Hot off the presses! Apr 01 Nat Biotech

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Latest Articles Include:

• Sharing secrets
  - Nat Biotech 29(4):291 (2011)
  Nature Biotechnology | Editorial Sharing secrets Journal name:Nature BiotechnologyVolume: 29,Page:291Year published:(2011)DOI:doi:10.1038/nbt.1848Published online08 April 2011 The launch of Nature Biotechnology's Trade Secrets blog reflects the growing importance of biotech in emerging markets. View full text Additional data
• Genzyme-Sanofi buyout is second largest biotech deal ever
  - Nat Biotech 29(4):293-294 (2011)
  Nature Biotechnology | News Genzyme-Sanofi buyout is second largest biotech deal ever * Mark Ratner1Journal name:Nature BiotechnologyVolume: 29,Pages:293–294Year published:(2011)DOI:doi:10.1038/nbt0411-293Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Michael Fein/Bloomberg via Getty Images Sanofi's Chris Viehbacher (left) and Genzyme's Henri Termeer seal the $20.1 billion deal that gives France's drugmaker a portfolio of treatments for rare diseases. On March 7, the board of directors of Genzyme recommended that shareholders accept a buyout offer from global pharma giant Sanofi-aventis of Paris, presumably ending the most visible and noisy acquisition negotiation in biotech history. When finalized, it will become the second largest biotech transaction ever, behind only Roche's acquisition of Genentech (Table 1). View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * Cambridge, Massachusetts * Mark Ratner Author Details * Mark Ratner Search for this author in: * NPG journals * PubMed * Google Scholar
• Amylase corn sparks worries
  - Nat Biotech 29(4):294 (2011)
  Nature Biotechnology | News Amylase corn sparks worries * Emily WaltzJournal name:Nature BiotechnologyVolume: 29,Page:294Year published:(2011)DOI:doi:10.1038/nbt0411-294Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. istockphoto/Istankov Corn millers have voiced quality concerns. A genetically modified (GM) variety of corn intended for ethanol production is drawing objections not only from anti-GM organizations but also from some biotech supporters. The crop, approved in February by the US Department of Agriculture, and developed by Basel-based Syngenta and marketed as Enogen, expresses an α-amylase enzyme, which helps break down the starch in corn more efficiently during ethanol production. The trait could cut costs for the ethanol industry by reducing water, energy and chemical use. But if it enters the food processing stream, it could damage corn-based food quality, resulting in sticky tortillas, dense corn puffs and gummy bread, say corn millers and food processors. Wayne Moore, a food scientist and independent consultant hired to review Syngenta's data by the North American Millers' Association in Washington, DC, says, "I'm concerned that if it gets into food processing it could cause some serious problems." A Syngenta spokesperson said the! re is validity to the Millers' Association complaints. "I think they have a legitimate concern," says Jack Bernens, head of technology acceptance at Syngenta. Bernens adds, however, that the probability of amylase corn getting into the food supply is "very, very low." In its proposed voluntary containment plan Syngenta says growers will sign contracts that specify how the corn will be transported and how delivery and harvest equipment will be cleaned. Farmers will not be allowed to grow amylase corn within certain distances—usually 40 miles—of food corn mills. The supply of seed will be limited at first to growers working within the vicinity of certain ethanol plants, and will ramp up slowly. Syngenta's plan "looks good on paper," says Moore, "but I don't know that it's going to work in practice." View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Emily Waltz Search for this author in: * NPG journals * PubMed * Google Scholar
• Amgen spikes interest in live virus vaccines for hard-to-treat cancers
  - Nat Biotech 29(4):295-296 (2011)
  Nature Biotechnology | News Amgen spikes interest in live virus vaccines for hard-to-treat cancers * Charlie Schmidt1Journal name:Nature BiotechnologyVolume: 29,Pages:295–296Year published:(2011)DOI:doi:10.1038/nbt0411-295Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Amgen Amgen's R&D muscle will spur BioVex's oncolytic virus immunotherapies. Oncolytic viruses have a long, checkered history in cancer therapy—perceived as safe but ineffective. So Amgen's announcement in January that it would pay BioVex of Woburn, Massachusetts, $425 million in upfront cash and $575 million in milestones, provided an endorsement of tumor-targeting viruses, placing them under a new spotlight. Thousand Oaks, California–based Amgen based its purchase on promising phase 2 results in 50 patients with metastatic melanoma. After treatment with the genetically modified virus OncoVEX, the company's lead candidate, detectible disease was completely eliminated in eight individuals. In four others who received treatment, disease burden decreased by at least 30%. "What we've seen so far is impressive—durable responses and shrinking tumor masses in a cancer that's notoriously difficult to control," says Roger Perlmutter, Amgen's executive vice president for R&D. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * Portland, Maine * Charlie Schmidt Author Details * Charlie Schmidt Search for this author in: * NPG journals * PubMed * Google Scholar
• Large drugs outdo small
  - Nat Biotech 29(4):296 (2011)
  Nature Biotechnology | News Large drugs outdo small * Bethan HughesJournal name:Nature BiotechnologyVolume: 29,Page:296Year published:(2011)DOI:doi:10.1038/nbt0411-296aPublished online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Biologics are twice as successful as novel small-molecule drugs in gaining market approval, according to a new study. At the 13th Annual Biotechnology Industry Organization (BIO) CEO and Investor Conference, BIO and BioMedTracker, of San Diego, presented their analyses of the approval rates of 4,275 drugs in development from 2003 to 2010. They found that drug success rates from phase 1 to approval was 9% for all indications. Overall rates for secondary indications rates were lower: 14.5% for lead indications and 3.2% for secondary. A further analysis of the types of drugs achieving approval showed that biologics were almost twice as likely as new molecular entities (NMEs) to get approved for a lead indication (26% and 14% respectively). Notably, over 85% of the NMEs are small-molecule drugs. In addition, "The biologics do not include vaccines," says Michael Hay, senior biotechnology analyst at BioMedTracker, who listed the biologics included in the data set as bacterial ! products, cellular therapies, monoclonal antibodies, natural and synthetic proteins, nonviral gene therapies, viral gene therapies, peptides and polyclonal antibodies. Hay also observed that, "Monoclonal antibodies make up over half of the biologic drugs in the data set." Worth noting, non-NMEs were most likely to get approved for any indication (lead or secondary, 41% and 10%, respectively), suggesting that developers of follow-on products benefit from the experience of drug developers who forge the first regulatory pathway for a new drug class. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Bethan Hughes Search for this author in: * NPG journals * PubMed * Google Scholar
• Irish bioprocessing school
  - Nat Biotech 29(4):296 (2011)
  Nature Biotechnology | News Irish bioprocessing school * Jennifer RohnJournal name:Nature BiotechnologyVolume: 29,Page:296Year published:(2011)DOI:doi:10.1038/nbt0411-296bPublished online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The National Institute for Bioprocessing Research and Training (NIBRT) opened its doors in Dublin on February 21 to provide research, training and education for all aspects of bioprocessing. According to its new director, Professor Ian Marison, the 6,500 m2, purpose-built building will provide infrastructure ranging from small-scale pilot suites to a factory-scale production environment, and will focus on biologics and small molecules. The government-funded NIBRT will be run as a collaborative effort by four Irish universities. The aim is to support local companies and to attract new industrial partners both at home and abroad. Marison says that what makes NIBRT special is that its activities will be solely driven by industry need. Once a biomanufacturing need is identified, the NIBRT will put together diverse expertise to solve it in collaboration with industry. If a problem is deemed especially important, the NIBRT may recruit a basic research laboratory to work on it long! term. The ethos is flexibility. The institute might engage in contract research for companies or can collaborate as equal partners. The NIBRT can also host visiting industrial scientists, and vice versa. This flexibility will also be reflected in new intellectual property, which can be generated and owned by the universities, by the industrial stakeholders or as a partnership. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Jennifer Rohn Search for this author in: * NPG journals * PubMed * Google Scholar
• Pharma interest surges in antibody drug conjugates
  - Nat Biotech 29(4):297-298 (2011)
  Nature Biotechnology | News Pharma interest surges in antibody drug conjugates * Sarah Webb1Journal name:Nature BiotechnologyVolume: 29,Pages:297–298Year published:(2011)DOI:doi:10.1038/nbt0411-297Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Genentech T-DM1 combines Genentech's blockbuster antibody Herceptin and the antimitotic cytotoxic DM1 using ImmunoGen's linker technology. In January, Seattle Genetics of Bothell, Washington, entered a $208 million deal with Pfizer to use the biotech firm's monoclonal antibody (mAb)-drug conjugate (ADC) technology for a single oncology target. The agreement comes on the heels of a partnership inked by Novartis to access ImmunoGen's tumor-activated prodrug (TAP) linker technology. The Basel-based pharma agreed to pay ImmunoGen of Waltham, Massachusetts, $45 million upfront and up to $200 million per target for constructing 'souped up' antibodies for several cancer targets. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * Brooklyn, New York * Sarah Webb Author Details * Sarah Webb Search for this author in: * NPG journals * PubMed * Google Scholar
• Benlysta makes history
  - Nat Biotech 29(4):298 (2011)
  Nature Biotechnology | News Benlysta makes history * Mark RatnerJournal name:Nature BiotechnologyVolume: 29,Page:298Year published:(2011)DOI:doi:10.1038/nbt0411-298aPublished online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The first new drug for lupus in almost 50 years has been approved by the US Food and Drug Administration (FDA). Human Genome Sciences (HGS) obtained the agency's go-ahead for its first-in-class drug Benlysta (belimumab) on March 9. The Rockville, Maryland, biotech and its partner, London-based GlaxoSmithKline (GSK), will sell Benlysta, a human monoclonal antibody, at an annual treatment cost of $35,000 to a target market of 200,000 US patients. The agency's approval, the first for lupus since 1956, was based principally on two clinical studies involving 1,684 lupus patients (Nat. Biotechnol.27, 779, 2009). Notably, African American individuals and people with African heritage did not appear to respond to treatment with Benlysta, raising concerns that labeling may be restricted. But FDA decided "the studies lacked sufficient numbers to establish a definite conclusion," and HGS will conduct an additional study in people with those backgrounds. Also, although the regulator ! recommended against treating patients with severe active lupus nephritis or central nervous system lupus—groups not included in the pivotal studies—there was no black box warning excluding them from treatment. Joseph Schwartz of Leerink Swann in Boston called the broad label for Benlysta the "best case scenario" for the company. HGS and GSK expect an approval decision on Benlysta in Europe in the second half of 2011. Schwartz estimates US Benlysta sales will exceed a billion dollars annually in the US by 2014. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Mark Ratner Search for this author in: * NPG journals * PubMed * Google Scholar
• Open access consortium
  - Nat Biotech 29(4):298 (2011)
  Nature Biotechnology | News Open access consortium * Stephen StraussJournal name:Nature BiotechnologyVolume: 29,Page:298Year published:(2011)DOI:doi:10.1038/nbt0411-298bPublished online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. The first public-private partnership aimed at tackling inefficiencies in drug validation to speed up drug discovery held its inaugural brain storming session on February 16. This open access consortium known as Arch2POCM was instigated by University of Toronto biologist Aled Edwards, head of the Structural Genomics Consortium, Stephen Friend of Sage Bionetworks and Chas Bountra, of the University of Oxford. This initiative was set up to move high-risk disease targets to the point of proof of clinical mechanism. That first meeting in Toronto included 43 representatives of industry, academia, regulatory agencies and patient groups (http://www.sagebase.org/partners/Arch2POCM.php). They discussed ways of getting around the privacy and intellectual property (IP) roadblocks that today cause pharma companies to waste time and money repeating experiments with novel compounds their competitors already know will fail. What sets Arch2POCM apart from similar endeavors (Nat. Biotechnol.2! 8, 631–634, 2010) is their insistence on a practical agenda to implement open sourcing by both the public and private sectors. "Each of our groupings agreed to have one or two people work closely in the development of a business plan," said Edwards. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Stephen Strauss Search for this author in: * NPG journals * PubMed * Google Scholar
• Researchers cut loose as Pfizer and Merck shutter European sites
  - Nat Biotech 29(4):299-300 (2011)
  Nature Biotechnology | News Researchers cut loose as Pfizer and Merck shutter European sites * Nidhi Subbaraman1Journal name:Nature BiotechnologyVolume: 29,Pages:299–300Year published:(2011)DOI:doi:10.1038/nbt0411-299Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. l94/ZUMA Press/Newscom Over the next two years, 2,400 people will be leaving Pfizer's R&D site in Sandwich, Kent. At the beginning of February, Pfizer announced as part of its fourth-quarter and full-year earnings report that it would close its 56-year-old research center in Sandwich, Kent, by the end of 2012. The move could terminate 2,400 UK research positions, adding to the growing ranks of scientists laid off from pharmaceutical R&D. On March 16, the UK took another blow with news that Novartis of Basel would slash 550 positions from its West Sussex facility. Europe has been hit particularly badly by layoffs in the drug industry, with large centers of commercial R&D closing in both the UK and the Netherlands over the past 12 months. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * New York * Nidhi Subbaraman Author Details * Nidhi Subbaraman Search for this author in: * NPG journals * PubMed * Google Scholar
