Engineered mosquitoes proposed for release in Malaysia

According to the World Health Organisation, spread of dengue fever since the 70s has put 2.5 billion people at risk, with an estimated 50 million cases per year.
Dengue fever is a disease caused by a family of viruses that are transmitted by mosquitoes. It is an acute illness of sudden onset that usually follows a benign course with headache, fever, exhaustion, severe joint and muscle pain, swollen glands (lymphadenopathy), and rash. The presence (the "dengue triad") of fever, rash, and headache (and other pains) is particularly characteristic of dengue.
Malaysia's Academy of Science, located in a country severely suffering from dengue, is keen on proposing a novel strategy to the government. The method is called "sterile insect technique' and involves the release of genetically engineered male Aedes Aegypti over a wide area to mate with the native insects that are present. Native females that mate with the sterile males produce non viable eggs, leading to a decline in the target pest population.
According to the inspirers in Oxitec, a biotech company based in Oxford, UK and founded by University of Oxford geneticist Luke Alphey, the technology is supposed to be environment-friendly, species-specific and has been described as “birth control for insects”.
This 'sterile insect technique' has been successful in the past, in eliminating the parasitic screworm (Cochliomyia hominivorax) from the US and most of Central America. This parasitic fly lays its eggs in the living tissue of warm-blooded animals, including humans. The larvae hatch and 'screw' into the surrounding tissue as they feed, causing severe tissue damage and sometimes death. At that approach, the screw worms used were sterilized using radiation. This has been a certain problem because irradiated mosquitoes are unable to compete wild-type males to mate with females.
Oxitec integrated a genetic element, LA 513, into the DNA of the mosquitoes. This genetic modification kills any offspring in the larval stage if they are not fed the drug tetracycline. When in lab, the mosquitoes fed with the antibiotic, grow in huge numbers. In nature, where tetracycline will not be provided, the modified gene will be able to crash the reproduction of the local A.Aegypti population.
Recent media reports claimed that the strain would be released on Pulau Ketam, an island fishing village near Kuala Lumpur. C. P. Ramachandran, who chairs the relevant committee of Malaysia's Academy of Sciences mentioned that, “any risks related to genetically modified organisms must be balanced against the potential benefits”.

Reference journal
Hoang Kim Phac et al, Late-acting dominant lethal genetic systems and mosquito control. BMC Biology 2007 5:11

Foldit! A game for protein structure design

Considering from a structural biologist's point of view, unravelling the exact way that proteins are folded will certainly lead to a Nobel nomination, with the same magnitude as the determination of Myoglobin structure from J.Kendrew in 1957. But apart from all that glitters, protein structure is more about handing a message in a bottle that appears to be a tough riddle.
Proteins are the work units in our cells. Main roles that are assigned to them are catalytic activity, polymerization for forming necessary cellular components, enabling blood cells to recognize antigens and others. The way that a protein is functional is based primarily to its 3D structure. The natural process, that a protein will reach its final 3D conformation, is called folding.
Dr Baker, a biochemist at the University of Washington, and a team of computer designers have developed a game with a purpose to aid in determining optimal folding ways of certain protein targets as well as structure-based design of novel crucial protein inhibitors that could lead to drug development for threats as HIV, cancer and malaria. Such an experimental endeavor requires exquisite computational time and rational in silico processing.
The project is a reincarnation of an older project called Rosseta@home. That was a screensaver that was installed from about 200.000 people around the world. It was using the available processing time of their systems, when they would otherwise be idle, for aiding in research on folding problems. When the screensaver was being launched one could see the protein structure (that was currently handled) floating on his screen. But since a human eye is always more efficient than a computer -and this is one of the main facts among structural biology community- the users of the screensaver were not able to contribute with "suggestions" on how the protein could be more stable.. Not until the game Foldit made its appearance. Dr. Baker thought of posing to the users of Rosseta and others a challenge of solving puzzles and gaining points for stable foldings. When the computer doesn't know what the best next step is, it changes the structure randomly. But what if people working with computers can solve a hard problem that computers can't solve alone? Voila! That was the idea.
In order to play the game one has not to be a scientist with a PhD on issues of protein structure determination. Friendly tutorials on known folded proteins aid the user to understand the general rules - or else the "game rules"- that govern how a protein is taking its final shape in nature. The better the manipulation of the protein in order to reach a favorable energetic state that could form a functional protein, the more points the user gets. Users do that by pulling protein parts, forming hydrogen bonds, move residual side chains, stabilizing residual backbone as if they were using latest high-tech protein graphics software, normally used by educated researchers!
Once a user finishes the 40 tutorial puzzles is entering the challenge puzzles were he deals with important target proteins, for which the optimal folding state is unknown. So by playing one could actually assist in doing cutting-edge research on structure-based computer protein design. Dr. Baker's next plans are to import a whole list of new features that will allow users to change residues and parts of the protein as they wish, in order to come to a better fold, or else to design manually prospective novel proteins with new functions!!
It seems that there is threat for World of Warcraft, and from the parents point of view what better than a game that educates and promotes rationality?

