Tagged Questions

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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5
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2answers
33 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 ...
1
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0answers
10 views

How were the synaptic areas identified in the somatic sensation pathways?

I'm studying the somatic sensation pathways in neuro-anatomy and I was wondering what was the experimental procedure for identifying the number and location of the synapses in these pathways? ...
2
votes
2answers
44 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
0answers
42 views

How can oxygen production during photosynthesis be measured?

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 ...
6
votes
1answer
127 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 ...
1
vote
1answer
28 views

A question on exclusion of study participants for an Exome genotyping array

I'm reading a paper that used whole exome sequencing on an African American and European populations to discover novel low frequency and rare variants associated with lipid levels & the risk of ...
3
votes
1answer
94 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, ...
0
votes
0answers
20 views

What models are used for the different pathways of apoptosis?

We are trying to find references for experimental models of different pathways of apoptosis (caspase-dependent and -independent intrinsic apoptosis, death receptor type-1 and -2 mediated apoptosis, ...
0
votes
1answer
21 views

Simple experimental design of a chemostat without pumps

A chemostat is a device to maintain a cell culture in equilibrium, by continually pumping nutrients in and pumping excess cells and nutrients out. What's the simplest design of a chemostat one can ...
0
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0answers
28 views

Degenerate primer design for DIG in situ hybridization

New to molecular and have learned to design primers from google/youtube so any info would help Would someone be willing to share their protocol for degenerate primer design? Breakdown: Trying to ...
1
vote
1answer
33 views

Book on yeast reproduction, evolution and on the use of yeast as model organism

I am looking for a good book in: Yeast reproduction mating types Recombination mating type determination mechanism Yeast evolution Yeast as model organism and its use in experimental biology It ...
0
votes
2answers
199 views

How to design an experiment with scent triggered memory recall in humans?

I've recently learned that scents can trigger memory recall in humans, and am thinking about setting up an experiment where I would attempt to induce memory recall through exposure to scents. In ...
2
votes
2answers
91 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 ...
3
votes
1answer
97 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 ...
7
votes
1answer
98 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 ...
1
vote
0answers
36 views

Are there mice pedometers?

I am seeking to make treatments for arthritis. Earlier, I asked a question about Protocol for measuring stamina of arthritic mice, and I also know that some earlier studies have used pedometers. As a ...
6
votes
4answers
121 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 ...
1
vote
1answer
380 views

What should be evaluated in food decomposition experiment?

Briefing Some days ago I noted that 3 cookies left on my desk since 3 months ago are still "fresh", and by that I mean... not spongy like some cookies that get soft after some time outside. However ...
1
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0answers
34 views

Randomized experimental design in genetic experimentation.

I am struggling to find out if randomization is used in traditional genetic breeding experimentation with model organisms, especially in lab contexts? And why this should be so? This is part of a ...
2
votes
3answers
1k 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 ...
5
votes
2answers
138 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 ...
1
vote
1answer
481 views

Role of Fbx15 in ES cells and its use in assaying for iPS cells (Yamanaka paper and others)?

I am trying to understand the assay for iPS cells in the Takahashi & Yamanaka 2006 paper. They inserted a beta-geo cassette, which contains the neomycin resistance gene, into the Fbx15 gene. The ...
2
votes
1answer
475 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
1answer
462 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 ...
2
votes
2answers
628 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 ...
0
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0answers
52 views

what's an ethics-friendly way to measure the protocol of electric shocking mice?

We have to measure the protocol of electric shocking mice. The mice are head-fixed, we have to guarantee that the electric current is significant to make the mice learn, but not too big to make the ...
3
votes
0answers
787 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 ...
6
votes
4answers
164 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 ...
0
votes
2answers
48 views

Manipulating Gut flora in vivo

I am tasked with designing an in vivo experiment in humans that requires manipulating the gut flora in one sample group to gauge its effect. Please suggest ways of doing this besides administering ...
5
votes
1answer
84 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 ...
5
votes
1answer
385 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 ...
3
votes
0answers
50 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 ...
1
vote
0answers
68 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
64 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 ...
5
votes
3answers
515 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
138 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 ...
6
votes
1answer
189 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 ...
4
votes
1answer
94 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 ...
20
votes
3answers
1k 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 ...
11
votes
3answers
505 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 ...
16
votes
3answers
237 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 ...