This is just a homework question: Q: Let’s assume that there is an unknown set of E. coli genes that are required for biofilm formation. Describe a genetic experiment you could perform to try to ...
5
votes
2answers
172 views

How is gene expression estimated?

I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles and one ...
5
votes
3answers
635 views

When to measure resting heart rate and blood pressure for following day-to-day trend?

I'd like monitor my resting heart rate and blood pressure to see how they are affected by regular cardiovascular training and other events in life. When should I take the measurements in order to ...
5
votes
3answers
185 views

Can we knock out Caspase-9 *and* avoid breast cancer phenotype in our mouse model?

I am trying to design a wet lab experiment with no wet lab experience to name. Right now, in my dream land, it would be excellent if it were possible to create a Caspase-9 knockout mouse (damage to ...
5
votes
1answer
94 views

Resource for model organism anatomy/physiology for biological experiments

I'm looking for a resource that best surveys the anatomy and physiology of common genetic model organisms, and how their characteristics are particularly useful for biological experiments. For ...
4
votes
1answer
42 views

Medium for Pseudomonas?

What is a good minimal medium for Pseudomonas bacteria? Do I need different media for different Pseudomonas species?
4
votes
1answer
114 views

Best method for measuring very young plant growth?

Is there a preferable method for measuring plant growth for a plant before the "sprout" stage? Preferably at the microgreen stage? I assume it would not involve some type of leaf based measurument, ...
4
votes
1answer
123 views

When should endocytosis inhibitors be used in cell binding assays?

I'm beginning to do some cell-binding assays and I would like for my proteins to not be endocytosed by my mammalian cells. Typical suggestions are for the cells to be kept on ice and that the binding ...
4
votes
1answer
97 views

Is there a cheap and easy way to check for potentially unsafe UV exposure?

My lab has an older large Fotodyne tabletop UV transilluminator for visualizing gels. It has a UV blocking cover that hopefully reduces UV that passes through, but I've always been suspcious as to ...
4
votes
2answers
44 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, ...
4
votes
1answer
68 views

Productive turnover and generations in the fruit fly

I was reading about the Lenski experiments on the evolution of E. coli bacterium and Dr. Elders's experiments on the evolution of the guppy. These two experiments absolutely fascinated me, and seemed ...
3
votes
1answer
2k views

What is the purpose of back-crossing mice for multiple generations?

Occasionally I will come across articles that refer to back-crossing mice of one strain onto the background other another strain (e.g., C57Bl6). They do not explicitly state the purpose for doing so, ...
3
votes
1answer
87 views

DNA length and annealing kinetics

I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the ...
3
votes
1answer
231 views

Drosophila melanogaster eclosion

Is there any published data which shows the number of Drosophila melanogaster fruit flies eclosing (hatching out of the pupae) against time since egg oviposition? I'm thinking there should be ...
3
votes
1answer
1k views

Where to put the gene after eukaryotic promoter for best expression levels?

As far as I know there is an optimum distance between a promoter and the gene for the best expression levels. What is that distance for common promoters like CMV, SV40? If you have a first hand ...
3
votes
0answers
21 views

What techniques can be used to link environmental conditions to crop yield?

Im interested in how we can determine what are the optimal conditions for crops and how deviations from these optimal conditions affect yield. In the literature I have found two main approaches and I ...
3
votes
1answer
474 views

Storing Taqman plates with polymerase in fridge before running

I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, ...
3
votes
0answers
412 views

Can't resolve protein with native PAGE

This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After ...
3
votes
0answers
2k views

What are the factors to consider when determining the sample size for a given study?

Say I'm designing a retrospective study (where I'd collect data from various schools for the last 5 years) to see if consuming milk can contribute to childhood obesity. How do I decide on how many ...
3
votes
0answers
57 views

Help with designing the analysis of radio telemetry study [closed]

I was wondering if there are any spatial ecologists out there who can provide some insight on the trouble I'm having with my Masters research. I am looking at the association a bat species to high ...
2
votes
1answer
175 views

What exactly is neuroplasticity, and can it be demonstrated with a simple experiment?

As far as I know, neuroplasticity is about restoring brain functions by moving some functions to other still functional. Neuroplasticity is more prominent in children than in adults. What are other ...
2
votes
2answers
159 views

What does it mean to perform in vitro experiments with mutant bacteria?

I came across the following sentence while reading the paper: Nanchen, Annik, et al. "Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose ...
2
votes
2answers
118 views

Is it possible to create an experiment in house conditions to prove the existence of germs?

I realise that the best way to prove the existence of germs or single-celled organisms is by looking at them through a microscope. But I don't have a microscope at my home, how can I design an ...
2
votes
2answers
2k views

Primer design for Gibson assembly

I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid. I am unsure how to design my primers for ...
2
votes
2answers
1k views

How prevalent is Taq polymerase in adding 3' A overhangs to the PCR product?

I am conducting a mutagenesis on a gene in vivo of which I need to ligate into an expression vector. The primers I have designed overlap restriction sites of which I plan to use to ligate into the ...
2
votes
1answer
39 views

Is there some research paper which focus on the influence of using cancer cell as experimental materials on experimental result? [closed]

Cancer cell is unstable cell and high variation, but there are many experiment use cancer cell as experimental materials. I always wonder how much influence can using cancer cell as experimental ...
2
votes
1answer
40 views

Microinjection method in C. elegans

I have a question about the experiment that using microinjection to inject RNAi into the C. elegans. To prepare the dsRNA for injection, fist have to clone the gene of interest from the worm genome ...
2
votes
1answer
28 views

Summarising ChIP-seq and controls needed

As part of my study I have to present on a method of discerning binding sites of proteins to DNA, for which I have looked at ChIP-seq. This is a brief overview of what I have so far, and was wondering ...
2
votes
1answer
941 views

Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?

Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions. On a slide, it said that expression might be ...
2
votes
0answers
12 views

Does level of bats activity differs from day to day?

Say we measure bats activity as number of passes through given area. Can it differ significantly depending from day to day or it stays on average roughly the same? I am wondering whether the following ...
2
votes
0answers
106 views

Does antibody staining / immunolabeling block or inhibit protein function?

In dissociated live cells, does staining them with an antibody block the protein's function? I am sorting cells based on their expression of a few marker genes, and culturing them post-sort for ...
2
votes
0answers
52 views

How can oxygen production during photosynthesis be measured? [duplicate]

I'm curious how people measure quantitatively photosynthetic rate in labs. I've seen many qualitative examples with direct observations of bubbles forming in water due to photosynthetic output of ...
1
vote
3answers
40 views

Statistically, why is the number of mutated genes in eggs treated with chemical mutagenesis one?

Excerpted from the Guide to Research Techniques in Neuroscience [1]: In chemical mutagenesis, a scientist applies a mutagenizing chemical, such as ethyl methane sulfonate (EMS) or ...
1
vote
1answer
120 views

Disadvantage of using Drosophila for breeding experiment

What should be the disadvantage of using Drosophila for experiments? a)small size of larva. b)short life cycle. c)mating soon after emergence of flies. d)large number of offsprings. Options (b) and ...
1
vote
1answer
49 views

what are examples of experimental designs on exposing materal for degradation

if one wanted to compare how sources of DNA would degradate in various conditions(environmental) how would they do this in an experimental fashion but also be best comparable to real world examples of ...