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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1answer
37 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 ...
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0answers
18 views

Determining hyaluronic acid hydrolysis via dye-binding assay

I have a protein that I am reasonably sure hydrolyzes hyaluronic acid, and I'm trying to design an experiment to test that. I was told that a dye binding plate assay where clear zones will indicate ...
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1answer
63 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 ...
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1answer
49 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 ...
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1answer
27 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 ...
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1answer
64 views

How to statistically test the predictability of evolution? [closed]

Can anyone recommend me an experimental study which tries to test the predictability of evolution? The closest works I found are the studies of fluctuation tests (f.e. classical study of Luria & ...
2
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1answer
21 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 ...
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1answer
21 views

Ways to identify that proteins are regulating different genes experimentally

As part of my study I have been given this hypothesis: HIF 1a and HIF 2a regulate different genes in multiple myeloma What ways do we have to identify that these proteins are regulating ...
4
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1answer
104 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, ...
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1answer
32 views

What would be the estimated cost sequencing?

I'm a newbie to the world of NGS, but I thought it might be a suitable and cheaper alternative to doing traditional Sanger sequencing for this particular application. However, I'm not so sure on how ...
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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 ...
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3answers
266 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 ...
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0answers
40 views

How to measure the biomass of hydroponic plants in netpot/rockwool DWC system?

I'm doing an experiment with 4 kale plants, each in their own small deep water culture (DWC) system. Each plant was transplanted in rockwool with netpots and clay pebbles. But I need to periodically ...
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1answer
92 views

Choosing the best assay for my experiment? [closed]

Which of the following assays can be used to determine whether cell death specifically due to apoptosis has occurred in a given cell sample? Choose all that apply. WST-1 Assay Caspase Colorimetric ...
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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 ...
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1answer
156 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 ...
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0answers
270 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
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1answer
68 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 ...
6
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2answers
614 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 ...
5
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3answers
156 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 ...
2
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1answer
135 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 ...
3
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0answers
288 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 ...
2
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0answers
95 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 ...
4
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1answer
41 views

Medium for Pseudomonas?

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

Optimization of E. coli growth in D₂O (heavy water)

I would like to find a method of increasing the biomass of my D2O cultures because my current method is not yielding enough protein. I would like to also minimize the amount of H2O in my culture. My ...
5
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2answers
168 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 ...
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0answers
12 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? ...
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2answers
137 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 ...
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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 ...
6
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1answer
2k 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
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1answer
88 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 ...
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1answer
30 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
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1answer
1k 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
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1answer
45 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 ...
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1answer
46 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 ...
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1answer
50 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 ...
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2answers
491 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
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2answers
109 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
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1answer
190 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
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1answer
161 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 ...
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4answers
211 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 ...
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1answer
701 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 ...
2
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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 ...
5
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2answers
163 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 ...
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1answer
944 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
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1answer
853 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 ...
3
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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 ...
2
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2answers
972 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 ...
3
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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 ...
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4answers
307 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 ...