The study of the molecular processes of the nucleus and cell function.
10
votes
1answer
73 views
When running a gel, what could cause a standard to run “faster” than usual?
We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too ...
0
votes
0answers
99 views
Text Book on Cancer Genomics/Biology [closed]
Could anyone of you suggest few of the best text book(s) for Cancer Genomics/Biology from basic to advance level.
4
votes
2answers
419 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 ...
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? ...
14
votes
2answers
624 views
How and where, in the human brain, are memories stored?
Background
I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work.
Context ...
5
votes
1answer
279 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)? ...
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, ...
8
votes
2answers
109 views
How are antibodies designed?
Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.
This ability is harnessed as a tool in research to purify target structures in ...
15
votes
2answers
392 views
How long can I store extracted RNA?
If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before ...
7
votes
1answer
105 views
How realistic is to use DNA for long term storage?
This is mainly a followup question to the recent paper Next-Generation Digital Information Storage in DNA.
Personally, while I agree about the data density of the format, I can't help point out the ...
9
votes
1answer
138 views
Is there a program that simulates biology on a molecular level?
Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
4
votes
2answers
184 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?
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 ...
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. ...
9
votes
3answers
1k views
How long can E. coli stocks be stored at -20°C?
I'm volunteering for a biohacker lab - biocurious in Sunnyvale. The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet.
I'd like to set up some ...
6
votes
5answers
186 views
What is the lowest common denominator of cancer?
What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?
21
votes
4answers
250 views
How are the boundaries of a gene determined?
What statistical processes and methods are used by geneticists/molecular biologists to know where one gene starts and one ends?
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, ...
8
votes
1answer
78 views
Why is propanoic acid often added to the diet of C. elegans?
And what are its effects on C. elegans?
The paper is Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects ...
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 ...
10
votes
1answer
158 views
What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?
Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
8
votes
2answers
163 views
Do antibiotics attenuate immune response on subsequent exposure to same bacteria?
A healthy immune response to a bacterial infection includes "memory" to permit the body to thwart subsequent exposure to same bacteria. What are the dynamics of using antibiotics on initial exposure ...
8
votes
1answer
266 views
What did Richard Feynman contribute to molecular biology?
Some time ago, I read James Gleick's "Genius: The Life and Science of Richard Feynman", a wonderful biography of Feynman and, by extension, most of modern physics.
In this book, the author mentions ...
0
votes
0answers
86 views
which free videos with 3d animations simulating protein processes are there? [closed]
I have found a group that creates free videos that show life within (or outside) a cell as it really is, at the near molecular level. They use real protein structures with in-molecule dynamics ...
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 ...
2
votes
1answer
78 views
In cancer, why do cells duplicate themselves?
In regards to cancer why do cells replicate themselves? If it's a mutation, what kind of mutation would this be classified as?
2
votes
0answers
58 views
Optimization of annealing temperature
I am trying to optimize annealing temperature for some primer pairs. I have tried optimization using cDNA, genomic DNA, Taq polymerase, phusion polymerase etc., but every time I am either getting ...
8
votes
1answer
10k views
Absorption ratios 260/280 and 260/230 for RNA
I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And ...
7
votes
1answer
136 views
How fast do different organs turn over cells?
It is said that the human body turns over all cells or molecules in 7 year cycles. This is not quite correct, because there are different organs changing at different speeds. My interest is what is ...
3
votes
1answer
97 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
2answers
117 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 ...
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 ...
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 ...
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 ...
9
votes
1answer
612 views
How does translational coupling work in prokaryotes?
Today I heard about a phenomenon called "translational coupling", where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. ...
10
votes
1answer
477 views
Is the eukaryotic nucleus composed of a single or double membrane?
I know that it is usually considered a double membrane like those surrounding mitochondria and chloroplasts, but I read a review that stated "according to topological details it is actually a single ...
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 ...
0
votes
1answer
64 views
If inhibiting S6 kinase decreases protein translation, then could inhibiting S6 kinase could possibly slow down long-term potentiation in neurons?
From http://en.wikipedia.org/wiki/P70S6_kinase...
Phosphorylation of S6 induces protein synthesis at the ribosome.
P70S6 kinase is in a signaling pathway that includes mTOR (the
mammalian ...
6
votes
1answer
370 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
551 views
Purpose of poly(A)+ RNA?
I am learning RNA-seq analysis. I always encounter this phase "poly(A)+ RNA". After searching, I got this: "Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection ...
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 ...
2
votes
0answers
73 views
Mouse meta-globin mRNA problem
This is an mRNA strand of mouse meta-globin:
5'-ccccagauacggaauucgaau-3'
A) Which small RNA (below) is most likely to regulate expression of
meta-globin?
...
10
votes
2answers
187 views
What is the highest competency possible for E coli?
I am looking to find a highly competent E coli strain. I am making a library of a ~6.6kb plasmid and I am not getting high enough efficiency. Does anyone have a suggestion of a strain/protocol with ...
19
votes
1answer
194 views
Regulation of chromatin structure
Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary ...
15
votes
5answers
447 views
Online Molecular and Cellular Biology Video Lectures?
I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge ...
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 ...
9
votes
4answers
166 views
How can I avoid digesting protein-bound DNA?
I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion.
When digesting protein-bound DNA, is all of the unbound DNA ...
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 ...
9
votes
1answer
121 views
How are there alternative initiation codons?
According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the ...
8
votes
2answers
5k views
Why is SOC medium recommended for transformations?
In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating.
I've usually substituted LB medium for ...