European Commission urges for a healthy EU research labour environment

Brussels, 27 May 2008.

European Commission aims to establish a motivation strategy for preventing the immigration of talented European researchers and scientists to the USA and other continents. Primary goals in the agenda are functional expansion of the research organizations and covering the gap of a unified social insurance system for research personnel.
The committee focuses on the issues that young researchers face at EU work environments. Most of them are being employed in short term posts, while career development is usually based on years of experience and not on professional ability and aptitude.
A partnership among member states is being proposed, aiming to broaden the mobility of research workers between member states, research centres, in academia and industry.

According to E.C. until the end of 2010 the following targets must have been accomplished:
- systematically open recruitment by research institutions to all European researchers
- meet the social security and supplementary pensions needs of mobile researchers
- provide attractive employment and working conditions, such as improved contractual terms, salaries and opportunities for career development
- ensure researchers have the necessary skills to turn knowledge into results including by creating stronger links between universities and industry

Coordinated action between the Commission and the Member States, alongside renewed efforts on existing initiatives such as the European Charter for Researchers and Code of Conduct for the Recruitment of Researchers, would help to create a genuine European labour market for researchers. This will balance the supply and demand for research personnel, boost productivity growth, increase knowledge transfer and facilitate the development of centres of excellence throughout the EU. It will also create more effective international connections for collaborative research and the economic exploitation of research results, and help to create more attractive conditions for industrial investment in research.

At 2010 a general evaluation of the partnership's outcome and progress will take place, and any need for certain action, on EU's behalf, will be determined.
“We need to free the potential of our excellent researchers if we are to achieve Europe's wider Lisbon agenda ambitions and make the European Research Area a reality. Too many of them have to wait too long for the chance to become independent researchers in their own right due to outdated national legislation and practices.” stated by the European Commissioner for Science and Research, Janez Potočnik.

Genetically modified bacteria used as "living computers"

Scientists at the biology and the mathematics departments of Davidson College, North Carolina and Missouri Western State University, Missouri, USA, genetically engineered bacteria -Escherichia coli-, resulting to a platform that could handle a popular mathematical problem called the Burnt Pancake Problem (BPP).
The Burnt Pancake Problem can be visualized as a stack of various sized “pancakes”, each consisted of a burnt side and a golden side, arranged in an arbitrary order. In order for the problem to be solved the stack must be sorted by flipping individual or subsets of adjacent pancakes until the stack is ordered like this: from smallest to largest with each pancake oriented golden side up. Both order and orientation (burnt OR golden side up) are changed, when flipping is performed. The less the flips needed to solve the riddle, the more successful the implemented “solving tool” is considered.

(image credit: Derrick Coetzee)

Now the role of the spatula, shown at the figure above, is played by the algorithm that is applied to solve the problem. If you are using a conventional computational system, that would be done with a computer. Haynes et al have shown that addressing the problem is now feasible, using E.coli – without a single “click”.
Imagine that instead of pancakes we have DNA fragments inside an E.coli. The researchers added genes from Salmonella typhimurium, whose function was carrying out the flipping. They also engineered the E.coli with a reporter gene, that conferred resistance to a certain antibiotic, but do so only when the DNA fragments are flipped in the correct order. Because of the nature of the genes that researchers added to E.coli bacteria, flipping occurs at random. The time point at which the BPP is first solved reflects the minimal number of flips required to solve the problem.
This quite simple experimental system could be of considerable importance in the field of comparative genomics, since flippable DNA arrays could serve as an excellent model that could assist in understanding genome rearrangements throughout evolution. Phylogenetic relationships between species can be inferred by using BPP mathematical modeling to compute the minimum number of rearrengements that could link 2 genomes.

Reference journal
Karmella A Haynes et al. Engineering bacteria to solve the Burnt Pancake Problem. Journal of Biological Engineering (in press)