Hot off the presses! Aug 01 Nat Biotechnol

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• In this issue
  - Nat Biotechnol 29(8):vii-viii (2011)
  Article preview View full access options Nature Biotechnology | In This Issue In this issue Journal name:Nature BiotechnologyVolume: 29,Pages:vii–viiiYear published:(2011)DOI:doi:10.1038/nbt.1953Published online05 August 2011 Prostate cancer lincRNAs Noncoding RNAs may contribute to human disease, as demonstrated by last year's discovery that enforced expression of the long intergenic noncoding (linc) RNAs HOTAIR promotes breast cancer metastasis. Whereas the authors of that previous study used a targeted method based on knowledge of loci involved in disease, Chinnaiyan and colleagues show how the assembly of transcripts from RNA-Seq data can be used for less biased discovery of disease-associated noncoding RNAs throughout the genome. Studying prostate cancer, the researchers first sequence polyadenylated RNA from a cohort of 102 prostate tissues and cell lines, including benign tissue, localized tumors and metastatic tumors. The resulting reads are then assembled into transcripts. Of the assembled unannotated noncoding RNAs, one in particular, termed PCAT-1, is markedly upregulated in both localized and metastatic tumors. Subsequent experiments link the expression of PCAT-1 to the oncoprotein EZH2 and uncover a role for! PCAT-1 as transcriptional repressor capable of modulating cell proliferation in vitro. This strategy based on assembly of RNA-Seq data should be applicable to discovering unannotated RNAs involved in other biological processes and diseases. CM RNA-Seq enables polyploid crop linkage analysis Linkage maps based on single-nucleotide polymorphism (SNP) markers are of critical value in crop breeding. Genome resequencing now provides the simplest option for SNP discovery in diploid crops, but remains challenging for most polyploid species. Bancroft and colleagues describe a workflow that uses gene expression profiling to both identify SNPs in the tetraploid crop oilseed rape (Brassica napus) and align them with genome sequences of the two progenitors from which B. napus originated. Because the sequence data set used to detect polymorphisms and score markers also describes transcript abundances, they are able to monitor both sequence and expression variation simultaneously. The authors use their linkage data for detailed comparison of B. napus with the extensively characterized related model species Arabidopsis thaliana and even for identifying errors in the assemblies of the progenitor species Brassica rapa and Brassica oleracea. The availability of >23,000 B. napus ! linkage markers will be a valuable resource for those involved in improving this important source of cooking oil. Moreover, application of the approach to other polyploid crops will enable construction of high-density linkage maps at a fraction of the cost needed for approaches dependent on genome resequencing. PH Isolating pancreatic cell types Transplantation of allogeneic pancreatic islets into the liver has shown efficacy in treating diabetes, but the supply of islets available for this therapy is limited. Human embryonic stem cells (hESCs) might provide an additional and unlimited source of islets if they could be differentiated efficiently in vitro into appropriate cell types. A differentiation method developed by researchers at Viacyte (San Diego) produced a heterogeneous population of pancreatic cells, some of which became functional beta cells after a period of maturation in vivo (Nat. Biotechnol.24, 1392–1401, 2006 and Nat. Biotechnol.26, 443–452, 2008). To pinpoint the subpopulation of cells that became beta cells, a Viacyte team headed by Olivia Kelly now identifies antibodies that allow the isolation of two likely progenitor cell types: pancreatic endoderm cells and polyhormonal endocrine cells. Surprisingly, transplantation studies show that the polyhormonal endocrine cells generate mostly glucagon! cells, whereas the pancreatic endoderm cells give rise to beta cells. [] KA Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• Pushing the envelope
  - Nat Biotechnol 29(8):669 (2011)
  Nature Biotechnology | Editorial Pushing the envelope Journal name:Nature BiotechnologyVolume: 29,Page:669Year published:(2011)DOI:doi:10.1038/nbt.1956Published online05 August 2011 The US Food and Drug Administration (FDA) should follow its advisory panels and rescind metastatic breast cancer from Avastin's label. View full text Additional data
• E. coli crisis opens door for Alexion drug trial
  - Nat Biotechnol 29(8):671 (2011)
  Article preview View full access options Nature Biotechnology | News E. coli crisis opens door for Alexion drug trial * Lucas Laursen1Journal name:Nature BiotechnologyVolume: 29,Page:671Year published:(2011)DOI:doi:10.1038/nbt0811-671Published online05 August 2011 Pixwork/istockphoto Seeds used for sprouting were the likely source of the E. coli outbreak in Germany and France. Alexion stepped in to provide an expensive antibody treatment to those who fell ill. This spring's outbreak of a virulent form of Escherichia coli in Germany and France provoked a rapid response from public health authorities and the research community. Not only did the response represent a triumph of global collaboration in rapidly characterizing the Shiga toxin–producing strain but it also prompted an on-the-fly clinical trial of one of the world's most expensive biotech drugs—Alexion's humanized monoclonal antibody Soliris (eculizumab)—previously approved for the rare disease paroxysmal nocturnal hemoglobinuria (PNH). As thousands fell ill with the enterohemorrhagic E. coli (EHEC) strain O104:H4 from eating tainted food—a substantial fraction developing potentially fatal hemolytic uremic syndrome (HUS)—German and then French doctors turned to Soliris, which prevents the cleavage of complement component 5 (C5) and activation of the hemolytic cascade. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Zurich * Lucas Laursen Author Details * Lucas Laursen Search for this author in: * NPG journals * PubMed * Google Scholar
• TNF-α blockers and tumors
  - Nat Biotechnol 29(8):672 (2011)
  Article preview View full access options Nature Biotechnology | News TNF-α blockers and tumors * Nuala MoranJournal name:Nature BiotechnologyVolume: 29,Page:672Year published:(2011)DOI:doi:10.1038/nbt0811-672aPublished online05 August 2011 A Danish study has found no increase in cancer risk in people taking tumor necrosis factor alpha (TNF-α) inhibitors over a long period. The authors (Ann. Rheum. Dis. (suppl. 3), 410, 2011) cross-referenced data from 5,598 patients included in DANBIO, the national Danish Rheumatological registry set up in 2000 to monitor individuals treated with biologic drugs, with the Danish Cancer Registry. They concluded that, "No overall or specific elevation of cancer risk was observed during up to nine years of follow-up." The cohort, mainly treated for rheumatoid arthritis with TNF-α blockers Humira (adalimumab), Remicade (infliximab) and Enbrel (etanercept) from 2000 to 2008, will continue to be followed. Given the cytokine's role in immune surveillance for cancer, it was always anticipated that blocking anti-TNF-α might leave patients open to a higher risk of malignancies. This led to black box warnings and, in August 2009, the US Food and Drug Administration (FDA) added spec! ific information about the risk of lymphomas and other rare cancers in pediatric patients. But the overall level of risk remains unclear. As recently as December 2010, a meta-analysis, commissioned by the European Medicines Agency, of 74 randomized controlled trials involving 15,418 patients treated with TNF-α blockers, could neither "refute nor verify" any link. The recent results do not mean TNF-α blockers are in the clear yet. Lead author Lene Dreyer of the Department of Rheumatology at Gentofte University Hospital in Denmark said, "Drugs targeting TNF can influence the development of tumors, although the extent of this impact remains unclear." Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Nuala Moran Search for this author in: * NPG journals * PubMed * Google Scholar
• Swiss food giant enters diagnostics
  - Nat Biotechnol 29(8):672 (2011)
