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

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2answers
110 views

How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_R1$, $O_R2$, $O_R3$ - ...
3
votes
1answer
42 views

What is a protective epitope?

What is a protective epitope? An epitope is basically a part of antigen. So does it mean that when the epitope combines with an antibody, it helps in the functioning of the antibody instead of going ...
3
votes
1answer
31 views

Efficiency of plasmid DNA isolation from frozen E. coli cell cultures

Has anyone isolated plasmid DNA from frozen (at -20degrees) E. coli cell cultures (not pellets)? Has that worked and if so, with what yields? What would be the quality of the isolated plasmid DNA if ...
3
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1answer
58 views

What is “bacto” peptone?

Standard recipes for yeast medium often include "bacto-peptone". Is this the same as bacteriological peptone? Is there an authoritative source that spells it out?
3
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1answer
103 views

Do macrophages engulf mtDNA?

Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment. We know that mtDNA inheritance is solely matrilineal. So the question is, If your mitochondrial DNA ...
3
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1answer
146 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?
3
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1answer
38 views

How do you express and detect GLP-1 receptors?

I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors. The cell line used is Min-6. How do I detect ...
3
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3answers
848 views

Knockdown of long noncoding RNA (lncRNA) - how is it done?

I don't work at the wet lab and don't know all the details about the knockdown techniques. My question is: How lncRNA knockdown is done? For example - you have lncRNA that is functional in the ...
3
votes
1answer
131 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
3
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1answer
454 views

Difference between “transcriptional activity” and “RNA expression”

I am working with a network object where the nodes are different events in molecular biology. Specifically; Catalytic activity of X, RNA expression of X, GTP-bound activity of X, Kinase activity of ...
3
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1answer
100 views

What is the extent of the effect of Tris on E. coli?

I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H2O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane ...
3
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2answers
176 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 ...
3
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1answer
627 views

How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
3
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1answer
391 views

How to secrete a recombinant protein from E. coli?

What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli? I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells. For now I ...
3
votes
2answers
73 views

Why not use Cu(OH)2 as a dye for protein electrophoresis?

As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?
3
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2answers
475 views

Just how light-sensitive is ethidium bromide?

One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in ...
3
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1answer
122 views

What are centromeres *really*?

I've gathered that a centromere is a a region* where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark ...
3
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1answer
95 views

205 nm UV-Vis readings

Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.
3
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1answer
94 views

Real-time PCR delay in Cq due to insertion SNP in primer

I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. I am most interested in how much there is a delay in ...
3
votes
1answer
75 views

Transposons and the net amount of DNA

The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost ...
3
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1answer
662 views

What is the exact principle of capillary isotachophoresis?

I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.
3
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1answer
757 views

What is the purpose of Y-shaped adapters in Illumina sequencing?

Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. ...
3
votes
1answer
380 views

Why re-label the strand ends in 3' DNA labelling?

I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works. I took a diagram from my lesson and tried to understand with it; this is what I understood. If I’m ...
3
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1answer
106 views

High protein turnover rate and protease inhibitors?

I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular). I have a problem: when I measure the mRNA and protein ...
3
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1answer
110 views

Optimization of annealing temperature

I am trying to optimize annealing temperature for some primer pairs. I have tried optimization using cDNA, genomic DNA, Taq polymerase, phusion polymerase etc., but every time I am either getting ...
3
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0answers
15k views

Does CPH4 exists? [closed]

I just see the film Lucy, it talks about a molecule called CPH4 which increase human capabilities. Of course it's a film and so it's not scientific facts. During an interview the producer says that ...
3
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0answers
26 views

Cross section of actin network in neurites

for a simulation I am developing I would like to know how the actin network in neurites is distributed. Is actin confined to the periphery or is the whole neurite shaft containing actin with a rather ...
3
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0answers
35 views

Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
3
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0answers
59 views

Large scale reverse transcription?

I need to make RNA:DNA duplexes. I can make 100 to 200 ug of mRNA through in vitro transcription, and I know how to use reverse transcription to make a cDNA library, but I have questions with this. ...
3
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0answers
66 views

Will eukaryotic RNA fold in the same way in prokaryotes?

As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any ...
3
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0answers
77 views

How does LCR compare to Assembly PCR

The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction ...
2
votes
3answers
926 views

Improving Gel Extraction yields

How can I improve my Gel Extraction yields. We use the standard protocol from Qiagen, gel extraction, dissolve in QG buffer at 42C and purify via anion exchange columns. However, with 500 ng we ...
2
votes
4answers
78 views

determine longest poly-purine tract

how to determine/ find the longest poly-purine tract in any genome and this needs to be on the E. coli genome . is it to figure out the polypurine tract and then figure out the longest chain ? or is ...
2
votes
3answers
97 views

What equipment would one use to modify a virus? [closed]

Would anyone be so kind as to give me a few examples of the equipment involved when modifying a virus? Otherwise my novel may end up reading Eva entered the lab and modified a virus. Not much back ...
2
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2answers
72 views

Assays during drug discovery

After researching the definition of Assay, I am left with the idea that an assay refers to scientific screening. It could be of chemicals, microbes, etc. I understand that during drug-discovery ...
2
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1answer
48 views

How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
2
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1answer
188 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
4answers
83 views

Theoretically, what technique would one use to modify a virus so that it only affected a subset of the population?

I'm writing a novel and i would like to know some of the equipment and techniques involved with modifying a virus. Is it feasible for a virus to be engineered to only affect certain people? It ...
2
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3answers
57 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
68 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
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4answers
100 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?
2
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1answer
80 views

Is the protein in teardrops still attached to cells, or is it released and free-flowing?

A ScienceDaily article says that the protein in teardrops can kill bacteria. But how does it reach the bacteria?
2
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1answer
61 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, ...
2
votes
2answers
119 views

Prenatal Marketing

This is for a short story idea. Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...
2
votes
3answers
80 views

Is DNA mutation locally energetically stabilizing the DNA molecule

I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done ...
2
votes
1answer
40 views

Why do oncogenes show genetic dominance?

As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of ...
2
votes
1answer
35 views

Why does the pET- expression vector contain a LacI gene additionally to the one in the genome?

The pET plasmid is used for protein expression with T7 promotor in expression strains, such as E.coli BL21(DE3) It contains a lacI gene which codes for the lac repressor protein, a protein of ...
2
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1answer
30 views

Trimming of tRNA precursors

From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) : Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, and these are ...
2
votes
1answer
141 views

What's the physical meaning of Svedberg unit?

Sedimentation coefficients, using a centrifuge, are expressed using Svedberg unit (symbol S, sometimes Sv). Wikipedia states that $S = 10^{-13}$ sec but I also saw in a book that actually $S = ...
2
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2answers
70 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?