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SciTech #ScienceSunday Digest - Week 29 of 2012
A Top 10 selection of the scientific and technological advances that I discovered this week.

1. First Complete Computer Model of an Organism.
Computational biology takes a massive step forward with the creation of the first complete computer model of an organism, albeit a single-celled one The model takes account of every molecular interaction that takes place in the life cycle of the bacterium Mycoplasma genitalium. This in silico model of a cell can be probed with real research questions and used to formulate hypotheses for later wet-lab verification. While the immediate promise of biological computer aided design is immense the research group have set their sights on far loftier goals - to move from a single bacterial cell to a complete human model. 

2. Interlocked Rotating Molecular Machines Within Solid Materials.
The first solid material has been created that consists of an array of linked and interlocked molecules that include a freely-rotating rotaxane molecule The rotating molecule speeds up when the bulk material is heated and slows to a stop when it is cooled. While this is just an exciting proof-of-principle, the team believe and have set their sights on creating related solid molecular structures that can be formed into switches and machines. 

3. An Overdue Boost for Atomtronics.
A new and simpler design was proposed for a quantum logic gate that could be the foundation for a new generation of atomtronic computing devices, which involves the manipulation of neutral atoms using lasers in a way that mimics the behviour of electrons in wires, transistors, and logic gates Why might this be useful? Well atomtronics would allow classical electronic devices to connect to quantum computers, which is but one example application. 

4. Molecularly Programmed Nanoparticles for Selectively Destroying Viruses.
A research team has created nanoparticles made of gold that are covered in (i) a specific short DNA oligonucleotide sequence and (ii) an enzyme that chops up any target mRNA sequence that is complementary to / recognises the sequence of the neighbour DNA oligonucleotide In tests this particle was able to shut down Hepatitis C replication in cells and reduce viral levels by nearly 100% - the oligonucleotide had been designed to be specifically complementary to an mRNA produced by the virus and crucial for its replication. This is a very interesting platform technology with personalised medicine applications; the specific oligonucleotide could be used to target many different viruses and other genetic problems such as cancer. 

5. Lithium-Air and Silicon-Sponge Batteries.
Sooner or later we will have a breakthrough battery / energy storage technology that actually reaches market. Promising contenders include this week’s (i) new lithium-air battery designs that do not have the recharging problem that has plagued the platform and (ii) new structured porous silicon sponges capable of holding four times their weight in lithium and many times more than competitor materials such as graphite

6. Artificially Exercised Engineered Muscle Implants.
Researchers have discovered that placing cells derived from muscle tissue on a strip of biocompatible material that is then exercised in the lab results in a muscle-like implant that can prompt muscle regeneration and significant functional recovery when implanted into muscle wound sites While this is great news for those with muscle defects or injuries, I’m waiting for this technology to mature into fully-fledged in vitro meat for food production and consumption purposes. 

7. Artificial Finger for Robotics & Prosthetics.
A research group has developed a prototype of the first sensitive artificial finger that works via an array of pressure sensors that mimic the spatial resolution, sensitivity and dynamics of human neural tactile sensors and can be directly connected to the central nervous system Attaining a human-like sense of touch for both robotics and prosthetics has been a long sought-after goal and I can’t wait to see if these guys can complete their program over the next year or two. 

8. Using Light to Steer Sound to Focus Light.
It turns out that when light strikes an optical fibre it compresses the material and creates a phonon - or unit of sound - that not only travels along the fibre but changes the refractive index and so bending the light and changing its frequency Further, that the incident light is able to controllably steer the sound travelling through the material. While applications include information transmission, processing, computing, and perhaps even holography I bet there are many applications that we today simply won’t be able to think of. 

9. Solving the Delivery of Interfering RNAs for RNAi Therapies.
RXi Pharmaceuticals has begun its first clinical trial for a dermal scarring therapy based on RNA interference - which is a therapeutic approach that has long been hailed as a powerful tool to down- and up-regulate the genetic activity of cells but until now has lacked a suitable delivery method in large living organisms like humans - It turns out that RNAi is now being tested in no less than 20 clinical trials The perfection of delivery systems like this should open up the RNAi therapeutic platform as a whole to allow a whole new generation of target drugs to be created. 

10. Interspecies Chimeras and Xenotransplantation. The Possibility of a Pig with a Human Brain.
One way to solve the shortage of organs for transplantation to save human lives is to harvest similar organs from animals such as pigs but this carries with it the disadvantage of immune rejection. One way around this is to take the organ and strip it of its cells (decellularization), then load the remaining collagen scaffold / skeleton of the organ with human cells and grow a new organ before implantation - this has met with some success with simple organs such as tracheas over the years. Another way around this is to engineer the embryo of the animal to lack the genes required to form a particular organ and introduce pluripotent human stem cells into the embryo - as it grows the animal develops the organ it is not supposed to be able to grow, but this organ is comprised entirely of human cells and in theory could be safely transplanted into a human. This was first done in 2010 with a mouse growing up and living with a functional rat pancreas and the same group repeated their success this week with a mouse growing up with functional rat kidneys So . . . this is a proof-of-principle that a pig could be grown that had organs comprised entirely of human cells - a pig with a human heart or lungs or kidney. What about a pig with a human brain??? 
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ad 1 A really important paper that will change a lot

This Cell paper is just so exiting: A Whole-Cell Computational Model Predicts Phenotype from Genotype 

The dry lab will increase in importance. More and more scientist can move from the pipette to the computer key board. The future work of a scientist is coding and designing abstraction. 

It is although worth to notice that they work on the base of object oriented programming. Objective-C might be the language of choice for the synthetic  biologist.

As we have the option to print DNA, we might have less need to use engineering concepts to engineer from parts. Instead we might focus more on the information management. #objectOrientedProgrammming   instead of #biobricks ?

Maybe we will in #SynBio  move form the #biobrick  concept inspired by modern engineering to  #objectOrientedSyntheticBiology  

see also this nice video: A Whole-Cell Computational Model Predicts Phenotype from Genotype A Whole-Cell Computational Model Predicts Phenotype from Genotype
and their webpage: 
I will make my judgement whenever they can model eurkaryotic disease, or even just predict novel phenotypes of yeast. 525 genes is a whole different game than 6000 genes. But if they can do it, and what they predict can be recreated in wet space...I will have to quit my life and begin anew.

I will be waiting!
I am developing some new hashtags, like a series.
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