  Article preview View full access options Nature Biotechnology | News Swiss food giant enters diagnostics * Karen CareyJournal name:Nature BiotechnologyVolume: 29,Page:672Year published:(2011)DOI:doi:10.1038/nbt0811-672bPublished online05 August 2011 Nestle's buyout of San Diego–based Prometheus Laboratories marks a strategic shift by the Vevey, Switzerland–based food company into personalized medicine. Prometheus is a specialty pharma and diagnostics firm, focused on gastroenterology and oncology services to guide the use of targeted therapies. The financial terms were not disclosed, though the transaction is estimated at over $1.1 billion, and is being conducted by Nestle Health Science, a subsidiary formed in January to specialize in health nutrition. "I know there's not any other food company in the world that has created a division specifically to explore and exploit the overlap between pharmaceuticals and food," says independent food industry consultant, James Amoroso, of Walchwil, Switzerland. By adding Prometheus, Nestle acquires a Crohn's disease prognostic test and a diagnostic for inflammatory bowel disease among others. It also pulls in rights to cancer drugs Proleukin, originated by Novartis of Basel! , and Rencarex (girentuximab), a targeted antibody for targeting solid tumors licensed from Munich-based Wilex. Also recently, Nestle added nutritional products manufacturers Vitaflo of Liverpool, UK, and CM&D Pharma, of Munich. Nestle spent $1.9 billion on R&D in 2010. "They've got enough pure research going on, as well as applied research," Amoroso says, "that they know there are areas to exploit." Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Karen Carey Search for this author in: * NPG journals * PubMed * Google Scholar
• US court bolsters biotech patent protection
  - Nat Biotechnol 29(8):672-673 (2011)
  Article preview View full access options Nature Biotechnology | News US court bolsters biotech patent protection * Charlotte Harrison1Journal name:Nature BiotechnologyVolume: 29,Pages:672–673Year published:(2011)DOI:doi:10.1038/nbt0811-672cPublished online05 August 2011 Haraz N. Ghanbari/AP The US Court of Appeals for the Federal Circuit's recent ruling on inequitable conduct is viewed as positive for biotech. On May 23, the US Court of Appeals for the Federal Circuit's (CAFC) ruling in Therasense vs. Becton Dickinson & Company raised the standards for charging inequitable conduct. This is good news for biotech companies, as the ruling will likely stem inequitable conduct charges, a litigation tactic often used by patent infringers to render an innovator's patent unenforceable or to delay settlement. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Canterbury, UK * Charlotte Harrison Author Details * Charlotte Harrison Search for this author in: * NPG journals * PubMed * Google Scholar
• FDA approves first cell therapy for wrinkle-free visage
  - Nat Biotechnol 29(8):674-675 (2011)
  Article preview View full access options Nature Biotechnology | News FDA approves first cell therapy for wrinkle-free visage * Charles Schmidt1Journal name:Nature BiotechnologyVolume: 29,Pages:674–675Year published:(2011)DOI:doi:10.1038/nbt0811-674Published online05 August 2011 Credit zoran mircetic Fibrocell's laViv is a cosmetic cell therapy injected into dermal layers. In June, after a nearly ten-year review, the US Food and Drug Administration (FDA) approved laViv (azficel-T), a first-in-class personalized cell therapy for eliminating fine wrinkles or nasolabial folds around the nose and mouth. Issued to its developer, Fibrocell Science, in Exton, Pennsylvania, the approval marks a regulatory first for ex vivo manipulated cell cosmetics in the US and could serve as a test case for future decisions on other cosmetic cell therapies. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Charles Schmidt Author Details * Charles Schmidt Search for this author in: * NPG journals * PubMed * Google Scholar
• FDA inspections online
  - Nat Biotechnol 29(8):676 (2011)
  Article preview View full access options Nature Biotechnology | News FDA inspections online * Bethan HughesJournal name:Nature BiotechnologyVolume: 29,Page:676Year published:(2011)DOI:doi:10.1038/nbt0811-676aPublished online05 August 2011 The US Food and Drug Administration (FDA) has released an online database of its final inspection classifications conducted in fiscal years 2009 and 2010. "We believe that disclosure of the compliance status of establishments will provide the public with a rationale for the agency's enforcement actions and may deter future violations and increase compliance with FDA regulations," says Howard Sklamberg, director of the FDA's Office of Enforcement. This includes inspections of clinical trial investigators, institutional review boards, and facilities that manufacture, process, pack or hold an FDA-regulated product that is currently marketed. The FDA will update the database every six months. In addition, the FDA is posting summaries of the most frequently cited regulations during inspections conducted by the FDA from fiscal years 2006 to 2010. "Disclosure of the inspection observations and number of times cited will provide industry with information that can be used to in! form compliance efforts," adds Sklamberg. "The database information should be a reminder to all regulated industry that the FDA is out there, inspecting your facilities and that it is not a matter of if, but when, the agency will show up at your door. If this leads to a better understanding of how important it is to have solid systems and processes in place, then the database will have served a significant purpose," says Jack Garvey, founder and principal at Compliance Architects in Robbinsville, New Jersey. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• Australian biotechs rejoice
  - Nat Biotechnol 29(8):676 (2011)
  Article preview View full access options Nature Biotechnology | News Australian biotechs rejoice * Jennifer RohnJournal name:Nature BiotechnologyVolume: 29,Page:676Year published:(2011)DOI:doi:10.1038/nbt0811-676bPublished online05 August 2011 The Australian Department of Innovation, Industry, Science & Research and The Treasury jointly announced an AUS $1.8 ($1.9) billion R&D tax credit last month aimed at boosting biotech companies and other innovation-oriented firms. In a bid to stimulate smaller businesses, companies with an aggregated turnover of less than AUS $20 ($21) million will benefit the most, with a 45% refundable tax credit on R&D expenditure. It is seen as being especially useful for startup biotech firms trading in loss. But larger companies exceeding the AUS $20 million benchmark will still enjoy a 40% nonrefundable offset. The reform, which is expected to pass the Senate in August and be backdated to July 1, has cross-party support and is the result of significant consultation and negotiation since at least 2008. Anna Lavelle, the CEO of AusBiotech, an industry organization representing more than 3,000 Australian biotech companies, said that the announcement represented the "most significant po! sitive news" that the industry has had for a number of years. She predicts that the move will stimulate new investment and the production of more intellectual property, and will allow companies to begin their clinical trials earlier and reach their end goal of entering the market faster than before. She added, "All biotechnology companies will benefit from the reform to some degree and the majority will benefit dramatically." Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• FDA panel votes to pull Avastin in breast cancer, again
  - Nat Biotechnol 29(8):676 (2011)
  Article preview View full access options Nature Biotechnology | News FDA panel votes to pull Avastin in breast cancer, again * Mark Ratner1Journal name:Nature BiotechnologyVolume: 29,Page:676Year published:(2011)DOI:doi:10.1038/nbt0811-676cPublished online05 August 2011 Roche The cancer treatment Avastin binds to VEGF secreted by the tumor. For the second time in a year, a panel of US Food & Drug Administration (FDA) advisors has stated that Genentech's blockbuster cancer drug Avastin (bevacizumab) confers no meaningful clinical benefit when used with chemotherapy as an initial treatment for metastatic breast cancer and that its approval should therefore be rescinded. The forum for the current pronouncement was a two-day public hearing in late June requested by Genentech, the S. San Francisco, California, unit of Swiss pharmaceutical giant Roche. Avastin, a humanized monoclonal antibody that binds to vascular endothelial growth factor (VEGF), was approved in 2008 for use with chemotherapy in metastatic breast cancer under the agency's accelerated approval process. But last December, the FDA rescinded approval for the drug in that indication, prompting the drugmaker to request a hearing—the first time a drugmaker has ever contested such a move by the regulator (Nat. Med.17, 233, 2011). Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• Novel schemes skirt NICE barrier
  - Nat Biotechnol 29(8):677 (2011)
  Article preview View full access options Nature Biotechnology | News Novel schemes skirt NICE barrier * Suzanne Elvidge1Journal name:Nature BiotechnologyVolume: 29,Page:677Year published:(2011)DOI:doi:10.1038/nbt0811-677aPublished online05 August 2011 Roel Smart/istockphoto Costly cancer treatments could be made available through the newly launched Cancer Drug Fund. A £600 ($968) million fund that gives cancer specialists the power to prescribe drugs not recommended by the UK's National Institute for Health and Clinical Excellence (NICE) in London could clear the path of expensive biotech drugs to market. At the same time, a clarification of how medical practitioners and hospitals can engage in risk-sharing agreements with drugmakers—in all areas, not just cancer—could benefit companies producing innovative biologics, although the systems' intricacies could be hard to navigate. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Stockport, UK * Suzanne Elvidge Author Details * Suzanne Elvidge Search for this author in: * NPG journals * PubMed * Google Scholar
