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

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258 views

Why Isolated, recombinant plasmid DNA without any restriction is often detected in agarose gel electrophoresis as three DNA bands?

I don't understand why three bands are found without any restriction digest. Please answer me as soon as possible. Thank you
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1answer
51 views

difference between ischemia and oxygen-glucose deprived medium

Ischemia is roughly defined as insufficient blood flow to a specific region of the body and in the literature it is generally considered as causing oxygen and glucose deprivation in the tissue and ...
4
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1answer
84 views

Do mitochondria use ATP in order make another ATP from glucose?

Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?
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1answer
220 views

What is Pan for in pan-caspase?

A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?
2
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2answers
162 views

Single stranded DNA in gel electrophoresis

From http://www.nfstc.org/pdi/Subject05/pdi_s05_m01_01.htm : ... The separation medium contains a denaturant in order that the electrophoresis is conducted on single-stranded DNA fragments. ...
6
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1answer
269 views

How tolerant are ants to cold?

There was a trail of what are commonly known as sugar ants (small, brown, hyperactive) in my kitchen. Three of them walked onto an ice tray placed in their path. They only walked a short distance on ...
5
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1answer
419 views

What is the definition of a stringent/relaxed plasmid?

I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are: Relaxed control of plasmid replication. Relaxed control ...
4
votes
1answer
92 views

Are there any organisms that lack ATP synthase?

ATP synthase is used by cells to synthesise ATP from ADP using energy from a proton gradient. Depending on which sites I look at, this is either a universal feature of living cells, or it's "almost ...
4
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2answers
102 views

A photosynthesizing mouse?

N. Shubin's Your Inner Fish makes the point several times that there is a lot of functional similarity between some seemingly remote gene cousins. If that needed reinforcing we have the spider-goat, ...
3
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1answer
78 views

What is “bacto” peptone?

Standard recipes for yeast medium often include "bacto-peptone". Is this the same as bacteriological peptone? Is there an authoritative source that spells it out?
2
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1answer
59 views

How was Restriction Site of EcoRI sequenced?

The sequence of restriction site of EcoRI - GAATTC was identified in the early 1970s, before Sanger Sequencing was invented.(1977) How was the restriction site of EcoRI sequenced ?
2
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1answer
36 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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53 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 ...
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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 ...
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1answer
81 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
158 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
votes
1answer
437 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
45 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
118 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
284 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
97 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
34 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
1k 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
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1answer
49 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?
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2answers
128 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
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1answer
108 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
82 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
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1answer
110 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
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3answers
78 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
780 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
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3answers
92 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
68 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
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2answers
211 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
227 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
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1answer
110 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 ...
1
vote
1answer
116 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
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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
78 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
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1answer
27 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
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1answer
72 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
56 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
59 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
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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
113 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
87 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
75 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
61 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
182 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?