The study of the molecular processes of the nucleus and cell function.
6
votes
1answer
92 views
What are the different ways an exon gets spliced?
Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.
6
votes
2answers
81 views
DAM enzyme distances move along the genome
I am fusing a protein with a Dam enzyme (http://en.wikipedia.org/wiki/Dam_(methylase)). The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, ...
6
votes
1answer
124 views
Effect of histidine on the binding affinity of HisP
I was asked the following question by my teacher:
A gene regulatory protein called HisP regulates the enzymes for
histidine biosynthesis in the bacterium E. Coli. HisP is a protein
whoes ...
6
votes
1answer
692 views
The effect of the start codon GTG on translation in E. coli
Translation in E. coli is initiated at the start ATG codon, which encodes for the amino acid Methionine (Met). In some cases, the start codon can be GTG, which within the open reading frame (ORF) ...
6
votes
1answer
47 views
Why does not the host produce any immune response to antiserum antibodies?
When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is:
Why don't the injected antibodies ...
6
votes
1answer
367 views
Does anyone have any TOPO directional cloning tips? [closed]
I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?
6
votes
1answer
123 views
In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?
Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine ...
6
votes
1answer
94 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 ...
6
votes
1answer
37 views
circulating microRNAs are functional?
In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
6
votes
1answer
68 views
Bicoid regulation of hunchback
I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
6
votes
1answer
144 views
How Do Adherent Cells In Culture Attach To A Plastic Dish?
I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are hemidesmosomes involved in anchoring the cells to the plastic dish? What (if any) other molecules are ...
6
votes
1answer
51 views
Is there a Reverse Transcription optimization for long, 9kb, transcripts?
Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep. It will be trivial to make internal primers sets for the PCR that ...
6
votes
0answers
44 views
Does the MS2 RNA binding protein have any translational repression effects?
Reposted from Quora: http://www.quora.com/Does-the-MS2-RNA-binding-protein-have-any-translational-repression-effects
I'm thinking of the MS2 protein binding to its RNA hairpin target. Would the ...
5
votes
4answers
286 views
What are good resources for self-learning modern molecular biology concepts? [closed]
My learning of molecular biology ended in the early 90's (and with early 90's era information). While I don't aspire to be a molecular biologist, I do aspire to better understand modern approaches ...
5
votes
1answer
182 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 ...
5
votes
2answers
1k views
Primer design for introduction of restriction sites flanking a gene of interest
I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods.
1) Primer first partially hybridises to the gene, has a mis-match where the ...
5
votes
2answers
51 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 ...
5
votes
1answer
171 views
What's the state of the art in designing and creating your own life forms?
What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have ...
5
votes
1answer
672 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?
5
votes
1answer
276 views
High Glucose vs Low Glucose DMEM for Cell Culture
I've noticed that in mammalian cell culture, there are often two types of DMEM available. High Glucose and Low Glucose. Does it matter which type I use for culturing of cells (e.g. Hela or HEK293)? ...
5
votes
1answer
186 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 ...
5
votes
0answers
56 views
What is the fastest way to build an alanine scanning library?
For interfacial studies, I would like to build an alanine scanning library for one of my proteins examining 20 sites. I will ultimately express the gene using E.coli cell-free protein synthesis. I ...
5
votes
1answer
52 views
Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans?
Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene?
The paper is Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, ...
4
votes
4answers
291 views
What is a good miniprep protocol for the class room?
I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found:
Using phenol/chloroform
extract with phenol:chloroform:isoamylalcohol,
isopropanol precipitation, ...
4
votes
2answers
95 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 ...
4
votes
2answers
183 views
DNA as an acid? [duplicate]
Possible Duplicate:
Does DNA react in all of the ways most other acids do?
Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
4
votes
2answers
414 views
What are the advantages and disadvantages of using beta-galactosidase compared to luciferase as a reporter gene?
In the University labs, we have used Beta-galactosidase as a reporter gene to quantify the expression initiated by the stress-response promoter in yeast. This was done by exposing one of the two ...
4
votes
1answer
82 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 ...
4
votes
1answer
48 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 ...
4
votes
1answer
76 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 ...
4
votes
1answer
108 views
Why am I getting low transformation efficiency with DB3.1 E.coli cells?
I am making competent cells using DB3.1 E. coli cells. Even after following the exact protocol (Inoue method for ultracompetent cells) given in 'Sambrook and Russel', I am not getting transformation ...
4
votes
1answer
47 views
How to find ion/water channel related genes
We now have a collection of transcripts at hand. We would like to investigate some particular ones, which are ion/water channel related. How to perform this? Could anybody point out how to find the ...
3
votes
2answers
75 views
How do proteins and genes participate in learning?
I am a computer scientist that studies biology and bioinformatics.
In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and ...
3
votes
1answer
52 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 ...
3
votes
2answers
38 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 ...
3
votes
2answers
68 views
Do Yeast Insertion constructs revert?
If I insert a new gene with a yeast integrating plasmid and select with a drop out culture once, can I assume that the newly integrated gene will stay in the strain without putting selective pressure ...
3
votes
3answers
74 views
Is DNA mutation locally energetically stabilizing the DNA molecule
I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done ...
3
votes
2answers
116 views
Do the simplest bacteria have ribosomes and helicase?
I find it interesting that all life on earth use DNA. I've seen video on how helicase and ribosomes work together to copy DNA sequences (to RNA) with helicase then recreate them using ribosomes. Does ...
3
votes
1answer
37 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 ...
3
votes
1answer
53 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 ...
3
votes
1answer
25 views
What is the extent of the effect of Tris on E. coli?
I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H2O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane ...
3
votes
1answer
45 views
What's the difference between shotgun sequencing and clone based sequencing?
What are the main differences between shotgun sequencing and clone based sequencing?
3
votes
1answer
56 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.
3
votes
1answer
55 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 ...
3
votes
1answer
96 views
How do I create a probe for in situ hybridization?
I tried to make the probe several times but it failed again and again. It usually turns out that the probe after hydrolysis is very very short (maybe around 50bp). I did not check the RNA before ...
3
votes
1answer
99 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 ...
2
votes
3answers
83 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 ...
2
votes
1answer
71 views
Is the protein in teardrops still attached to cells, or is it released and free-flowing?
A ScienceDaily article says that the protein in teardrops can kill bacteria.
But how does it reach the bacteria?
2
votes
2answers
81 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 ...
2
votes
1answer
74 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 ...
