The study of the molecular processes of the nucleus and cell function.
2
votes
1answer
17 views
Why is allolactose the LacI inducer?
For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
3
votes
1answer
106 views
Why re-label the strand ends in 3' DNA labelling?
I have a problem with a molecular biology question; I don’t understand how DNA 3’ labelling works.
I took a diagram from my lesson and tried to understand with it; this is what I understood.
If I’m ...
3
votes
3answers
134 views
Why do neurones use chemical signalling at synaptic junctions?
Problem. When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical brownian diffusion signalling with ...
4
votes
1answer
49 views
How can I save bacillus strains on filter paper without an -80 degree freezer?
I want to save my bacillus strains but I don't have access to a -80 degree freezer. What are possible alternatives?
1
vote
1answer
39 views
How do viroids propagate to other hosts?
As viroids are simply non-encapsidated non-coding RNA molecules, it is difficult to imagine a mechanism for their continual infection, other than horizontal transfer which doesn't seem to be the case. ...
1
vote
0answers
34 views
Low RNA yield, low 260/230 ratio
I extracted total RNA from animal tissue using the Qiagen RNeasy kit, however my RNA yield was extremely low and the 260/230 ratio was around 0.3. This is the protocol I followed:
The animal ...
3
votes
2answers
45 views
Just how light-sensitive is ethidium bromide?
One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in ...
2
votes
2answers
94 views
Prenatal Marketing
This is for a short story idea.
Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...
6
votes
1answer
39 views
Intracellular lipid transport
I know that lipids are carried around the body in the blood either as micelles or by lipid-binding proteins which allow them to be solved.
Lipids can't always be integrated in a membrane though, the ...
2
votes
1answer
54 views
Optogenetics - How do microbial opsins work?
I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things.
So we have Retinal and Opsin that form Rhodopsin molecule that ...
6
votes
2answers
983 views
What is the function of the RNA primer in DNA replication?
During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
2
votes
1answer
35 views
What are centromeres *really*?
I've gathered that a centromere is a a region* where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark ...
5
votes
2answers
92 views
What's the difference between shotgun sequencing and clone based sequencing?
What are the main differences between shotgun sequencing and clone based sequencing?
1
vote
1answer
33 views
In vitro enzyme production
I need to express a protein in vitro but I don't know where to start. I will likely do a T7 transcription protocol but for translation I am not sure what to do. Are there any good kits?
0
votes
0answers
35 views
Hardy-Weinberg applied to three alleles and stimation of allele frequencies
I have this equation:
Corresponds to HW in equilibria with three alleles:
$(p+q+r)^2=1$
Expanding the square results:
$p^2+2pq+r^2+2pr+q^2+2qr = 1$
I need to separate homozygous and ...
2
votes
1answer
51 views
Histone marks mechanism
I am slightly confused about the mechanisms that makes histone modifications associate with gene expression.
That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in ...
1
vote
0answers
26 views
What mammalian cell lines are easiest to grow and transfect?
I'm working with HEK293 cells, which are very easy to transfect. Does anyone have other suggestions for cell lines with very high transfection efficiency? Ideally the chromosomes would also be diploid ...
2
votes
3answers
119 views
Knockdown of long noncoding RNA (lncRNA) - how is it done?
I don't work at the wet lab and don't know all the details about the knockdown techniques.
My question is:
How lncRNA knockdown is done?
For example - you have lncRNA that is functional in the ...
2
votes
0answers
37 views
What is the purpose of Y-shaped adapters in Illumina sequencing?
Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library.
The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary.
...
5
votes
2answers
114 views
Is wiping with RNAse Zap enough to destroy RNAse activity?
From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH?
Some other links suggest there is some NaOH as well.
The Ambion site states that RNAseZap destroys RNAse ...
1
vote
1answer
67 views
Why is Sanger sequencing inferior for detecting SNPs in cancer cells?
I am familiar with Sanger sequencing, but at the level of an undergraduate. A lecturer of mine tried to describe Sanger sequencing as losing the sequence information in noise when used to detect ...
1
vote
1answer
31 views
What is solid-phase bridge amplification?
During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
2
votes
1answer
53 views
Does bleach destroy RNAse activity, and if so, how does it do it?
I am working with RNA samples, and I'm trying to be very careful about RNAse contamination.
I have some questions about bleach, though. Some people say that a solution of bleach is enough to destroy ...
0
votes
1answer
34 views
How can I clean phenol extracted RNA?
I extracted RNA from skin and quantified it in an Nanodrop machine. The 260/230 ratio was very low and two peaks appeared in the absorbance curve, but the RNA is ressuspended in RNAse free water. How ...
5
votes
1answer
351 views
Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?
Agar is a relatively cheap substance from red algae. And it contains a saccharide agarose as well as a small amount of pectin.
Agar is used for culture plates as is, but for DNA gels a grade of ...
