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

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Growing E. coli at room temperature?

If I were to do a blue/white selection of transformed E. coli on LB agar ampicillin plates at room temperature (23⁰C) for about 2 days and 18 hours, will I run into the issue of satellite colonies or ...
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Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme

The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends ...
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46 views

Enzyme Assay - pectinase

During assaying an enzyme at high temperature, the substrate (Pectin) is degraded by the high temperature rather than by enzyme, so, how can I minimize degradation of the substrate by the temperature? ...
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Receptors for red and far-red light in plants: Shade avoidance

Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading. My question is: which receptor is ...
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38 views

Adenosine metabolism

Are adenosine or its catabolites increased in inflamed airways? How can I assess this? I am trying to use inhibitors for adenosine deaminase, xanthine oxidase, and purine nucleoside phosphorylase, but ...
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92 views

How does LCR compare to Assembly PCR

The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction ...
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22 views

How to prevent e coli from clumping (for FACS)?

I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells. I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run ...
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30 views

Is it possible that a set of functionally related proteins in a pathway fulfill different functions?

Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific ...
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13 views

Resource for finding Repressive/Inhibitory factors for a given gene?

I have a list of genes for each of which I'd like to find: A list of transcription factors that up-regulate the gene A list of inhibitory factors that down-regulate it. I used this tool on ...
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16 views

Metabolism that generates methanol

I've been looking for help topics about methanol in metabolism. Specifically I wish to know What is a common dietary component that generates methanol following metabolism and comment on its ...
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25 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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128 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, ...
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214 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, ...
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173 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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7 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
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14 views

how to get truseq's gel size selection when preparing libraries for exome enrichment?

i would normally use a 6 minute fragmentation as quoted by agilent but this gives post exome enrichment libraries of around 300bp or slightly over. Truseq want libraries to be 100bp larger. i am ...
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27 views

recombinant peptide MHC complex

What is recombinant peptide-MHC complex??? Recombinant DNA means "to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological ...
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What keeps resting potential of neurons constant at -70mV?

I know the sodium-potassium pump pumps out 3 Na+ ions and pumps in 2 K+ ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and ...
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38 views

Assembling DNA fragments with ~10kb overlap in vitro

Let's say I have two fragments of bacterial DNA (~50kb in length each) that overlap on the ends by roughly ~10kb; the overlap sequences are unknown. I would like to assemble these into longer ...
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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 ...
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1k views

Bacterial 16S rRNA PCR amplification with universal primers

I am doing an experiment to amplify the 16S rRNA gene from bacteria present in gut contents of fish. After extracting DNA, I perform one-step PCR with universal bacterial primers (27F, 1492R) and I ...
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11 views

What genetic distance model should be used when calculating genetic differences in Arelquin?

I'm using Arelquin to look at the genetic structure between a number of different populations. I want to compare the populations by producing pairwise FST values, however I don't know what model for ...
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24 views

Superpatients for Cancer resistance

I was reading an article on MIT Technology review about superpatients for low cholesterol that got me thinking whether such patients exist for cancer. The article is ...
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Sequence based method for prediction of continuous B cell epitope

What is Sequence based method for prediction of continuous B cell epitope? What is the algorithm/procedure of this method? Can someone please explain this to me in simple language?
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MHC restricted peptide

What is an MHC restricted peptide? "MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host ...
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11 views

border zone of the infarcted heart

I did myocardial infarction experiments on mice and I am a newbie in this area. I need to isolate RNA and protein from the remote and the border zone. Where should I cut the heart so i can separate ...
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33 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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How do you amplify a specific AFLP marker?

I'm trying to clone a specific AFLP marker out of Medicago truncatula. I know the selective bases I need for the end of the primers. My problem is that all the AFLP cloning kits I have found are ...