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

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2
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2answers
124 views

Image analysis of GFP-tagged protein localization bursts

I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent ...
2
votes
1answer
66 views

What are the Gateway clonase enzymes?

The Gateway cloning system utilizes what Life Technologies refers to as "Clonase enzyme mix" to catalyze the BP and LR reactions. What is in this enzyme mix? Is there a sequence for them?
3
votes
2answers
132 views

Do RNA molecules bind each other?

I have a question, maybe a naive one. Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA ...
2
votes
2answers
95 views

Modern alternatives of DNA footprinting

Since DNA footprinting is an old method I thought there may be some more recent and effective methods to identify a DNA sequence, do you know any of them?
4
votes
1answer
119 views

Topology of closed circular DNA

Why are covalently closed circular plasmid DNAs naturally found in an underwound state ? Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it ...
2
votes
3answers
130 views

Why doesn't the cytosol dissolve the polar structures?

we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why ...
2
votes
1answer
126 views

Role of isopropanol in plasmid isolation

In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? ...
2
votes
0answers
226 views

Image Processing Suite for bacterial microscopy: Schnitzcells or MicrobeTracker?

I am looking to start doing some work tracking the size and growth of individual bacterial cells in the microscope. In order to analyze the images I need software that can segment the cells, ...
1
vote
1answer
69 views

Missing 4$H_2O$s (per glucose) in Cellular Respiration… Where can they be?

I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $H_2O$ molecules. Generally, cellular respiration is written thus : $C_6H_{12}O_6 + ...
2
votes
1answer
167 views

Troubleshooting for Agarose Gel Electrophoresis

SI ran my 2% agarose gel on constant voltage (100 V). For a few times it worked at CV but, after a week or so the machine would automatically switch to constant current by itself. And this only ...
11
votes
1answer
2k views

How does translational coupling work in prokaryotes?

Today I heard about a phenomenon called "translational coupling", where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. ...
4
votes
2answers
152 views

Is AT or GC content important in electrophoresis?

Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?
2
votes
1answer
63 views

Do you have experience with PacBio?

I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have ...
3
votes
1answer
89 views

How to measure quality and quantity of DNA?

I would like to mesure DNA. I quantify the concentration with Qubit fluorometer, but I would like to know also quality of DNA. I try BioAnalyzer (Agilent),but without success. Bioanalyzer measure DNA ...
2
votes
1answer
83 views

Substitute 25mM dNTPs mix with 10mM dNTPs

I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, ...
1
vote
2answers
79 views

Functioning of EDTA

I know that EDTA chelates metal ions. It weakens bacterial cell wall and inactivates the DNases. What is the reason why it can do so ? I guess it can inactivate DNases by altering the ...
2
votes
1answer
33 views

Transport of mammalian insulin in vivo

What is the mechanism for transport of insulin in mammalian cells?
11
votes
2answers
5k views

How do I clean phenol contaminated RNA without losing any of the sample?

I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went ...
2
votes
0answers
134 views

Gibson assembly using NeBuilder

I am supposed to construct a plasmid that contains features from two other plasmids. My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, ...
1
vote
1answer
66 views

Why bacteria produce light?

After seeing this video I am curious to know why the free living bacteria produce light. What advantage will they have ? Or is it just an "unintentional" result of one of their pathways ?
14
votes
6answers
1k views

Online Molecular and Cellular Biology Video Lectures?

I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge ...
6
votes
1answer
507 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
2
votes
1answer
63 views

Would expression of GroEL and GroES in erythrocytes be a potentially effective therapy for sickle cell disease?

Would expression of GroEL and GroES in erythrocytes be a potentially effective therapeutic strategy for sickle cell disease? Why or why not?
4
votes
1answer
219 views

What is the minimum length required for a circular DNA ligation?

What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?
13
votes
1answer
964 views

What did Richard Feynman contribute to molecular biology?

