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

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What are some atypical examples of positive transcriptional cooperativity?

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...
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474 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?
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184 views

Synthetic construct with multiple ORFs not expressing

I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation ...
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3k 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 ...
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284 views

What is the extent of the effect of Tris on E. coli?

I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane ...
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74 views

Can difference in the expression potential of alleles lead to dominance?

Several hour ago I was in thoughts what allele dominance really means on molecular level. As we know from basic genetics, if the organism had Aa type of some gene ...
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251 views

Why is E.coli used as a model?

Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?
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301 views

Western blotting with multiple antibodies

Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a ...
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110 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 - ...
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95 views

What is Colloidal biology and does it have any scientific background?

There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007: “MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940* written by PhD ...
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144 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 ...
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129 views

Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?

Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I ...
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66 views

Do non-enzyme catalysed reaction pathways exist?

Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google. I have almost no background in biology, ...
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257 views

How can E. coli proliferate so rapidly?

The E. coli has a genome with approximately 5×106 bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~103 nucleotides ...
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5k views

How does formaldehyde cause protein-DNA crosslinking?

How does formaldehyde cause protein-DNA crosslinking? I would guess it's because the strongly polar water molecule interacts strongly with polar residues on a protein-DNA complex, and adding a less ...
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2k views

High Glucose vs Low Glucose DMEM for Cell Culture

I've noticed that in mammalian cell culture, there are often two types of DMEM available. High Glucose and Low Glucose. Does it matter which type I use for culturing of cells (e.g. Hela or HEK293)? ...
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74 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
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87 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 ...
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76 views

Can bacteria, viruses, and cancer cells be destroyed by resonance?

Radiotherapy has been used to treat cancer. Can the resonances by coordinated electromagnetic waves (and/or other forms of waves), of various frequencies, amplitudes and pulse rates, directed from ...
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73 views

Why do some medicines induce sleep? [closed]

I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and ...
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106 views

SDS Laemmli Gel that did not solidify [closed]

In my lab class this week my partner and I were making a SDS-PAGE Laemmli Gel. We made the resolving gel solution which was made of 30% Acrylamide, DI water, 1.5 M Tris-HCL pH8.8, and 20% SDS. We ...
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94 views

Why would we overexpress Sir2 by overexpressing its hypomorph (dSir2-EP2300) in C. elegans?

Can't we just overexpress regular Sir2 in the paper? Rather than overexpress a reduced-function gene? The paper is Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, ...
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742 views

What is a good miniprep protocol for the class room?

I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found: Using phenol/chloroform extract with phenol:chloroform:isoamylalcohol, isopropanol precipitation, ...
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349 views

Question about equilibrium potential formula

My biology book says, that the equilibrium potential for an ion with a charge of +1 is: $$E_{ion}= 62mV \biggl(\log\frac{[ion]_{outside}}{[ion]_{inside}}\biggr)$$ Where does the 62 mV come from? How ...
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258 views

In cancer, why do cells duplicate themselves?

In regards to cancer why do cells replicate themselves? If it's a mutation, what kind of mutation would this be classified as?
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On which strand does the promoter sit?

My book keeps giving different indicators as to whether the promoters are on the coding or template strand. It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...
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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 ...
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What's a protein pulldown assay?

I'm reading a paper and the authors mention a "protein pulldown" assay. I've never done this before, and googling doesn't bring up much. Could I get a rundown of the basic theory behind it? Also ...
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210 views

Theoretically, what technique would one use to modify a virus so that it only affected a subset of the population?

I'm writing a novel and i would like to know some of the equipment and techniques involved with modifying a virus. Is it feasible for a virus to be engineered to only affect certain people? It ...
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107 views

How do proteins and genes participate in learning?

I am a computer scientist that studies biology and bioinformatics. In the last weeks, I have been trying to study new research directions, and I would like to deepen my knowledge on the role and ...
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184 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
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665 views

Why proteinase K doesn't degrade itself?

Can anyone tell me why proteinase K doesn't degrade itself? If possible please provide me the source.
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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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35 views

How much time do the different mechanisms of gene regulation need to take effect?

I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference. If non-active regulator genes using each of the different ...
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3k views

How can histidine be classified both as positively charged and hydrophobic?

I saw the chart in this post Histidine aromaticity. Since I'm not allowed to comment and post a question instead of an answer, I have to ask my question in a separate thread. How can histidine be ...
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1answer
1k 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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186 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, ...
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516 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 ...
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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 - $O_{R1}$, $O_{R2}$, $O_{R3}$ - ...
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83 views

How to safely conserve my current DNA methylation marks?

I read the Wikipedia article on DNA methylation Let's say I want to extract and then stock my current DNA methylation marks somewhere so that I can use it safely 20 years in the future for a medical ...
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171 views

Nomenclature of genes and proteins

With respect to this paper: Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen In the abstract, I found names such as Rab6 and Vps35 and TNPO3. So Rab6 ...
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1k views

Why AZT is selective towards HIV and doesn't impair human DNA replication?

I've found this article, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics). ...
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544 views

Can concentration of a protein be determined from a gel quantitatively (rough estimation)?

I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which ...
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127 views

How small does a nanobot have to be to “swim through the brain” and access any neuron it wants to?

I read on this question What is in the space between neurons in a brain? that there is actually not much empty space in a brain. But my question is slightly different. Is there a visual demonstration ...
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209 views

Transmembrane Protein Problem

Problem A transmembrane protein has 1000 aa. The 5th aa is found on the external side of the cell membrane. It interacts with the aqueous environment outside the cell. Amino acid 90 is inside the ...
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1answer
64 views

Protein Isolation from mammalian cells

What non-SDS buffer can I use to isolate protein from mammalian cells? The protein is intended for testing electron transport chain complexes.
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161 views

Western Blot: Fischer ECL substrate 2:1 instead of 1:1?

i recently developed a b-actin-ab-incubated PVDF-WB-Membrane with the Thermo Scientific Pierce ECL Kit. According to the manufacterers orders i mixed Reagent 1 and Reagent 2 1:1. But unfortunately i ...
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411 views

What is a protective epitope?

What is a protective epitope? An epitope is basically a part of antigen. So does it mean that when the epitope combines with an antibody, it helps in the functioning of the antibody instead of going ...
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378 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 ...