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

learn more… | top users | synonyms

1
vote
2answers
66 views

The role of antibodies interacting with cancer

I'm learning about antibodies. As I understand it, antibodies detect stranger cells/bacterial/viruses by the molecules present in their membranes. In cancer cells, the cancer cell have produce some ...
3
votes
1answer
56 views

Self pairing in DNA

I know that ssRNA molecule can fold over itself (e.g. in t-RNA). Can DNA do the same? Is there any example of this in nature? Why is this phenomenon more common in RNA than in DNA?
1
vote
1answer
66 views

DNA preparation for sequencing

In shotgun sequencing method or some related method that DNA is break up into random fragment. The fragment that have about 3kb in size is inserted into plasmid by enzyme ligase and then plasmid ...
2
votes
1answer
60 views

How do cells figure out the big-picture shape?

I'm wondering what makes cells to divide (and stop) in such a way that they make our hands the shape that our hands are...
4
votes
1answer
181 views

Cloning two fluorescent proteins with different promoters in the same plasmid?

I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and ...
5
votes
1answer
81 views

Will eukaryotic RNA fold in the same way in prokaryotes?

As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any ...
1
vote
1answer
61 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
0
votes
1answer
194 views

Why not use SDS-PAGE as a method to detect viruses?

Recently, I have been researching about DNA and I know the most popular method for detecting viruses is based on DNA. After learning about proteins, I wonder why we do not detect viruses based on ...
0
votes
2answers
145 views

Problem on finding sequence of Taq polymerase

As i know, Taq Polymerase can be found in Thermus aquaticus, so i do a search for protein list of Thermus aquaticus and have this : http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053 . ...
1
vote
1answer
117 views

Preparation of normal DNA polymerase

i don't need Taq polymerase. Just need normal DNA polymerase. So the main idea is preparation polymerase directly from Lactobacillus without using cloned vector. My idea is electrophoresis using ...
1
vote
2answers
130 views

Finding a easy and cheap method for dyeing dNTP

I want to measure OD to know the concentration of dNTP. Any idea for dyeing dNTP at cheapest price and easiest way ?
2
votes
2answers
390 views

Beginning with centrifuge experiment

This is the first time I do a centrifuge experiment with my own centrifuge machine, it's just simple made by a rotor that can rotate the tube at high speed. As I know a centrifuge machine can be using ...
2
votes
0answers
182 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
2
votes
1answer
90 views

Should I design a primer to detect virus based on NCBI genebank?

When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?
2
votes
2answers
167 views

Realtime PCR plate cleaning

Have anyone used realtime PCR, is that the plate for realtime PCR is one-time using or not ? Otherwise how to clean the plate after reaction to prevent wrong result in next time using ?
3
votes
2answers
86 views

How does the DNA know which chain has error in repairing?

As we know, the DNA has more stability than RNA, if one chain has broken or accidentally distorted, it can be repaired by the other one. Suppose there is a segment AGTC, its peer is GACT. Now its ...
0
votes
1answer
63 views

Some question about materials for PCR

I'm planning to order oligo, polymerase, nucleotide, buffer for my first diy PCR experiment (now I have nothing), so I have some questions. How and how long I can storage them? I have only a fridge ...
0
votes
1answer
57 views

Carotenoid biosynthesis in yeast

Does Budding Yeast Sacchromyces cerevisiae produces significant amount of carotenoids? Have anybody estimated the ratio of flux going in branches 1. Cholesterol synthesis(via squalene) 2. Coenzyme Q6 ...
5
votes
2answers
209 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
5
votes
3answers
133 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
0
votes
3answers
134 views

Pump to separate protein/DNA instead of electrophoresis?

I know that DNA molecules or proteins can be separated in electrophoresis because the electrical charge is used to pull the DNA through the gel. So instead of using electrical, can I using physical ...
3
votes
1answer
922 views

What is the exact principle of capillary isotachophoresis?

I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.
3
votes
2answers
78 views

Why not use Cu(OH)2 as a dye for protein electrophoresis?

As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?
6
votes
1answer
3k views

What causes the colors we see in eyes?

Genetics aside, what are the biochemical reasons the different colours of human irises? Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue, ...
2
votes
1answer
952 views

Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
1
vote
1answer
793 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. ...
7
votes
1answer
59 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
2answers
123 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 ...
3
votes
2answers
718 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
1answer
617 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 ...
3
votes
1answer
162 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 ...
1
vote
1answer
42 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?
1
vote
1answer
104 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 ...
3
votes
3answers
663 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 ...
3
votes
1answer
1k 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. ...
3
votes
3answers
1k 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
1answer
924 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
475 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?
5
votes
2answers
6k views

What's the difference between shotgun sequencing and clone based sequencing?

What are the main differences between shotgun sequencing and clone based sequencing?
4
votes
1answer
67 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?
4
votes
2answers
419 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 ...
5
votes
2answers
2k 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 ...
0
votes
1answer
89 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 ...
1
vote
1answer
35 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
177 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 ...
2
votes
1answer
583 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 ...
4
votes
1answer
245 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 ...
1
vote
1answer
435 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 ...
3
votes
1answer
112 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.
2
votes
3answers
1k 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 ...