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

learn more… | top users | synonyms

1
vote
0answers
30 views

Study case of the inheritance system of Oenothera

I've been told some interesting facts about oenothera. Apparently in this species some lineages have been through some translocations and in results to these translocations and in consequence, some ...
2
votes
2answers
52 views

In genome research, what is the problem in Mapping that may be caused by reads being too short?

In the following scenario: You were given short sequence reads of plant RNA obtained from a next-generation sequencing machine (fragments of 20–30 nucleotides in length). You attempt to map them back ...
4
votes
2answers
73 views

Detecting food fraud

There's undoubtedly more than one way to do this, but if a DIY biologist were to attempt to detect food fraud (e.g. as done by students from Stanford University and Trinity School, Manhattan with ...
2
votes
1answer
77 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
4
votes
2answers
372 views

What is the difference between transformation and transfection?

What is the difference between transformation and transfection? How do both of these methods work?
2
votes
2answers
110 views

Image analysis of GFP-tagged protein localization bursts

I'm reading an article (full text here) that analyze the dynamics of localization of a GFP-tagged transcription factor (Crz1) over the time at the single-cell level, by taking movies in a fluorescent ...
2
votes
1answer
37 views

What are the Gateway clonase enzymes?

The Gateway cloning system utilizes what Life Technologies refers to as "Clonase enzyme mix" to catalyze the BP and LR reactions. What is in this enzyme mix? Is there a sequence for them?
3
votes
0answers
55 views

Selection on linked loci in a diploid population

Let’s consider two linked loci $A$ and $B$ that are both bi-allelic. In consequence, we have four different possible haplotypes $A_1B_1$, $A_1B_2$, $A_2B_1$, $A_2B_2$, which frequencies are $X_1$, ...
3
votes
2answers
112 views

Do RNA molecules bind each other?

I have a question, maybe a naive one. Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA ...
2
votes
2answers
67 views

Modern alternatives of DNA footprinting

Since DNA footprinting is an old method I thought there may be some more recent and effective methods to identify a DNA sequence, do you know any of them?
4
votes
1answer
102 views

Topology of closed circular DNA

Why are covalently closed circular plasmid DNAs naturally found in an underwound state ? Is it because this makes it easier for the DNA replication machinery to access and unwind DNA ? Or is it ...
5
votes
1answer
81 views

What are the costs associated with carrying lots of genetic material

What are the costs (if any) associated with carrying lots of genetic material? energy for copying? raw material for copying? space in the cell? Maintenance cost (matter and energy)? time to copy is ...
2
votes
3answers
52 views

Why doesn't the cytosol dissolve the polar structures?

we know that cytoplasm of cells are filled with water molecules and other hydrophilic molecules so my question is why the water of cytosol doesn't dissolve the ionic part of the lipid bilayer or why ...
2
votes
1answer
44 views

Role of isopropanol in plasmid isolation

In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? ...
2
votes
0answers
150 views

Image Processing Suite for bacterial microscopy: Schnitzcells or MicrobeTracker?

I am looking to start doing some work tracking the size and growth of individual bacterial cells in the microscope. In order to analyze the images I need software that can segment the cells, ...
3
votes
2answers
94 views

How can CI repressor both activate and repress $P_{RM}$ promoter found in $\lambda$ phage?

I'm reading a paper where the authors constructed a toggle switch that uses bidirectional $P_R/P_{RM}$ promoter found in the $\lambda$ phage. There are 3 binding sites - $O_R1$, $O_R2$, $O_R3$ - ...
3
votes
1answer
124 views

Why does methylation not occur in viral DNA?

Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?
1
vote
1answer
46 views

Missing 4$H_2O$s (per glucose) in Cellular Respiration… Where can they be?

I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $H_2O$ molecules. Generally, cellular respiration is written thus : $C_6H_{12}O_6 + ...
1
vote
1answer
74 views

Troubleshooting for Agarose Gel Electrophoresis

SI ran my 2% agarose gel on constant voltage (100 V). For a few times it worked at CV but, after a week or so the machine would automatically switch to constant current by itself. And this only ...
10
votes
1answer
1k 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. ...
4
votes
2answers
86 views

Is AT or GC content important in electrophoresis?

Will it make a difference in running speed if we run samples of same no of bases but different AT - GC content ?
1
vote
0answers
86 views

Which mutagen is responsible for pancreatic cancer [closed]

Which mutagen, aflatoxin or acridine orange (an intercalating dye) would most likely lead to an increased incidence of pancreatic cancer. Why?
1
vote
1answer
53 views

Do you have experience with PacBio?

