Tag: DNA sequencing

Food for Thought: Weekly Wrap-Up

Sascha Karberg in Frankfurter Allgemeine Sonntagszeitung (FAS) features the latests attempts of biologists to understand and replicate the endosymbiosis of cyanobacteria and cells of eucaryotes that led to the chloroplasts found in all green plants. Already in the 1970s, biologists successfully incorporated cyanobacteria into an amoeba and meanwhile, several animals carrying endosymbionts providing them with extra energy from the sun have been discovered. This is now replicated in the lab. Using genetically engineered cyanobacteria, scientist recently created zebrafish larvae as well as mice and hamster cells with endosymbionts that not only survive but replicate. Karberg also explains why this will not lead to green cows living on sunlight.

Silvia von der Weiden in Die Welt introduces novel findings about the role of water molecules in protecting and maintaining the DNA geometry. Reducing or expanding the size of the water sheath covering the DNA changes the conformation of the molecule as if activating a switch. The findings may be used to create novel DNA-based nanotools or develop DNA-binding drugs to influence gene activation.

In Forbes, Mattew Herper features a graph proving Moore’s law wrong – at least in the decline of cost of DNA sequencing: the cost of getting DNA data (i.e. cost per genome as well as per megabyte of DNA sequence) is dropping way faster than the cost of processing data on computers. In a separate article, Herper endorses Wall Street’s forecast, that Pfizer’s Prevnar 13 vaccine against pneumococcus infections will be the company’s biggest seller in five years.

The Economist features an Italian engineering firm developing a system to collect oil spills in the sea that is based on wool. Already the company has been granted a patent of its containerized, ship-based kit. After absorbing the oil, the wool is pressed to recover the oil and the reused.

Andrew Pollack in the New York Times reports about setbacks in the development of treatments based on stem cells. Experiments recently  showed that induced pluripotent stem cells – which are thought to be superior both ethically and technically to embryonic stem cells – are rejected by the immune system. However, it is not yet clear whether the results obtained in mice hold true for humans, too.


Food for Thought: Weekly Wrap-Up

MacGregor Campbell reports in the New Scientist that DNA can stretch to nearly twice its length without breaking and explains how this feature can lead to the development of new drugs to fight cancer. Ferris Jabr in the same magazine reports about the first discovery of a virus infecting nematode Caenorhabdis elegans, a workhorse of developmental biology. The discovery will now enable biologists to study virus-host interactions in this model organism.

The Economist introduces a technology developed by Planar Energy (Orlando, Florida) which turns rechargeable batteries into thin, solid devices by printing lithium-ion batteries onto sheets of metal or plastic. The magazine quotes the company by saying the cells will be more reliable than conventional lithium-ion cells, will be able to store two to three times more energy in the same weight and will last for tens of thousands of recharging cycles. They could also be made for a third of the cost. The trick is done by using a ceramic electrolyte which can be printed and appears solid while it allows free passage to lithium ions.

Matthew Herper in Forbes reports on PerkinElmer’s entry into the DNA sequencing market by creating a service business. Researchers can send in DNA for sequencing by PerkinElmer and subsequently access and analyze the genetic data in a computer cloud. Focus will be on human exam sequencing. Matthew also features a video interview with Mischa Angrist, author of “Here is a Human Being: At the dawn of personal genomics” about what it means to look at one’s own sequence data and whether these data should be private or be available for science.

Also in Forbes, Robert Langreth introduces research by William DeGrado, of the University of Pennsylvania trying to breath new life in peptide drugs to fight infectious diseases. DeGrado uses supercomputer simulation to create antibiotics that mimic natural ones but are far simpler to produce and more stable. The first drug designed by DeGrado, PMX-30063 by PolyMedix to treat staphylococcus skin infections is now in clinical trials.

The New York Times also deals with infectious diseases. Sindya N. Bhanoo outlines efforts of researchers from seven countries to analyze how a single strain of Streptococcus pneumoniae bacteria has morphed over 30 years and spread across the world, as a result of evolutionary pressure by antibiotics and vaccines. Within three decades, the strain turned over about 75% of its genome by recombination and mutation. The study appeared in Science.

German papers feature two stories on drugs that surprisingly show efficacy in indications they have not been developed for: Cinthia Briseno in Der Spiegel reports on a study featured in Science on cancer drug Taxol paclitaxel which is able to stimulate the growth of nerve fibers that have been cut in two. The researchers are now planning clinical studies in paraplegics. Nicola von Lutterotti in Frankfurter Allgemeine Zeitung reports a Lancet Neurology study on Prozac fluxetin which is able support the recovery from palsy in stroke patients.

Food for Thought: What Would You Do With a Personal Sequencer?

Basically, it is the smallest pH meter in the world, but its impact on science, medicine, and even daily life is likely to be huge. The pH meter developed by Ion Torrent sits on a semiconductor chip beneath very tiny wells containing a single-stranded DNA probe and DNA polymerase in a buffer. The wells are flooded by the nucleotides A, T, G and C in a sequential manner, and incorporation is recorded by measuring the proton released in the reaction. Thereby, the pH meter can be used to sequence DNA. The chip contains 1.3 million wells, the device measures about 60x50x55 cm (24x20x21 inches), costs $50,000 and is named  PGM – Personal Genome Machine.

Already on the market, it puts DNA sequencing within the reach of nearly every lab, doctor’s practice, clinic, and even college. While it still has certain limitations – it can read only 20 genes at once at present – DNA sequencing never has been easier and less error-prone. Other devices with similar elegance and even more speed are around the corner – as an example, scientists from Imperial College of London last month demonstrated in NanoLetters that they can sequence genes by propelling a DNA strand at high speed through a tiny 50 nanometre (nm) hole cut in a silicon chip, using an electrical charge. As the strand emerges from the nanopore, its coding sequence is read by a ‘tunnelling electrode junction’. This 2 nm gap between two wires supports an electrical current that interacts with the distinct electrical signal from each base code. The speed is unbelievable and translates into sequencing an entire human genome in 5 minutes.

Certainly, these machines will have a huge impact on the amount of data generated for the development of personalized medicine and individualized therapies. But now that DNA sequencing is approaching a mass market, it will inevitably reach anyone, just like cameras, computers and mobile phones that turned from “professional only” machines into commodities. The statement that no one needs such a machine is refuted by history: when the telephone was invented, US president Rutherford B. Hayes could not think of anyone wanting to use it, XEROX once was sure that the world market for photocopiers would be around 50 machines, and even Intel’s founder Gordon Moore could not think of using personal computers at home for anything meaningful other than “maybe filing cooking recipes”.

What would you do with a personal sequencer at home? Screen your blood for disease on a daily basis? Check your food for microbial contamination? Classify the bugs and shrubs in your garden to find new ones? Secretly sequence the DNA of you neighbors, boss or affair to find out about genetic weaknesses? In a decade, ads might state once again: “There is an APP for that!”