Some time ago, I read James Gleick's "Genius: The Life and Science of Richard Feynman", a wonderful biography of Feynman and, by extension, most of modern physics. In this book, the author mentions ...
2
votes
1answer
620 views

Orientations of codon and anticodon

So 5'-AUG-3' is the start codon on an mRNA transcript Does that mean that the tRNA anticodon is 5'-CAU-3'? Here, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify ...
4
votes
1answer
75 views

What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
5
votes
1answer
747 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
4
votes
1answer
83 views

Ribosomal RNA amount in a Drosophila cell

I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to ...
7
votes
1answer
134 views

Does the MS2 RNA binding protein have any translational repression effects?

Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the ...
-1
votes
2answers
113 views

PAH gene mutation

Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a patient with phenylketonuria revealed a mutation in the protein coding region whose predicted effect would be to replace the amino ...
2
votes
2answers
1k views

Explanation of the terms “downstream signaling” and “upstream signaling”

In molecular biology, what's the meaning of the terms "downstream signaling" and "upstream signaling"? What's the difference between them?
0
votes
1answer
48 views

RNase and EtOH issue

I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes ...
1
vote
1answer
113 views

How to relate human metabolic model reactions and cancer drug targets / reactome items?

Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model. Essentially, I would like to know ...
3
votes
2answers
199 views

How do I create a probe for in situ hybridization?

I tried to make the probe several times but it failed again and again. It usually turns out that the probe after hydrolysis is very very short (maybe around 50nt). I did not check the RNA before ...
10
votes
1answer
25k views

Why do we add salt when precipitating DNA?

All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?
3
votes
4answers
132 views

Translation of mRNA?

We inserted an insulin gene from human into bacteria. Will translation of the gene (protein formation) occur in bacteria? If translation occurs then why does it occurs, give a reason for this?
0
votes
2answers
183 views

How to determine the actual flux in the human metabolic model of a cell line?

The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model. As far as I understand, a good way to do that would be to use gene ...
1
vote
1answer
84 views

Do “transcription factor binding site” and “operator” mean the same thing?

Can the terms "transcription factor binding site" and "operator" be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding ...
2
votes
1answer
116 views

Cloning of a sheep.. Dolly?

Dolly the sheep was a clone. When she was born she was eight years old on her 1st day of birth, her mother (from which she was cloned) was also eight years old. What is a molecular reason behind this ...
8
votes
2answers
2k views

Why is the number of PCR cycles limited?

I've been told that the maximum number of cycles in PCR is between 20 and 30. Is this true, and what are the reasons for this limitation?
5
votes
1answer
61 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
2
votes
1answer
91 views

Should I design a primer to detect virus based on NCBI genebank?

When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?
1
vote
1answer
106 views

Hardy-Weinberg applied to three alleles and stimation of allele frequencies

I have this equation: Corresponds to HW in equilibria with three alleles: $(p+q+r)^2=1$ Expanding the square results: $p^2+2pq+r^2+2pr+q^2+2qr = 1$ I need to separate homozygous and ...
2
votes
1answer
275 views

Elution of biotinylated RNA

I am using Neutravidin Agarose beads to isolate biotinylated RNA. The thing is, in the manual it says to use 8M Guanidine-HCl, pH 1.5 for elution biotinylated molecules. As far as I know it is a very ...
-1
votes
1answer
58 views

What is the impact of prolonged electromagnetic exposure on human health?

What are the health effects of being exposed to a very strong electromagnetic field caused by two resonating superconductive coils (not static magnets) for a period of years?
1
vote
1answer
71 views

In vitro transcription, contamination problem

I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination. Instead of perform the in vitro transcription again, ...
1
vote
1answer
63 views

Dilution question about RNA

I have a basic and probably silly question. I am isolating RNA with TRIzol. I have performed the basic steps and dissolved the pellet in 50 uL water. I ve measured the concentration and it was 3313 ...
8
votes
2answers
2k views

why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon ? Why is there a need for an initiation codon ? Can't translation start with different codons?
1
vote
1answer
83 views

Transcribing DNA to mRNA with introns

I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem: Given the following DNA sequence, ...