I prepare a experiment and I found $PacBio SMRT$ as the great way to sequence my PCR products. I find the cost: library preparation 655 dollars + sequencing 435 dollars. It seems very low. Do you have ...
2
votes
1answer
61 views

How to measure quality and quantity of DNA?

I would like to mesure DNA. I quantify the concentration with Qubit fluorometer, but I would like to know also quality of DNA. I try BioAnalyzer (Agilent),but without success. Bioanalyzer measure DNA ...
2
votes
1answer
55 views

Substitute 25mM dNTPs mix with 10mM dNTPs

I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, ...
1
vote
2answers
44 views

Functioning of EDTA

I know that EDTA chelates metal ions. It weakens bacterial cell wall and inactivates the DNases. What is the reason why it can do so ? I guess it can inactivate DNases by altering the ...
2
votes
1answer
28 views

Transport of mammalian insulin in vivo

What is the mechanism for transport of insulin in mammalian cells?
10
votes
2answers
4k views

How do I clean phenol contaminated RNA without losing any of the sample?

I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went ...
2
votes
0answers
58 views

Gibson assembly using NeBuilder

I am supposed to construct a plasmid that contains features from two other plasmids. My strategy is to generate three fragments form the two other plasmids. I was encouraged to try Gibson assembly, ...
1
vote
1answer
53 views

Why bacteria produce light?

After seeing this video I am curious to know why the free living bacteria produce light. What advantage will they have ? Or is it just an "unintentional" result of one of their pathways ?
14
votes
6answers
938 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 ...
6
votes
1answer
259 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
2
votes
1answer
57 views

Would expression of GroEL and GroES in erythrocytes be a potentially effective therapy for sickle cell disease?

Would expression of GroEL and GroES in erythrocytes be a potentially effective therapeutic strategy for sickle cell disease? Why or why not?
4
votes
1answer
126 views

What is the minimum length required for a circular DNA ligation?

What is the minimum length of a DNA molecule for the ends to come in close enough contact that they can ligate. Assume there are free divalent cations in solution. Does anyone have any idea?
2
votes
0answers
85 views

RNA isolation from Drosophila head

I need to isolate RNA from Drosophila head. I basically chop the head off and first homogenize it with a homogenizer (similar to this: ...
12
votes
1answer
726 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 ...
2
votes
1answer
145 views

Orientations of codon and anticodon

So 5'-AUG-3' is the start codon on an mRNA transcript Does that mean that the tRNA anticodon is 5'-CAU-3'? Here, I see that the tRNA anticodon for methionine is UAC, and the chart doesn't specify ...
4
votes
1answer
58 views

What is the relation between plasmid concentration and mRNA levels?

Suppose a simple synthetic construct, consisting of a constitutive promoter and a single gene: One of the simplest ways to model GFP transcription is to use an ODE: $\frac{d [GFP_{mRNA}]}{dt} = a - ...
5
votes
1answer
335 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
0
votes
0answers
52 views

Are DNA molecular motors described by cellular automata rules?

While watching this Molecular Visualizations of DNA it struck me how much the motion resembles Conway's Game of Life. And not only visually; each molecule/atom is described by a finite set of ...
4
votes
1answer
60 views

Ribosomal RNA amount in a Drosophila cell

I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to ...
7
votes
1answer
101 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 ...
-1
votes
2answers
66 views

PAH gene mutation

Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a patient with phenylketonuria revealed a mutation in the protein coding region whose predicted effect would be to replace the amino ...
2
votes
2answers
230 views

Explanation of the terms “downstream signaling” and “upstream signaling”

In molecular biology, what's the meaning of the terms "downstream signaling" and "upstream signaling"? What's the difference between them?
2
votes
1answer
164 views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
0
votes
1answer
35 views

RNase and EtOH issue

I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes ...
1
vote
1answer
56 views

How to relate human metabolic model reactions and cancer drug targets / reactome items?

Trying to find a way to take a cancer drug (from CancerDR, for instance) and infer the metabolic reactions that are affected by it in the Human Metabolic Model. Essentially, I would like to know ...
3
votes
2answers
172 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 50nt). I did not check the RNA before ...
9
votes
1answer
15k views

Why do we add salt when precipitating DNA?

All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?
-1
votes
1answer
147 views

How to convert nanogram to picomole? [closed]

I have lets say 10ng/uL of RNA. How can I convert it to picomole? I need it to calculate how much magnetic beads I need. This is the product: ...