1
vote
1answer
21 views
Amount of reverse transcriptase in µg or mM for qRT-PCR
I am trying to calculate a titration amount for a molecule which I would like to use in my PCR samples. Different molecules have different densities so I would like to calculate the appropriate ...
3
votes
1answer
58 views
High protein turnover rate and protease inhibitors?
I work with mice, and I want to see what happens to some specific proteins in the mouse brain after IL-1b injection (intracerebroventricular).
I have a problem: when I measure the mRNA and protein ...
9
votes
2answers
2k views
Why is PEG important for efficient yeast transformation?
One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient ...
3
votes
1answer
42 views
What molecular processes are involved in pseudopodial extension?
I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
1
vote
1answer
61 views
Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?
Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions.
On a slide, it said that expression might be ...
1
vote
0answers
35 views
Can I heat Trizol?
I wonder if I can heat Trizol reagent for 30 min 65C. The goal is to disrupt protein-RNA complex while inhibiting nucleases. (I can't use RNasin cause it's inactivated in 65C, and can't use RVC cause ...
4
votes
1answer
95 views
How does formaldehyde cause protein-DNA crosslinking?
How does formaldehyde cause protein-DNA crosslinking? I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less ...
3
votes
1answer
60 views
205 nm UV-Vis readings
Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.
7
votes
1answer
107 views
How Antioxidants affects Human Metabolism?
I'd like to know how antioxidants affects the human metabolism and which ones are essential for metabolism processes.
1
vote
1answer
36 views
Why does the hydrolysis of ATP increasing entropy increase the Phosphoryl-‐transfer Potential?
I am currently taking a biology class. I do not understand this concept. I understand that the electrostatic repulsion of the negative charges, resonance stabilization and hydration stabilization all ...
1
vote
0answers
28 views
Experience with Detox Cloning
I just saw this paper.
A Highly Efficient Molecular Cloning Platform that Utilises a Small Bacterial Toxin Gene
I was curious if anyone had experience with this cloning strategy using the IbsC ...
2
votes
3answers
104 views
Improving Gel Extraction yields
How can I improve my Gel Extraction yields. We use the standard protocol from Qiagen, gel extraction, dissolve in QG buffer at 42C and purify via anion exchange columns. However, with 500 ng we ...
4
votes
1answer
61 views
What is a simple protocol for staining cells in suspension?
I am an engineering student studying how electric fields affect cells, specifically the phenomena of electroporation in living cells.
I know that electroporation is widely used for introducing genes ...
3
votes
0answers
25 views
How does LCR compare to Assembly PCR
The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction ...
9
votes
1answer
83 views
E. coli values for [enzymes], [metabolites] and kinetic rates
In my attempt to create a metabolic model of E. coli, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is E. coli model iJO1366 (more ...
2
votes
1answer
76 views
What in soy are people allergic to and will these allergens be passed along if an animal that has eaten soy is consumed?
I have two related questions about soy allergies and possible reactions.
What is it that are humans who have soy allergies actually allergic to? What is the allergen?
If an animal eats soy, are ...
3
votes
1answer
58 views
Can I use PCR buffer instead of cDNA synthesis buffer?
I am using Fermentase First strand cDNA synthesis kit but its buffer is over. I need to work today but I have not access to any sorce currently. I have PCR buffer in the lab. Can I use PCR buffer ...
4
votes
1answer
86 views
Can forensic DNA analysis be used to generate a visual approximation of a suspect?
In light of the current US supreme court case, I'm curious if enough information can be teased out of a DNA sample to get a "reasonable" approximation of the suspect (never mind the legality). I ...
6
votes
1answer
109 views
How does Topoisomerase II inhibition affect cancer cells?
Topoisomerase II poisons represent some of the most important and
widely prescribed anticancer drugs currently in clinical use. These
drugs encompass a diverse group of natural and synthetic ...
3
votes
1answer
57 views
Difference between “transcriptional activity” and “RNA expression”
I am working with a network object where the nodes are different events in molecular biology.
Specifically;
Catalytic activity of X,
RNA expression of X,
GTP-bound activity of X,
Kinase activity of ...
5
votes
1answer
259 views
Very high 260/230 absorbance ratio of an RNA sample
After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25).
I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
9
votes
2answers
465 views
What is the difference between SOLiD, 454, and Illumina next-gen sequencing?
I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
4
votes
2answers
100 views
Question about equilibrium potential formula
My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$
Where does the 62 mV come from? How ...
1
vote
0answers
53 views
Molecular cause of cramps, spasms and strengthening in muscles? (incl. intro to muscle contraction)
When motor neurons are stimulated to trigger an action potential, this potential propagates down the spine, eventually reaching a neuromuscular junction, causing the release of acetylcholine (ACh).
...
3
votes
2answers
41 views
How common is bacterial mediated transformation? In plants? In animal cells?
The most common method to transform plants is by soaking plant tissue in cultures of agrobacteria (this is not their current classification) which transfer DNA into the plants.
Is lateral gene ...