• Architects meet stem cells
  - Nat Biotech 29(4):300 (2011)
  Nature Biotechnology | News Architects meet stem cells * Stephen StraussJournal name:Nature BiotechnologyVolume: 29,Page:300Year published:(2011)DOI:doi:10.1038/nbt0411-300Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Mark Citret, Bruce Damonte UCSF's new stem cell building. The University of California at San Francisco opened in February a bold new $123 million building to house its stem cell research facility. The Ray and Dagmar Dolby Regenerative Medicine Building is an example of cutting edge architecture specifically designed to ramp up research productivity. "The point of the building is to accelerate the work we do here, and one way it does this is by creating neighborhoods where you have clusters of investigators working on similar problems," says Arnold Kriegstein director of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, which will be housed in the new facility. One design strategy for achieving this goal was to have open bench laboratory areas. The building's roughly 300 scientists and technicians would share the same work space and equipment even if they were working on different areas of research. The result says Kriegstein is "the feeling that this is just one large enterprise." Another des! ign innovation to create a sense of working intimacy was a split-level, open glass, partition design that effectively makes the four floors of the building only half a floor apart. "The open stairways and glass partitions allow for a seamless floor-to-floor relationship," is how Kriegstein describes it. Fetal surgeon Tippi MacKenzie, for instance, shares laboratory space with another group studying placental biology, a proximity that creates a synergy for exploring how implanted maternal stem cells might treat diseases while a child is still in the womb. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Stephen Strauss Search for this author in: * NPG journals * PubMed * Google Scholar
• p38 kinase inhibitor approved for idiopathic pulmonary fibrosis
  - Nat Biotech 29(4):301 (2011)
  Nature Biotechnology | News p38 kinase inhibitor approved for idiopathic pulmonary fibrosis * Nuala Moran1Journal name:Nature BiotechnologyVolume: 29,Page:301Year published:(2011)DOI:doi:10.1038/nbt0411-301Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Scan showing pulmonary fibrosis with scarred lung tissue. The first treatment for the debilitating and fatal lung disease idiopathic pulmonary fibrosis (IPF) has been approved in Europe. On March 3, the European Commission gave InterMune of Brisbane, California, the go-ahead to market the orphan drug Esbriet (pirfenidone)—a rare success in a disease that has recently thwarted drug development efforts at several companies. In December, Gilead Sciences of Foster City, California, suspended phase 3 studies in IPF for Letairis (ambrisentan), which was already approved to treat pulmonary arterial hypertension. Nine months earlier, Swiss biotech Actelion suspended a similar compound Tracleer (bosentan; also previously registered for pulmonary arterial hypertension) when it failed to show significance in phase 3 studies of IPF. Whereas the new drug Esbriet targets the p38 gamma kinase, Tracleer and Letairis both target the endothelin system. Getting the nod for Esbriet has not been without hitches—at least in Western markets. The US Food and Drug Administration refused to approve the small molecule last May, issuing InterMune with a complete response letter asking for an additional clinical trial. In 2008, under the trade name Pirespa, Osaka, Japan–based Shionogi had previously obtained approval for the use of pirfenidone against IPF in Japan. According to InterMune CEO Daniel Welch, the European approval has been built on the company's experience in IPF. Over the past 11 years, he says "we've studied more patients than any other company." Welch says one of the key difficulties in developing treatments has been in understanding the definition of the disease, in which the generation of fibrotic tissue composed of extracellular matrix (ECM) proteins, including collagen and fibronectin, incrementally—and fatally—reduces the oxygen-exchanging capacity of the lungs. "The medical community doesn't understand what causes IPF. If it did, it would be a lot easier trying to figure out how to stop it," Welch says. InterMune and others have kept trying (Table 1), not only because of the unmet medical need—IPF accounts for ~135,000 patients in Europe and 200,000 in the US—but also because an effective treatment for this orphan disease potentially would open the door to treatments of many other fibrotic diseases. Table 1 Full table Esbriet is a small-molecule p38 gamma kinase inhibitor that blocks the synthesis of transforming growth factor beta (TGF-β), which is involved in the process of producing fibrotic tissue. Stromedix, located in Cambridge, Massachusetts, also has TGF-β in its sights. The company expects to launch a phase 2 trial of STX-100, a humanized monoclonal antibody (mAb) against integrin α-v-β-6, an ECM protein that controls the activation of TGF-β, later this year. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Affiliations * London * Nuala Moran Author Details * Nuala Moran Search for this author in: * NPG journals * PubMed * Google Scholar
• GM crop cultivation surges, but novel traits languish
  - Nat Biotech 29(4):302 (2011)
  Nature Biotechnology | News | Data Page GM crop cultivation surges, but novel traits languish * Wayne Peng1Journal name:Nature BiotechnologyVolume: 29,Page:302Year published:(2011)DOI:doi:10.1038/nbt.1842Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Total planting area for transgenic crops exceeded 1 billion hectares in 2010. Syngenta's E3272 maize line, designed to facilitate biofuel production with a mutant alpha-amylase transgene, was approved in the US earlier this year. Although new approvals and field trials slowed down in the US and Europe, food and feed uses of existing transgenic crops keep expanding in Brazil, the Philippines and Korea. Global area by transgenic state Box 1: Global area by transgenic state Full box Global area of transgenic crops by country View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Wayne Peng is Emerging Technology Analyst, Nature Publishing Group Author Details * Wayne Peng Search for this author in: * NPG journals * PubMed * Google Scholar Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Mixed messages from Washington
  - Nat Biotech 29(4):303-305 (2011)
  Nature Biotechnology | News | News Feature Mixed messages from Washington * Jeffrey L. Fox1Journal name:Nature BiotechnologyVolume: 29,Pages:303–305Year published:(2011)DOI:doi:10.1038/nbt.1836Published online08 April 2011 With the economy sputtering toward recovery, federal outlays shriveling and the political scene in upheaval, the US biotech policy picture is more than a little blurred. Jeffrey L. Fox reports. View full text Additional data Affiliations * Washington, DC * Jeffrey L. Fox Author Details * Jeffrey L. Fox Search for this author in: * NPG journals * PubMed * Google Scholar
• For the records
  - Nat Biotech 29(4):306-309 (2011)
  
• Acceptable changes in quality attributes of glycosylated biopharmaceuticals
  - Nat Biotech 29(4):310-312 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Acceptable changes in quality attributes of glycosylated biopharmaceuticals * Martin Schiestl1 * Thomas Stangler1 * Claudia Torella1 * Tadej Čepeljnik1 * Hansjörg Toll1 * Roger Grau1 * AffiliationsJournal name:Nature BiotechnologyVolume: 29,Pages:310–312Year published:(2011)DOI:doi:10.1038/nbt.1839Published online08 April 2011 To the Editor: Since the first marketing approvals of recombinant biopharmaceuticals, the question of which changes in quality attributes, which comprise identity, strength and purity, are acceptable in the life cycle of these products without changing the product label has been debated extensively1. This question is especially important in the context of manufacturing process changes, which happen quite frequently and for various reasons (e.g., process improvements, scale changes or site transfers). Although companies and health authorities have been managing these quality changes for many years based on the principle that changes in quality attributes can be accepted only if they do not alter safety and efficacy, the lack of peer-reviewed data in the public domain has limited debates about product quality and variation to a discussion of principles rather than specifics. Here, we present a study that looks at variation in three major marketed biologics, the purpose of which is to provide! more transparency and to anchor the debate about acceptable changes in quality attributes on a firmer factual footing. Identifying such variations in quality attributes could help not only biotech companies in their development efforts but also the medical and scientific communities in understanding these products. By analyzing the quality profiles of the glycosylated recombinant therapeutic proteins Aranesp (darbepoetin alfa), Rituxan/Mabthera (rituximab) and Enbrel (etanercept) sourced from the market between 2007 and 2010, our data thus provide examples of acceptable variations for products that have remained on the market with unchanged product labels. Glycosylated proteins are complex molecules and even a well-controlled product may consist of several hundred or more glycoforms having the same amino acid sequence but different glycan composition. When making these products, the manufacturer has to deliver a consistent product quality to guarantee a reproducible clinical performance. Current analytical methods allow the detection of even small changes in quality attributes and can therefore enable sensitive monitoring of the batch-to-batch consistency and variability of the manufacturing process. Several different factors may account for changes in quality attributes. The first is the inherent batch-to-batch variability in the manufacturing process. Second, process drifts can lead to gradual changes of attributes. Such drifting events are not desired and normally trigger further investigations and corrective actions, or even redevelopment activities to ensure process consistency. Finally, larger and abrupt changes in quali! ty attributes can occur after implementation of manufacturing process changes, which are all too common in the pharmaceutical industry. Although manufacturers try to prevent associated changes in quality attributes, such changes cannot be avoided in every case. Changes in the biologics manufacturing process are tightly regulated by the health authorities. Manufacturers need to demonstrate that the process change does not alter the clinical safety or efficacy of the biologic product. The evaluation of such changes follows a comparability exercise between the pre- and post-change product, which is focused on the quality level and sometimes, depending on the magnitude of the change and the existing product understanding, also requires comparative data on the preclinical and clinical levels. The principles of the comparability exercise are regulated in guidelines, such as the International Conference on Harmonisation (ICH) Q5E (http://www.ich.org/fileadmin/Public_Web_Site/ICH_Products/Guidelines/Quality/Q5E/Step4/Q5E_Guideline.pdf), which acknowledges that "the demonstration of comparability does not necessarily mean that the quality attributes of the pre-change and post-change product are identical, but that they are highly similar ! and that the existing knowledge is sufficiently predictive to ensure that any differences in quality attributes have no adverse impact upon safety or efficacy of the drug product." Comparability decisions are difficult to make and require the complete assessment of the existing process and product including the knowledge of structure-function relationships. Others1 have already acknowledged that a collection of data would be extremely valuable to come to a more informed design and improved assessment of comparability studies. And yet, very little data on commercialized products can be found in the public domain. In an attempt to at least partially fill this gap, we have analyzed multiple batches of Aranesp, Rituxan/Mabthera and Enbrel to study the variability in the quality attributes of modern therapeutic proteins currently on the market. The data were generated as described in the Supplementary Methods, using the materials listed in Supplementary Tables 12. The active pharmaceutical ingredient of Aranesp, darbepoetin alfa, is an erythropoiesis-stimulating protein. It represents an engineered analog of human erythropoietin. It differs from endogenous erythropoietin mainly by an alteration of the amino acid sequence that introduces two additional N-glycosylation sites, which results in an elongated half-life in vivo. The biological activity and clinical effect of erythropoietins is influenced by the glycosylation profile, which needs to be tightly controlled during production2. We have characterized commercial batches sourced in the European Union (EU) by capillary zone electrophoresis, which separates isoforms with different charges resulting from varying numbers of sialic acids per molecule (Fig. 1 and Supplementary Fig. 1). The in vivo biological activity is known to be dependent on the number of sialic acid units per molecule, which is a result of the available sialylation sites, the antennarity of the N-glycans and the completeness of sialylation3. back to article Figure 1: Comparison of the pre- and post-change Aranesp batches measured by capillary zone electrophoresis. () Relative content of the individual isoforms of the pre-change (n = 18) and the post-change (n = 4) batches. () Representative electropherograms; peaks are labeled with the isoform number. View full text Figures at a glance * Figure 1: Comparison of the pre- and post-change Aranesp batches measured by capillary zone electrophoresis. () Relative content of the individual isoforms of the pre-change (n = 18) and the post-change (n = 4) batches. () Representative electropherograms; peaks are labeled with the isoform number. * Figure 2: Comparison of the different pre- and post-change batches of Rituxan/Mabthera. () Exemplary CEX chromatograms. () Amount of basic variants of the pre-change (n = 12) and post-change (n = 6) batches as measured by CEX. () ADCC potency of the pre-change (n = 11) and post-change (n = 8) batches. () Relative amount of the G0 glycan of the pre-change (n = 13) and post-change (n = 11) batches. () Exemplary glycan mapping chromatograms. () Glycan legend. * Figure 3: Comparison of the different pre- and post-change batches of Enbrel. () Relative amounts of basic variants of the pre-change (n = 6) and the post-change (n = 6) batches as measured by CEX.