• Cisgenic crop exemption
  - Nat Biotechnol 29(8):677 (2011)
  Article preview View full access options Nature Biotechnology | News Cisgenic crop exemption * Emily WaltzJournal name:Nature BiotechnologyVolume: 29,Page:677Year published:(2011)DOI:doi:10.1038/nbt0811-677bPublished online05 August 2011 Cisgenic plants could be allowed on the market without US Environmental Protection Agency (EPA) approval under a proposed rule change aimed at reducing the regulatory burden for biotech crops. Cisgenic plants are formed by moving genetic material between sexually compatible species, such as from one variety of corn to another, using molecular biology tools. Some industry supporters say they are hopeful that cisgenic exemption is a first step in a broader effort by EPA to fully accept biotech crops as safe, and to exempt all genetically modified (GM) plants. "The usefulness of the proposed exemption to crop developers will depend on how narrowly the cisgenic exemption is defined," says Adrianne Massey, managing director of scientific and regulatory affairs at the Biotechnology Industry Organization in Washington, DC. "We will learn these details only after EPA publishes the proposed rule and requests comments." At press time, the EPA had not released the draft rule to! the public. The agency in March shared a draft with the US Department of Agriculture (USDA), which also regulates biotech crops, and the US Department of Health and Human Services, for their review. According to EPA documents, the purpose of the exemption is to "encourage research and development of useful biotechnology" and to reduce the number of GM plants seeking registration. "It would not be surprising for USDA to take a similar action," says Doug Gurian-Sherman of the Union of Concerned Scientists in Cambridge, Massachusetts. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• EU tolerates GM
  - Nat Biotechnol 29(8):677 (2011)
  Article preview View full access options Nature Biotechnology | News EU tolerates GM * Anna MeldolesiJournal name:Nature BiotechnologyVolume: 29,Page:677Year published:(2011)DOI:doi:10.1038/nbt0811-677cPublished online05 August 2011 On June 24 the European Commission took a baby step forward by harmonizing regulations on unapproved genetically modified (GM) organisms found in trace amounts in animal feed imports. Up to 0.1% GM products will now be allowed in feed, in a move aimed at easing feed shortage fears. Lack of synchronicity in GM regulations between importing and exporting countries means that when traces of GM organisms find their way into feed and food, shipments are blocked and the risk of supply disruptions mounts. Val Giddings, senior fellow with the Information Technology and Innovation Foundation in Washington, DC, says, "The biotech industry will be affected indirectly. The new rules will make the lives of their biggest customers easier...They are the ones who ship harvest around the world and bear the brunt of exposure when detection methods of unprecedented power are linked with a regulatory regime unhinged from risk, reason or reality." The new threshold will apply only under cert! ain conditions (for instance, authorization pending in EU for over three months), and does not apply to food, however. "It's a limited stopgap, doing nothing for food and not enough for feed," Giddings adds. According to Carel du Marchie Sarvaas, from EuropaBio, "Longer-term solutions should include a more efficient and rapid processing of GM products through the EU system but there are no indications things might improve soon." Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Anna Meldolesi Search for this author in: * NPG journals * PubMed * Google Scholar
• Supreme Court ruling prompts universities to tighten employee contracts
  - Nat Biotechnol 29(8):678 (2011)
  Article preview View full access options Nature Biotechnology | News Supreme Court ruling prompts universities to tighten employee contracts * Josh P Roberts1Journal name:Nature BiotechnologyVolume: 29,Page:678Year published:(2011)DOI:doi:10.1038/nbt0811-678Published online05 August 2011 Dennis Brack/NewscomDebsphotos032895-John_Roberts_8. Chief Justice John Roberts rejected Stanford's claims. In June, the United States Supreme Court ruled 7–2 in favor of Roche Molecular Systems of Pleasanton, California, in a patent infringement dispute with Stanford University of Palo Alto, California, ending a six-year-long ordeal that many thought threatened to divide industry from academia. Stanford had sued Roche for marketing PCR-based HIV tests based on inventions made by Stanford post-doc Mark Holodniy while collaborating at Cetus. (Roche acquired rights to Cetus's PCR technology in 1991.) Some suggested that a ruling for Stanford would have given universities the right to any invention simply because a single federal dollar had been spent on it; others suggested that a ruling for Roche would have signaled the end of the Bayh-Dole Act—which allows universities to retain intellectual property (IP) rights to the results of federally funded research—as we know it. Instead, the ruling narrowly focused on the wording of the agreements signed by the inventor, Holodniy, wh! ich assigned the rights of his research to Cetus. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 * Minneapolis * Josh P Roberts Author Details * Josh P Roberts Search for this author in: * NPG journals * PubMed * Google Scholar
• Newsmaker: Lycera
  - Nat Biotechnol 29(8):679 (2011)
  Nature Biotechnology | News Newsmaker: Lycera * Ken Garber1Journal name:Nature BiotechnologyVolume: 29,Page:679Year published:(2011)DOI:doi:10.1038/nbt0811-679Published online05 August 2011 Galvanized by ex-Pfizer researchers, Lycera is pursuing allosteric inhibitors of the mitochondrial ATPase and a nuclear receptor in autoimmune and inflammatory diseases. View full text Additional data Affiliations * Ann Arbor, Michigan. * Ken Garber Author Details * Ken Garber Search for this author in: * NPG journals * PubMed * Google Scholar
• Drug pipeline: Q211
  - Nat Biotechnol 29(8):680 (2011)
  Article preview View full access options Nature Biotechnology | News | Data Page Drug pipeline: Q211 * Wayne Peng1Journal name:Nature BiotechnologyVolume: 29,Page:680Year published:(2011)DOI:doi:10.1038/nbt.1942Published online05 August 2011 There was a notable uptick in drug approvals by the US Food and Drug Administration (FDA) compared with the same period last year. The agency approved two hepatitis C drugs, Victrelis (boceprevir) and Incivek (telaprevir) as well as a second autologous cell therapy, laViv (azficel-T), for skin wrinkle reduction. The V600E mutation-specific B-RAF inhibitor vemurafenib for melanoma, translation modulator ataluren for cystic fibrosis and monoclonal antibody teplizumab for diabetes showed proof of efficacy in trials. Notable regulatory approvals (Q2 2011) Box 1: Notable regulatory approvals (Q2 2011) Full box Notable regulatory setbacks (Q2 2011) Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * Print * Email * 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 Additional data
• Move over ZFNs
  - Nat Biotechnol 29(8):681-684 (2011)
  Nature Biotechnology | News Feature Move over ZFNs Journal name:Nature BiotechnologyVolume: 29,Pages:681–684Year published:(2011)DOI:doi:10.1038/nbt.1935Published online05 August 2011 A new technology for genome editing may put the zinc finger nuclease franchise out of business, some believe. Not so fast, say the finger people. Laura DeFrancesco reports. View full text Additional data
• Commercializing a disruptive technology
  - Nat Biotechnol 29(8):685-688 (2011)
  
• IMI moves forward
  - Nat Biotechnol 29(8):689-690 (2011)
