Tag: Craig Venter

Food for Thought: Weekly Wrap-Up

Hildegard Kaulen in Frankfurter Allgemeine Zeitung (FAZ) reports from the 61st Lindau Meeting of Nobel Laureates on the need for novel antibiotics. She features the talk of Thomas A. Steitz from Yale University on ribosomes and novel antibiotics. Steitz in 2009 received the chemistry nobel prize for the structure determination of ribosomes together with Ada Yonath and Venkatraman Ramakrishnan. This discovery has led to novel insights on antibiotics binding to these cellular organelles – an important prerequisite for the design of novel antibiotics as bacterial ribosomes still are the most important targets for antibiotics. Among others, the scientists learned that the larger the contact area of ribosomes and an antibiotic, the more mutations are necessary to evade the binding and anti-microbial activity of the compound. Steitz therefore recommends linking antibiotics. He also co-founded a company, Rib-X Pharmaceuticals, which is designing novel antibiotics by structure-based design. Its most advanced compound successfully completed a Phase II study this year.

Richard Friebe, also in FAZ, reports on a breakthrough in synthetic biology accomplished by a team of German, French and Dutch scientists and published in Angewandte Chemie. Other than Craig Venter, who rebuilt an organism by chemically synthesizing its DNA, the group designed a partially artificial organism. Using automated selection, the researchers transformed an E. coli strain unable to synthesize thymine nucleotides into an organism incorporating the artificial thymine analogue 5-chlorouracil instead of thymine into its entire DNA. The goal of the project was to demonstrate that it is possible to develop a generic technology for evolving the chemical constitution of microbial populations by using the simplest possible algorithms. Members of the team recently co-founded Heurisko USA Inc.

Die Welt reports on novel insights into the medical role of Helicobacter pylori, a bacterium living in the human stomach and known for its ability to cause gastritis, gastric ulcer and stomach cancer. Christian Taube from the University of Mainz and colleagues from Zurich University recently published findings that early infections with Helicobacter can protect against allergic asthma. In newborn mice, an early infection impaired maturation of dendritic cells in the lung and increased enrichment of regulatory T cells responsible for oppressing asthma. Resistance is lost once Helicobacter is eradicated with antibiotics. The researchers therefore think that the increase of allergic asthma may be caused by today’s widespread use of antibiotics.

Type 2 diabetes can be cured by a strict diet, reports Christina Berndt in Süddeutsche Zeitung (SZ). In a UK study comprising 11 type 2 diabetics, in 7 of the patients insulin production normalized and the liver started to respond to the hormone properly after they were put on a strict 600 kcal diet for 8 weeks. The cure even worked in patients suffering from diabetes for 4 years and the effects were lasting, provided the patients did not overeat subsequently.

William Pentland in Forbes writes that the US Defense Advanced Research Projects Agency (DARPA) is a driving force behind a new effort to harness biology as a manufacturing platform. The “Living Foundries” program is designed to fund projects that enable on-demand manufacturing capabilities for the production of advanced materials and devices. “Key to success,” DARPA writes, “will be the democratization of the biological design and manufacturing process, breaking open the field to those outside the biological sciences.” As examples, DARPA mentions next-generation DNA synthesis and assembly technologies, modular genetic parts and systems, and cell-based fabrication systems.

In a Forbes interview conducted by Alex Howard,  Charlie Quinn, director of data integration technology at the Benaroya Research Institute, talks about the necessity of new tools and strategies to cope with today’s data deluge. Quinn, who is dealing with genomics, maintains that it is not only about novel technologies but also about cultural changes to create greater value by sharing data and establishing open source and even open data projects, sharing data much earlier than it is done now. Thereby, novel ideas can be spread earlier. “What we’ve been doing is going around and trying to convince people that we understand they have to keep data private up to a certain point, but let’s try and release as much data as we can as early as we can.”

