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

learn more… | top users | synonyms

2
votes
2answers
60 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 ...
5
votes
2answers
297 views

Signaling through G protein Coupled Receptors?

There are two different cell lines but we do not know that these cell lines have Gs or Gi proteins, associated with their G-protein coupled receptors. If we wants to know about this. Can we design a ...
4
votes
2answers
107 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 ...
1
vote
0answers
35 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 ...
5
votes
2answers
2k 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
1answer
66 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
2answers
132 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 ...
4
votes
1answer
119 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 ...
2
votes
2answers
95 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?
3
votes
1answer
134 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 ...
5
votes
3answers
89 views

Hebbian theory “fire together” clarification

Donald Hebb states it as follows: "Let us assume that the persistence or repetition of a reverberatory activity (or "trace") tends to induce lasting cellular changes that add to its stability.… ...
2
votes
1answer
2k views

How does a TOPflash/FOPflash assay work to detect beta-catenin protein expression?

I am reading an article (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596711/) wherein a TOPflash/FOPflash assay is used to detect beta-catenin protein levels in a COS-7 cell line. I can't find a good ...
1
vote
1answer
34 views

Degenerate primer design for DIG in situ hybridization

New to molecular and have learned to design primers from google/youtube so any info would help Would someone be willing to share their protocol for degenerate primer design? Breakdown: Trying to ...
2
votes
3answers
130 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
126 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? ...
4
votes
2answers
364 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
2answers
338 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?
9
votes
1answer
119 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 (Big genome size)? energy for copying? raw material for copying? space in the cell? Maintenance cost (matter and ...
2
votes
1answer
167 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 ...
2
votes
1answer
63 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 ...
3
votes
1answer
89 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 ...
0
votes
1answer
28 views

Property of E.coli harboring F element

From Genetics by Ursula Goodenough E.coli harboring an F element are endowed with a number of phenotypic traits : 1.They are sensitive to infection by ssRNA phages and certain ssDNA phages. ...
2
votes
1answer
83 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
1answer
69 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
2answers
79 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
33 views

Transport of mammalian insulin in vivo

What is the mechanism for transport of insulin in mammalian cells?
2
votes
0answers
134 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, ...
7
votes
1answer
88 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 $X_1$, ...
5
votes
1answer
87 views

enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops. I have read that cohesin is one of ...
2
votes
1answer
63 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
219 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?
4
votes
1answer
236 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: ...
6
votes
1answer
507 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 ...
4
votes
1answer
75 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
747 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
4
votes
1answer
83 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 ...
2
votes
2answers
1k 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?
-1
votes
2answers
113 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 ...
1
vote
1answer
407 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
48 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
votes
1answer
408 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: ...
2
votes
6answers
213 views

Sequence analysis software suites

I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what ...
1
vote
1answer
84 views

Do “transcription factor binding site” and “operator” mean the same thing?

Can the terms "transcription factor binding site" and "operator" be used interchangeably in all contexts when referring to a DNA sequence, e.g. regardless of a cell type, whether or not the binding ...
3
votes
4answers
132 views

Translation of mRNA?

We inserted an insulin gene from human into bacteria. Will translation of the gene (protein formation) occur in bacteria? If translation occurs then why does it occurs, give a reason for this?
2
votes
1answer
116 views

Cloning of a sheep.. Dolly?

Dolly the sheep was a clone. When she was born she was eight years old on her 1st day of birth, her mother (from which she was cloned) was also eight years old. What is a molecular reason behind this ...
8
votes
2answers
2k views

Why is the number of PCR cycles limited?

I've been told that the maximum number of cycles in PCR is between 20 and 30. Is this true, and what are the reasons for this limitation?
3
votes
1answer
44 views

How do you express and detect GLP-1 receptors?

I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors. The cell line used is Min-6. How do I detect ...
0
votes
2answers
183 views

How to determine the actual flux in the human metabolic model of a cell line?

The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model. As far as I understand, a good way to do that would be to use gene ...
1
vote
1answer
113 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 ...
2
votes
1answer
90 views

Does biotin affect downstream experiments, such as RT-qPCR?

I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the ...