  Article preview View full access options Nature Biotechnology | Opinion and Comment | Correspondence IMI moves forward * Rudolf Strohmeier1, 2 * Ruxandra Draghia-Akli1, 2 * Andrzej Rys1, 2 * Pedro Ortun Silvan1, 2 * Theodius Lennon1, 2 * Carlo Incerti2, 3 * Richard Bergström2, 3 * Salahdine Chibout2, 3 * Roch Doliveux2, 3 * Peter Hongaard Andersen2, 3 * AffiliationsJournal name:Nature BiotechnologyVolume: 29,Pages:689–690Year published:(2011)DOI:doi:10.1038/nbt.1944Published online05 August 2011 To the Editor: As members of the Governing Board of the Innovative Medicines Initiative (IMI), we wish to respond to two recent articles published in Nature Biotechnology that cast unfounded gloom over IMI1, 2. In the June issue, Gunjan Sinha reports on a series of incorrect allegations on the funding rules and intellectual property (IP) policy of IMI1 on the basis of an interview with the head of European Research and Development at University College London, and a letter published in September 2010 by the League of European Research Universities. Sinha writes, "For an academic partner, IMI funds cover only 75% of direct projects costs and 20% of indirect project costs, which results in loss-making projects. This diverges from the [European Union's] EU's Framework Programme 7, which covers 100% of direct costs and 60% of indirect costs—a disincentive to participate." We would like to clarify that for academic investigators, the 75% funding rate of direct eligible costs is exactly the same in IMI as in collaborative research projects supported directly from the EU 7th Framework Programme. As far as the coverage of indirect costs is concerned, IMI now offers the possibility to! claim for actual indirect costs. This new measure is aligned with the objective of IMI to support research activities on the basis of real costs, in a transparent manner. Regarding IP, Sinha reports "IMI's intellectual property agreement heavily favors the industrial partner's financial interests." In fact, IMI designed a policy that aims to promote knowledge disclosure and to reward innovation through a fair allocation of rights. Each participant to an IMI project remains the exclusive owner of the know-how and IP rights held before becoming a partner of the IMI consortium. In the course of an IMI project, partners who generate results are the owners of corresponding information and IP rights. Access rights to IP are granted to consortium partners or third parties upon specific request, under terms that vary according to the foreseen use of the IP. As a matter of fact, the IP policy of IMI has been designed to allow the flexibility necessary to accommodate the specific situation of each consortium, as explained in a guidance note accessible on the IMI website (http://www.imi.europa.eu). Furthermore, the IMI executive office acts as a neu! tral third-party to facilitate agreement between participants when necessary. Whatever the causes of the misperceptions and misrepresentations of IMI rules and policy, the projects selected after the first two calls for proposals attracted 298 academic teams, several of which originated from major institutions. Indeed, 75 research groups from the UK are represented in IMI projects, the highest number among European countries. This trend is confirmed after the third call for proposals with 5 out of 7 applicants' consortia being coordinated by UK organizations. In the July issue, the editorial focuses on the supposed lack of interest of IMI in biotech companies2. This does not correspond to the strategic vision of IMI and is contradicted by the significant involvement of such businesses in ongoing IMI projects. Above all, the IMI governing board fully realizes the critical role of biotech enterprises in the development of the pharmaceutical sector at large and is developing actions in this direction. As a matter of fact, 45 small and medium-size enterprises (SMEs) participate in 19 out of the 23 ongoing IMI projects and 15.79% of IMI funding is currently allocated to SMEs. Thirty-two SMEs are indeed biotech companies whereas 10 are specialized in information technologies (IT) and data analysis, which is aligned with the objectives of many projects to share data and to build large-scale databases. Only three SMEs are dedicated to project management or consultancy. When asked about their interest in being involved in IMI, SME partner! s emphasize the access to new business opportunities and the enhanced visibility offered by IMI. It is true that the European Federation of Pharmaceutical Industries and Associations (EFPIA) is driving the scientific research agenda of IMI; however, EFPIA companies do not receive any public funding and actually invest significant resources in IMI projects, matching the public funds provided by the EU Commission. Thus, although these two articles reflect a negative view of the impact of IMI by some pressure groups, the facts speak for themselves as the first IMI projects are already reporting significant achievements. For instance, the NEWMEDS consortium (http://www.newmeds-europe.com/en/consortium.php) has created the largest database ever on schizophrenia, gathering extensive information and material from more than 20,000 patients enrolled in trials conducted by several pharmaceutical companies3. This consortium has also assembled a database on more than 2,000 patients with major depression, which already delivered new clues to predict therapeutic responses. In the area of drug safety, the SAFE-T consortium (http://www.imi-safe-t.eu/biomarker/drug-induced-injury/consortium) identified 153 biomarker candidates for drug-induced injury of the kidney, the liver and the vascular system and established a generic strategy to qualify biomarkers4, whereas the eTOX consortium (http://www.e-t! ox.net/consortium.html), which includes four IT solution SMEs, developed an innovative multi-scale modeling strategy allowing the in silico prediction of drug effects on the heart using electrocardiogram simulations5. In parallel, four education and training projects are running, covering different areas of pharmaceutical sciences, including pharmacovigilance, of direct relevance to industry and regulatory authorities. Therefore, the alarmist and negative description of IMI reported in this journal does not reflect reality. In an era where biopharmaceutical companies rely more and more on noncompetitive research and open collaboration to develop new models for drug development, IMI offers unique opportunities for academic groups and SMEs interested in translating results of their endeavors into innovative therapies. The update of the IMI Scientific Research Agenda has just been completed and will result in a series of even more ambitious projects based on sharing of data and know-how to address major unmet medical needs. The currently running 4th Call for Proposals (Table 1) already contains two 'Think Big' projects with a transformational potential: the first aims at developing a European framework for patient-level health information, which will be exploited for investigations on major diseases in adult and pediatric populations; the second will focus on the use of induced pluripotent stem cells derived from patients as innovative tools for drug discovery and safety assessment. The budget of each project will be around 50 ($70) million, with equal contributions from the European Commission and companies in EFPIA (the European Federation of Pharmaceutical Industries and Associations), the latter in the form of in-kind contributions. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * European Commission, Brussels, Belgium. * Rudolf Strohmeier, * Ruxandra Draghia-Akli, * Andrzej Rys, * Pedro Ortun Silvan & * Theodius Lennon * Innovative Medicines Initiative (IMI), Brussels, Belgium. * Rudolf Strohmeier, * Ruxandra Draghia-Akli, * Andrzej Rys, * Pedro Ortun Silvan, * Theodius Lennon, * Carlo Incerti, * Richard Bergström, * Salahdine Chibout, * Roch Doliveux & * Peter Hongaard Andersen * European Federation of Pharmaceutical Industries and Associations, Brussels, Belgium. * Carlo Incerti, * Richard Bergström, * Salahdine Chibout, * Roch Doliveux & * Peter Hongaard Andersen Competing financial interests S.C. is with Novartis, R.D. is with UCB, P.H.A. is with Lundbeck and C.I. is with Genzyme. Author Details * Rudolf Strohmeier Search for this author in: * NPG journals * PubMed * Google Scholar * Ruxandra Draghia-Akli Search for this author in: * NPG journals * PubMed * Google Scholar * Andrzej Rys Search for this author in: * NPG journals * PubMed * Google Scholar * Pedro Ortun Silvan Search for this author in: * NPG journals * PubMed * Google Scholar * Theodius Lennon Search for this author in: * NPG journals * PubMed * Google Scholar * Carlo Incerti Search for this author in: * NPG journals * PubMed * Google Scholar * Richard Bergström Search for this author in: * NPG journals * PubMed * Google Scholar * Salahdine Chibout Search for this author in: * NPG journals * PubMed * Google Scholar * Roch Doliveux Search for this author in: * NPG journals * PubMed * Google Scholar * Peter Hongaard Andersen Search for this author in: * NPG journals * PubMed * Google Scholar Correspondence should be addressed to Michel Goldman, Executive Director, Innovative Medicines Initiative (IMI), Brussels, Belgium. e-mail: michel.goldman@imi.europa.eu Additional data
• Biosimilars—why terminology matters
  - Nat Biotechnol 29(8):690-693 (2011)
