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8

The minimum requirement for E. coli and other bacteria to grow and survive is called minimal medium. It's even defined at Merriam-Webster: a medium that contains only inorganic salts, a simple carbon source (as carbon dioxide or glucose), and water Water and glucose are pretty easy, but the source of salts may often change; regardless, you really need ...


7

To be honest, you really shouldn't be buying such things if you're not prepared to handle them properly. If you work with a proper lab, you will be inindated with vendors trying to sell you these and many others. But to answer your question, if you are looking to purchase many such items ATCC is an excellent resource. Not only will you have to meet ...


7

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 all your plasmid as an ori region that contains so called iteron: In many cases, the origin of replication contains directly repeated sequences, termed iterons,...


7

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 expression data Stanford MicroArray Database (use the search tool to find relevant organisms) Colombos (COLlection Of Microarrays for Bacterial OrganismS) ...


5

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, the consensus is to start the induction at OD 0.6, and for most chemically competent cells, the optimal OD ranges from 0.3 to 0.8 depending on the competency ...


5

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 organism”. They worked with it because they were bacteriologists and it was a convenient bacterium to use. As Joshua Lederberg wrote in Microbiology Today (2004): ...


4

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 always do 2000 rpm, 20 minutes, 4C if I'm doing a midi or maxi sized prep and harvesting bacteria in a 50ml conical. If I'm doing a miniprep I will take the 1....


4

Yes, but no. In other words, this quote is not probably not true in the ways you'd think. Bacteria can survive on practically nothing for long periods of time, but whether you call that life is subjective. Nitrogen is necessary for all the co-enzymes and proteins to sustain life. In order to get energy, if E coli. needs to metabolize nitrogen to waste at ...


4

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 the reaction, the aldehyde from the C1 is oxidized to a carboxylic acid which in a second step is turned into a phosphoester. To do so, a cysteine from the ...


4

Let me first clarify the difference between anaerobic respiration and fermentation. Literally respiration refers to breathing, but its definition has been extended to include cellular metabolism that leads to ATP generation. Fermentation, as you said depends on substrate level phosphorylation. Anaerobic respiration on the other hand just means ATP ...


4

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 take in oxygen and one that produces oxygen. All three consumers of oxygen in E.coli are the oxidation of ubiquinone by at two sites in cytochrome-bcl or by ...


4

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


4

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

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 in the physiology of microorganisms does not provide any justification. Similarly, a recent review by Blount, 2015, eLife: The unexhausted potential of E. coli ...


4

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 smelling.


3

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). See my answer on your previous post and the linked paper. Also look for coherent feed forward network motifs.


3

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 or don't produce sufficient quantities of these enzymes. An organism that doesn't use oxygen for metabolism but is also not relatively harmed by it can be ...


3

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 with the peptidase Trypsin (10g/l) Yeast extract, made by autolysis of the cells (5g/l) Sodium chloride (10g/l) The original formulation of Bertani from 1951 (...


3

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 lead to a groups of cells that have non-independent cell orientations. For more information, including how people have induced it to do otherwise, see this ...


3

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 number of cells in a Petri dish (N). (We assume a stable population in a saturated medium.) $$ B \times P \times D \times N $$ I've looked up some articles and ...


2

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. In this form the predator can't attack E. coli and it lives among the amoeba for extended periods. It does not look like a simple point mutation to me, which ...


2

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902570/ In addition to the other answer(s), E. coli has been shown to have filamentous spikes even under controlled conditions. This is not the same situation as it sounds like you have a non synchronized culture in which this happens, but it could be related.


2

According to this data sheet, the genotype of the strain RosettaTM(DE3)pLysS is F- ompT hsdS (r- m-) gal dcm (DE3) pLysSRARE (CamR). This strain carries certain tRNA genes on the same plasmid as the LysS gene, and these tRNAs boost expression from genes containing rare (in E. coli) codons. The plasmid encodes chloramphenicol resistance (CamR). If you have ...


2

In terms of naturally-occurring "genes" I think that the record is probably held by the attenuator peptides. In bacteria, the regulatory mechanism known as transcription attenuation involves the ribosomal biosynthesis of very short peptides. In the trp operon, where the phenomenon was first described by Yanofsky's group, the peptide, MKAIFVLKGWWRTS, ...


2

There are three variables being shown here: The amount of time samples were stored in the freezer to allow $^{32}$P decay (x-axis), The length of time samples were allowed to grow in a nonradioactive environment before being frozen (points with different symbols), and The rate of $\beta$-galactosidase production when cells were thawed and grown in the ...


2

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 cell should be intact except for lacing one gene, which would mean that the response is in vivo. The knockouts were performed inside the E. coli cells and, as ...


2

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

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 after the dot (period) in NCBI accession numbers, denotes the version. From NCBI: VERSION is made of the accession number of the database record followed by ...


2

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 exchanging the E.coli polymerases with other polymerases displaying higher error rates (or with less proofreading capabilities). A lot of errors are quickly ...


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