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Spidermonkey's Sporadic Lab Stuff

by Spidermonkey

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Hello World from the lab!

Part spider - part lab monkey, will do science for cash, strawberries, or for a place to be that's out of the rain (but preferably for cash).

The rest of what I get up to goes into the Tunnel of Goats :)

Urgent Science Stuff:

Please help reform English libel law
Current UK libel laws are very bad for science and free speech.


Cool science stuff:

RCSB Protein data bank: Molecule of the Month in alphabetical order

The PCR Song It's the little things that keep you going...

NCBI's Entrez Gene My favourite starting point for finding out what is known about any gene of interest.

NCBI's PubMed Where to go to find pretty much all research published in the last 30 years or so (may go back a lot further now). All newly published research is quickly added to the site.

The Genetic Code - table of the DNA/RNA triplet codes for amino acids. This is how DNA codes for protein.

Another PCR song Disco frenzy :)


Recent visitors

Staying alive

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The colonies are very tiny and slow growing, but hopefully they still contain the plasmid (so they will make my bit of DNA for me). Have bunged some into culture over night (in the broth from the bottom pic)It was impossible to pick single colonies as they are so tiny and so slow growing so I've just taken several dabs of a couple of the stripes of bugs and am hoping some of them will grow up overnight in liquid culture. Then I can steak some of that out onto new plates and pick single colonies later. In the meantime I can try to isolate the DNA from these and then (if I get enough) I can see if it will work with the mammalian cells (middle pic). In other words I'll be able to actually do an experiment!
Will see how things look in the morning.
30th Nov 2009, 23:56  

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billion says:

I have to ask... which mammal(s) are the mammalian cells from?

1st Dec 2009, 12:26

Spidermonkey says:

These ones here are a human liver cancer cell line (HuH7). We use human-derived cell lines for most things we do, mostly liver cancer and breast cancer lines. Cancer cells are useful here for the very reason they are bad in a person i.e. because they have escaped the usual controls on growth and division, they can be kept going outside of the body. This also makes them an imperfect model for the same reasons so work with cell lines must therefore always be interpreted with care, but they are mighty useful.

1st Dec 2009, 15:18

billion says:

"they can be kept going outside of the body..."

so the cancer cells you're working on are alive and reproducing constantly?

2nd Dec 2009, 12:00

Spidermonkey says:

They grow and divide, grow and divide, yes. So long as I keep them happy by changing their medium when they need it (every 2-4 days for these cells) and split them into new flasks just before they become to crowded.

Some immortalized cell lines are made from non-cancerous cells by infecting them with Epstein Barr Virus which causes some of the same changes needed for independence.

Non-cancerous cells (primary cell cultures) e.g. from tissue biopsies can be kept going for a few rounds of cell division if you treat them right before they senesce and die. The trick is to do your experiment while they are at their best (or as close as possible) before they die.

You can usually freeze some back in liquid nitrogen if you don't need them for a while (and to have back-up stocks of course). They can take a little coaxing back to life again sometimes.

Mostly we try to keep the number of times we change the flasks as low as possible (i.e. a low passage number), as the longer cells are maintained in culture the more likely they are to evolve into a slightly different cell type from the initial population you started with. By growing cells in culture, you are of course applying a selective pressure for cells that grow well in those conditions/can cope outside the body. Any cells which do not thrive in such conditions die out leaving a population of subclones that do. Evolution works on so many levels.

2nd Dec 2009, 15:36

billion says:

for sure... it's interesting, I went to a public talk recently where a biologist was talking about, amongst other things, craig venter's work. as I understand it he is using a method of eliminating "unnecessary" sections of dna from (microscopic) organisms so that only the dna essential for their survival and function remains. the talker also stated this work could lead to various new kinds of genetic engineering. one method proposed was that the organism could be engineered to not adapt to any new environment, in effect stopping evolution in its tracks. I couldn't think of any practical benefits of doing this at the time, but maybe it would be useful in your line of work?

2nd Dec 2009, 16:49

Spidermonkey says:

It's fascinating stuff alright. Stopping evolution would be very useful in the lab (and for making 'tools' to do jobs like in bioreactors for clearing up toxins, making energy out of waste etc), though I don't think he's doing this with mammalian cell lines yet. Scientists all over the world are using the same cell lines, but the further they are from the original stocks (in terms of number of divisions) the more divergent they become. Imagine a whole lot of scattered tiny populations all being grown by different people, in slightly different batches of medium, with more or less rough handling, all acquiring the odd mutations and chromosomal rearrangements as they go. I'm amazed anything works at all sometimes! You really do have to know the limitations of the system you're working with.

2nd Dec 2009, 17:16

billion says:

so... are the "odd mutations" what ultimately allow the cells to adapt to new conditions? and do "chromosomal rearrangements" occur only in cancerous cells?

2nd Dec 2009, 23:55

Spidermonkey says:

Odd mutations that prove advantageous by providing a growth advantage will inevitably be selected for, mutations which do no harm will accumulate and those which are damaging (make the cells grow more slowly for instance) will be selected against.
Chromosomal rearrangements can occur in any cell really but they are more likely in cancer cells. Cancer cells frequently have all sorts of defects in in their DNA repair pathways. In normal cells the DNA repair processes are what catch the majority of mutations either fixing them or directing the cell to undergo programmed cell death is the damage is too much to cope with. People who have cancer susceptibility syndromes like Nijmegen breakage syndrome for example, have defects in these pathways and hence are more prone to cancers of various sorts.

3rd Dec 2009, 22:00