June 26, 2006

Synthetic Biology

Follow-up to Group meeting: Boston and Jerusalem from Schreibfaul in Warwick

…and it comes back to haunt you. Need to make an overview of the Heidelber conference. Let's look at the Collins talk first :

Title: "Integrating synthetic biology and systems biology"
Collins, J. J., 20 Oct 2005

  1. Building synthetic gene networks: Gene toggle and RNA swithces
  2. Applications in microbiology: (anti)toxins and cell death pathways
  3. Inferring genetic networks: using the network model to infer the mode of action of drugs

To one. Synthetic gene networks:

  • Forward Engineering. Design switch, simple modeling,produce plasmids and see if it works. Gardner in Nature 2000. (Toggle switch in E.coli).
  • moving from e. coli up to yeast and mammalian systems. coupling to natural systems.
  • RNA based synthetic biology: Enginieered ribo–regulators. Issacs Nature Biotechnology 2004

To two. Applications in microbiology:

  • biosensors and programmable cells
  • wirkung von toxins. Afif 2001 CcdB
  • gradielles anschalten von toxins, antibiotics. following along the cell death pathway. iron comes in at later stage. unpublished at the time.

To Three. Infering genetic networks:

  • Reverse engineering gene networks
  • overexpress genes of interest, obtain expression profiles, feed into NIR algorithm, reverse engineer regulatory network
  • Yeung PNAS 2002 and Tegner PNAS 2003
  • Example with E Coli SOS pathway: Gardner Science 2003
  • 9 gene subnetwork. perturb gene expression. output by real time pcr. algorithm gives graphs, sign and strength of interaction.
  • next step: use result to find key players with most influence over the other genes. recA, lexA which confirms previous biological results.

  • Most exciting application: Infer the mode of action of compounds.
  • drugs: know drug hits some target. but: what else does that drug hit? difficult
  • now if you know the network and you know the output, you can infer what the input was.
  • test approach with the sos pathway by upregulating recA, lexA, measure output, run NIR and infer that recA, lexA was upregulated. horay.

  • up to higher organism. very costly to turn genes up or down. So you are only left with the output. hope is that by a lot of perturbations like drugs, mutations etc. might still infer network. Bernardo Nature Biotechnology 2005

*Future applications:"

  • Mammalian Systems
  • Network based drug development
  • Multi–scale approaches

June 21, 2006

A work of pure genius

Writing about web page http://o.tearne.org/G103/

The Blockbuster of this summer. G103 can be watched here soon.

June 10, 2006

Targeted Killings

Writing about Zarqawi dies in Iraq from The International Current Affairs Society

Is this a war now or not? See my comment there.

May 26, 2006

Who benefits from the Da Vinci code?

The pope doesn't like it. And pagans do.
And now, also Protestants embrace it.
So everyone's a winner now?

May 24, 2006

Bread and Butter

Where on earth will I find bread? I would give a lot for bread from a good bakery – but mail order bread ? Maybe this list will yield some other solutions…

At least I have still one more loaf in the freezer.

May 18, 2006

Dinge, die die Welt nicht braucht: Teenage Mosquito Repellent

Writing about web page http://www.jnemarketing.com/

Payback time. Youngsters Beware! Or maybe, rejoice. After all, the sonic teenage fright removes the necessety for stronger measures like leashes or muzzles. So as the high pitch whistle principle has improved the life for dogs, it is certainly fit to do the same for the teenage population. The audio repellent will also save me from the chore to engage in direct interaction, which allways makes me terribly uncomfortable. Education becomes easy. Kids can be safely ignored, and if they become a nuisance – just blow the whistle and enjoy their anger. That will teach them a lesson and probably turn them into better persons.

Who produced these terrible kids anyway? Can't we send them away (not to Coventry, please)? To Glasgow maybe. Then they can eat deep freid Mars bars all day, which will impair their health and render them unable to do much harm.

If it weren't for these human rights issues:

These louts can infringe on our rights to run a profitable shop for the community yet we can't dare infringe on their right to loiter and make life a misery for our shoppers

This annoyed shop owner should claim his human right (the lesser known Article 31) to run a profitable shop. Or would it be the right to inflict pain on random people walking by his profitable shop? (Article 32)

May 02, 2006

Cycling for Coventry

Writing about web page http://www.coventrycyclist.org.uk/

Aha. A cycling campaign for coventry. Maybe have a look at their magazine see what that is about.

Good idea anyway, I know some roads that could do with a bike lane.

April 18, 2006

Orange Alert

Writing about web page http://www.guardian.co.uk/attackonlondon/story/0,,1755303,00.html

Now that is just hillarious. I am looking forward to when the BBC weather forecast will be amended to include an update on the immediate terrorism threat. "Relaxed and secure in the morning, getting a bit more tense in the early afternoon while we have some serious anxiousness later ahead on the possibility of some panic attacks."

Best still to rely on your own judgement for a local threat update. Just look out of the window and check if the neighbourhood looks a bit ominous today.

Blessed be these happy times, where we don't have anything else to worry about!

March 28, 2006

Pedophile Hysteria

Writing about web page http://www.kuro5hin.org/story/2000/10/5/153129/842

"Defending our children" has become a rallying cry for people who actually want to control our adults. When you take the worst that society has to offer and use it as the norm by which everyone's actions are measured, freedom is no longer a word that contains any meaning.

wrote Kuro5hin.org in 2000, commenting the public opinion in the States.

A bit dramatic maybe, but following recent media coverage and public opinion, I belive that this article is pretty relevant to the situation in present day Britain.

March 12, 2006

Tipping in England

I always was amazed at the absence of tipping in England and kept wondering, what the service staff is actually thinking about it. Here we have a personal insight from Ele .

Also looks like there is a new discussion brewing up…

Ulrich Janus

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