Tag: Synthetic biology

Food for Thought: Weekly Wrap-Up

Die Welt this week reports on plans by BayerCropScience, a division of Bayer AG, to develop new, heat- and drought-resistant wheat varieties. To accomplish this goal, BayerCropScience will refrain from introducing novel genes into the wheat genome for fear of protests in Europe. However, the company is cooperating, among others, with Israel-based Evogene to also develop genetically engineered crops for other markets.

Michael Simm in Focus features the latest accomplishments of synthetic biology in which researchers control artificially introduced networks of genes in cells and tissue. As an example, scientists from the Department of Biosystems Science and Engineering (D-BSSE) in Basle, Switzerland, have inserted genes for hormone production into cells. By adding genetic control elements that can be switched on by irradiation with blue light these genes can be controlled from outside. As an example, the researchers in vitro introduced a genetic network for the production of insulin into human tissue which subsequently was micro encapsulated and transplanted to the skin of diabetic mice. After a meal, blue light is applied to switch on insulin production in order to normalize blood sugar levels. The model works well so that the researchers are thinking about clinical trials. Already, the use of light to switch on genes has led to the new scientific discipline of optogenetics which is exploring light-controlled genes and cells to treat diseases such as Parkinson’s or epilepsy. D-BSSE researchers also developed cells carrying a network of genes that is able to normalize uric acid levels in gout patients.

Siegfried Hofmann in Handelsblatt is introducing various therapeutic approaches of biopharmaceutical companies in a series entitled “future lab 2020.” Topics range from personalized medicine to stem cell therapies to novel immune therapies.

David Shaywitz in Forbes provides a thoughtful article explaining why Silicon Valley failed to make a dent in the healthcare space: “most tech-savvy entrepreneurs lack an in-depth appreciation for the complexity of medicine in general, and the nuances of the doctor-patient dynamic they are confidently trying to influence or replace.” He goes on to say that management of high-tech companies needs to understand the science: “When a science-driven business is led by leaders who don’t even know what they don’t know, and who actually believe that the crisp powerpoint slides that bubble up for their review actually and adequately represent the science involved – then you risk making some very ignorant decisions.”

The New Scientist this week features a story on how cancer cells can be poisoned with  2-deoxyglucose. The sugar dislodges a protein protecting a suicide switch which subsequently can be triggered by ABT-263 navitoclax, a molecule under development at Genentech. The magazine also reports on a call for proposals by DARPA, the US military’s research arm, to develop small interfering RNA (siRNA) to fight bacteria. DARPA is seeking ideas for adaptable nanoparticles that can be reprogrammed “on the fly” by loading up specific siRNA to deal with outbreaks among troops.

And finally, the Economist features people pioneering the backyard generation of fuel to power their diesel cars. The recipe starts with collecting used kitchen oil, which after some filtering is broken down into esters and glycerol by adding sodium hydroxide and methanol and heating. Glycerol is drained away and the remainder is washed with water to get rid of impurities. Removing residual water and moisture is done with an aquarium bubbler. The resulting biodiesel, the article states, can be used in diesel cars without any modification. Already, British company Oilybits is selling devices to produce 120 liter batches of biodiesel in a more professional way.

Food for Thought: Weekly Wrap-Up

Solar cells can become cheap bulk ware, even for developing countries, writes Manfred Lindinger in Frankfurter Allgemeine Zeitung (FAZ). He introduces a technology for printing a sheet of zinc oxide, a polymer containing fullerenes and an electrode made from polymers on paper. The technology developed at Technical University Chemnitz can use ordinary printing machines and paper, and the resulting solar paper can be bended and folded. However, the efficiency is still very poor (1.3% at 5 V compared to 10 or more with conventional ones). Life span will amount to a few months. For other approaches to make cheaper solar cells, see this post.

Martina Lenzen-Schulte, also in FAZ, explains how measle viruses leave cells to enter the airway. Today it is known that they do not proliferate in the outer epithelium cells but in lymph nodes. The way back is facilitated by the membrane protein nectin-4, which acts as a transporter carrying the virus through epithelial cells. Lenzen-Schulte also reports that the effect may explain why cancer cells, which often overexpress nectin-4, are vulnerable to measle and other viruses. This might pave a way to develop new oncolytic viruses.

Ernst-Ludwig Winnacker, the nestor of the German biotechnology industry, makes the case for green biotechnology in the weekly Die Zeit. Winnacker criticizes the concept of coexistence that tries to avoid a blending of genetically modified and conventionally bred plants by defining a minimum distance between cultivated areas. In Germany, a farmer cultivating GMOs is liable for every case of cross-breeding, a provision that effectively prohibits GMO cultivation as there is a zero threshold for “contamination”. Winnacker also criticizes the strategy of patenting genetically modified plants instead of protecting them with the traditional plant variety rights that allow for exemptions for the further use of GMOs by breeders and farmers. Green biotechnology, he writes, has – at least in Europe – become the scapegoat for everything that is wrong with modern agriculture, from monoculture to declining biodiversity to the death of bees, although Europe is almost free from GM plants. As 25 years of research into the risk of green biotechnology have not been able to reveal any real danger, Winnacker proposes to amend the German law on genetic engineering and to simply omit the measures restricting the cultivation of GMOs.

Diabetics may soon be able to measure blood sugar without pricking, reports Der Spiegel. A new technology developed by researchers of John’s Hopkins University enables measuring of blood sugar in tear fluid.

In Wirtschaftswoche, Matthias Hohensee introduces US-based 23andme company which offers genetic testing at a rate of $99 plus a flat fee of $9 per month for access to the data. The company, which was criticized for exaggerating the benefits of personal genetic testing, also changed its business model and is now offering its records comprising the data of 125,000 people for research purposes, e.g. to find out why certain hereditary diseases display incomplete penetrance in different carriers of the respective genes.

Theres Lüthi in Neue Zürcher Zeitung (NZZ) reports on clinical studies by Roche and Novartis in people suffering from Down’s or fragile X syndrome in an attempt to improve cognitive abilities.

Alyson Krueger in Forbes reports on a talk on synthetic biology given by Andrew Hessel of Singularity University during the Technonomy 2011 conference. Hessel describes synthetic biology as computer-assisted genetic design that goes from an idea to printing DNA to ultimately booting DNA and forecasts it will render the task of engineering life as straightforward as programming software, or creating a vaccine as simple as Tweeting.

Alex Knapp, also in Forbes, describes a “cyborg yeast” designed by researchers from the University of California at San Francisco and ETH Zurich, Switzerland. In the yeast, the expression of a certain gene can be switched on and off by different shades of red light. The technique may lead to advances in the production of proteins by yeast cultures.

The Economist reports on the first computational pathologist which can can distinguish between grades of breast-cancer cells to provide a more accurate prognosis than a human pathologist can manage.

And finally, scientists found a single gene which can make you appear kinder, reports Catherine de Lange in New Scientist. In experiments conducted at the University of Toronto, people with the so-called GG version of the oxytocin receptor gene were judged to be kinder than those with GA or AA versions. Those with GG variations used significantly more non-verbal empathetic gestures in their storytelling such as smiling and nodding which made them appear kinder.

 

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.

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