() Relative amount of the G2F glycan of the pre-change (n = 25) and the post-change (n = 9) batches. () Exemplary CEX chromatograms. () Exemplary glycan mapping chromatograms. Author information * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Sandoz Biopharmaceuticals, Kundl, Austria. * Martin Schiestl, * Thomas Stangler, * Claudia Torella, * Tadej Čepeljnik, * Hansjörg Toll & * Roger Grau Competing financial interests The authors are employees of Novartis/Sandoz, which is developing, manufacturing and marketing biopharmaceuticals, including biosimilar products. Author Details * Martin Schiestl Search for this author in: * NPG journals * PubMed * Google Scholar * Thomas Stangler Search for this author in: * NPG journals * PubMed * Google Scholar * Claudia Torella Search for this author in: * NPG journals * PubMed * Google Scholar * Tadej Čepeljnik Search for this author in: * NPG journals * PubMed * Google Scholar * Hansjörg Toll Search for this author in: * NPG journals * PubMed * Google Scholar * Roger Grau Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (451Kb) Supplementary Figures 1—3, Supplementary Tables 1,2 and Supplementary Methods Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Research Assistant - Analytical * ITC Ltd. (R&D Centre) * Bangalore, Karnataka, India * Scientist Positions * Rajiv Gandhi Centre for Biotechnology * Trivandrum, India * PostDoc Position * Max-Planck-Institut fur Kognitions- und Neurowissenschaften Leipzig * Leipzig, Germany * Post a free job * More science jobs Related content Articles * Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21 Nature Genetics 25 Jan 2009 * Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells Nature Biotechnology 08 Apr 2011 * Automated monitoring and analysis of social behavior in Drosophila Nature Methods 08 Mar 2009 * Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues Nature Methods 27 Dec 2009 * Genome-wide association study identifies three loci associated with melanoma risk Nature Genetics 05 Jul 2009 View all Open innovation challenges * RNAi Sequences Targeted to the Asian Citrus Psyllid Genome Deadline:May 03 2011Reward:$100,000 USD The non-profit Citrus Research and Development Foundation, desires proposals for RNA sequences that … * Chordoma Cancer Cell Lines Needed to Save Lives! Deadline:Jun 13 2011Reward:$10,000 USD The Chordoma Foundation requests cell lines or animal models that can be used for research into chor… * Powered by: * More challenges Top content Emailed * Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors Nature Biotechnology 26 Oct 2008 * Fresh from the biologic pipeline—2010 Nature Biotechnology 09 Mar 2011 * Biosimilars encircle Rituxan, US debates innovator exclusivity Nature Biotechnology 09 Mar 2011 * Label-free quantification of membrane-ligand interactions using backscattering interferometry Nature Biotechnology 13 Mar 2011 * Advancing RNA-Seq analysis Nature Biotechnology 01 May 2010 View all Downloaded * Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes Nature Biotechnology 20 Mar 2011 * Systematic exploration of essential yeast gene function with temperature-sensitive mutants Nature Biotechnology 27 Mar 2011 * Label-free quantification of membrane-ligand interactions using backscattering interferometry Nature Biotechnology 13 Mar 2011 * Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology 02 May 2010 * Beyond natural antibodies: the power of in vitro display technologies Nature Biotechnology 09 Mar 2011 View all Blogged * Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts Nature Biotechnology 30 Nov 2007 * Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology 19 Dec 2010 * Are the current ontologies in biology good ontologies? Nature Biotechnology 01 Sep 2005 * An orally delivered small-molecule formulation with antiangiogenic and anticancer activity Nature Biotechnology 29 Jun 2008 * Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds Nature Biotechnology 22 Jun 2008 View all * Nature Biotechnology * ISSN: 1087-0156 * EISSN: 1546-1696 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells
  - Nat Biotech 29(4):313-314 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Karotypic abnormalities in human induced pluripotent stem cells and embryonic stem cells * Seth M Taapken1 * Benjamin S Nisler1 * Michael A Newton2 * Tori L Sampsell-Barron1, 3, 4 * Kimberly A Leonhard1 * Erik M McIntire1 * Karen D Montgomery1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:313–314Year published:(2011)DOI:doi:10.1038/nbt.1835Published online08 April 2011 To the Editor: Although induced pluripotent stem cells (iPSCs) resemble embryonic stem cells (ESCs) with regard to pluripotency1, 2, reports of transcriptional, epigenetic and genetic differences between the two cell types emphasize the need for large-scale comparative analyses. We have performed karyotype analysis on >1,700 human iPSC and ESC cultures collected from 97 investigators in 29 laboratories. Our data reveal no notable differences in the incidence of chromosomal aberrations in iPSCs and ESCs: 12.50% of 552 cultures from 219 human iPSC lines have abnormal karyotypes, compared to 12.90% in 1,163 cultures from 40 human ESC lines (Table 1). Recurrent aberrations are summarized in Figure 1 and detailed in Supplementary Table 1. The unselected data set was carefully screened to avoid sampling redundancies that may result in ascertainment bias. back to article Figure 1: Recurrent chromosomal abnormalities in human ESC and iPSC cultures. "Other" refers to nonrecurring structural or numerical abnormalities; full karyotypes for these abnormalities appear in Supplementary Table 2. Abnormalities of chromosome 12 are divided into two categories: full trisomy 12 and partial trisomy 12, due to either isochromosome 12p (i(12)(p10)) or an inverted duplication of 12p (dup(12)(p13p11.2)). () Frequency of abnormalities in each cell type as a percentage of total abnormalities; raw data shown in Supplementary Table 1. () The number of each abnormality found in iPSC cultures according to the method of reprogramming1, 3. View full text Author information * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * WiCell Research Institute, Madison, Wisconsin, United States. * Seth M Taapken, * Benjamin S Nisler, * Tori L Sampsell-Barron, * Kimberly A Leonhard, * Erik M McIntire & * Karen D Montgomery * Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States. * Michael A Newton * Research and Development, Life Technologies, Inc., Madison, Wisconsin, United States. * Tori L Sampsell-Barron * Biotechnology Department, Madison Area Technical College, Madison, Wisconsin, United States. * Tori L Sampsell-Barron Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Karen D Montgomery Author Details * Seth M Taapken Search for this author in: * NPG journals * PubMed * Google Scholar * Benjamin S Nisler Search for this author in: * NPG journals * PubMed * Google Scholar * Michael A Newton Search for this author in: * NPG journals * PubMed * Google Scholar * Tori L Sampsell-Barron Search for this author in: * NPG journals * PubMed * Google Scholar * Kimberly A Leonhard Search for this author in: * NPG journals * PubMed * Google Scholar * Erik M McIntire Search for this author in: * NPG journals * PubMed * Google Scholar * Karen D Montgomery Contact Karen D Montgomery Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (418Kb) Supplementary Figures 1,2, Supplementary Tables 1—4 and Supplementary Methods Additional data * Journal home * Current issue * For authors * Subscribe * E-alert sign up * RSS feed Science jobs from naturejobs * Scientist Positions * Rajiv Gandhi Centre for Biotechnology * Trivandrum, India * President / CEO * Critical Path Institute * Tucson, United States * Open Faculty Appointments * UCLA * Los Angeles, CA * Post a free job * More science jobs Related content Articles * Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis Nature Genetics 25 Jan 2009 * Chemical phylogenetics of histone deacetylases Nature Chemical Biology 07 Feb 2010 * Mutation of DNASE1 in people with systemic lupus erythematosus Nature Genetics 01 Aug 2001 * Nanoparticles can cause DNA damage across a cellular barrier Nature Nanotechnology 05 Nov 2009 * Acceptable changes in quality attributes of glycosylated biopharmaceuticals Nature Biotechnology 08 Apr 2011 View all Open innovation challenges * Immortalized Insect Cell Line for Neuronal Studies Deadline:Jun 06 2011Reward:$100,000 USD The Seeker requires an insect neuronal cell line expressing specific functional markers and amenable… * Equipment and Processes for Continuous-flow Solids-based Chemical Synthesis Deadline:May 04 2011Reward:$10,000 USD The goal of this Challenge is to create a comprehensive list of equipment and processes used for con… * Powered by: * More challenges Top content Emailed * Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors Nature Biotechnology 26 Oct 2008 * Fresh from the biologic pipeline—2010 Nature Biotechnology 09 Mar 2011 * Biosimilars encircle Rituxan, US debates innovator exclusivity Nature Biotechnology 09 Mar 2011 * Label-free quantification of membrane-ligand interactions using backscattering interferometry Nature Biotechnology 13 Mar 2011 * Advancing RNA-Seq analysis Nature Biotechnology 01 May 2010 View all Downloaded * Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes Nature Biotechnology 20 Mar 2011 * Systematic exploration of essential yeast gene function with temperature-sensitive mutants Nature Biotechnology 27 Mar 2011 * Label-free quantification of membrane-ligand interactions using backscattering interferometry Nature Biotechnology 13 Mar 2011 * Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology 02 May 2010 * Beyond natural antibodies: the power of in vitro display technologies Nature Biotechnology 09 Mar 2011 View all Blogged * Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts Nature Biotechnology 30 Nov 2007 * Haplotype-resolved genome sequencing of a Gujarati Indian individual Nature Biotechnology 19 Dec 2010 * Are the current ontologies in biology good ontologies? Nature Biotechnology 01 Sep 2005 * An orally delivered small-molecule formulation with antiangiogenic and anticancer activity Nature Biotechnology 29 Jun 2008 * Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds Nature Biotechnology 22 Jun 2008 View all * Nature Biotechnology * ISSN: 1087-0156 * EISSN: 1546-1696 * About NPG * Contact NPG * RSS web feeds * Help * Privacy policy * Legal notice * Accessibility statement * Terms * Nature News * Naturejobs * Nature Asia * Nature EducationSearch:Go © 2011 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.partner of AGORA, HINARI, OARE, INASP, CrossRef and COUNTER
• EU legitimizes GM crop exclusion zones
  - Nat Biotech 29(4):315-317 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence EU legitimizes GM crop exclusion zones * Maite Sabalza1, 4 * Bruna Miralpeix1, 4 * Richard M Twyman2, 4 * Teresa Capell1 * Paul Christou1, 3 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:315–317Year published:(2011)DOI:doi:10.1038/nbt.1840Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. To the Editor: On July 13, 2010, the European Commission (EC) officially proposed to give member states the freedom to veto the cultivation of genetically modified (GM) crops on their own territory without having to provide any scientific evidence relating to new risks1. The objective of the legislation is ostensibly to make individual member states responsible for their own policy on GM crops, and therefore to speed up pending authorizations by removing the ability of those member states to veto approval throughout the European Union by avoiding a qualified majority (Fig. 1). However, we argue that the opt-out will have exactly the opposite effect to that intended, allowing the creation of arbitrary GM-free zones in Europe that will cause untold damage to the EU economy and its global scientific standing. Figure 1: The previous voting habits of the EU ministers on matters concerning GM crops. Europe divides into two roughly equal camps (pro-GM in green and anti-GM in red) based on votes cast on 19 GM proposals between 2003 and 2005. In 2005, the pro-GM camp had a slight advantage because several of the most populous member states were pro-GM. More recently, there has been a slip towards the anti-GM stance with Germany and France now adopting an anti-GM position, although they are more likely to abstain on proposals rather than actively oppose. This is reflected in the voting for the approval of the Amflora GM potato on February 18, 2008. (Data from Friends of the Earth; symbols represent votes for, against and abstentions; not all countries voted on every proposal; the authors thank Michael Green for assistance in the preparation of this figure.) * Full size image (329 KB) * Figures/tables index The removal of any need for scientific justification in decisions concerning GM crops effectively serves to legalize the currently illegal practice in which individual member states arbitrarily declare GM-free zones within their borders, or ban GM crops altogether2. The only GM crops currently grown in Europe are the pest-resistant maize variety MON810 and the Amflora potato variety engineered to produce modified starch. Both are banned in Austria, Hungary and Luxembourg, and the MON810 event is also banned in France, Greece and Germany (Table 1). Poland is currently drawing up legislation to ban all GM seeds, and other member states are considering similar proposals. Although these existing and proposed bans are technically in breach of EU regulations, at least those member states implementing a ban have to make some sort of effort to justify their decision on scientific grounds, even if the evidence used in such cases is dubious (the 'safeguard clause'). When the legal ame! ndment enters into force, member states will be free to restrict or prohibit the cultivation of all or particular GM crops within their territory, including crops that have already been authorized for cultivation under Directive 2001/18/EC and Regulation EC 1829/2003, and will be able to do so without explanation. This places the future of GM agriculture in Europe at the whim of politicians who may feel compelled to act in response to the media or activist propaganda. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Primary authors * These authors contributed equally to this work. * Maite Sabalza, * Bruna Miralpeix & * Richard M Twyman Affiliations * Departament de Producció Vegetal I Ciència Forestal, University of Lleida, Lleida, Spain. * Maite Sabalza, * Bruna Miralpeix, * Teresa Capell & * Paul Christou * Department of Biological Sciences, University of Warwick, Coventry, UK. * Richard M Twyman * Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, Barcelona, Spain. * Paul Christou Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Paul Christou Author Details * Maite Sabalza Search for this author in: * NPG journals * PubMed * Google Scholar * Bruna Miralpeix Search for this author in: * NPG journals * PubMed * Google Scholar * Richard M Twyman Search for this author in: * NPG journals * PubMed * Google Scholar * Teresa Capell Search for this author in: * NPG journals * PubMed * Google Scholar * Paul Christou Contact Paul Christou Search for this author in: * NPG journals * PubMed * Google Scholar Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. 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• Intellectual property rights in publicly funded biobanks: much ado about nothing?
