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

learn more… | top users | synonyms

2
votes
0answers
20 views

Can mutation rate be increased for instance by mutagenesis targeting the DNA polymerase?

I am studying a non-cultivable bacterium living in an insect host, and I would like to generate some random mutants of this bacteria while preserving the insect. I am wondering if one way to do so ...
0
votes
2answers
22 views

If a given DNA oligo is an aptamer, will the corresponding RNA oligo with the same sequence be an aptamer aswell?

Functionality of aptamers depends upon the oligo's sequence and secondary structure. So, if I take a DNA aptamer and make an RNA oligo of the same sequence (T replaced with U obviously), will this RNA ...
-1
votes
1answer
35 views

definition of phenotype

I'm no biologist but I'm trying to enter molecular biology from a perspective. I notices that genotype is quite well defined and phenotype not as well. If I understand well, gene expression builds up ...
3
votes
2answers
80 views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
0
votes
0answers
21 views

How can we determine the polarity of fat molecules?

I'm trying to solve a question in a biochemistry quiz, which is asking for classifying a set of lipidic derivatives, by increasing polarity. Unfortunately, we didn't cover the classification of ...
2
votes
0answers
20 views

How much salt [NaCl] is too much in DNA precipitation?

In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the ...
0
votes
0answers
10 views

Concentration at equilibrium calculations given initial concentrations and Keq [closed]

Consider the reaction: A + B ↔ C + D. The Keq for the reaction is 1. The initial conditions of a reaction mixture are: [A] = 1 μM, [B] = 0.05 μM, [C] = 0.5 μM, [D] = 0.4 μM. What is the ...
2
votes
0answers
19 views

BSA for trouble shooting failed PCRs?

I am using PCR to amplify a 1000bp region of the CytB mt gene. Some of the samples had not amplified and I wish to change the reaction components (or use additives like BSA) to attempt at getting ...
1
vote
1answer
22 views

How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices." There is a statement in the abstract which I don't understand: "The ...
1
vote
1answer
39 views

How to synthesize and isolate single stranded cDNA from an RNA template?

I would like to have pure single stranded cDNA of my choice. I am thinking of reverse transcription from RNA (obtained by in vitro transcription), degrading RNA from RNA-DNA hybrid with RNase-H, ...
3
votes
0answers
36 views

L-tryptophan in mammalian cell culture

Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells? It's an essential amino acid, so I cannot fathom why low concentrations as opposed to ...
1
vote
0answers
21 views

Is a Ribonuclease Inhibitor protein the only mechanism employed by the human cell to protect cellular RNA from degradation by endoribonuclease?

Are there any other methods of protection for cellular RNA from degradation by endonuclease (specifically the Pancreatic Ribonuclease RNase II (Eosinophil-derived neurotoxin) and RNase III (Eosinophil ...
2
votes
1answer
19 views

Is there a good site or software to see if a primer pair spans an exon junction?

I am going to perform some RT-qPCR tests to validate an experiment.  I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been ...
2
votes
1answer
98 views

What is a functional screen?

I was going through this paper, but did not understand a term. What is the meaning of functional screen? (I am not a biology student, I don't understand much, and a small simple explanation would ...
1
vote
0answers
17 views

What is the lifetime of the vasopressin receptor V2?

I was looking at the production of vasopressin receptor 2, also known as V2R or ADH-R. What I found is that it is coded by the AVPR2 gene and degraded by the Alix protein (source). But I did not get ...
3
votes
0answers
35 views

What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I am searching for the catalyst behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, they form a relationship ...
0
votes
1answer
24 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
0
votes
0answers
16 views

What is the effect of the RNA 2' OH group on its structure and stability? [duplicate]

I've read that the 2'-hydroxyl group plays "fundamental roles" in both the structure and the function of RNA, and that it is a major difference between RNA and DNA. I would like to know more ...
3
votes
1answer
77 views

Is nuclear DNA immuno-privileged?

It is well known that if DNA occurs in the cytoplasm of eukaryotic cells, an immune response may be triggered through a myriad of DNA receptors and pathways as part of the immuno response. Yet, ...
-2
votes
0answers
46 views

Importance of Biodegradation pathway over other pathways

What is the importance of biodegradation pathway over other pathways? This question occured when I saw this paper: Fenner K, Gao J, Kramer S, Ellis L, Wackett L. Data-driven extraction of relative ...
4
votes
2answers
50 views

How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?

I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest. In order to validate the type of cells I have collected using this ...
1
vote
2answers
43 views

Does ATP hydrolysis reaction have a high or low activation energy?

