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

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How is the protein removed from the DNA preparation? [on hold]

to determine how much DNA you have, you measure the absorption of the DNA.
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what makes different materials to have different tastes? [on hold]

what makes different materials to have different tastes? For example: what we know as different colors is due to different frequencies of light and what we know as sound is due to the different ...
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1answer
33 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 ...
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40 views

What are the 5 most expensive machines that can be found in a bio-lab? [closed]

What are the 5 most expensive machines that are specific to a biology laboratory? In this case the type of biology laboratory that specialises in molecular biology and bioinformatics (study of cell ...
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1answer
63 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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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
516 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?
3
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1answer
22 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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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
29 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
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 ...
0
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1answer
14 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
31 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
39 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
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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
53 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
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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
43 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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151 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
24 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
48 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
17 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
51 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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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 ...
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27 views

C. elegans and 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?
6
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1answer
61 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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63 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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104 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
78 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
54 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
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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 ...
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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
76 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?
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27 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
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1answer
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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 ...
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188 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.
4
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1answer
185 views

How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude? I am interested in RNA ...
3
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1answer
51 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? ...
4
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1answer
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protein-binding sRNAs

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on A bit of background and context: In bacteria, a regulatory protein ...
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Sequence based method for prediction of continuous B cell epitope

What is Sequence based method for prediction of continuous B cell epitope? What is the algorithm/procedure of this method? Can someone please explain this to me in simple language?
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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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1answer
46 views

A monkey typing Shakspeare? [closed]

I think that the ultimate and most important question of biology and science is the origin of life. Was it the result of pure probability? Or was it the result of the law of physics? In other words, ...
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1answer
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Determining and Differentiating specific ATPases

In respects to this certain ATPase transporter. What do i look for in respects to determining what specific kind it is out of: F-ATPases V-ATPases A-ATPases P-ATPases E-ATPases Im assuming that ...
2
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2answers
66 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a ...
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recombinant peptide MHC complex

What is recombinant peptide-MHC complex??? Recombinant DNA means "to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological ...
4
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2answers
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Transmembrane Protein Problem

Problem A transmembrane protein has 1000 aa. The 5th aa is found on the external side of the cell membrane. It interacts with the aqueous environment outside the cell. Amino acid 90 is inside the ...
2
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1answer
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epitope prediction/ mapping

B-CELL EPITOPE PREDICTION Regarding this article: "Such a molecule can be synthesized or, in case of a protein, its gene can be cloned into an expression vector."----- is a particular line in ...
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How does Temperature influences the rate of protein turnover? [duplicate]

Question How (quantitatively speaking) does temperature influences rate of turnover of transcription factors? Which protein? As I am not looking for any accurate number I am talking about an ...