  - Nat Biotech 29(4):319-323 (2011)
  Nature Biotechnology | Feature | Patents Intellectual property rights in publicly funded biobanks: much ado about nothing? * Saminda Pathmasiri1 * Mylène Deschênes1 * Yann Joly2 * Tara Mrejen2 * Francis Hemmings3 * Bartha Maria Knoppers3 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:319–323Year published:(2011)DOI:doi:10.1038/nbt.1834Published online08 April 2011 Should biobanks be involved in downstream intellectual property rights developed from accessing materials contained in them, and to what extent? View full text Figures at a glance * Figure 1: IPRs developed in the context of biobanks. * Figure 2: Innovation cycle in publicly funded biobanks. Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Saminda Pathmasiri and Myléne Deschênes are at the Public Population Project in Genomics (P3G) Consortium, Montreal, Quebec, Canada * Mylène Deschênes * Yann Joly, Tara Mrejen and Bartha Maria Knoppers are at McGill University, Montreal, Quebec, Canada * Francis Hemmings is at the University of Montreal, Montreal, Quebec, Canada. * Bartha Maria Knoppers Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Saminda Pathmasiri Author Details * Saminda Pathmasiri Contact Saminda Pathmasiri Search for this author in: * NPG journals * PubMed * Google Scholar * Mylène Deschênes Search for this author in: * NPG journals * PubMed * Google Scholar * Yann Joly Search for this author in: * NPG journals * PubMed * Google Scholar * Tara Mrejen Search for this author in: * NPG journals * PubMed * Google Scholar * Francis Hemmings Search for this author in: * NPG journals * PubMed * Google Scholar * Bartha Maria Knoppers Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Recent patent applications in gene expression
  - Nat Biotech 29(4):324 (2011)
  Nature Biotechnology | Feature | Patents Recent patent applications in gene expression Journal name:Nature BiotechnologyVolume: 29,Page:324Year published:(2011)DOI:doi:10.1038/nbt.1850Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• SiRNA delivery with exosome nanoparticles
  - Nat Biotech 29(4):325-326 (2011)
  Nature Biotechnology | News and Views SiRNA delivery with exosome nanoparticles * Jasper G van den Boorn1 * Martin Schlee1 * Christoph Coch1 * Gunther Hartmann1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:325–326Year published:(2011)DOI:doi:10.1038/nbt.1830Published online08 April 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. A natural system for ferrying RNA between cells is used to transport siRNA to the mouse brain. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Jasper G. van den Boorn, Martin Schlee, Christoph Coch and Gunther Hartmann are at the Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Gunther Hartmann Author Details * Jasper G van den Boorn Search for this author in: * NPG journals * PubMed * Google Scholar * Martin Schlee Search for this author in: * NPG journals * PubMed * Google Scholar * Christoph Coch Search for this author in: * NPG journals * PubMed * Google Scholar * Gunther Hartmann Contact Gunther Hartmann Search for this author in: * NPG journals * PubMed * Google Scholar Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Biofuels from protein
  - Nat Biotech 29(4):327-328 (2011)
  Nature Biotechnology | News and Views Biofuels from protein * Jonathan R Mielenz1Journal name:Nature BiotechnologyVolume: 29,Pages:327–328Year published:(2011)DOI:doi:10.1038/nbt.1838Published online08 April 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Rerouting nitrogen flux in bacteria allows renewable production of biofuels from proteins. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Jonathan R. Mielenz is at the Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA. e-mail: Competing financial interests The author declares no competing financial interests. Author Details * Jonathan R Mielenz Contact Jonathan R Mielenz Search for this author in: * NPG journals * PubMed * Google Scholar Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• A new look at membrane protein binding
  - Nat Biotech 29(4):328-329 (2011)
  Nature Biotechnology | News and Views A new look at membrane protein binding * Charles A Lunn1Journal name:Nature BiotechnologyVolume: 29,Pages:328–329Year published:(2011)DOI:doi:10.1038/nbt.1820Published online08 April 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. An optical spectroscopy method can measure the affinities of ligands to membrane receptors that are embedded in their native membranes. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Charles A. Lunn is at Merck Sharp and Dohme Corp., Kenilworth, New Jersey, USA. e-mail: Competing financial interests The author is employed by Merck Sharp and Dohme Corp. Author Details * Charles A Lunn Contact Charles A Lunn Search for this author in: * NPG journals * PubMed * Google Scholar Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Bessel beams for light relief
  - Nat Biotech 29(4):329 (2011)
  Nature Biotechnology | News and Views Bessel beams for light relief * Peter HareJournal name:Nature BiotechnologyVolume: 29,Page:329Year published:(2011)DOI:doi:10.1038/nbt.1844Published online08 April 2011 Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. E. Betzig, T. Planchon & L. Gao The damaging effects of prolonged exposure to light have long stymied analysis of dynamic processes in single living cells at high spatial resolution in real time. Photobleaching, which often results from light that illuminates parts of the sample outside the area in focus, further cuts into microscopists' so-called photon budget. Reporting in Nature Methods, Planchon et al.1 describe the use of Bessel beam plane-illumination microscopy to address these challenges. The ability to acquire two-dimensional image planes at rates approaching 200 frames s−1 enables them to assemble, within <10 s, three-dimensional images with resolutions down to ~0.3 μm. The approach is the first application of plane-illumination microscopy to single cells. Plane illumination confines excitation to the area in focus by shining a sheet of light through the side of the sample and illuminating only the specific plane that the objective above the sample is focused on. However, the broad sheets of light produced by the Gaussian beams used to image multicellular structures at single-cell resolution are too thick to monitor subcellular events. To circumvent this limitation, Planchon et al. turned to Bessel beams—very narrow nondiffracting light rays each surrounded by concentric rings of less intense light. The key challenge lay in eliminating the phototoxicity, photobleaching and out-of-focus haze caused by the weaker peripheral light. The authors addressed this problem by using two-photon excitation and an approach called structured illumination, either alone or together. Structured illumination involves rapidly switching the beam on and off instead of sweeping it across the sample continuously. The combination of both approaches is slightly superior to either alone, but comes at the expense of slower image acquisition than can be obtained using a continuously swept beam. As depicted in this montage, the authors use the approach to image (clockwise from left) internal architecture and vacuoles in a monkey kidney cell (gold), membrane ruffles at the surface of a monkey kidney cell (orange), microtubules in a pig kidney cell (green), mitochondria in a human osteosarcoma cell (blue and blue-green) and chromosomes during mitosis of a pig kidney cell (orange). Two-color live imaging at the same level of four-dimensional spatiotemporal detail is possible for processes that occur at rates compatible with the time needed to collect frames at the desired spatial resolution. Proteins that participate in processes with faster dynamics can be monitored by labeling them with the same fluorescent tag, as long as they are known a priori to remain spatially segregated during analysis. View full text Read the full article * Instant access to this article: US$18Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data
• Research highlights
  - Nat Biotech 29(4):330 (2011)
  Nature Biotechnology | Research Highlights Research highlights * Kathy Aschheim * Laura DeFrancesco * Peter Hare * Craig MakJournal name:Nature BiotechnologyVolume: 29,Page:330Year published:(2011)DOI:doi:10.1038/nbt.1853Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Cross-linked multilammelar vesicles Subunit vaccines seldom activate the potent T-cell responses needed to counteract many viral diseases and cancers because of inefficient presentation of antigens to naive CD8+ T cells. Success to date in encapsulating antigens and adjuvants within unilamellar and multilamellar lipid vesicles is thought to arise from an enhancement of antigen stability and the mimicking of cues normally associated with a protective immune response. Moon et al. build on these efforts by covalently crosslinking the concentric membrane bilayers that encapsulate a core filled with model antigen ovalbumin (blue in picture) and embedding the lipid-like Toll-like receptor 4 (TLR4) agonist monophosphoryl lipid A (MPLA; red in picture) within the bilayers. Comparisons with simple liposomes and multilamellar liposomes of the same lipid composition reveal that the new polyethylene glycol–decorated, interbilayer–crosslinked multilamellar vesicles (ICMVs) elicit T-cell and antibody responses to the mo! del antigen ovalbumin in mice comparable to those for strong, live-vector vaccines. Stapling of the bilayers appears to prolong persistence of the vaccine in the serum while optimizing vaccine delivery to antigen-presenting cells. It remains to be seen whether these promising effects will translate to better protective immunity in disease models. (Nat. Mater.10, 243–251, 2011) PH Immunity through IL-17 Pediatric Streptococcus pneumoniae infections represent a significant health problem, despite the existence of effective vaccines. Vaccines cover only a fraction of the extant serotypes, and the population of S. pneumoniae colonizing the nasal mucosa is dynamic, necessitating the production of new vaccines. Moffitt et al. use a genomic approach to design serotype-independent vaccines that trigger immune responses in mouse models and in human cells. Based on prior work showing that mucosal-derived immunity in adults resistant to S. pneumoniae is mediated by IL-17–secreting CD4+ T cells, the researchers first screened a library of pneumococcal proteins for those that stimulate IL-17 secretion in vitro. They identified 17 proteins that were present in all 22 of the sequenced S. pneumoniae genomes and did not cross-react with human or other bacterial proteins. From those, five that were expressed at high levels in Escherichia coli were selected for further testing. Two selecte! d proteins (both components of transport systems) stimulated mouse splenocytes and human peripheral blood monocytes to secrete IL-17. In addition, mice immunized intranasally with those antigens were protected from infection with clinical strains of S. pneumoniae; this protection was abrogated by depleting the animals of CD4+ T cells or by inhibiting the IL-17 pathway. The work identifies a new route to immunity as well as a novel set of antigens—none of the antigens overlaps with those that elicit antibody responses. In addition, this approach may be applicable to other mucosal pathogens, of which several exist in humans. (Cell Host Microbe, 158–165, 2011) LD View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data Author Details * Kathy Aschheim Search for this author in: * NPG journals * PubMed * Google Scholar * Laura DeFrancesco Search for this author in: * NPG journals * PubMed * Google Scholar * Peter Hare Search for this author in: * NPG journals * PubMed * Google Scholar * Craig Mak Search for this author in: * NPG journals * PubMed * Google Scholar
• John Storey
  - Nat Biotech 29(4):331-333 (2011)
  Nature Biotechnology | Computational Biology | Profile John Storey * H. Craig Mak1Journal name:Nature BiotechnologyVolume: 29,Pages:331–333Year published:(2011)DOI:doi:10.1038/nbt.1831Published online08 April 2011 John Storey provides his take on the importance of new statistical methods for high-throughput sequencing. View full text Additional data Affiliations * H. Craig Mak is Associate Editor, Nature Biotechnology Author Details * H. Craig Mak Search for this author in: * NPG journals * PubMed * Google Scholar