  Article preview View full access options Nature Biotechnology | Opinion and Comment | Correspondence Biosimilars—why terminology matters * Martina Weise1, 9 * Marie-Christine Bielsky2, 10 * Karen De Smet3, 9 * Falk Ehmann4 * Niklas Ekman5, 10 * Gopalan Narayanan2, 10 * Hans-Karl Heim1, 9 * Esa Heinonen5, 10 * Kowid Ho6, 10 * Robin Thorpe7, 10 * Camille Vleminckx4 * Meenu Wadhwa7, 10 * Christian K Schneider8, 9 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:690–693Year published:(2011)DOI:doi:10.1038/nbt.1936Published online05 August 2011 To the Editor: As members of the Biosimilar Medicinal Products Working Party (BMWP) at the European Medicines Agency (EMA; London), we would like to draw readers' attention to problems arising from imprecise usage of the term biosimilar (similar biological medicinal product) in the literature. We have repeatedly noticed misinterpretations of the biosimilar concept as well as inconsistent use of terminology and are concerned about potential implications of this, such as negative perception and impaired acceptance of biosimilars among prescribing physicians and patients. Here we outline the scientific principles underlying the biosimilar concept in the European Union (EU; Brussels). We also address problems in terminology in the context of global emergence of copy biologicals (including 'true' biosimilars) and 'biobetters', and the potential for unjustified concerns about the efficacy and safety of biosimilars in their stricter sense. The recent expiry of data protection or patents for the first biopharmaceuticals has opened up the possibility of developing biological products similar to these original products and to rely for licensing, in part, on the extensive knowledge gained with the originator products. Although copy versions of original biopharmaceuticals are already available in different parts of the world, there are no consistent worldwide requirements for their registration. In Europe, the EMA's Committee for Medicinal Products for Human Use (CHMP) is responsible for the scientific assessment of human medicines that follow the European 'centralized procedure of marketing authorization'. According to this legislation, all recombinant proteins must undergo this route for licensing1. As most biosimilars are recombinant proteins, they usually have to follow this centralized route. According to the EU, a biosimilar medicinal product is a copy version of an already authorized biological medicinal product (the reference product) with demonstrated similarity in physicochemical characteristics, efficacy and safety, based on a comprehensive comparability exercise2, 3. Biological medicinal products are derived from living cells or organisms and consist of relatively large and highly complex molecular entities that are often difficult to fully characterize by currently available analytical methods. Because of the inherent variability of the biological system used as manufacturing process, the resulting biological product will also display a certain degree of variability ('microheterogeneity'). Developers of biosimilars usually do not have access to either the originator companies' proprietary data, including details on the manufacturing process, or the active ingredient of the reference medicine. Therefore, they need to engineer their own manufacturing process that is capable of manufacturing a product as similar as possible to the reference product. Because of unavoidable differences in the manufacturing process, which may include the use of different expression systems, fermentation and purification processes, as well as different excipients, the quality attributes of the biosimilar and the reference medicinal products will not be strictly identical. Such variability may not be a matter of concern but rather is a scientific fact that has been accepted by the scientific and regulatory community since the introduction of biotech for the production of biological medicines. As a biosimilar is highly unlikely to be identical to its reference product, the standard 'generic' approach (that is, demonstration of bioequivalence in comparative bioavailability studies, established for small chemically derived and easily characterized molecules) is not sufficient for the development, regulatory assessment and licensing of such a product. For this reason, we argue that the term biogeneric is scientifically incorrect and should not be used for a biosimilar. In the EU, any biosimilar submitted for approval is assessed through a thorough comparability exercise with the reference product, including a comparison of the quality attributes and followed by comparative nonclinical studies, if considered necessary for safety reasons, and clinical studies, to ensure close resemblance in physicochemical characteristics, safety and efficacy. It should be noted that a comparability exercise is also required for originator biological medicinal products when changes to the manufacturing process are made4. Indeed, such changes are frequently introduced throughout a product's lifecycle (e.g., to improve the quality or to increase the yield of the product). As a consequence, the quality profile of the biological product may evolve over its life cycle but would still be considered as comparable to the product before changes were made as long as relevant impact on safety and efficacy has been excluded with sufficient confidence5. The scientific principles underlying the comparability exercise required for changes in the manufacturing process of a given biological product and for the development of a biosimilar product are the same. Even so, data requirements for the latter are higher and, at least in the EU, always include clinical studies because, due to the completely independent manufacturing processes, some differences between the biosimilar and the reference product can be expected, and the potential impact of these differences on safety and efficacy cannot be predicted from analytical assessment alone. Therefore, biosimilars approved in the EU have always been clinically tested in addition to being characterized physicochemically and biologically. As for any biosimilar, the biological reference medicine will have been authorized and in clinical use for several years and a large body of knowledge on its efficacy and safety will be available. A biosimilar is intended to be used at the same dose(s) and dosing regimen(s) to treat the same disease(s) as the reference product. Therefore, the focus of biosimilar development is not to establish patient benefit per se—this has already been done for the reference product—but to convincingly demonstrate similarity to the reference product as the basis for relying, in part, on efficacy and safety experience gained with the reference product. The various general and product class–specific EU guidelines for biosimilars define the nonclinical and clinical studies that need to be carried out to show that the biosimilar medicine is indeed similar and as safe and effective as the biological reference medicine2. A repetition of the entire development program of the reference produ! ct would, on scientific grounds, not add relevant information (e.g., phase 2 proof-of-concept studies) and thus could even be considered unethical. Clinical biosimilarity is established by use of a 'sensitive' clinical test model, able to detect potential differences between the biosimilar and the reference product. For example, differences in the efficacy of two insulins would be more likely to be detected in insulin-sensitive, normal-weight healthy people or individuals with type 1 diabetes mellitus than in those who are obese and have insulin-resistant type 2 diabetes. A valid conclusion on similarity can only be made based on reassurance that relevant differences would indeed have been detectable by the 'model' used in the clinical studies. This also implies that the clinical trial design may be different from that for a novel molecular entity and may also use different (clinical or pharmacodynamic), more sensitive endpoints. Demonstration of equivalent (that is, clinically not showing relevant lower or higher) efficacy is needed to adopt the dose recommendations established for the reference product. In the case of lower potency, a higher dose would be needed to achieve the same effects as the reference product. In the case of higher potency, safety concerns could arise when using the dose(s) recommended for the reference product, especially for products with a narrow therapeutic margin. Relevant differences in efficacy would therefore contradict the assumption of similarity and would likely preclude extrapolation of efficacy and safety data to other indications of the reference product, particularly those with different dose requirements. These points make it clear that, although a reduction in the data requirements is possible for biosimilars, the prelicensing data package is nevertheless substantial. Similarity in physicochemical characteristics is a prerequisite for a possible reduction in nonclinical and clinical data requirements. The amount of possible data reduction depends on how well the molecule can be characterized by state-of-the-art analytical methods, on observed or potential differences between the biosimilar and the reference product, and the clinical experience gained with the reference product and/or the substance class. The above description outlines the requirements for the licensing of biosimilar