Escherichia coli, a gram-negative, rod-shaped bacterium commonly found in the lower intestines of warm-blooded animals. Used extensively in laboratory research.

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Anaerobic respiration choice in E. coli

Under anaerobic conditions E. coli has two options to generate ATP: fermentation (substrate-level phosphorylation), and respiration (proton gradient, chemisomotic phosphorylation). Which is favored? ...
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Regulation of Cra protein level in E coli

Catabolite Activator/Repressor, Cra protein (formerly known as Fructure Repressor FruR) plays a significant role in central carbon metabolism of E coli. Its activity is inhibited by ...
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What would cause E. coli to change from filamentous growth to normal growth?

In my lab we've observed a phenomenon in which a culture of E. coli is found to shift from normal rod growth to filamentous growth and then back to normal rod growth again several times over the ...
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How long can E. coli stocks be stored at -20°C?

I'm volunteering for a biohacker lab - biocurious in Sunnyvale. The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet. I'd like to set up some ...
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Problem with bacterial transformation with electroporation

I have a problem with a bacterial transformation of a yeast gene that I can not solve. I isolated yeast DNA and did a PCR to get my product. I am using pCGCUm vector with a GFP construct. I digest ...
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explanation of conjugation experiment in bacteria

In this paper (On the expression of a structural gene) I am confused about what is being plotted in Figure 6. The x-axis contains the fraction of radioactive day and y-axis contains the enzyme ...
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How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
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Can Escherichia coli survive on glucose and water alone?

I am novice to biochemistry and biology in general. I am reading Lehninger Principles of Biochemistry, and I found the following sentence at the beginning of the chapter on glycolysis: A bacterium ...
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116 views

Effect of pH on life? Use buffer or HCl? How about lactic acid?

I'm trying to find the effect of pH on living things like E. coli and such. At first I thought of using a buffer solution which maintains its level of pH, but it's possible that the inactive ions of ...
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256 views

The antibiotic 'kanamycin' in the growing of culture E. coli

I'm a first year student and I'm not sure if I understand correctly the role played by the antibiotic 'kanamycin' in the growing of culture E. coli (Rosetta). Can anybody explain me why we use ...
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Is there are practical lower limit to gene length in E. coli?

Question is rather self-explanatory. Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been ...
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158 views

How to obtain bacteria samples?

Would anyone know how to go about obtaining samples of Salmonella or E. coli for purely educational purposes? Note: I just want to look at the stuff under a microscope.
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E. coli, risk of infection?

There has been a warning about E. coli contaminated water in South Florida. Now I'm wondering are there empirical data or historic cases which show a correlation between E.coli levels in tap water and ...
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Whence fecal E. coli (et al.) if swallowing it is dangerous?

I don't know much about medicine, and I know even less about microbiology, but I understand that there are organisms in the lower gastrointestinal tract (and in feces) of a human, like Escherichia ...
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168 views

What makes E. coli yellowish?

LB, TB media, and yeast extract are also yellow but at the heart of the question. What chemical(s) make E. coli yellow?
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Growth kinetics of E.coli on media containing lactose and casein

I did this experiment last month using E.coli isolated from raw milk and have following data via uv-spec: ...
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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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Why is it sometimes difficult to resuspend E. coli in P1?

It's a curiosity question. When I'm doing minipreps after pelleting the bacteria sometimes it's very easy to resuspend them in P1 (Qiagen kit), but sometimes they form a rubbery clump that is very ...
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312 views

How useful are vitamin and trace element additions in E. coli culture medium?

In protocols for minimal media for growing bacteria I often see that a vitamin mix or a mix of various trace metals is added. But at least for E. coli I know that those are not strictly necessary, ...
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Survival of E. coli on agar plate at -20 degree C without glycerol stock

If I kept E. coli transformed with plasmid at -20˚C without making glycerol stock, will it survive? Actually I have kept it this way for 18 hours. What will happen with it? Will it grow in fresh ...
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Salvaging a plasmid from a cell culture stored at the incorrect temperature

I have E. coli with transformed plasmid on agar in a vial. It has been stored at -20 degree C without glycerol stock for 18 hours. This is a continuation of: Survival of E. coli on agar plate at -20 ...
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Literature about putative epigenetic state changes in mammal sequences after cloning steps in Escherichia coli

I would like you to point me out some literature about putative epigenetic state changes in mouse/mammal sequences after cloning steps in Escherichia coli. This are the last search details I used in ...
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What is the appropriate method to send a strain?

We are planning to send an ecoli strain to another lab. What is the appropriate way to do so. No MTA is required but the options seem to be using filter paper or sending a glycerol stock on dry ice.
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Measuring reverse transcriptase activity in E. coli

Goal: To quantify the HIV-1 reverse transcriptase (RT) activity for a number of mutated RTs. Idea: Put RT into a vector in E.coli. Deliver GFP mRNA to E.coli. RT will process the mRNA. The ...
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How long does it take for E. coli to shift feedstocks?

With our fermentations we're noticing that it takes an appreciable amount of time for E. coli (K12 variant) to change from being metabolically streamlined on amino acids to being metabolically ...
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Which cryogenic vials and caps are ideal for storing glycerol stocks?

There are internally threaded, externally threaded, natural caps. For the vials, there are skirts, star-footed, and various bottoms. Why do any of these things matter?
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How do you knockout an E. coli gene without disrupting the rest of the gene cluster?

I'm familiar with the method to build Keio collection using single-gene deletion with an antibiotic cassette. However, what happens when there are gene clusters or overlapping ORFs and you still only ...