I was recently studying about ATP and how it functions as an energy carrier to all biological processes; however, I came across a confusing and paradoxical statement from two sources: (at 7:36) and ...
1
vote
2answers
55 views

What happens when we re-start a PCR reaction?

Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be ...
0
votes
1answer
25 views

Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
1
vote
1answer
43 views

shRNA knockdown not showing with Western

I've recently been performing shRNA transfections and was hoping to get some advice on why I'm not seeing any knockdown via western blot I transfected by MDAMB468 breast cancer cell lines with shRNA ...
1
vote
1answer
14 views

What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
2
votes
1answer
33 views

What happens to IP3 molecules after release from IP3 receptors?

IP3 molecules bind to IP3 receptors and open up the calcium channels on the endoplasmic reticulum. I am wondering what happens to IP3 molecules after they have been released from the IP3 receptor? Do ...
6
votes
1answer
71 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
1
vote
1answer
59 views

Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using ...
6
votes
1answer
263 views

How bad is ethidium bromide in your plasmid for downstream applications?

I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired ...
5
votes
0answers
67 views

Why do some medicines induce sleep? [closed]

I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and ...
1
vote
0answers
55 views

Where do the H+ ions come from in light reactions?

In the light-dependent reactions of photosynthesis, H+ ions pass to the thylakoid space. Where do these protons come from?
6
votes
3answers
76 views

Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
0
votes
1answer
42 views

What is a selectively neutral genotypic change?

I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions. Firstly, from my understanding, genotypic neutrality means the ...
3
votes
1answer
42 views

What makes a strong polyadenylation signal a strong signal?

I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?
3
votes
2answers
75 views

Neomycin resistance gene in E. coli stb3 cells

We use a lentivirus packaging vector called pLenti_puro_DEST. We use puromycin to select for the cloned gene in 293T cells. However, the pLenti_Neo_Dest has been discontinued, so I'm cloning a ...
4
votes
1answer
43 views

Why do some protocols require prewarming a liquid medium before inoculating?

For example, in this protocol for E. coli competent cell preparation, it says: Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours). Prepare 500 mL SOB medium ...
3
votes
0answers
46 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
1
vote
1answer
43 views

Plasmid gene knockout

How do delete a single gene encoded in an operon on a plasmid using E. coli? Could you use the same principle as when knocking out a gene from the bacterial chromosome which is e.g. suicide ...
3
votes
1answer
62 views

Walk me through microsatellite markers and PCR

Three polymorph microsatellite markers are used to try and narrow down the location of a disease locus, with the use of PCR with 2 flanks on each side of the actual polymorphic area. The PCR ...
0
votes
0answers
32 views

Primer heterodimer problem

I design my primers in Primer3PLUS and analyze them in Oligoanalyzer3.1, A big problem that I have this is that I got very nice output in NCBI-Primer BLAST for their specificity but a very negative ΔG ...
3
votes
1answer
55 views

Why increasing the vector concentration does not increase the effeciency of bacterial transformation?

I was reading some old description of the protocols used for the transformation of bacterial cells. In the description I read that the transformation works best with low amount of DNA, and if we ...
3
votes
3answers
78 views

Looking for good reference book in molecular biology [closed]

I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques. I would be interested in a ...
3
votes
1answer
113 views

Restriction sites

I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases: ATTGCAGTCTG and I want ...
2
votes
1answer
88 views

Is the amount of dNTPs rate limiting for very long PCR products?

I'm using the Q5 system and I'm PCRing a product that will have a final length of around 9500 bases. I have noticed that the product is there but very faint. The primer seems to be used up. So my ...
2
votes
1answer
36 views

Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?

As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to ...
4
votes
2answers
118 views

What are the “minimum requirements” for a single cell?

I saw a description of the "minimum requirements" for a cell at http://creation.com/origin-of-life in the section called "What are the minimum requirements for a cell to live?" and I'm wondering if ...
2
votes
1answer
22 views

What is the protein sequence taken as input in the Path-A prediction system

Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a ...
1
vote
0answers
63 views

Recommend any Molecular lab LIMS (Laboratory Information Management System)

We are looking to develop or customize a LIMS for our molecular lab. Do you know of a LIMS that you've used in a molecular lab before, or one that could be used. Thanks for the help (Edit) Some of ...
7
votes
2answers
251 views

What is the difference between sequence, reads, and contigs of genetic material?

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example? I am new to bioinformatics, and I have not found any conclusive ...