• Overcoming barriers to membrane protein structure determination
  - Nat Biotech 29(4):335-340 (2011)
  Nature Biotechnology | Research | Perspective Overcoming barriers to membrane protein structure determination * Roslyn M Bill1 * Peter J F Henderson2 * So Iwata3 * Edmund R S Kunji4 * Hartmut Michel5 * Richard Neutze6 * Simon Newstead7 * Bert Poolman8 * Christopher G Tate9 * Horst Vogel10 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:335–340Year published:(2011)DOI:doi:10.1038/nbt.1833Published online08 April 2011 Abstract * Abstract * Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank. View full text Figures at a glance * Figure 1: Progress in solving prokaryotic and eukaryotic membrane protein structures. () Trends in the use of host cells for the production of recombinant membrane proteins used in structural studies. The number of unique α-helical integral membrane protein structures deposited in the Protein Data Bank each year since 1985 is broken down according to whether the structure was derived from natural (black) or recombinant (orange) sources. Inset: a pie chart showing the breakdown of various recombinant host sources. () Trends in phasing methods for new membrane protein structures. The number of unique structures solved using either experimental (black) or molecular replacement (orange) methods is shown. Inset: a pie chart showing the breakdown of various experimental phasing methods. MIR(AS), multiple isomorphous replacement (with anomalous scattering); MAD, multiwavelength anomalous dispersion; SAD, single wavelength anomalous dispersion; SIR(AS), single isomorphous replacement (with anomalous scattering). Unique structures are defined according to http://blan! co.biomol.uci.edu/Membrane_Proteins_xtal.html. * Figure 2: Strategies for crystallizing membrane proteins. () Structures of βAR achieved using different approaches. β2AR engineered with T4 lysozyme inserted into intracellular loop 3 was crystallized in lipid cubic phase with cholesteryl hemisuccinate added to stabilize the receptor (left); the structure of thermostabilized β1AR-m23 purified in octythioglucoside was determined by vapor diffusion crystallization (center); β2AR stabilized in bicelles and bound to a Fab antibody fragment was crystallized by vapor diffusion (right)55. The receptors are shown in rainbow coloration, and T4 lysozyme and Fab antibody fragment are shown in gray. () The relative sizes of the detergent micelles surrounding a small membrane protein. The mitochondrial ATP/ADP carrier (30 kDa) was purified in detergents of the alkyl-maltoside series with decreasing hydrocarbon chain length from tridecylmaltoside (purple) to octylmaltoside (red). The dimensions of the detergent micelles were inferred from the Stokes radii of the free and protein-detergent mi! celles determined by size exclusion chromatography90. Author information * Abstract * Author information Affiliations * School of Life and Health Sciences, Aston University, Birmingham, UK. * Roslyn M Bill * Astbury Centre for Structural Molecular Biology, Institute of Membrane and Systems Biology, University of Leeds, Leeds, UK. * Peter J F Henderson * Membrane Protein Crystallography Group, Division of Molecular Biosciences, Imperial College London, London, UK. * So Iwata * MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, UK. * Edmund R S Kunji * Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany. * Hartmut Michel * Department of Chemistry, Biochemistry and Biophysics, University of Gothenburg, Gothenburg, Sweden. * Richard Neutze * Department of Biochemistry, University of Oxford, Oxford, UK. * Simon Newstead * Department of Biochemistry, University of Groningen, Groningen, The Netherlands. * Bert Poolman * MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK. * Christopher G Tate * Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. * Horst Vogel Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Roslyn M Bill Author Details * Roslyn M Bill Contact Roslyn M Bill Search for this author in: * NPG journals * PubMed * Google Scholar * Peter J F Henderson Search for this author in: * NPG journals * PubMed * Google Scholar * So Iwata Search for this author in: * NPG journals * PubMed * Google Scholar * Edmund R S Kunji Search for this author in: * NPG journals * PubMed * Google Scholar * Hartmut Michel Search for this author in: * NPG journals * PubMed * Google Scholar * Richard Neutze Search for this author in: * NPG journals * PubMed * Google Scholar * Simon Newstead Search for this author in: * NPG journals * PubMed * Google Scholar * Bert Poolman Search for this author in: * NPG journals * PubMed * Google Scholar * Christopher G Tate Search for this author in: * NPG journals * PubMed * Google Scholar * Horst Vogel Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes
  - Nat Biotech 29(4):341-345 (2011)
  Nature Biotechnology | Research | Letter Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes * Lydia Alvarez-Erviti1, 2 * Yiqi Seow1, 2 * HaiFang Yin1 * Corinne Betts1 * Samira Lakhal1 * Matthew J A Wood1 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:341–345Year published:(2011)DOI:doi:10.1038/nbt.1807Received22 September 2010Accepted09 February 2011Published online20 March 2011 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg To realize the therapeutic potential of RNA drugs, efficient, tissue-specific and nonimmunogenic delivery technologies must be developed. Here we show that exosomes—endogenous nano-vesicles that transport RNAs and proteins1, 2—can deliver short interfering (si)RNA to the brain in mice. To reduce immunogenicity, we used self-derived dendritic cells for exosome production. Targeting was achieved by engineering the dendritic cells to express Lamp2b, an exosomal membrane protein, fused to the neuron-specific RVG peptide3. Purified exosomes were loaded with exogenous siRNA by electroporation. Intravenously injected RVG-targeted exosomes delivered GAPDH siRNA specifically to neurons, microglia, oligodendrocytes in the brain, resulting in a specific gene knockdown. Pre-exposure to RVG exosomes did not attenuate knockdown, and non-specific uptake in other tissues was not observed. The therapeutic potential of exosome-mediated siRNA delivery was demonstrated by the strong mRNA (6! 0%) and protein (62%) knockdown of BACE1, a therapeutic target in Alzheimer's disease, in wild-type mice. View full text Figures at a glance * Figure 1: Targeting peptide expressed with Lamp2b is expressed on the external surface of exosomes. () Schematic representation of production, harvest and re-administration of targeted self-exosomes for gene delivery. () Schematic representation of the modified Lamp2b protein. SP, signal peptide; TP, targeting peptide; TM, transmembrane domain; CT, C terminus. () FLAG and Lamp2b western blots of dendritic cells and their corresponding exosomes. () Lamp-1 western blots of samples after exosome pulldown with either anti-Ago1 or anti-FLAG beads. Anti-FLAG beads retain FLAG-exosomes better than unmodified exosomes and anti-Ago1 does not retain either type of exosome. () qPCR of dendritic cells transfected with MSP-Lamp2b (MSP) or RVG-Lamp2b (RVG) with primers specific for MSP-Lamp2b or RVG-Lamp2b. () Size distribution of RVG exosomes as measured by NTA peaking at 88 nm diameter. () Electron micrograph of phosphotungstic acid stained RVG exosomes. Control is untransfected dendritic cells and exosomes, FLAG is dendritic cells transfected with FLAG-Lamp2b and derivative exosomes.! Full-length blots are presented in Supplementary Figure 9a,b. * Figure 2: In vitro delivery of siRNA by targeted exosomes. (,) qPCR of GAPDH normalized against 18S in Neuro2A cells and C2C12 cells 2 d after application of medium (Control), naked siRNA (siRNA), siRNA delivered with Lipofectamine 2000 (siRNA + LP), unmodified exosomes (Exosomes), MSP exosomes or RVG exosomes. (,) Representative images of Neuro2A and C2C12 cells 2 d after application of Cy5-labeled GAPDH siRNA delivered with siRNA + LP, RVG exosomes (RVG exos) or MSP exosomes (MSP exos). () 25, 50 and 100 pmoles (50, 100 and 200 nM) of each BACE1 siRNA was complexed with Lipofectamine 2000 or RVG exosomes (3 μg per 50 pmoles of siRNA) and applied to Neuro2A cells in the presence or absence of 500 nM of α-bungarotoxin. RNA was harvested 2 d later and assayed with qPCR normalized against 18S. * indicates P < 0.05 versus untreated control. The results represent the mean and s.d. of three independent experiments, each carried out with a new batch of exosomes to internalize batch-to-batch variation. For and , data are means plus s.d. * Figure 3: In vivo delivery of siRNA with targeted exosomes results in brain-specific gene knockdown. (,) GAPDH qPCR in the striatum, midbrain, cortex, quadriceps muscle, spleen, liver, kidney and heart of mice 3 d after intravenous injection of 150 μg naked GAPDH siRNA or siRNA encapsulated in RVG exosomes normalized to untreated controls (100%) (n = 3 for each group). (,) GAPDH qPCR and representative western blot of mice injected with RVG exosome–encapsulated GAPDH siRNA (150 μg) on two separate occasions 7 and 3 d before euthanization (n = 3). Mice were injected intravenously with RVG exosomes (n = 5), 150 μg each of two BACE1 siRNAs encapsulated in 150 μg of RVG exosomes (n = 8), complexed with in vivo transfection reagent (n = 5) or RVG-9R peptide (n = 5) and compared with untreated control (n = 8). (–) Animals were euthanized 3 d after injection and cortical sections were assayed with BACE1 qPCR (), BACE1 western blot (,) and β-amyloid 1-42 ELISA (). All qPCR was normalized to 18S RNA levels. *, ** and *** indicates P < 0.05, P < 0.01 and P < 0.001 versus unt! reated control. All error bars reflect s.d. (n = 5). Full-length blots are presented in Supplementary Figure 9c,d. Author information * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Lydia Alvarez-Erviti & * Yiqi Seow Affiliations * Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. * Lydia Alvarez-Erviti, * Yiqi Seow, * HaiFang Yin, * Corinne Betts, * Samira Lakhal & * Matthew J A Wood Contributions L.A.-E., Y.S. and M.J.A.W. designed the experiments. L.A.-E. and Y.S. performed the experiments and analyzed the data except for intravenous injection, CFSE proliferation assay. H.Y. performed intravenous injections. C.B. assisted with dissection and harvesting of tissue. S.L. performed the CFSE proliferation assay. L.A.-E., Y.S. and M.J.A.W. wrote the manuscript. Competing financial interests The authors have filed a patent application related to the work in this paper. Corresponding author Correspondence to: * Matthew J A Wood Author Details * Lydia Alvarez-Erviti Search for this author in: * NPG journals * PubMed * Google Scholar * Yiqi Seow Search for this author in: * NPG journals * PubMed * Google Scholar * HaiFang Yin Search for this author in: * NPG journals * PubMed * Google Scholar * Corinne Betts Search for this author in: * NPG journals * PubMed * Google Scholar * Samira Lakhal Search for this author in: * NPG journals * PubMed * Google Scholar * Matthew J A Wood Contact Matthew J A Wood Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (2M) Supplementary Tables 1,2 and Supplementary Figs. 1–9 Additional data
• Conversion of proteins into biofuels by engineering nitrogen flux
  - Nat Biotech 29(4):346-351 (2011)