Food for Thought: Weekly Wrap-Up

In Germany, science pages were dominated by Japan’s nuclear disaster. Apart from topics such as radioactivity as a threat to human health and the environment, Christiane Hucklenbroich in Frankfurter Allgemeine Zeitung (FAZ) deals with an upcoming new definition of autism. Instead of seeing autism as a defined disease category, physicians have come to the conclusion that one should rather use the term “autism spectrum”, comprising several aspects of autism. The medical community also has started focusing on co-morbidity aspects as well as autism-like symptoms in other psychiatric diseases.

Susanne Kutter in Wirtschaftswoche summarizes latest advances in stem cell medicine. Among others, she features a clinical trial conducted at the University of Rostock in which the heart muscle of patients suffering from an infarction is injected with adult stem cells to initiate regeneration of muscle. The trial includes more than 150 patients and will be finished end of 2012. A method already successful has been established in India, where more than 700 people with blindness caused by Vitamin A deficiency regained eyesight after injection of stem cells into the cornea.

Roni Caryn Rabin in The New York Times reports on a Lancet study that pooled data from 58 studies involving more than 220,000 people with a mean age of 58 to find out whether the idea that obese people with an apple shape (carrying the overweight predominantly in the belly) are more at risk for heart disease than overweight people with a pear shape. The answer is: they are not. Overweight matters, but shape does not.

Ferris Jabr in New Scientist introduces a small implantable device developed by researchers from the  Massachusetts Institute of Technology (MIT) that can track tumor growth in the body of cancer patients. The device contains magnetic nanoparticles covered with monoclonal antibodies able to bind cancer-related molecules, e.g. human chorionic gonadotrophin (hCG), a hormone released by testicular and ovarian cancers. The first generation had read-out by MRI scans that detect formation of clusters within the device due to binding of the molecules. However, the researchers now improved detection so that readout can now be done by a hand-held device. The principle can also be adapted to monitor other changes in the body, e.g. silent heart attacks.

For blood transfusion, medical doctors need to carefully choose the right blood group from 29 possible combinations of the AB0, Rhesus, the MNS and other systems. This challenge sometimes needs to complications and logistic problems. The Economist reports on a successful approach by researchers from the University of Montreal to disguise the antigenic proteins from red blood cells. The trick is done by first dressing the fatty surface membrane of the cells and then attaching another cover so that the immune system does not pay attention to the cells. The cover is fully permeable by oxygen and carbon dioxide.

David Whelan in Forbes calls for a psychological study of people investing in biotech stocks, in particular those writing rude comments on articles featuring the ups and downs of stocks. He claims the phenomenon is only seen with articles on biotech stocks.

And finally, David M. Ewalt in Forbes reports about errors in Craig Venter’s first synthetic life form in which Venter inserted DNA composed on a computer. The DNA included quotes from James Joyce and Richard Feynman, however Craig used the Joyce quote without written permission from Joyce’s estate and misquoted Feynman by obtaining the quote from the internet. Craig said he was now going back to the organism to correct the error.

Food for Thought: Synthetic Biology

A lot has been written since last week’s publication of Craig Venter’s latest coup – the creation of the first cell controlled by a synthetic genome. While the reactions span from the  alarmist (“playing god”) to the dismissive (“nothing new”), most commentaries overlook that Venter has demonstrated that life – for now, bacteria – can be customized to an extend that by far exceeds conventional genetic technologies which merely introduce a few new genes into existing organisms.

For now, it is impossible to forecast the success of building and introducing synthetic genomes to manufacture organisms that spill out biofuel or clean up polluted shores at unprecedented efficiency. Synthetic genomes have only recently become available as the technology to accurately synthesize and assemble large pieces of DNA has made tremendous progress and has led to decreasing prices for synthetic DNA. Venter used 1078 cassettes of 1080 base pairs each which were assembled to a genome of 1.08 million base pairs. In comparison, the E. coli genome consists of about 4.6 million base pairs.

The real challenge now is understanding and commanding the interplay of the multiple genes that make up a functioning genome. Venter’s new bacteria provide an exciting testing ground for this kind of research, and that’s why the first companies to profit from this innovation will be the ones providing the technologies to synthesize and assemble large and complex genes.

In the meantime, the place to look at the field’s progress on a regular basis, is SyntheticBiology and the Biobricks Foundation.