Thursday, May 20, 2010

B Fwd: Re: JCVI publishes booted synthetic genome

---------- Forwarded message ----------
From: "Anselm Levskaya" <>
Date: May 21, 2010 1:19 AM
Subject: Re: JCVI publishes booted synthetic genome
To: <>

I'd like to point out that the -real- news here is the vast array of
techniques that venter's group (led by daniel gibson) has pioneered in
order to build the "assembly stack" to get from noisy 80-mer dna
pieces to a verified megabase.  The techniques are a big deal and
venter is one of the few people adequately funding this kind of purely
technical research.

Two techniques in particular:
- one-step, isothermal assembly of DNA in vitro:
- whole assembly of oligo-tiles into genes in yeast spheroplasts:

are extremely important improvements on past methods both in terms of
efficacy and in terms of their power to construct combinatorial

If any of y'all do cloning in your dayjobs I heavily recommend that
you check out the former method.  I and my colleagues are switching
our entire cloning pipeline to utilize this method.


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Tuesday, May 18, 2010

B Fwd: [WebBio] PepStr

---------- Forwarded message ----------
From: "Raghava" <>
Date: May 18, 2010 12:41 PM
Subject: [WebBio] PepStr
To: "webbio: Web Servers for Biologists" <>

Name: PepStr

Pepstr is a de novo method for prediction of tertiary structure of
small peptides. It uses 3 steps:
In first step, the regular secondary structure states (helix, β-strand
and coil) and β-turn types are predicted using BetaTurns method.
Secondly, initial or starting conformation for a given sequence is
generated using the Tleap module of Amber version6 with phi, psi
values corresponding to the secondary structure states predicted in
step I. The side chain angles are asigned using standard Dunbrack
backbone dependent rotamer library.
This initial conformation is then subjected to energy minimization and
molecular dynamics simulations using Sander module of Amber. It
consists of few initial cycles of steepest descent minimization
followed by dynamics which is carried out for 25ps at 300K using 1-fs
time steps. Finally, this is followed by minimization using a
combination of steepest descent and cojugate gradient algorithms.
The final coordinates are saved in PDB format.

Tuesday, May 4, 2010

B Fwd: Metamodern (1 new item)

---------- Forwarded message ----------
From: "Newsfeed to Email Gateway" <>
Date: May 4, 2010 3:04 PM
Subject: Metamodern (1 new item)
To: <>

Metamodern (1 new item)

Item 1 (05/04/10 19:19:36 UTC): Globe Form afterword & environmental posts

I'm back from Globe Forum 2010, a meeting that brings together leaders of innovative businesses focused on sustainability. A major theme at the meeting was, of course, greenhouse gases and climate change. My talk emphasized that high CO2 levels will persist for decades (even with heroically deep cuts in CO2 emissions) unless we implement large-scale atmospheric CO2 capture.

Thermodynamics says that removing the anthropogenic excess CO2 will require work of compression amounting to about 3 TW-decades of energy (preferably not from coal). Since 3 TW is more than the total time-average electric power production of the human race today, this highlights the importance of new modes of production that can make solar arrays and carbon-capture apparatus economically, sustainably, and at low cost. This is one of many motivations for developing high-throughput APM.

Here are a few Metamodern posts relevant to climate change:

Greenhouse Gases and Advanced Nanotechnology discusses the under-appreciated stubbornness of the problem and how it can be solved when the human race achieves a basic competence in fabricating physical objects.

Ocean Acidification: The Other CO2 Problem discusses the chemical side of changing the composition of the atmosphere. Planetary sunscreen wouldn't address this problem.

To improve US fuel economy, stop talking about MPG! suggests that switching to a more direct description of fuel consumption would dispel a costly illusion about automobile performance and help to correct crazy R&D priorities. (Miles per gallon describes inverse fuel consumption, a strange and confusing metric, and 2,000 mpg car would be a surprisingly low-value miracle.)

One Watt, One year, One dollar (pass it on) tells how bloggers (or anyone else able to communicate) can help reduce energy waste, immediately and with little effort, by helping to popularize a simple, memorable fact about the retail cost of electric power. (In other words: please link to this post and be pleased that you've done something to save the planet.)