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

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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 ...
4
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1answer
303 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 ...
7
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1answer
89 views

Double stranded nucleic acids are more 'durable' than single stranded nucleic acids?

I'm struggling with a question I've been asked. "Why is double stranded genetic material more 'durable' than single stranded one?" I know that double stranded genetic material is more stable due to ...
3
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2answers
64 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 ...
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1answer
57 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 ...
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2answers
121 views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
3
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1answer
851 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.
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2answers
293 views

Growing E. coli at room temperature?

If I were to do a blue/white selection of transformed E. coli on LB agar ampicillin plates at room temperature (23⁰C) for about 2 days and 18 hours, will I run into the issue of satellite colonies or ...
2
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1answer
50 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 ...
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0answers
26 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 ...
1
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0answers
34 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 ...
3
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2answers
73 views

Need help in codon optimization

I want to chemically synthesize a GFP gene for expressing in rice.I am using the IDT Codon Optimization program and found that not all the codons are 100% optimized. Some of them are the 2nd or 3rd in ...
2
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1answer
45 views

Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme

The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends ...
5
votes
4answers
764 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?
5
votes
3answers
335 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 ...
2
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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 ...
4
votes
1answer
128 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
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1answer
101 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 ...
2
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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
3k 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?
4
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1answer
43 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 ...
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0answers
16 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 ...
1
vote
1answer
66 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). ...
2
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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 ...
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1answer
48 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
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1answer
39 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 ...
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1answer
77 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 ...
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2answers
967 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 ...
5
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1answer
253 views

Restriction Mapping - Homework question

I have trouble in solving this exercise. Exercise A circular plasmid of 10,000 base pairs (bp) is digested with two restriction enzymes,A and B, to produce a 3000 bp and a 2000 bp bands when ...
6
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2answers
105 views

Can an organism process H₂O into H₂O₂?

In an answer to a recent question on Worldbuilding, I suggested that an organism convert $H_2O$ into $H_2O_2$. I suggested a few processes that yielded the desired final result ($2H_2O \rightarrow ...
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2answers
35 views

C.elegans and antioxidants

How would you test the effect of antioxidants on C.elegans lifespan? Is this done through feeding E.coli with antioxidants and then C.elegans with E.coli, or is there another method?
0
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1answer
198 views

Apoptosis vs necroptosis

I understand that apoptosis and necroptosis share the same upper part of the pathway, but I cannot seem to distinguish when is each one activated? From my readings, it seems that when procaspases 8 or ...
1
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2answers
1k views

Book Recommendations: GRE Subject Test In Biochemistry, Cell And Molecular Biology

There are probably a lot of really good answers that may vary significantly in terms of content. I'm looking for a set of books that I can read in preparation for the GRE Subject Test In ...
3
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1answer
34 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
4
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1answer
105 views

How small does a nanobot have to be to “swim through the brain” and access any neuron it wants to?

I read on this question What is in the space between neurons in a brain? that there is actually not much empty space in a brain. But my question is slightly different. Is there a visual demonstration ...
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1answer
24 views

Centriole genes Knock-out Experiment in Common experimental animals?

Anyone know of any experiments that have knocked out the genes for producing centrioles in a worm, mouse, fish, fly or whatever animal? Are the genes for centrioles even identified? It has been shown ...
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1answer
110 views

How to separate peptide on SDS PAGE?

I want to separate 1600 Da peptide on SDS PAGE, on 20% GEL I didn't get any band, How can I separate on PAGE? Can I use 25% SDS PAGE?
4
votes
2answers
610 views

How can histidine be classified both as positively charged and hydrophobic?

I saw the chart in this post Histidine aromaticity. Since I'm not allowed to comment and post a question instead of an answer, I have to ask my question in a separate thread. How can histidine be ...
2
votes
1answer
59 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?
7
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1answer
81 views

How exactly can dsRNA be introduced to a cell?

Is it just by viruses or are there other means by which it gets into cells, such as plasmid uptake?
4
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1answer
98 views

Redundancy of the genetic code

One particular codon codes only for one amino acid, but an amino acid can be coded for by several different codons. Now according to the genetic code, the codon UUU ...
8
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2answers
573 views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
8
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1answer
138 views

Can a human cell live indefinetely in a controlled environment?

How long can a human cell live in a controlled environment, given all necessary nutrients, temperatures, mechanisms for waste removal, and other requirements are provided for? Put differently: Can a ...
2
votes
2answers
475 views

How does non-homologous end joining (NHEJ) work?

I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it ...
6
votes
2answers
756 views

Alternatives to trypsin for cell detachment?

I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin. I was wondering if there are ...
1
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2answers
84 views

How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here? Binding of the triphosphate ...
2
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1answer
2k views

What are some of the general characteristics of the DH5 alpha strain?

I can not find some useful sources unfortunately. Please tell me about some important characteristics of DH5 alpha. What makes DH5 alpha suitable for the gene cloning?
0
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1answer
33 views

Does adding antibiotic after 5-10 mins of innoculation affect the protein yield or growth?

I've asked a lab colleague the same question. She said, it would loosen the bacterial cells in the LB medium and plasmids would come out. Is that true? and why?
2
votes
1answer
190 views

Active & passive transport question

If an element, ion or molecule is found in a cell is it possible to tell which method of transport was used? for example if a hydrogen or sodium ion was found in the cell could you tell if it got ...
4
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2answers
395 views

Why proteinase K doesn't degrade itself?

Can anyone tell me why proteinase K doesn't degrade itself? If possible please provide me the source.