medicinal products in the EU. But what of other types of nonbrand biologics that may not fall under this definition of biosimilars? Various terms have emerged in different parts of the world for copy versions of original biological medicinal products, including biosimilars, follow-on biologicals/biologics, subsequent-entry biologicals/biologics, similar biopharmaceuticals, me-too biologicals/biologics, biogenerics or noninnovator proteins. In addition, different definitions of the same term in different geographical locations add to the semantic confusion. In recent chemical analyses of various 'noninnovator epoetins', significant differences (compared with the supposed originator product) with regard to physicochemical characteristics and potency were observed6, whereas almost superimposable quality characteristics were demonstrated for a 'biosimilar' epoetin7. The main difference between these two seemingly contradictory findings is that one paper6 analyzed proteins that are not biosimilars, as we wish to define them, whereas the other article7 analyzed a true biosimilar (Binocrit8). We acknowledge that the authors in both publications used the terms in an appropriate manner. In addition, some of these noninnovator epoetins exhibited very high batch-to-batch variability, exceeding self-declared specifications for several batches9, 10 or were found to be associated with severe adverse reactions (pure red cell aplasia)11. In our opinion, some low molecular weight heparins already marketed outside the EU and the United States should also not be labeled biosimilars because it is not clear whether they were developed in a comparative manner12. Furthermore, different formulations of botulinum toxin A recently described by Wenzel et al.13 do not qualify as true biosimilars because of obvious differences in physicochemical characteristics, doses and dosing regimens13. Another misinterpretation of the biosimilar concept is to brand second-generation proteins—analogs with differences in the primary structure—as biosimilars. Our understanding of the term second-generation proteins are biologicals or biologics that have been structurally and/or functionally altered to gain an improved, or different, clinical performance. An example would be a chimeric monoclonal antibody and a subsequently developed fully human monoclonal antibody, directed against the same antigen or a cytokine product and its counterpart decorated with polyethylene glycol. As these would clearly exhibit differences in the structure of the active substance and different clinical behavior due to different potency or immunogenicity, the second-generation products cannot be biosimilar to each other. The most striking misinterpretation of the term biosimilar was noted by one of us (C.K.S.) during a conference, where a physician expressed his doubts about biosimilars because "they may not even contain active substance." Here the term biosimilar was obviously conflated with counterfeit medicine, which according to the World Health Organization (WHO; Geneva) definition is "deliberately and fraudulently mislabeled with respect to identity and/or source."14. Counterfeiting has recently, for example, been reported for epoetins15, 16. For these reasons, we suggest that any copy version of a therapeutic protein, which has not been developed and assessed in line with the scientific principles of a strictly comparative development program against a reference product, should not be termed biosimilar. We do not wish to imply that other products are of lower quality, efficacy or safety, but simply that they may not qualify as biosimilars according to the understanding of this term in the EU and potentially other regions, and thus may require different terminology to enable a clear distinction between the different products. Using a consistent and clear terminology will prevent confusion between biosimilars and other copy versions of original biological medicinal products, and ensure their safe use. Indeed, recently, the WHO has adopted a 'Guideline on evaluation of similar biotherapeutic products' to provide globally acceptable principles for licensing of biotherapeutic products that are claimed to be similar to biotherapeutic products of assured quality, safety and efficacy, based on a reduced data package17. Despite the use of a slightly different term (that is, "similar biotherapeutic product"), the scientific principles laid down in this document are generally in line with the EU requirements. We expect that this WHO guideline will facilitate the employment of sound global standards for the development and licensing of similar biotherapeutic products. Of particular note, the US Food and Drug Administration (FDA) previously used the informal term 'follow-on protein products' to refer to "proteins and peptides that are intended to be sufficiently similar to a product already approved under the Federal Food, Drug, and Cosmetic Act or licensed under the Public Health Service Act to permit the applicant to rely on certain existing scientific knowledge about the safety and effectiveness of the approved protein product"18. With the recent enactment of an approval pathway for such products, the term was changed to biosimilars19. However, whereas the new legislation in the United States foresees the licensure of biological products as biosimilar or interchangeable, the EU legislation and guidelines do not mention the issue of interchangeability, mainly because any decision on automatic substitution has to be made at the national level of individual EU member states. FDA guidelines defining the data requirements for biosimilar ! and interchangeable biologicals are awaited. We believe that terminology covering biosimilars is important because demonstrated close resemblance to the reference product is a key feature of biosimilars with inherent implications that the prescribing physician must be able to rely upon. A proposal for a more precise terminology is provided in Table 1. In conclusion, we would like to propose a narrow definition of biosimilars as follows: Table 1: Proposal for a more precise terminology. Full table A biosimilar is a copy version of an already authorized biological medicinal product with demonstrated similarity in physicochemical characteristics, efficacy and safety, based on a comprehensive comparability exercise. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Bundesinstitut für Arzneimittel und Medizinprodukte (BfArM), Bonn, Germany. * Martina Weise & * Hans-Karl Heim * Medicines and Healthcare products Regulatory Agency (MHRA), London, UK. * Marie-Christine Bielsky & * Gopalan Narayanan * Federal Agency for Medicines and Health Products (FAGG), Brussels, Belgium. * Karen De Smet * European Medicines Agency (EMA), London, UK. * Falk Ehmann & * Camille Vleminckx * Finnish Medicines Agency (FIMEA), Helsinki, Finland. * Niklas Ekman & * Esa Heinonen * L'Agence française de sécurité sanitaire des produits de santé (Afssaps), Paris, France. * Kowid Ho * National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK. * Robin Thorpe & * Meenu Wadhwa * Paul-Ehrlich-Institut (PEI), Langen, Germany, and Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany. * Christian K Schneider * Member of the Working Party on Similar Biological (Biosimilar) Medicinal Products (BMWP) of the Committee for Medicinal Products for Human Use (CHMP), EMA, UK. * Martina Weise, * Karen De Smet, * Hans-Karl Heim & * Christian K Schneider * Expert of the BMWP, EMA, UK. * Marie-Christine Bielsky, * Niklas Ekman, * Gopalan Narayanan, * Esa Heinonen, * Kowid Ho, * Robin Thorpe & * Meenu Wadhwa Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Martina Weise Author Details * Martina Weise Contact Martina Weise Search for this author in: * NPG journals * PubMed * Google Scholar * Marie-Christine Bielsky Search for this author in: * NPG journals * PubMed * Google Scholar * Karen De Smet Search for this author in: * NPG journals * PubMed * Google Scholar * Falk Ehmann Search for this author in: * NPG journals * PubMed * Google Scholar * Niklas Ekman Search for this author in: * NPG journals * PubMed * Google Scholar * Gopalan Narayanan Search for this author in: * NPG journals * PubMed * Google Scholar * Hans-Karl Heim Search for this author in: * NPG journals * PubMed * Google Scholar * Esa Heinonen Search for this author in: * NPG journals * PubMed * Google Scholar * Kowid Ho Search for this author in: * NPG journals * PubMed * Google Scholar * Robin Thorpe Search for this author in: * NPG journals * PubMed * Google Scholar * Camille Vleminckx Search for this author in: * NPG journals * PubMed * Google Scholar * Meenu Wadhwa Search for this author in: * NPG journals * PubMed * Google Scholar * Christian K Schneider Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Reply to: IMI moves forward
  - Nat Biotechnol 29(8):690 (2011)