  Nature Biotechnology | Research | Letter Conversion of proteins into biofuels by engineering nitrogen flux * Yi-Xin Huo1 * Kwang Myung Cho1, 2 * Jimmy G Lafontaine Rivera1 * Emma Monte1 * Claire R Shen1 * Yajun Yan1 * James C Liao1, 2 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:346–351Year published:(2011)DOI:doi:10.1038/nbt.1789Received30 November 2010Accepted26 January 2011Published online06 March 2011 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Biofuels are currently produced from carbohydrates and lipids in feedstock. Proteins, in contrast, have not been used to synthesize fuels because of the difficulties of deaminating protein hydrolysates. Here we apply metabolic engineering to generate Escherichia coli that can deaminate protein hydrolysates, enabling the cells to convert proteins to C4 and C5 alcohols at 56% of the theoretical yield. We accomplish this by introducing three exogenous transamination and deamination cycles, which provide an irreversible metabolic force that drives deamination reactions to completion. We show that Saccharomyces cerevisiae, E. coli, Bacillus subtilis and microalgae can be used as protein sources, producing up to 4,035 mg/l of alcohols from biomass containing ~22 g/l of amino acids. These results show the feasibility of using proteins for biorefineries, for which high-protein microalgae could be used as a feedstock with a possibility of maximizing algal growth1 and total CO2 fixati! on. View full text Figures at a glance * Figure 1: Screening of regulatory mutants for improved isobutanol production. All strains contain overexpressed isobutanol pathway genes (alsS, ilvC, ilvD, kivD, AdhA). Error bars indicate s.d. (n = 3). () Isobutanol titer from 20 strains containing different single-gene knockouts relative to the titer produced by the wild-type host (JCL16). (,) Deletion of quorum-sensing genes in YH19 (the high amino acid–consuming mutant) improved isobutanol production () and growth (). * Figure 2: Nitrogen-centric metabolic engineering strategy in E. coli. Error bars indicate s.d. (n = 3). Amino acids that are directly deaminated are shown in Supplemental Figure 5. Others are deaminated through the reprogrammed transamination and deamination cycles (–). Overexpressed enzymes shown in red. Deletion of gdhA and glnA blocks ammonia re-uptake and provides a metabolic driving force to direct the nitrogen flux out of the cell. () The amino groups in Asp and Ala are transferred to 2-ketoglutarate (2-KG) to yield pyruvate (Pyr) and Glu through a series of reactions (not shown). () IlvE transfers the amino group from Glu to 2-ketomethylvalerate (KMV) or 2-ketoisocaproate (KIC) to yield Ile and Leu, respectively. The heterologous LeuDH from Thermoactinomyces intermedius then deaminates Ile and Leu to regenerate KMV and KIC, respectively. NH3 is excreted but cannot be reassimilated because of ΔgdhA and ΔglnA. () IlvE also can transfer the amino group from Glu to 2-ketoisovalerate (KIV) and generate Val. AvtA then transfers the amino group from Val to Pyr to generate ! L-Ala, which is then converted to D-Ala and deaminated to yield Pyr. Excretion of NH3 is used as a driving force. () SerC transfers the amino group from Glu to 3-phosphohydroxypyruvate (3-PHP) to yield 3-phosphoserine (3-P-Ser), which is then converted to Ser by SerB. Ser is deaminated by SdaB to generate Pyr. Pyr can be recycled to 3-PHP or used for fuel synthesis. Again, NH3 excretion is used to drive the nitrogen flux. () Engineered keto acid pathways that produce ethanol (EtOH), isobutanol (iBOH), 2-methyl-1-butanol (2MB) and 3-methyl-1-butanol (3MB)9. () Enzyme activities of the overexpressed genes. For LeuDH and KivD, the substrates of specific reactions are given in parentheses. The substrate for YqhD is isobutyraldehyde. () Biofuel produced (EtOH, iBOH, 2MB, 3MB) from various engineering steps. Biofuel titers and the corresponding percentage of theoretical yield are marked. (,) Biofuel production and optical density (OD600) () and chain-length distribution () from E! . coli engineered using the nitrogen-centric metabolic enginee! ring strategy shown in (–). The strain is YH83 (YH19ΔglnAΔgdhAΔlsrA/overexpression of alsS, ilvC, ilvD, avtA, LeuDH, kivD, yqhD, ilvE, ilvA and sdaB). * Figure 3: Biofuel production and biorefining scheme from algal or bacterial protein sources. () The proposed protein-based biorefinery scheme. Amino acids are deaminated to various keto acids, which are then used to produce fuels, chemicals and pharmaceutical intermediates. The colors link products and intermediates to the amino acids from which they are derived. () Biofuel (EtOH, iBOH, 2MB, 3MB) produced from the engineered E. coli strain YH83 grown in flasks using algal or bacterial cell hydrolysates. Small laboratory-scale reactors (1 liter or 30 liters) were used to grow bacterial and algal cells individually. The algal biomass mixture includes C. vulgaris, P. purpureum, S. platensis and S. elongatus. All protein sources were adjusted to contain 21.6 g/l peptides and amino acids. Error bars indicate s.d. (n = 3). OAA, oxaloacetate; 2-KB, 2-ketobutyrate. Author information * Author information * Supplementary information Affiliations * Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California, USA. * Yi-Xin Huo, * Kwang Myung Cho, * Jimmy G Lafontaine Rivera, * Emma Monte, * Claire R Shen, * Yajun Yan & * James C Liao * Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA. * Kwang Myung Cho & * James C Liao Contributions Y.-X.H. designed and performed experiments, designed the theoretical calculation, analyzed data and wrote the manuscript; K.M.C. designed and performed experiments and analyzed data; J.G.L.R. designed and performed theoretical calculation; E.M. performed part of the experiments in Table 1; C.R.S. performed the chemical mutagenesis; Y.Y. designed and performed carbon-flux driven biofuel production; J.C.L. designed experiments, theoretical calculation, analyzed data and wrote the manuscript. Competing financial interests J.C.L. is a cofounder of Easel Biotechnoloiges, which licensed this technology from the University of California, Los Angeles. Corresponding author Correspondence to: * James C Liao Author Details * Yi-Xin Huo Search for this author in: * NPG journals * PubMed * Google Scholar * Kwang Myung Cho Search for this author in: * NPG journals * PubMed * Google Scholar * Jimmy G Lafontaine Rivera Search for this author in: * NPG journals * PubMed * Google Scholar * Emma Monte Search for this author in: * NPG journals * PubMed * Google Scholar * Claire R Shen Search for this author in: * NPG journals * PubMed * Google Scholar * Yajun Yan Search for this author in: * NPG journals * PubMed * Google Scholar * James C Liao Contact James C Liao Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (2M) Supplementary Tables 1–7 and Supplementary Figs. 1–11 Additional data
• Fluorescent peptides highlight peripheral nerves during surgery in mice
  - Nat Biotech 29(4):352-356 (2011)
  Nature Biotechnology | Research | Letter Fluorescent peptides highlight peripheral nerves during surgery in mice * Michael A Whitney1 * Jessica L Crisp2 * Linda T Nguyen3 * Beth Friedman1 * Larry A Gross4 * Paul Steinbach4 * Roger Y Tsien1, 2, 4 * Quyen T Nguyen3 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:352–356Year published:(2011)DOI:doi:10.1038/nbt.1764Received03 August 2010Accepted04 January 2011Published online06 February 2011 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Nerve preservation is an important goal during surgery because accidental transection or injury leads to significant morbidity, including numbness, pain, weakness or paralysis. Nerves are usually identified by their appearance and relationship to nearby structures or detected by local electrical stimulation (electromyography), but thin or buried nerves are sometimes overlooked. Here, we use phage display to select a peptide that binds preferentially to nerves. After systemic injection of a fluorescently labeled version of the peptide in mice, all peripheral nerves are clearly delineated within 2 h. Contrast between nerve and adjacent tissue is up to tenfold, and useful contrast lasts up to 8 h. No changes in behavior or activity are observed after treatment, indicating a lack of obvious toxicity. The fluorescent probe also labels nerves in human tissue samples. Fluorescence highlighting is independent of axonal integrity, suggesting that the probe could facilitate surgical r! epair of injured nerves and help prevent accidental transection. View full text Figures at a glance * Figure 1: Whole-body survey of nerves in mice (n = 3) 4 h after injection with 450 nmoles of FAM-NP41. (,) Brachial plexus. Reflectance image () showing left brachial plexus (arrow). Smaller branches (~50–100 μm) are easily seen (arrowheads) with fluorescence labeling () but not in reflectance image. (,) Sciatic nerve. Reflectance image () showing right sciatic nerve (arrow). Many more small branches (~50–100 μm) are seen (arrowheads) with fluorescence imaging () compared to reflectance. (,) Phrenic nerve. Reflectance image () showing left phrenic nerve (arrow) descending from the mediastinum to innervate the diaphragm. Note that the nerve is seen as a single linear fluorescent structure (arrow, ) compared to the bundle of nerve and connective tissue seen with reflectance (arrow, ). Arrowhead points to an intercostal nerve which is easily seen with fluorescence but not with reflectance. (,) Dorsal cutaneous nerves. Reflectance image () showing the dorsal musculature. Fluorescence imaging highlights the dorsal intercostal nerves (arrows, ) that are not easily seen with r! eflectance. (,) Facial nerve. Main facial nerve branches (arrows) are easily seen with both reflectance () and fluorescence (). However, a small branch of nerve arborization (arrowhead) leading to the upper face can be distinguished from surrounding tissue with fluorescence but not with reflectance. Insert shows arborizations (~50 μm diameter) of the lower division of the facial nerve that can be easily seen with fluorescence labeling. (,) Dorsal view of skull base. Reflectance image () showing left facial nerve (large arrow) wrapping around the ear, trigeminal nerves (small arrows), optic nerves (large arrowhead) and optic chiasm (small arrowhead). Fluorescence image () shows fluorescence labeling of the facial and trigeminal nerves (peripheral nervous system) but not the optic nerves and chiasm (central nervous system). Scale bar (–), 5 mm; inserts ( and ), 1 mm. * Figure 2: Time course and dose response of FAM-NP41 binding to nerve and nonnerve tissue. (–) Nerve fluorescence peaked at around 10 min after administration (), then declined (half-life ~50 min) to a plateau sustained between 3 and 6 h (see inset with expanded intensity scale, Student's t-test, two–tailed, P = 0.002 at 2 h, 0.0007 at 3 h, 0.0007 at 4 h, 0.003 at 5 h, 0.006 at 6 h). In contrast, muscle fluorescence was highest immediately after intravenous administration of the peptide, then declined steadily with a half-life of ~20 min (). Serum half-life was calculated at ~10 min (). Useful contrast between nerve and surrounding muscle developed by 2 h and lasts several hours (). Nerve-to–surrounding tissue contrast ratio increased with increasing amount of peptide injected, concentration from 15 to 5,000 nmoles per mouse injected (n = 2) (), because surrounding nonnerve tissue fluorescence seems more saturable than nerve binding with increasing peptide concentration (inset). * Figure 3: Cy5-NP41 (acetyl-SHSNTQTLAKAPEHTGC-(Cy5)-amide) labeling of sciatic nerve in Thy1-YFP transgenic mice. () Low-power brightfield view of left exposed sciatic nerve. Inset shows magnified view of central boxed region. () Same nerve as in with YFP fluorescence (pseudocolored yellow) superimposed on the brightfield image, showing transgenic expression of YFP in axons. () Same nerve as in and viewed with Cy5 fluorescence (pseudocolored cyan for maximal contrast during live surgery) superimposed on the brightfield image, showing nerve labeling with Cy5-NP41. Arrows in and point to thin buried nerve branches that are better revealed by the long-wavelength Cy5 fluorescence than by brightfield reflectance or shorter-wavelength YFP fluorescence. There is some nonspecific labeling of skin (asterisk) and cut edges of muscle (arrowhead) by Cy5-NP41. Fortunately, such nonspecific labeling hardly ever has the filamentous appearance of nerves, so an experienced surgeon can usually distinguish nonspecific from specific targets. () Low magnification longitudinal section showing myelin within t! he sciatic nerve using differential interference contrast (DIC), pseudocolored blue. () Same nerve as in showing axoplasmic YFP pseudocolored green (arrows). () Same nerve as in and , showing Cy5-NP41 labeling (pseudocolored red) of epineurium (arrows) and endoneurium (arrowheads). () Composite image of , and showing that NP41 labeling does not colocalize with either myelin or axoplasm. (–) Cross-sectional images corresponding to panels –. * Figure 4: NP41 can highlight buried nerve branches invisible by standard illumination. (–) Right facial nerve and its arborizations in a thy1-YFP mouse treated with Cy5-NP41, viewed by () white light reflectance, () Cy5 fluorescence (pseudocolored cyan) overlaid on reflectance and () YFP fluorescence (pseudocolored yellow), also overlaid on reflectance. The short arrow marks a nerve branch visible by all three