The study of the molecular processes of the nucleus and cell function.

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3
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1answer
107 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
2
votes
1answer
38 views

Why is the resting potential of a neuron so close to the equilibrium potential of K⁺?

I know this has something to do with the K+ leak channel. I just don't understand how. I know that 3 Na+ are pumped out for every 2 K+ pumped in. This makes the cell interior net negative. I know ...
8
votes
2answers
569 views

What is it about the housekeeping genes that makes them almost immune to gene regulation?

When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently ...
1
vote
0answers
18 views

How to engineer chromosomal duplications?

Specific genetic engineering of chromosomal aberrations like deletions, inversions and translocations are doable by using the CRISPR/Cas system or the other programmable nuclease systems. Insertions ...
6
votes
1answer
77 views

Receptors for red and far-red light in plants: Shade avoidance

Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading. My question is: which receptor is ...
0
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0answers
23 views

Cannot conjugate Biotin-labeled DNA to Streptavidin-labeled solid surface

I have been trying to immobilize DNA by the bioconjugation of biotin and streptavidin, but I cannot get this work. I added EDC and streptavidin to COOH ...
2
votes
0answers
13 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
2
votes
1answer
52 views

How do C. elegans manage nutrition?

If there is ample amount of food, do C. elegans worms know when to stop eating or do they store extra energy? Could they put this extra energy to use by moving faster or putting more eggs?
4
votes
1answer
289 views

RNA isolation from Drosophila head

I need to isolate RNA from Drosophila head. I basically chop the head off and first homogenize it with a homogenizer (similar to this: ...
1
vote
1answer
21 views

Why does a tumour's genome change depending on the environment?

According to the book "Primer of The Molecular Biology of Cancer" by Vincent, Theodore and Ateven, the tumour cell is changed depending on its environment. performed genome-wide analysis on three ...
3
votes
0answers
78 views

How to prevent e coli from clumping (for FACS)?

I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells. I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run ...
6
votes
1answer
275 views

why is DNA antiparallel? Can it be parallel?

My biology textbook mentions that DNA is antiparallel and it got me wondering... Can DNA be parallel? What would happen if it was parallel? could DNA still replicate right?
3
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0answers
41 views

Why is ATP the main nucleoside triphosphate used to exchange energy? [duplicate]

Out of all of the nucleoside triphosphates what makes ATP the most used? Is it its structure? The amount of energy it contains? Why is GTP not used as much? What is the deal with the other nucleoside ...
4
votes
3answers
369 views

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? The book's answer is $20^{12}$. However, I disagree. This result ...
9
votes
3answers
2k views

Does a man contain all the genes needed to make a woman?

This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so ...
3
votes
2answers
52 views

What does the gene name “lexA” stand for?

It is an important gene expressed in E. coli that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence ...
13
votes
5answers
2k views

Why are some genes dominant over others? What is the mechanism behind it?

If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain ...
4
votes
1answer
207 views

Can concentration of a protein be determined from a gel quantitatively (rough estimation)?

I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which ...
2
votes
2answers
769 views

What is Pan for in pan-caspase?

A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?
3
votes
1answer
298 views

Does sample buffer require EDTA for protein separation on SDS PAGE?

In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE.
1
vote
1answer
49 views

Protocol for checking pipette calibrations using absorbance readings of a dye in solution?

I've been looking around the net looking for a nice protocol to validate micropipette calibrations using absorbance readings of a dye in solution. Does anyone have one they can share? I'd highly ...
4
votes
1answer
173 views

DNA content in plant seeds vs. fruit flesh

Is there a publication comparing DNA yield and/or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits? I would prefer a ...
5
votes
4answers
403 views

What is SDS PAGE gel polymerization time?

I am working on 20% SDS PAGE. I want to know optimum polymerization time for 20% resolving gel and 6% stacking gel. If I increase the time then would it affect the band pattern?
1
vote
1answer
439 views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
2
votes
1answer
26 views

Concentration of degenerate primers should you dilute to?

I'm a little embarrassed to ask but when you have for example four degenerate primers and the end protocol says that the final primer concentration should be 10 µM working stock, should you make the ...
0
votes
0answers
18 views

What genetic distance model should be used when calculating genetic differences in Arelquin?