  Article preview View full access options Nature Biotechnology | Opinion and Comment | Correspondence Reply to: IMI moves forward Journal name:Nature BiotechnologyVolume: 29,Page:690Year published:(2011)DOI:doi:10.1038/nbt.1951Published online05 August 2011 Nature Biotechnology replies: We continue to urge the IMI governing board to do more to engage SMEs in setting the agendas for IMI projects. Success in recruiting SMEs into projects is different from providing SMEs with a voice at the table that can contribute to setting the innovation agenda. We recognize this is difficult—for one thing, people at SMEs very often don't have time to devote employees to outside projects, such as IMI. Our editorial attempted to highlight the problem that the innovative agenda of EFPIA members may not be as broad as the innovative agenda put forward by less established and smaller companies who seek to disrupt conventional approaches. For example, it is clear that cells derived from human induced pluripotent stem cells offer considerable potential in drug discovery screens and safety assessment, and this has been demonstrated by the investment by the pharmaceutical industry in these approaches in recent years. But what about the potential of such products as experimental ! therapies in themselves? Clearly, a focus for many SMEs and academic groups but not a major focus for many major pharmaceutical companies. Perhaps IMI could play a role in moving such unconventional approaches forward, especially if the funding and expertise from EU and EFPIA could be used to help SMEs focus their efforts to address the formidable manufacturing, regulatory and reimbursement issues that cell therapies face before reaching the market. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• Synergies between synthetic biology and metabolic engineering
  - Nat Biotechnol 29(8):693-695 (2011)
  Article preview View full access options Nature Biotechnology | Opinion and Comment | Correspondence Synergies between synthetic biology and metabolic engineering * Jens Nielsen1 * Jay D Keasling2, 3, 4 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:693–695Year published:(2011)DOI:doi:10.1038/nbt.1937Published online05 August 2011 To the Editor: Your focus issue on 'Synthetic Biology' (December 2009) highlighted some of the ambiguities in defining the fields of metabolic engineering and synthetic biology. Here we provide our interpretation of the scope of each of these fields and then provide suggestions for how they could be dovetailed synergistically to facilitate the design and construction of efficient cell factories. Metabolic engineering has evolved into an area of research that encompasses detailed metabolic analyses with the objective of identifying targets for manipulation and directed genetic modification (through the use of recombinant DNA technology) for the improvement and/or design of cells. Improvement may focus on a range of different strategies, including enhancement of substrate range, production of novel products, increase of yield and productivity, and/or augmentation of cellular robustness (e.g., improved tolerance towards toxic compounds). Recent years have also witnessed the emergence of synthetic biology, both as a means to reconstruct small, artificial biological systems (e.g., to assemble a novel biological regulon or oscillators that can be used to regulate gene expression in response to a specific input)1 and as an approach for synthesizing DNA and complete chromosomes, as illustrated by the recent culmination of several decades of work attempting to reconstruct a complete bacterial genome2. In industrial biology, synthetic biology offers some tremendous opportunities to create cell factories tailor-made for efficient production of fuels and chemicals. In most cases, though, the design and construction of cell factories for use in industrial biology requires both synthetic biology and metabolic engineering (Fig. 1). In many instances, a well-known, safe, platform cell factory is used as a chassis for production of a new chemical compound. The first step is to reconstruct a completely synthetic pathway in this cell factory and, thereafter, the regulation of the carbon fluxes is altered such that there is a sufficient flux toward the product of interest to allow an economically feasible process. There are several reasons why this combined approach is widely used in cell factory design. Figure 1: Illustration of the overlap between metabolic engineering and synthetic biology by the use of three different approaches to produce a desirable product. () The first approach is a traditional approach in biotech where a naturally producing organism is selected as the cell factory for production of the desirable product. Typically the flux toward the product is naturally low but through the use of classical strain improvement or the use of directed genetic modifications, that is, metabolic engineering, it is possible to increase the flux toward the product. () In the second approach, the platform cell factory does not naturally produce the product of interest. Through insertion of a synthetic pathway in the organism (illustrated by the red pathway), the cell factory can produce the product, often in small amounts initially. However, through pathway optimization the flux through this synthetic pathway can be increased to ensure a high flux toward the product. This approach clearly applies concepts from both metabolic engineering and synthetic biology. () In the last approach a complete synthetic cell is constructed such that i! t is dedicated to produce the desirable product. * Full size image (113 KB) First, there is in industry much interest in applying a limited number of platform cell factories for production of a wide range of fuels and chemicals as this allows flexibility of production facilities, which are very capital intensive. This is best illustrated by the production of industrial enzymes, where the main commercial producers have consolidated around the use of a few (fungal and bacterial) cell factories. It is also evident in the area of antibiotic production where, for example, the production of adipoyl-7-amino-3-deacetoxycephalosporanic acid (adipoyl-7-ADCA), a precursor for cephalexin, has been accomplished through the engineering of a highly efficient, penicillin-producing strain of Penicillium chrysogenum3. In addition, in the field of fuel production, much interest has centered on the yeast Saccharomyces cerevisiae for production of novel fuels, as it is already well adapted to industrial conditions and thus can be applied as a plug-and-play solution. Oth! er important platform cell factories are Escherichia coli and Corynebacterium glutamicum. As industry has a preference for these platforms, it follows that the production of new compounds can only be obtained through reconstruction of pathways that lead to their synthesis, followed by the engineering of metabolism to ensure that these products are produced at a high yield and in high titers. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. * Jens Nielsen * Joint Bioenergy Institute, Emeryville, California, USA. * Jay D Keasling * Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California, USA. * Jay D Keasling * Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. * Jay D Keasling Competing financial interests Jay Keasling is a founder of and has a financial interest in Amyris and LS9. Corresponding author Correspondence to: * Jay D Keasling Author Details * Jens Nielsen Search for this author in: * NPG journals * PubMed * Google Scholar * Jay D Keasling Contact Jay D Keasling Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Knockout rats generated by embryo microinjection of TALENs
  - Nat Biotechnol 29(8):695-696 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Knockout rats generated by embryo microinjection of TALENs * Laurent Tesson1 * Claire Usal1 * Séverine Ménoret1 * Elo Leung2 * Brett J Niles2 * Séverine Remy1 * Yolanda Santiago2 * Anna I Vincent2 * Xiangdong Meng2 * Lei Zhang2 * Philip D Gregory2 * Ignacio Anegon1 * Gregory J Cost2 * Affiliations * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:695–696Year published:(2011)DOI:doi:10.1038/nbt.1940Published online05 August 2011 To the Editor: The recent description of highly active transcription activator-like effector nucleases (TALENs)1 prompted us to explore their utility for in vivo genetic engineering in the laboratory rat. The rat is a valuable experimental animal because of its suitability for modeling human disease and toxicology. Zinc-finger nuclease (ZFN) technology and the isolation of rat embryonic stem cells have enabled targeted modifications of the rat genome2, 3, 4, 5. Recently, Xanthomonas-derived transcription activator-like (TAL) effector proteins have elicited much interest because of their apparently simple rules for sequence-specific DNA recognition6, 7. Several investigators have fused the FokI nuclease domain to TAL effector proteins to create TALENs1, 8, 9, 10, 11, 12. However, only optimal truncation of the TAL effector protein allowed high-frequency gene disruption of endogenous loci and targeted DNA integration1, 13, 14. Here we use TALENs to disrupt the rat IgM locus, creating heritab! le mutations that eliminate IgM function. Our results establish the use of TALEN technology for in vivo gene knockout in mammals. 