imaging modes. The arrowheads point to branches that are difficult to differentiate from muscle fascia in reflectance, but clearly distinguishable in both fluorescence images. The long arrow indicates a deeply buried branch visible only by Cy5-NP41 due to the better penetration of far-red wavelengths. (–) Left sciatic nerve (arrow) and its arborization in a mouse with a syngeneic 8119 mammary tumor graft17, 18, viewed by () white light reflectance, () FAM fluorescence 2 h after intravenous injection of NP41 (150 nmoles) (pseudocolored cyan, overlaid on reflectance) and () Cy5 fluorescence (pseudocolored green, overlaid on reflectance) from conjugates! of activatable cell-penetrating peptides and dendrimers (ACPPDs). The large arrowheads in and point to a nerve branch buried under tumor, visible only by FAM fluorescence. Small arrowheads in denote tumor. See Supplementary Video 1. Author information * Author information * Supplementary information Affiliations * Department of Pharmacology, University of California at San Diego, La Jolla, California, USA. * Michael A Whitney, * Beth Friedman & * Roger Y Tsien * Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA. * Jessica L Crisp & * Roger Y Tsien * Division of Otolaryngology-Head and Neck Surgery, University of California at San Diego, La Jolla, California, USA. * Linda T Nguyen & * Quyen T Nguyen * Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, USA. * Larry A Gross, * Paul Steinbach & * Roger Y Tsien Contributions M.A.W. designed and performed experiments, interpreted data and wrote manuscript. J.L.C. designed and performed experiments and interpreted data. L.T.N. designed and performed experiments and interpreted data. B.F. designed and performed experiments and interpreted data. L.A.G. designed and performed experiments and interpreted data. P.S. provided computer support for experiments, R.Y.T. designed experiments, interpreted data and wrote manuscript. Q.T.N. designed and performed experiments, interpreted data and wrote manuscript. Competing financial interests M.A.W., R.Y.T. and Q.T.N. are scientific advisors for Avelas Biosciences, Inc., who has licensed the technology described above from the University of California San Diego. Corresponding author Correspondence to: * Quyen T Nguyen Author Details * Michael A Whitney Search for this author in: * NPG journals * PubMed * Google Scholar * Jessica L Crisp Search for this author in: * NPG journals * PubMed * Google Scholar * Linda T Nguyen Search for this author in: * NPG journals * PubMed * Google Scholar * Beth Friedman Search for this author in: * NPG journals * PubMed * Google Scholar * Larry A Gross Search for this author in: * NPG journals * PubMed * Google Scholar * Paul Steinbach Search for this author in: * NPG journals * PubMed * Google Scholar * Roger Y Tsien Search for this author in: * NPG journals * PubMed * Google Scholar * Quyen T Nguyen Contact Quyen T Nguyen Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (12M) Supplementary Table 1, Supplementary Figs. 1–8 and Supplementary Video 1 Additional data
• Label-free quantification of membrane-ligand interactions using backscattering interferometry
  - Nat Biotech 29(4):357-360 (2011)
  Nature Biotechnology | Research | Letter Label-free quantification of membrane-ligand interactions using backscattering interferometry * Michael M Baksh1 * Amanda K Kussrow3 * Mauro Mileni2 * M G Finn1 * Darryl J Bornhop3 * Affiliations * Contributions * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:357–360Year published:(2011)DOI:doi:10.1038/nbt.1790Received12 April 2010Accepted26 January 2011Published online13 March 2011 Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Although membrane proteins are ubiquitous within all living organisms and represent the majority of drug targets, a general method for direct, label-free measurement of ligand binding to native membranes has not been reported. Here we show that backscattering interferometry (BSI) can accurately quantify ligand-receptor binding affinities in a variety of membrane environments. By detecting minute changes in the refractive index of a solution, BSI allows binding interactions of proteins with their ligands to be measured at picomolar concentrations. Equilibrium binding constants in the micromolar to picomolar range were obtained for small- and large-molecule interactions in both synthetic and cell-derived membranes without the use of labels or supporting substrates. The simple and low-cost hardware, high sensitivity and label-free nature of BSI should make it readily applicable to the study of many membrane-associated proteins of biochemical and pharmacological interest. View full text Figures at a glance * Figure 1: Experimental components. () Backscattering interferometry instrumentation. () Schematic representation of the small unilamellar vesicles (SUVs) on which BSI measurements were made in this work. * Figure 2: Representative plots of BSI signal versus ligand concentration for the determination of binding constants for the following pairs of molecules (membrane-bound species + ligand). The control ligand in each case was tested at the highest concentration to verify its nonbinding nature (plotted in blue). Unless otherwise indicated, the membrane-bound partner was displayed in SUVs as described in the text. () GM1 + cholera toxin B subunit, control is full-length tetanus toxin. (–) FAAH + small-molecule inhibitors at pH 7.4, control is cholesterol; , OL-135; , FAR-1-216; , JGII-145. (–) As in –, at pH 9.0. () Vesicles derived from the membrane of SUP-T1 cells, natively expressing CXCR4. Ligand, CXCL12. Control, fully denatured CXCL12. (–) Vesicles derived from the membrane of CHO cells overexpressing the GABAB receptor + small-molecule substrates, agonists or antagonists. Ligands: , GABA; , baclofen; , SKF-97541; , CGP-54626. Controls: (–) L-alanine, () cholesterol. Each data point represents the average of at least four independent measurements; error bars are plus and minus the full value of s.e.m. in each direction. Repeat determinations of th! e binding curves gave very similar Kd values. Author information * Author information * Supplementary information Affiliations * Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA. * Michael M Baksh & * M G Finn * Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA. * Mauro Mileni * Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA. * Amanda K Kussrow & * Darryl J Bornhop Contributions M.M.B. developed methods for sample preparation, prepared samples for analysis and processed the raw BSI data; A.K.K. performed BSI measurements and processed the raw data; M.M. prepared the FAAH protein; M.M.B., A.K.K., M.G.F. and D.J.B. designed the project and wrote the manuscript. Competing financial interests D.J.B. has a financial interest in a company that is commercializing BSI. The other authors declare that they have no competing financial interests. Corresponding authors Correspondence to: * M G Finn or * Darryl J Bornhop Author Details * Michael M Baksh Search for this author in: * NPG journals * PubMed * Google Scholar * Amanda K Kussrow Search for this author in: * NPG journals * PubMed * Google Scholar * Mauro Mileni Search for this author in: * NPG journals * PubMed * Google Scholar * M G Finn Contact M G Finn Search for this author in: * NPG journals * PubMed * Google Scholar * Darryl J Bornhop Contact Darryl J Bornhop Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (856K) Supplementary Methods and Supplementary Figs. 1–3 Additional data
• Systematic exploration of essential yeast gene function with temperature-sensitive mutants
  - Nat Biotech 29(4):361-367 (2011)
  Nature Biotechnology | Research | Resources Systematic exploration of essential yeast gene function with temperature-sensitive mutants * Zhijian Li1, 8 * Franco J Vizeacoumar1, 8 * Sondra Bahr1 * Jingjing Li1 * Jonas Warringer2 * Frederick S Vizeacoumar3 * Renqiang Min1 * Benjamin VanderSluis4 * Jeremy Bellay4 * Michael DeVit5 * James A Fleming5 * Andrew Stephens6 * Julian Haase6 * Zhen-Yuan Lin1 * Anastasia Baryshnikova1 * Hong Lu1 * Zhun Yan1 * Ke Jin1 * Sarah Barker1 * Alessandro Datti3, 7 * Guri Giaever1 * Corey Nislow1 * Chris Bulawa5 * Chad L Myers4 * Michael Costanzo1 * Anne-Claude Gingras1 * Zhaolei Zhang1 * Anders Blomberg2 * Kerry Bloom6 * Brenda Andrews1 * Charles Boone1 * Affiliations * Contributions * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:361–367Year published:(2011)DOI:doi:10.1038/nbt.1832Received13 January 2011Accepted01 March 2011Published online27 March 2011 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Conditional temperature-sensitive (ts) mutations are valuable reagents for studying essential genes in the yeast Saccharomyces cerevisiae. We constructed 787 ts strains, covering 497 (~45%) of the 1,101 essential yeast genes, with ~30% of the genes represented by multiple alleles. All of the alleles are integrated into their native genomic locus in the S288C common reference strain and are linked to a kanMX selectable marker, allowing further genetic manipulation by synthetic genetic array (SGA)–based, high-throughput methods. We show two such manipulations: barcoding of 440 strains, which enables chemical-genetic suppression analysis, and the construction of arrays of strains carrying different fluorescent markers of subcellular structure, which enables quantitative analysis of phenotypes using high-content screening. Quantitative analysis of a GFP-tubulin marker identified roles for cohesin and condensin genes in spindle disassembly. This mutant collection should facilit! ate a wide range of systematic studies aimed at understanding the functions of essential genes. View full text Figures at a glance * Figure 1: Profiling the temperature sensitivity of ts strains. () Left panel; general interpretation of high-resolution liquid growth profiles of strains harboring ts alleles. Growth rate (population doubling time) was determined by measuring the slope of the exponential phase of the growth curve. Lag was given by the intercept of the initial density and the slope, and growth efficiency was calculated as the total change in density for cells having reached stationary phase. Right panel; sample growth curves of the strains with the act1-105 ts allele, obtained by micro-cultivation over a temperature range. () The fraction of all ts strains that exhibit significant (P < 0.001) temperature sensitive defects in growth rate (blue), lag (green) and/or efficiency (red) phases compared to wild type (WT) at the indicated temperatures. () Uncentered hierarchical clustering of ts allele growth profiles over all three growth variables. Profile similarity was measured using a Pearson similarity metric and average linkage mapping. The ts-strain sensi! tivity ratio is expressed as log2(WT/ts strain) at temperature X − log2(WT/ts strains) at 22 °C. ER, endoplasmic reticulum. * Figure 2: Zaragozic acid rescues bet2-1 and cdc43-2 ts phenotype. () Isoprenoid pathway in S. cerevisiae. The solid lines indicate one step and the dashed lines indicate multiple synthetic steps in the ergosterol and protein prenylation pathways44, 45, 46. () A pool of 440 barcoded ts mutants was grown in rich (YPD) medium in the presence of 4 mM of zaragozic acid A (ZA) or DMSO at 36.5 °C. Genomic DNA was prepared from cells after five generations of growth. Molecular barcodes were amplified by PCR and hybridized to a microarray (GeneChip Genflex Tag 16K Array v2, Affymetrix). The x axis represents the 440 ts strains ordered alphabetically by systematic name. The y axis represents the log2 ratio of barcode hybridization intensity between the ZA treatment and the solvent (DMSO) treatment. Mutants with highest log2 ratios at the restrictive temperature were identified as suppressors. () Yeast cells were grown in YPD with or without ZA in a 96-well plate at 36.5 °C. Fitness was defined as the ratio of doubling times measured in DMSO compar! ed to ZA treatment. Error bars represent s.d. for four independent experiments. * Figure 3: High-content screening of the ts allele collection identifies abnormal spindle morphology associated with cohesin and condensin mutants. () Fluorescent reporters introduced into the ts collection. The left panels show the localization of six different GFP/RFP-tagged marker proteins expressed in wild-type cells as well as the corresponding computationally processed