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

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What are the practical techniques used for the assessment of blood for abnormalities? [on hold]

Any practical laboratory techniques used for the assessment of blood in hematological investigations?
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14 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 ...
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19 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 ...
5
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1answer
147 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?
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40 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 ...
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3answers
252 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 ...
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28 views

Is it possible that a set of functionally related proteins in a pathway fulfill different functions?

Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific ...
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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 ...
4
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1answer
141 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 ...
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2answers
40 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
38 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 ...
2
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1answer
28 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?
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1answer
76 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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1answer
53 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
18 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
11 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 ...
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0answers
24 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 ...
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1answer
12 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 ...
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4answers
173 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?
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3answers
270 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
38 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
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1answer
49 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
72 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 ...
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13 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 ...
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3answers
569 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?
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1answer
26 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
14 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 ...
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1answer
36 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). ...
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1answer
24 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
22 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
33 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
46 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
99 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
71 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 ...
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95 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
28 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?
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1answer
54 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 ...
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2answers
329 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 ...
2
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1answer
28 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 ...
2
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1answer
62 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
20 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
53 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?
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2answers
98 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 ...
1
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1answer
31 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?
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1answer
64 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?
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1answer
69 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 ...
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2answers
134 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
95 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
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2answers
68 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 ...
5
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2answers
106 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 ...