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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3
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1answer
534 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, ...
-2
votes
0answers
18 views

How much level should I overexpress a protein without any diseases as references [on hold]

I am planning to overexpress this G protein alpha subunit by using adenovirus in HUVECs. Problem is, currently, no report showed that this protein expression is increased in any diseases. The only ...
1
vote
1answer
48 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 ...
0
votes
1answer
10 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 ...
3
votes
1answer
19 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 ...
4
votes
2answers
47 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-...
1
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0answers
47 views

How can I calculate Shannon-Wiener diversity index in caves with different kind of habitats and different sampling methods?

I would like to start a monitoring in different caves, compare caves of different age and length, and find out if there are any correlations between these factors and their diversity. I was thinking ...
1
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1answer
32 views

Pooling for qPCR

I am comparing miRNA expression levels in 3 different groups but I am low on money and time. I have to get some preliminary results to get the actual research going so I decided to pool my samples and ...
7
votes
1answer
645 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 ...
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 N-ethyl-N-...
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 ...
13
votes
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 ...
7
votes
1answer
81 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 ...
1
vote
1answer
50 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 ...
0
votes
0answers
22 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 ...
1
vote
1answer
128 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 ...
2
votes
1answer
41 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 ...
1
vote
1answer
86 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
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 ...
1
vote
1answer
23 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
votes
1answer
115 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, ...
0
votes
1answer
45 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 ...
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 ...
9
votes
3answers
435 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 ...
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 ...
1
vote
1answer
150 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 ...
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 ...
5
votes
3answers
188 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 ...
6
votes
1answer
114 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 ...
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?
6
votes
2answers
1k 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 ...
3
votes
1answer
93 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 ...
2
votes
1answer
183 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
votes
0answers
435 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 ...
4
votes
1answer
125 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 ...
1
vote
1answer
48 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
103 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 ...
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 ...
5
votes
2answers
224 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
vote
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? ...
2
votes
2answers
164 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 ...
6
votes
4answers
227 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
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 ...
1
vote
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
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, ...
0
votes
1answer
48 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
votes
2answers
542 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 ...
7
votes
4answers
362 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 ...
1
vote
1answer
51 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 ...
2
votes
2answers
121 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 ...