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

learn more… | top users | synonyms

3
votes
0answers
19 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
22 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 ...
-2
votes
0answers
16 views

Information about inactivation of restriction enzyme [on hold]

How can you be sure that a restriction enzyme has been inactivated? I tested restriction enzymes on a vector to see whether they were working or whether they were inactivated but I need a simpler ...
0
votes
0answers
15 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 ...
2
votes
1answer
54 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
44 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
41 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
29 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
48 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
38 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
13 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
30 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
67 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
259 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
53 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
66 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
61 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
41 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
39 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
61 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
29 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
52 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
62 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
67 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
32 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
104 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
59 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
241 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 ...
12
votes
2answers
104 views

How can we verify predictions of protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
0
votes
1answer
33 views

How is cancer associated with host pathogen interaction?

Does cancer by any chance fall under host pathogen interaction domain? What I mean to ask is that, is there pathogen interaction involved in cancer? I went through this article: ...
2
votes
0answers
26 views

Does blood typing still provide a use for ancient tissue analysis?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
2
votes
2answers
45 views

How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?

In this link, it states: It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding ...
0
votes
1answer
30 views

What is meant by clonal isolates?

With respect to this website: http://horfdb.dfci.harvard.edu/ what does the term clonal isolates mean?
3
votes
0answers
85 views

E. coli not growing in liquid medium

We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew ...
3
votes
0answers
83 views

Storing Taqman plates with polymerase in fridge before running

I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, ...
2
votes
1answer
36 views

specific numbers of neucleotides in okazaki fragments

Why there is specific number of nucleotides in okazaki fragments...? Okazaki fragments are form in lagging strand during the process of DNA replication.
1
vote
0answers
28 views

What will happen to transcription if histone acetyltransferases are removed from a eukaryotic cell?

If HATs are destroyed in a eukaryotic cell, how will gene expression level be affected? Will all gene expression be affected or just be slowed down and most gene will still be expressed?
0
votes
1answer
40 views

(Genetics) Is a silencer the same as gene silencing (heterochromatin)?

Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
1
vote
0answers
25 views

What is a “NuMA protein”?

I just got out of a lecture on mitosis and this part was incredibly confusing. After searching my textbook it doesn't cover it that well either. The professor mentioned a NUMA protein that is ...
1
vote
0answers
51 views

Importance of organic chemistry in biochemistry/molecular biology? [closed]

I'm halfway through my biochemistry and molecular biology degree in Australia and i'm concerned about a lack of organic chemistry. My friends studying biochemistry back home in Canada take units upon ...
3
votes
2answers
41 views

Macrophages and what they consume

Do macrophages in the dermis consume any foreign invader to the body, or simply pathogens and cellular debris? For example, would macrophages consume vitamins or medications injected into the dermal ...
5
votes
1answer
65 views

Is it possible to express a mutant gene only in a specific tissue?

Imagine that someone tries to develop a knockout mouse for a gene, but this result in lethality for the homozygous. Is it possible to express that mutant gene only in a specific tissue of interest to ...