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.

Filter by
Sorted by
Tagged with
0
votes
0answers
10 views

Conversion of 2E trans-2-enoyl CoA to 3E trans-2-enoyl CoA

I am working on a project that aims to synthesize a particular molecule from a purely synthetic route, in doing so I am attempting to create a strain of e.coli which would be able to use its trans ...
1
vote
1answer
52 views

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 ...
1
vote
1answer
39 views

What happens when the bacteria in the petri dish lack nutrients for long time?

If I put some E.coli in a petri dish filled with limited nutrition in room temperature and forget them for months or years. What will happen in the final after they overgrowth and used all nutrition ...
3
votes
0answers
36 views

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 ...
6
votes
3answers
225 views

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 ...
4
votes
1answer
108 views

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 ...
1
vote
0answers
130 views

E.coli fermentation - process flow

I have an engineering background and have been assigned a project to look into to failures during E.coli fermentation process using the data available before/during/after the process I have learnt ...
3
votes
2answers
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, ...
2
votes
1answer
202 views

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 ...
1
vote
0answers
34 views

Which viruses are fatal to E.Coli?

I am currently doing a bit of research into which viruses are specifically fatal to the E.Coli bacterium. Apart from the fact that this is merely interesting information for me, I would like to know ...
1
vote
1answer
136 views

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 ...
2
votes
2answers
116 views

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 ...
1
vote
2answers
549 views

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 ...
1
vote
1answer
75 views

How does a bacterium age without cell division?

If somehow a bacterium, let's say E. coli, is engineered in such a way that it loses the formation of ftsZ ring (or other ways that inhibit cell division), and if other conditions are optimal for ...
3
votes
2answers
561 views

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 ...
1
vote
1answer
1k views

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 × ...
1
vote
1answer
32 views

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 ...
13
votes
2answers
3k views

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 ...
4
votes
0answers
272 views

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 ...
1
vote
1answer
72 views

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?
1
vote
0answers
32 views

Will bacterial promoter without either -10 or -35 sequence allow no transcription?

I have a strong constitutive promoter on a plasmid inside of E.Coli, which expresses a gene. Having either -10 or -35 sequence modified to random sequence, will it ensure zero transcription from that ...
1
vote
1answer
2k views

What is the spacing between stop codon and transcription terminator?

When one tries to express a protein from a synthetic plasmid in E. coli, how many base pairs should there be between stop codon and the transcription terminator site?
3
votes
0answers
778 views

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 ...
2
votes
4answers
2k views

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 ...
9
votes
1answer
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 ...
6
votes
1answer
1k views

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 ...
3
votes
0answers
522 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 ...
0
votes
1answer
603 views

Exact location of E. coli in human body

E. coli lives in lower intestine. But exactly where can we find E. coli, and where is there none (or a really small amount) of it? I need the exact names of parts of the lower intestine where we can ...
1
vote
0answers
58 views

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

Are there any databases or papers that give recombination frequency as a function of position in the E coli genome?
4
votes
1answer
57 views

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 ...
4
votes
3answers
679 views

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 ...
3
votes
2answers
385 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 ...
5
votes
3answers
4k views

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 ...
4
votes
1answer
2k views

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 ...
2
votes
1answer
3k views

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? ...
2
votes
0answers
148 views

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-...
3
votes
1answer
2k views

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 ...
1
vote
1answer
169 views

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 ...
4
votes
1answer
5k views

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 ...
5
votes
2answers
3k views

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 ...
1
vote
1answer
408 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 ...
2
votes
2answers
4k 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 '...
5
votes
2answers
97 views

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 ...
1
vote
1answer
2k 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.
2
votes
2answers
123 views

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 ...
3
votes
2answers
141 views

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 ...
8
votes
3answers
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 ...
5
votes
1answer
804 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 ...
5
votes
2answers
1k 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, ...
2
votes
1answer
72 views

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 ...