I'm using Arelquin to look at the genetic structure between a number of different populations. I want to compare the populations by producing pairwise FST values, however I don't know what model for ...
0
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0answers
27 views

Superpatients for Cancer resistance

I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer. The article is ...
2
votes
1answer
44 views

How are lesions in the RNA corrected?

I quite understand why thymine is present in DNA. So we can mark it out where cytosine undergoes a reaction and is converted to uracil. Then we can repair the DNA. But how can we make that out in RNA ...
5
votes
3answers
304 views

In what sense is the “histone code” a code?

Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell ...
4
votes
2answers
2k views

On which strand does the promoter sit?

My book keeps giving different indicators as to whether the promoters are on the coding or template strand. It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...
8
votes
1answer
90 views

How to validate the regulatory interactions inferred from gene expression data?

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
5
votes
1answer
1k views

What is the definition of a stringent/relaxed plasmid?

I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are: Relaxed control of plasmid replication. Relaxed control ...
4
votes
1answer
72 views

Western blotting with multiple antibodies

Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a ...
8
votes
2answers
533 views

More variation in proteins than genes. Why?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
2
votes
0answers
17 views

Resource for finding Repressive/Inhibitory factors for a given gene?

I have a list of genes for each of which I'd like to find: A list of transcription factors that up-regulate the gene A list of inhibitory factors that down-regulate it. I used this tool on ...
6
votes
3answers
1k views

Should I dilute DNA with water or elution buffer?

I've extracted DNA using a kit and final step is eluted with buffer. If I must dilute my DNA samples, do I use the same elution buffer or can I use milliq water?
0
votes
1answer
35 views

Rosetta strain with chaperones for protein expression?

I am trying to purify a protein, and I was wondering if it is reasonably straightforward to obtain E.coli cells containing: -pGroe plasmids expressing chaperones. -Rosetta plasmids with codons that ...
4
votes
1answer
36 views

What's up with all the vague protocols? [closed]

I have lost count of how many protocols I've seen, including those supposed to be professionally written (such as manuals that come with kits from well known brands, or methods sections of papers in ...
0
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1answer
49 views

PCR directly on DNA binds to Ampure XP

During the library preparation it's possible to conserved Ampure beads during the different enzymatic reaction (it's the with beads strategy for improving yield, Fisher et al. Genome Biology 2011). ...
1
vote
0answers
15 views

how to get truseq's gel size selection when preparing libraries for exome enrichment?

i would normally use a 6 minute fragmentation as quoted by agilent but this gives post exome enrichment libraries of around 300bp or slightly over. Truseq want libraries to be 100bp larger. i am ...
2
votes
1answer
26 views

Separation of closely-sized isoforms

I have to separate two proteins of 86kDa and 80kDa respectively, however, I just cannot get a decent separation even in 6% polyacrylamide gel. To make matters worse, these two proteins are isoforms ...
3
votes
2answers
394 views

Why does methylation not occur in viral DNA?

Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?
1
vote
1answer
35 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 ...
4
votes
1answer
36 views

A few questions regarding immunology [closed]

I know that there is a variable region on antibodies which can recognize a wide variety of antigens, and that germinal centers create more "fit" antibodies to respond to an infection. So I was just ...
1
vote
1answer
63 views

Low copy numbers of plasmids

I have a plasmid with the P15A origin which apparently has a low copy number (see here). This would explain why my purification yeilds for subsequent digestion are low (gel shows the plasmid after ...
0
votes
2answers
430 views

Purifying a linear plasmid after restriction digest?

I expressed a yeast vector in E.coli and purified about 13µg of it. I then linearized it using a restriction enzyme, and attempted to gel purify it. I attempted this twice. The gel showed a clear ...
3
votes
1answer
68 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
2
votes
1answer
40 views

Kinesin-5 / cytoplasmic dynein spatial density distribution in neurons

Is there some way to experimentally determine the density distribution of Kinesin and Dynein in a Neuron? Fluorescence labeling would be impossible(?) as GFP markers would probably alter the motor ...
1
vote
1answer
210 views

Has anyone used Crispr/Cas to induce a knock-in in MEF cells?

Does anyone have experience with the crispr/cas9 platform performed on MEF? Or does anyone recall any relevent articles? Thanks
2
votes
1answer
102 views

Mouse meta-globin mRNA problem

This is an mRNA strand of mouse meta-globin: 5'-ccccagauacggaauucgaau-3' A) Which small RNA (below) is most likely to regulate expression of meta-globin? ...