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7 votes
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When do plasmids replicate relative to its host cell cycle?

I've found a nice review that has many details on plasmid replication in general, and several papers about pSC101 in detail, and I'll try to extract the key information from these papers. First of ...
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7 votes
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Where to find E.coli gene expression data?

There are some databases in which you can search for E.coli gene expression data: GenExpDB: E. coli Gene Expression Database Many Microbe Microarrays Database (M3D): A resource of microbial gene ...
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5 votes

Do I need to serially dilute E. coli cultures for optical density measures?

One is not normally required to serially dilute E. coli cultures for spectrophotometric measurements, at least in the experiments where the OD value is important. For most protein expression work, ...
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5 votes
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Did early 20th century researchers state why they used E. coli as a model organism?

Historical Fallacies implicit in the Question “…why a researcher chose to use E. coli as a model organism.” Researchers did not work with E. coli because they regarded it as a “model ...
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4 votes
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What is the mass of an E.coli cell?

Its simple: Mass = Density * Volume = 10^3 (Kg/m3) * (10^-18 m3) = 10^-15 Kg which is equal to 10^-12 gram or 1pico gram
4 votes

Why is it sometimes difficult to resuspend E. coli in P1?

Some things to consider. If you spinning too fast and too long, that is going to pack the pellet more. You can spin longer at a slower speed and you will notice your pellet is not as tightly packed. I ...
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4 votes
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Consumption of NAD+ in glycolysis

NAD+ is important in this step, since it is co-factor for the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), which acts as a acceptor for the hydrogen atom from the C1 (see below). If you look at ...
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4 votes

What is the mechanism of oxygen uptake in E. coli?

This question got me thinking about what are the metabolic enzymes that take oxygen up in E.coli. I searched the metacyc database for reactions that consume molecular oxygen and there are only 3 that ...
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4 votes

Recombination frequency as a function of genomic location in E coli?

A recombination map of the E. coli genome was recently published (several years after question was asked).
4 votes

Did early 20th century researchers state why they used E. coli as a model organism?

Very interesting question. Did early 20th century researchers state why they used E. coli as a model organism? In short: No (at least in the 1920ies). For instance: Werkman 1927: Vitamin Effects ...
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4 votes
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Why do coliform bacteria smell so bad?

E. coli and other bacteria metabolize tryptophan into odoriferous skatole and other indole compounds. If you're culturing these organisms in medium that contains tryptophan, that may be what you're ...
3 votes

Need for two oxygen sensors in E. coli

It is not uncommon for cells to have parallel pathways for same outcome. This ensures foolproof response and makes the system robust. E.coli also has another sensor for aerotaxis (Aer and Tsr proteins)...
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3 votes

Is it possible to grow E. coli K12 with algal amino acids as the sole carbon source?

E.coli can do that and in fact does this a lot in a commonly used bacterial medium: The popular LB Medium. This is composed of three components: Tryptone, a peptide mix made by digesting milk casein ...
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3 votes

What is the mechanism of oxygen uptake in E. coli?

The plasma membrane is quite permeable to oxygen and thus oxygen enters the cell simply by diffusion. Reactive oxygen species can be reduced enzymatically in aerobic organisms. Obligate anaerobes lack ...
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3 votes

Why do E.coli form parallel clusters?

Cell division happens by division at the middle of the rod, so the result is two daughter cells that are at nearly the same angle. Over time in the absence of agitation moving cells around, this will ...
3 votes

Mutations in a Petri dish overnight

We can calculate the number of base pair copy errors in a Petri dish per hour by multiplying the number of base pairs (B), the copy error rate (P), the number of divisions in an hour (D), and the ...
2 votes

What does it mean to perform in vitro experiments with mutant bacteria?

Answer clarified based on comment by @DurgaDatta What would it mean to say the enzyme activity was tested in vitro on the mutant? When we say the response of the a single gene knock out mutant, the ...
2 votes

What would cause E. coli to change from filamentous growth to normal growth?

I found that E. coli exposed to predators such as amoeba changes completely from normal form to filaments (on agar) that look wound up like spaghetti but are not only longer but significantly wider. ...
2 votes
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Why do two different E. coli reference genomes have different lengths?

U00096.2 is an updated version of U00096.1; you should preferably use the former for your analysis. In fact, even U00096.2 has been updated. The latest version is U00096.3. In general, the number ...
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2 votes
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Unwanted E. coli product in plasmid product

The root cause turned out to be a lying spec. Using a different one, it was revealed that there was next to no template DNA in the initial amplification. No DNA, no good plasmids.
2 votes
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Are there ways to genetically increase mutation rate of E.coli?

Mutations are caused by the insertion of the wrong bases during replication, or by chemical changes to bases, either by chemical agents or by radiation. The rate of mutations could be increased by ...
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2 votes

Why pellet and resuspend E. coli for plasmid prep

The reason this centrifugation/resuspension step is done has a simple reason: It concentrates the bacteria in a much smaller volume which is much easier to handle afterwards. For a maxiprep you ...
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1 vote

Plasmid specific DNA degradation

traditional method to remove a plasmid from E. Coli is to grow the cells with Etidium bromide. http://vlab.amrita.edu/?sub=3&brch=186&sim=1097&cnt=1
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1 vote

Why do two different E. coli reference genomes have different lengths?

As WYSIWYG answered, they are updated versions. The difference in length is mainly because that later versions are sequenced / aligned with better equipement and techniques, providing results that ...
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1 vote

Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

I wouldn't call them hypotheses, but the question is intriguing, and, as it seems to be ignored in the literature, I'll make a couple of suggestions. Perhaps it has something to do with recognition ...
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1 vote
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What nutrients are best suited for growing E.Coli

Optimal is a funny thing; it depends upon what you want. The purpose of the bacteria, is probably the most important aspect when considering the nutrients. There are many recipes capable of growing E. ...
1 vote

How does a bacterium age without cell division?

First of all, the growth of a bacterium is associated with an increase in cell biomass.So if a bacterium is restricted from replicating it does not grow. Coming to your later parts of the questions ...
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1 vote

Codon tables and the wobble hypothesis

This is a good question as, although in higher eukaroyotes codon usage does not necessarily correlate with translational efficiency, it does to a large extent in Escherichia coli (see e.g. Boël et al.,...
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1 vote

What is the spacing between stop codon and transcription terminator?

In general, there is no need for a spacing between stop codon and terminator. They can be right next to each other. When transcribed, transcription terminator forms a hairpin-like structure which ...
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