Tag: Ion Torrent

Food for Thought: Weekly Wrap-Up

This week, Frankfurter Allgemeine Zeitung (FAZ) deals with potential origins of the enterohemorrhagic E. coli (EHEC) epidemic in Germany. Christina Hucklenbroich details the consequences of feeding cattle mixed provender, a forage that changes the environment of the intestinal tract so that it becomes an ideal habitat for bacteria like E. coli. In a separate article the same author deals with an EHEC outbreak in 1997 in the US which affected mostly women – similar to the current epidemic in Germany. Back then, the source had been alfalfa sprouts used in salads. While the ultimate source had never been found, scientists suspected that already the seeds had been contaminated. Richard Friebe, also in FAZ, deals with slurry from pigs, cattle, and fowl that is know to contain all sorts of bacteria and viruses. It is used either directly as fertilizer (though not on vegetables and salad plants) or may contaminate adjacent fields through spillover, spray or via irrigation using water contaminated with slurry.

Susanne Kutter in Wirtschaftswoche introduces Holger Zinke, co-founder and CEO of BRAIN AG, a biotech company specialized on “white” biotechnology, using the skills of microbes to re-design industrial processes or to come up with entirely new ones. Thereby, pharma and chemical industry can save energy, money, and expenses for raw materials. The article is part of a series on pioneers of the “greentech-era”, trying to change the industry to make it more energy-efficient and sustainable.

In Forbes, Matthew Herper analyses why scientists in Germany and China used small desktop sequencers by Ion Torrent rather than big machines by Illumina, Life or 454 Life Sciences to decipher the sequence of the EHEC strain rampaging through Germany. Herper claims it is speed and cost. However, the choice was also influenced by the fact that the sequence of the new strain matched strains with sequences available in public databases relatively closely so that puzzling together the short sequence data generated by the machine was easy.

In reporting on this year’s annual conference of the American Society of Clinical Oncology (ASCO), Andrew Pollack in The New York Times (NYT) introduces two drugs for the treatment of melanoma: vemurafenib (developed by Genentech, part of Roche Group), which attacks a specific mutation accelerating tumor growth and Yervoi ipilimumab (developed by Bristol-Myers Squibb), which unleashes the body’s immune system to fight the cancer. Yervoi was approved by FDA in March this year. Pollack also features latest clinical results for Aromasin exemestane, a drug marketed for preventing recurrences of breast cancer.

Gina Kolata, also in NYT, deals with the phenomenon of “linguistic toxicity”, i.e. drug labels listing more and more side effects, even contradictory ones such as that a medication can cause diarrhea or constipation. As of today, drug labels in the US list an average of 94 side effects (the top numbers already are exceeding 500), despite efforts of FDA to make drug makers avoid listing of side effects that are infrequent and minor, commonly observed in the absence of drug therapy or not plausibly related to drug therapy. Main reason is pharma companies trying to protect themselves against lawsuits.

Last not least, New Scientist features the latest advice for those of you on diet: psychologist found that if you succeed convincing yourself that everything you eat bears enormous amounts of calories, your ghrelin hormone level will drop much lower after eating so that you feel being full faster.

Food for Thought: Weekly Wrap-Up

Andreas Menn in Wirtschaftswoche introduces the latest medical applications of smartphones for monitoring physical functions, ranging from the heartbeats of unborn children to blood sugar, blood pressure and pulse rates of elderly people to even pacers and other implants. According to Menn, the Mobile Health sector has a 19% market growth. In the US, patients are joining movements like The Quantified Self to collect health data for research purposes (and, as an example, to determine the ideal moment for wake-up). Contact lenses measure and report blood sugar levels, while tests strips or clothes with in-built wearable electronics control breathrate, wound swelling and urine for dangerous deviations. The field is still littered with startups, but big players like Siemens, Philips, sanofi aventis and Deutsche Telekom also have stepped in already.

Joachim Müller-Jung in Frankfurter Allgemeine Zeitung (FAZ) reports from the recent meeting of the Stem Cell Network North Rhine Westphalia. The debates focused on quality control of induced stem cells and the ability to derive motor neurons from such stem cells.

In The New York Times, Nicholas Wade reports on a recently discovered bundle of genes regulating the growth of heart muscles cells. The study published in Science will be of great interest for the development of novel therapeutics. It is known today that heart muscle cells are replaced in humans – however, the growth rate is too slow to replace the loss of many cells, e.g. in a heart attack. By modulating these genes, it might one day be possible to regenerate heart muscle in a targeted manner.

In Wired, Brandon Keim features a proposal by theoretical physicists that bacteria might transmit electromagnetic signals by using their DNA chromosomes as an antenna. The proposal is likely to trigger controversy as many biologists doubt that bacteria emit electric signals. French nobelist Luc Montagnier had already claimed in 2009 that bacteria do transmit radio signals in the 1 kHz range.

In the New Scientist, Ferris Jabr introduces a super twisty beam of laser light that is able to tell left-hand molecules from right-hand ones, with potential applications in drug development. Rowan Hooper reports on successful attempts to cure certain forms of blindness by introducing genes from algae into the eyes. The genes are encoding for channelrhodopsin-2 (ChR2), a photosensitive protein used by unicellular algae to orient towards light. The mice carrying a hereditary form of blindness were treated with subretinal injections of viruses carrying the algal gene and subsequently were able to use light beams for orientation in a maze. Trials in humans, the article states, might begin in two years. Finally, Andy Coghlan features findings that humans can be grouped by one of three gut ecosystems. These three “enterotypes” – dominated by three different species each – have been found all over the world and have a bias towards degradation of certain nutrients and production of certain vitamins.

And finally, for those of you who loved the Get a Mac ads by Apple (“I’m a Mac, I’m a PC”), please have a look at the ad campaign of Ion Torrent comparing its PGM sequencer to competitors such as MiSeq.

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!”