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

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35 views

Trimming of tRNA precursors

From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) : Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, and these are ...
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0answers
48 views

PQR files make from pdb2pqr are different to GROMACS

I have a pdb file and I would like to make a pqr one. In GROMACS, I use editconf -mead to produce pqr, with topol.top taken from pdb2gmx or use it to produce pdb file, then use pdb2pqr. Which one is ...
0
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0answers
30 views

What is the suitable terminology to describe this study approach?

I need to know the correct term(s) which are usually used in the parlance of both biology and bioinformatics for this study approach: About 11 transcripts were investigated using qPCR for a number of ...
1
vote
1answer
70 views

A question related to qPCR analysis

Here is the thing. I am using a method, called TU-Tagging, to isolate cell type specific RNA. You can find more about the method here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783170/ To explain ...
4
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1answer
142 views

how is the plasma membrane repaired after endocytosis?

When the vesicle is swallowed of course the lipid layer internalizes. My question is how will the top segment of membrane will bind back together when that vesicle took the membrane with it inside ...
2
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1answer
284 views

What's the physical meaning of Svedberg unit?

Sedimentation coefficients, using a centrifuge, are expressed using Svedberg unit (symbol S, sometimes Sv). Wikipedia states that $S = 10^{-13}$ sec but I also saw in a book that actually $S = ...
2
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1answer
43 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
3
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1answer
113 views

Do macrophages engulf mtDNA?

Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment. We know that mtDNA inheritance is solely matrilineal. So the question is, If your mitochondrial DNA ...
2
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2answers
58 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
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2answers
276 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
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2answers
94 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 ...
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0answers
33 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 ...
4
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2answers
896 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
45 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
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2answers
124 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
105 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
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2answers
74 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?
2
votes
1answer
102 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
74 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
457 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 ...
2
votes
3answers
81 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
53 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? ...
3
votes
2answers
151 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
189 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?
7
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1answer
96 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 ...
1
vote
1answer
104 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 ...
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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?
2
votes
1answer
60 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
75 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
25 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
68 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
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1answer
49 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
52 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
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0answers
97 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
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1answer
86 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 $X_1$, ...
2
votes
1answer
59 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
169 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
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0answers
128 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
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1answer
330 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
67 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
506 views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
4
votes
1answer
68 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
583 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
80 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
1answer
231 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
37 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
287 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
179 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 ...
0
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0answers
15 views

Testing gene against resistance and susceptible cultivars

I have one gene cloned from plant fungal pathogen using pure culture. Now I want to characterized this gene using molecular methods for which I have few resistance and susceptible cultivars of the ...