Questions tagged [ecoli]

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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13
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3answers
1k 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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Why and how is DNA synthesis so much faster then RNA synthesis in bacteria?

DNA synthesis in E. coli is 20x faster than RNA synthesis at 1000nt/s vs 50nt/s. (Mirkin'05) I find that perplexing since DNA polymerization has better proofreading than the RNA variety, which ...
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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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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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728 views

When do plasmids replicate relative to its host cell cycle?

For plasmids is so much shorter than their host cell's genome (about 1/1000 in my case), it will take only 1/1000 time for it to replicate. With respect to cell cycle, when will that replication ...
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334 views

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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1answer
633 views

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 ...
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702 views

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

I am investigating the early uses of E. coli as a model organism. Sadly, many early 20th century papers are not in English. In those that are, I have been unable to find explicit statements as to why ...
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1answer
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Where to find E.coli gene expression data?

I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc. I have ...
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339 views

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

How does E. coli uptake oxygen? Most of the literature I found is concerned with response to oxygen level supplied in the medium, as opposed to how much is actually transported inside. Can they shut ...
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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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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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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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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 media?...
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1answer
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Consumption of NAD+ in glycolysis

Out of 10 steps in glycolysis, only one reaction- Glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (PGP), uses NAD+ and thereby producing NADH. Furthermore, this very step is solely ...
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Need for two oxygen sensors in E. coli

E. coli has two oxygen sensors: FNR (fumarate-nitrate reductase) and ArcBA (Anoxic Redox Control, two component control systems). FNR directly senses the oxygen, while the interaction of ArcB with ...
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Plotting metabolic networks?

I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes ...
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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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E. Coli metabolization of paracetamol

For my science fair project, I did an experiment on how paracetamol and ibuprofen affected the growth of bacteria. By day 5, however, parts of the paracetamol blackened (image below). I am wondering ...
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Relative densitometry from SDS PAGE

I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software. My questions are ...
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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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386 views

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

I came across the following sentence while reading the paper: Nanchen, Annik, et al. "Cyclic AMP-dependent catabolite repression is the dominant control mechanism of metabolic fluxes under glucose ...
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284 views

Dissolving cell pellet after sonication

I was doing a protein prep and I made a mistake. After sonicating my cells, I was supposed to centrifuge and collect the supernatant (my protein is soluble and comes in the supernatant). I however, ...
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Codon tables and the wobble hypothesis

In E. coli, there are only 47 different tRNAs but 61 potential anticodons. This is because, from what I understand, the third base of the anticodon can pair by wobble rules. However, it is known that ...
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1answer
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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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1answer
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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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Low cost cell free expression system

I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like ...
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Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
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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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Do I need to serially dilute E. coli cultures for optical density measures?

I am expected to track cell growth by measuring the incubating culture's cell concentration every 30 minutes or so. So my questions are: Why do I need to do serial dilution (assuming that I do)? Why ...
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1answer
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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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2answers
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Why do two different E. coli reference genomes have different lengths?

I've downloaded two different reference genome of E. coli (E. coli K-12 MG1655: U00096.1 and E. coli K-12 MG1655: U00096.2) and they have different lengths. I searched for the meaning of reference ...
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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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1answer
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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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1answer
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Are there ways to genetically increase mutation rate of E.coli?

Are there ways to increase mutation rate of E.coli using genetic modifications? I know possible ways it can be done without genetic modifications by exposing the cells to stressful conditions like ...
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2answers
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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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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 fructose-1,6-...
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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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What is the mass of an E.coli cell?

I'm trying to get into Biology, reading introductory texts. A discussion on E.Coli estimates the mass of the cell from $$density =1g/mL=1g/cm^3$$ and $$volume=1µm^3$$ From this I get $$ mass=density × ...
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Is it possible to grow E. coli K12 with algal amino acids as the sole carbon source?

Instead of glucose or glycerol, is it possible for E coli to grow on an amino acid mixture as the sole carbon source and, if so, what should the concentration be?
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Why pellet and resuspend E. coli for plasmid prep

For maxipreps, cant you just add all the stuff that would be in P1 (RNase A, EDTA) then just add P2? Because if we pellet cells then resuspend theres got to be a reason, right? Is it slats and other ...
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Unwanted E. coli product in plasmid product

Using a TOPO XL Cloning kit, our lab took some amplified human DNA, inserted it into the vector, and attempted to clone it in E. coli. However, upon sequencing the purified plasmid product, the ...
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1answer
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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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Plasmid specific DNA degradation

I'm interested if there is a way to degrade the plasmid DNA inside an E.Coli cell specifically so that the method does no harm to the chromosomal DNA. First I was thinking about restriction ...
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What nutrients are best suited for growing E.Coli

I am looking to grow E.Coli (In a nutrient agar dish) to be used in an E.Coli lawn and was wondering what specific nutrients should be used to ensure the E.Coli grows optimally? Any answers or links ...