A minimal bacterial genome (2016)

Design and synthesis of a minimal bacterial genome
Science.  25 Mar 2016: 351 (6280):
http://science.sciencemag.org/content/351/6280/aad6253
Clyde A. Hutchison III, et al.

Designing and building a minimal genome
A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life.
In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm.
Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function.

journalistic version:

http://www.npr.org/sections/health-shots/2016/03/24/471307905/scientists-build-live-no-frills-cell-that-could-have-a-big-future

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A Whole-Cell Computational Model (2012)

A Whole-Cell Computational Model Predicts Phenotype from Genotype
Jonathan R. Karr, et al.
Cell 150(2):389–401, 20 July 2012
http://www.cell.com/abstract/S0092-8674%2812%2900776-3

Highlights
• An entire organism is modeled in terms of its molecular components
• Complex phenotypes can be modeled by integrating cell processes into a single model
• Unobserved cellular behaviors are predicted by model of M. genitalium
• New biological processes and parameters are predicted by model of M. genitalium

Understanding how complex phenotypes arise from individual molecules and their interactions is a primary challenge in biology that computational approaches are poised to tackle. We report a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium that includes all of its molecular components and their interactions. An integrative approach to modeling that combines diverse mathematics enabled the simultaneous inclusion of fundamentally different cellular processes and experimental measurements. Our whole-cell model accounts for all annotated gene functions and was validated against a broad range of data. The model provides insights into many previously unobserved cellular behaviors, including in vivo rates of protein-DNA association and an inverse relationship between the durations of DNA replication initiation and replication. In addition, experimental analysis directed by model predictions identified previously undetected kinetic parameters and biological functions. We conclude that comprehensive whole-cell models can be used to facilitate biological discovery.

journalistic version:

Synthesis of a Designer Eukaryotic Chromosome

Total Synthesis of a Functional Designer Eukaryotic Chromosome
Science. 27 March 2014
http://www.sciencemag.org/content/early/2014/03/26/science.1249252.abstract

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871–base pair designer eukaryotic chromosome, synIII, which is based on the 316,617–base pair native Saccharomyces cerevisiae chromosome III.
Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling.
SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII.
The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

related articles:

Scientists Move Closer to Inventing Artificial Life
Synthetic biology advances with a man-made chromosome inserted into live brewer’s yeast.
National Geographic. March 27, 2014
http://news.nationalgeographic.com/news/2014/03/140327-functional-designer-chromosome-synthetic-biology

Student Assembly Drives Yeast Project
Science 28 March 2014: 343(6178):1429
http://www.sciencemag.org/content/343/6178/1429.summary (PAID)

Building the Ultimate Yeast Genome
Elizabeth Pennisi
Science 28 March 2014: 1426-1429.
http://www.sciencemag.org/content/343/6178/1426.summary (PAID)

Paul Davies – The eerie silence: Are we alone in the Universe?

Paul Davies – The eerie silence: Are we alone in the Universe?
ANUchannel. June 12, 2012
http://www.youtube.com/watch?v=z5vPLSj3cNs

Quixotic quest

Probabilities exceedingly low. But if not tried, probabilities = 0

SETI
Novel by Karl Sagan

Jodie Foster uses headsets to hear for signals (fantasy)

habitability vs. habited: concepts frequently confused by the media

Origin of Matter: we know about it
Origin of life: ?

before: “Life is so complex, that it would never happen again”

19:13 Vital Dust (book):
“Life is a cosmic imperative”

19:45 a switch in sentiment NOT based on any science

We don’t know how life came to exist, therefore we can’t estimate the odds.

20:25 Hypothesis of the cosmic imperative. How can we test it?

22:30 If we find life on Mars, probably it came from Earth.

26:15 shadow biosphere

28:30 Traditional SETI: very anthropocentric

?galactic beacon

32:00 Terrestrial engineering. Astroengineering.

35:30 Fermi paradox

37:35 Earth could have been visited along 4.5 billion years

38:24 Alien footprints … 100 million years old
1. Buried nuclear waste
2. Buried quarries or mines on Earth, or surface mining traces on moon, asteroids, etc.
3. Biotechnology

55:50 The Hubble distance

see also:

journal Astrobiology
http://www.npr.org/blogs/thetwo-way/2014/01/16/263106030/in-search-for-habitable-planets-why-stop-at-earth-like

Is Mining on the Moon’s Horizon?
Dec. 8, 2013
http://www.npr.org/blogs/thetwo-way/2013/12/07/249503187/is-mining-on-the-moons-horizon

A Quixotic Quest to Mine Asteroids
The Wall Street Journal
April 23, 2012
http://online.wsj.com/news/articles/SB10001424052702303513404577356190967904210

https://franzcalvo.wordpress.com/2014/05/05/aaargh-physicists

A bacterium that can grow by using arsenic instead of phosphorus.
F. Wolfe-Simon, J. Switzer Blum, T.R. Kulp, G.W. Gordon, S.E. Hoeft, J. Pett-Ridge, J.F. Stolz, S.M. Webb, P.K. Weber, P.C.W. Davies, A.D. Anbar and R.S. Oremland
Science. (2011). 332: 1163-1166.
http://www.sciencemag.org/content/332/6034/1163.abstract
http://felisawolfesimon.com

To hype, or not to(o) hype: Communication of science is often tarnished by sensationalization, for which both scientists and the media are responsible
EMBO Rep. 1 April 2012: 303-307.
http://embor.embopress.org/cgi/reprint/13/4/303

https://en.wikipedia.org/wiki/Hypothetical_types_of_biochemistry

The technology of tomorrow: synthetic biology

Tired of Thinking? Google Says We Won’t Have To
Nov 13, 2013
http://blogs.wsj.com/digits/2013/11/13/tired-of-thinking-google-says-we-wont-have-to

Imagine a world where a computer tells you what to do and when—without having to log into your PC.
The Wall Street Journal talks with Google Executive Chairman Eric Schmidt on the technology of tomorrow.

Synthetic Biology: Making Diesel Fuel From Yeast

Put Down Oil Drill, Pick Up The Test Tube: Making Fuel From Yeast 
June 28, 2013
http://www.npr.org/2013/06/28/188431312/put-down-oil-drill-pick-up-the-test-tube-making-fuel-from-yeast

synthetic biology — genetic engineering taken to a whole new level.

His most successful project to date: Jay Keasling and his team inserted or tweaked a dozen genes in yeast cells and turned them into tiny factories that churn out a partially synthetic version of artemisinin, a key drug in the leading treatment of malaria. (The usual source of artemisinin is a tree known as sweet wormwood, and there are not enough to meet the global demand.)

And now Amyris, one of the companies Keasling founded, “has a factory in Brazil that’s using the engineered yeast, taking in sugar and spitting out a product that’s a diesel fuel,” Keasling says. Already, that diesel is in buses in Rio and Sao Paulo.

There is, of course, a catch: “This diesel is still more expensive than petroleum-based diesel by quite a long shot.”