images. Representative mutants with defects in localization of particular markers are shown on the right. Markers included a plasma membrane marker (Psr1p-GFP), a reporter of DNA damage (Ddc2p-GFP), a nuclear marker (Mad1p-NLS-RFP), a mitotic spindle reporter (GFP-Tub1), a mitochondrial marker (OM45p-GFP) and an actin reporter (Sac6p-GFP). () A sub-population of cohesin and condensin mutants exhibit abnormal spindle morphology. Spindle length and morphology were quantified in large-budded wild-type cells and strains harboring a cohesin (smc3-1) or condensin (smc2-1) mutant allele grown asynchronously at permissive (26 °C) and restrictive temperatures (32 °C). The fraction of cells exhibiting either short (upper panel) or fishhook-shaped spindles (! lower panel) were quantified in three independent populations; error bars represent s.d. across three independent experiments. () Ipl1p-GFP localization in cohesin (smc3-1) and condensin (smc2-8) mutants. Ipl1p-GFP localization to the mitotic spindle was monitored in wild-type, smc3-1 and smc2-8 mutants at permissive (26 °C) and restrictive temperatures (32 °C). Representative cells with short (top panels) and long (bottom panels) spindles are shown. White arrows indicate Ipl1p-GFP localization to the kinetochore in a cohesin mutant at the restrictive temperature. The fluorescent intensity line profile of Ipl1p-GFP for a representative cell is also shown. () Wild-type and mutant cells were divided into three separate groups based on spindle length (2–4 μm, 4–6 μm, >6 μm) as measured by assessment of an RFP-Tub1p marker. The percentage of cells in each spindle length group that exhibited mis-localized Ipl1p-GFP was measured at permissive and restrictive temperatures! . Error bars represent the s.d. across three independent exper! iments. * Figure 4: Relationship between cohesin, condensin and chromosomal passenger complexes (CPC). () Physical interaction network illustrating protein-protein interactions involving cohesin, condensin and CPC complexes. Nodes represent individual proteins and edges represent physical interactions. () Cohesin, condensin and CPC complex localization. Ipl1p-GFP, Smc3p-GFP and Smc4p-GFP localization was assessed with respect to the spindle pole marker, Spc29p-RFP in a wild-type strain. Fluorescent micrograph images illustrate representative single cells. Author information * Abstract * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Zhijian Li & * Franco J Vizeacoumar Affiliations * Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. * Zhijian Li, * Franco J Vizeacoumar, * Sondra Bahr, * Jingjing Li, * Renqiang Min, * Zhen-Yuan Lin, * Anastasia Baryshnikova, * Hong Lu, * Zhun Yan, * Ke Jin, * Sarah Barker, * Guri Giaever, * Corey Nislow, * Michael Costanzo, * Anne-Claude Gingras, * Zhaolei Zhang, * Brenda Andrews & * Charles Boone * Department of Cell and Molecular Biology, Göteborg University, Göteborg, Sweden. * Jonas Warringer & * Anders Blomberg * Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. * Frederick S Vizeacoumar & * Alessandro Datti * Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA. * Benjamin VanderSluis, * Jeremy Bellay & * Chad L Myers * FoldRx Pharmaceuticals Inc., Cambridge, Massachusetts, USA. * Michael DeVit, * James A Fleming & * Chris Bulawa * Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA. * Andrew Stephens, * Julian Haase & * Kerry Bloom * Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy. * Alessandro Datti Contributions Z.L., F.J.V., C.B. and B.A. conceived and designed the experiments. Z.L. and S.B. constructed the ts strains. J.W. and A.B. conducted and analyzed liquid growth profiling experiments. Z.L., F.J.V., F.S.V., J.L., R.M., K.J. and Z.Z. generated and analyzed the HCS data. M.C., A.B., B.V., J.B. and C.L.M. generated and analyzed the data. Z.Y.L. and A.C.G. performed mass spectrometry analyses. Z.L., Z.Y., M.D., J.A.F., C.B., G.G. and C.N. performed the chemical genetic experiments. Z.L., F.J.V., A.S., J.H. and K.B. performed the analysis on cohesin and condensin complexes. H.L., Z.Y., S.B., A.D., G.G., C.N., C.B., M.C., F.S.V., A.D., A.G., Z.Z. and K.B. provided technical support/reagents/materials/analysis tools. Z.L., F.J.V., M.C., B.A. and C.B. wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Brenda Andrews or * Charles Boone Author Details * Zhijian Li Search for this author in: * NPG journals * PubMed * Google Scholar * Franco J Vizeacoumar Search for this author in: * NPG journals * PubMed * Google Scholar * Sondra Bahr Search for this author in: * NPG journals * PubMed * Google Scholar * Jingjing Li Search for this author in: * NPG journals * PubMed * Google Scholar * Jonas Warringer Search for this author in: * NPG journals * PubMed * Google Scholar * Frederick S Vizeacoumar Search for this author in: * NPG journals * PubMed * Google Scholar * Renqiang Min Search for this author in: * NPG journals * PubMed * Google Scholar * Benjamin VanderSluis Search for this author in: * NPG journals * PubMed * Google Scholar * Jeremy Bellay Search for this author in: * NPG journals * PubMed * Google Scholar * Michael DeVit Search for this author in: * NPG journals * PubMed * Google Scholar * James A Fleming Search for this author in: * NPG journals * PubMed * Google Scholar * Andrew Stephens Search for this author in: * NPG journals * PubMed * Google Scholar * Julian Haase Search for this author in: * NPG journals * PubMed * Google Scholar * Zhen-Yuan Lin Search for this author in: * NPG journals * PubMed * Google Scholar * Anastasia Baryshnikova Search for this author in: * NPG journals * PubMed * Google Scholar * Hong Lu Search for this author in: * NPG journals * PubMed * Google Scholar * Zhun Yan Search for this author in: * NPG journals * PubMed * Google Scholar * Ke Jin Search for this author in: * NPG journals * PubMed * Google Scholar * Sarah Barker Search for this author in: * NPG journals * PubMed * Google Scholar * Alessandro Datti Search for this author in: * NPG journals * PubMed * Google Scholar * Guri Giaever Search for this author in: * NPG journals * PubMed * Google Scholar * Corey Nislow Search for this author in: * NPG journals * PubMed * Google Scholar * Chris Bulawa Search for this author in: * NPG journals * PubMed * Google Scholar * Chad L Myers Search for this author in: * NPG journals * PubMed * Google Scholar * Michael Costanzo Search for this author in: * NPG journals * PubMed * Google Scholar * Anne-Claude Gingras Search for this author in: * NPG journals * PubMed * Google Scholar * Zhaolei Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Anders Blomberg Search for this author in: * NPG journals * PubMed * Google Scholar * Kerry Bloom Search for this author in: * NPG journals * PubMed * Google Scholar * Brenda Andrews Contact Brenda Andrews Search for this author in: * NPG journals * PubMed * Google Scholar * Charles Boone Contact Charles Boone Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Author information * Supplementary information Excel files * Supplementary Table 1 (275K) * Supplementary Table 2 (200K) * Supplementary Table 3 (440K) * Supplementary Table 4 (20K) * Supplementary Table 5 (135K) * Supplementary Table 7 (64K) Other * Supplementary Table 6 (5.6M) PDF files * Supplementary Text and Figures (9.8M) Supplementary Figs. 1–6 Additional data
• Ease entry into an alternative career field by obtaining a specialized professional degree
  - Nat Biotech 29(4):368-369 (2011)
  Nature Biotechnology | Careers and Recruitment Ease entry into an alternative career field by obtaining a specialized professional degree * Nathan L Vanderford1Journal name:Nature BiotechnologyVolume: 29,Pages:368–369Year published:(2011)DOI:doi:10.1038/nbt.1841Published online08 April 2011 A professional science master's degree is specifically designed to add professional skills to those that are science-oriented, thus generating multi-skilled employees. View full text Author information Article tools * Full text * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Nathan L. Vanderford is at the University of Kentucky, Markey Cancer Center, Lexington, Kentucky, USA. Competing financial interests The author declares no competing financial interests. Corresponding author Correspondence to: * Nathan L Vanderford Author Details * Nathan L Vanderford Contact Nathan L Vanderford Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• People
  - Nat Biotech 29(4):370 (2011)
  Nature Biotechnology | Careers and Recruitment | People People Journal name:Nature BiotechnologyVolume: 29,Page:370Year published:(2011)DOI:doi:10.1038/nbt.1849Published online08 April 2011 Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. KaloBios Pharmaceuticals (S. San Francisco, CA, USA) has named (below, right) chief medical officer and as a member of the company's board of directors. Leff brings to KaloBios over 16 years' experience in biologics development, most recently as vice president and chief medical officer of Halozyme Therapeutics. Lyons has over 30 years of senior management experience in the biopharmaceutical industry. He is the former president and CEO of publicly held Neurocrine Biosciences. David W. Pritchard, KaloBios president and CEO, comments: "Their extensive track record in the development and commercialization of biologics will serve KaloBios well as we enter the next phase of our company's evolution as a developer of patient-targeted, monoclonal antibody-based therapeutics." has announced that he will transition from his role as CEO of Rexahn Pharmaceuticals (Rockville, MD, USA) to CSO. He will continue to serve as chairman of Rexahn's board of directors, and will serve as both CEO and CSO until the new CEO is named. Rexahn has initiated a search for a CEO to succeed Ahn. Genesis Biopharma (Los Angeles) has appointed to its board of directors. Andrews has three decades of experience in biotech R&D and currently serves as president and CEO of Sierra Sciences. Gentium (Villa Guardia, Italy) has announced that has been appointed to the new position of senior vice president, commercial operations. Haigh joins Gentium with 28 years of experience in the pharmaceutical and biotech fields. Most recently, he served as regional vice president of commercial operations for Biogen Idec. has been appointed to the board of directors of Cephalon (Frazer, PA, USA). Homcy is currently a partner at Third Rock Ventures and co-chairman of privately held Portola Pharmaceuticals, where he served as president and CEO from 2003 to 2010. Gene therapy developer Oxford BioMedica (Oxford, UK) has announced that its chairman, , will step down at the company's annual general meeting in May 2011. , nonexecutive director, senior independent director and deputy chairman, will then become chairman. Anadys Pharmaceuticals (San Diego) has appointed 20-year industry veteran to its board of directors. Labinger has served as executive vice president and chief commercial officer of Human Genome Sciences since August 2005. has been named chief medical officer for emerging company bluebird bio (Cambridge, MA, USA). LeBeaut has more than 20 years of experience working with specialty pharma companies. He was most recently CSO at Axcan Pharma and before that, he was vice president, US medical affairs at Sanofi-aventis Pharmaceuticals. Lithera (San Diego) has appointed president, CEO and a member of the company's board of directors. , founder and CEO of Lithera since its inception, will remain on the board of directors. Mahaffey has 24 years of industry experience, most recently serving as CEO of Peplin after its acquisition by LEO Pharma in 2009. Cell-based immunotherapy developer TxCell (Valbonne, France) has announced the appointment of (right) as its CEO. Meyer has more than 25 years of experience, beginning at Ciba-Geigy and continuing on at Sandoz, Rhône-Poulenc Rorer, Gencell and Aventis. Most recently he was CEO of Centelion. View full text Read the full article * Instant access to this article: US$32Buy now * Subscribe to Nature Biotechnology for full access: SubscribeLogin for existing subscribers Additional access options: * Use a document delivery service * Rent this article from DeepDyve * Login via Athens * Purchase a site license * Institutional access * British Library Document Supply Centre * Infotrieve * Thompson ISI Document Delivery * You can also request this document from your local library through inter-library loan services. Additional data