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 * INSERM UMR 643, Nantes, France; Platform Transgenic Rats Nantes IBiSA-CNRS; CHU Nantes, Nantes; Université de Nantes. * Laurent Tesson, * Claire Usal, * Séverine Ménoret, * Séverine Remy & * Ignacio Anegon * Sangamo Biosciences, Richmond, California, USA. * Elo Leung, * Brett J Niles, * Yolanda Santiago, * Anna I Vincent, * Xiangdong Meng, * Lei Zhang, * Philip D Gregory & * Gregory J Cost Competing financial interests E.L., B.J.N., Y.S., A.I.V., X.M., L.Z., P.D.G, and G.J.C. are employees of Sangamo BioSciences. Sangamo BioSciences provided financial support for research in I.A.'s laboratory. Sangamo BioSciences has filed a patent application on the basis of these results. Corresponding authors Correspondence to: * Gregory J Cost or * Ignacio Anegon Author Details * Laurent Tesson Search for this author in: * NPG journals * PubMed * Google Scholar * Claire Usal Search for this author in: * NPG journals * PubMed * Google Scholar * Séverine Ménoret Search for this author in: * NPG journals * PubMed * Google Scholar * Elo Leung Search for this author in: * NPG journals * PubMed * Google Scholar * Brett J Niles Search for this author in: * NPG journals * PubMed * Google Scholar * Séverine Remy Search for this author in: * NPG journals * PubMed * Google Scholar * Yolanda Santiago Search for this author in: * NPG journals * PubMed * Google Scholar * Anna I Vincent Search for this author in: * NPG journals * PubMed * Google Scholar * Xiangdong Meng Search for this author in: * NPG journals * PubMed * Google Scholar * Lei Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Philip D Gregory Search for this author in: * NPG journals * PubMed * Google Scholar * Ignacio Anegon Contact Ignacio Anegon Search for this author in: * NPG journals * PubMed * Google Scholar * Gregory J Cost Contact Gregory J Cost Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (5.7M) Supplementary Figures 1–3, Supplementary Tables 1–4, Supplementary Sequences and Supplementary Methods Additional data
• Targeted gene disruption in somatic zebrafish cells using engineered TALENs
  - Nat Biotechnol 29(8):697-698 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Targeted gene disruption in somatic zebrafish cells using engineered TALENs * Jeffry D Sander1, 2, 6 * Lindsay Cade3, 6 * Cyd Khayter1 * Deepak Reyon4 * Randall T Peterson3, 5 * J Keith Joung1, 2 * Jing-Ruey J Yeh3 * Affiliations * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:697–698Year published:(2011)DOI:doi:10.1038/nbt.1934Published online05 August 2011 To the Editor: Miller et al.1 recently described a transcription activator–like effector nuclease (TALEN) architecture for efficient genome editing in cultured human cells. We sought to determine whether the same framework could be used to efficiently disrupt endogenous genes in somatic cells of zebrafish and how the efficiency of TALENs compares with that obtained using engineered zinc-finger nucleases (ZFNs). 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 Primary authors * These authors contributed equally to this work. * Jeffry D Sander & * Lindsay Cade Affiliations * Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. * Jeffry D Sander, * Cyd Khayter & * J Keith Joung * Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA. * Jeffry D Sander & * J Keith Joung * Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA. * Lindsay Cade, * Randall T Peterson & * Jing-Ruey J Yeh * Department of Genetics, Development & Cell Biology; Interdepartmental Graduate Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, USA. * Deepak Reyon * Broad Institute, Cambridge, Massachusetts, USA. * Randall T Peterson Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Jing-Ruey J Yeh or * J Keith Joung Author Details * Jeffry D Sander Search for this author in: * NPG journals * PubMed * Google Scholar * Lindsay Cade Search for this author in: * NPG journals * PubMed * Google Scholar * Cyd Khayter Search for this author in: * NPG journals * PubMed * Google Scholar * Deepak Reyon Search for this author in: * NPG journals * PubMed * Google Scholar * Randall T Peterson Search for this author in: * NPG journals * PubMed * Google Scholar * J Keith Joung Contact J Keith Joung Search for this author in: * NPG journals * PubMed * Google Scholar * Jing-Ruey J Yeh Contact Jing-Ruey J Yeh Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (1.4M) Supplementary Figures 1–12, Supplementary Table 1 and Supplementary Methods Additional data
• Heritable gene targeting in zebrafish using customized TALENs
  - Nat Biotechnol 29(8):699-700 (2011)
  Nature Biotechnology | Opinion and Comment | Correspondence Heritable gene targeting in zebrafish using customized TALENs * Peng Huang1, 2 * An Xiao1 * Mingguo Zhou3 * Zuoyan Zhu1 * Shuo Lin2, 4 * Bo Zhang1 * Affiliations * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:699–700Year published:(2011)DOI:doi:10.1038/nbt.1939Published online05 August 2011 To the Editor: Studies of targeted gene modifications are of great interest in basic research as well as for clinical and agricultural applications1. In the February issue of Nature Biotechnology, two articles reported genomic modifications using transcription activator-like (TAL) effectors2, 3. Using fusion proteins, each comprising a TAL effector DNA binding domain and a FokI cleavage domain, Miller et al.2 reported that TAL effector nucleases (TALENs) successfully disrupted target genes in cultured human cells. Zhang et al.3 showed that TAL effectors can be used to regulate endogenous gene transcription. Compared with zinc-finger proteins4, 5, TAL effectors permit more predictable and specific binding to target DNA6, and therefore allow researchers to engineer genomes precisely without the need for laborious screening to identify a DNA binding domain with the requisite specificity. TALENs can induce DNA double-stranded breaks (DSBs) in yeast7. Gene targeting using TALENs has also been a! chieved in nematodes8 and human pluripotent cells9. However, it has not, to our knowledge, yet been demonstrated in a vertebrate organism. Here we report the use of TALENs to disrupt both of the two endogenous zebrafish genes we targeted and show that the mutations are transmitted through the germ line. 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 * Key Laboratory of Cell Proliferation and Differentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing, P.R. China. * Peng Huang, * An Xiao, * Zuoyan Zhu & * Bo Zhang * Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen University Town, Shenzhen, P.R. China. * Peng Huang & * Shuo Lin * College of Plant Protection, Nanjing Agricultural University, Nanjing, P.R. China. * Mingguo Zhou * Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA. * Shuo Lin Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Shuo Lin or * Bo Zhang Author Details * Peng Huang Search for this author in: * NPG journals * PubMed * Google Scholar * An Xiao Search for this author in: * NPG journals * PubMed * Google Scholar * Mingguo Zhou Search for this author in: * NPG journals * PubMed * Google Scholar * Zuoyan Zhu Search for this author in: * NPG journals * PubMed * Google Scholar * Shuo Lin Contact Shuo Lin Search for this author in: * NPG journals * PubMed * Google Scholar * Bo Zhang Contact Bo Zhang Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (1.2M) Supplementary Figures 1–7, Supplementary Tables 1–3, Supplementary Sequences and Supplementary Methods Additional data
• Finding the niche for human somatic cell nuclear transfer
  - Nat Biotechnol 29(8):701-705 (2011)
  Nature Biotechnology | Opinion and Comment | Commentary Finding the niche for human somatic cell nuclear transfer * Uta Grieshammer1 * Kelly A Shepard1 * Elizabeth A Nigh2 * Alan Trounson1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:701–705Year published:(2011)DOI:doi:10.1038/nbt.1933Published online05 August 2011 Does human somatic cell nuclear transfer have a future after the discovery of induced pluripotent stem cells? 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 * Alan Trounson, Uta Grieshammer and Kelly A. Shepard are at the California Institute for Regenerative Medicine, San Francisco, California, USA. * Elizabeth A. Nigh is with Science Editors in Palo Alto, California, USA. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Uta Grieshammer Author Details * Uta Grieshammer Contact Uta Grieshammer Search for this author in: * NPG journals * PubMed * Google Scholar * Kelly A Shepard Search for this author in: * NPG journals * PubMed * Google Scholar * Elizabeth A Nigh Search for this author in: * NPG journals * PubMed * Google Scholar * Alan Trounson Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Transgenic salmon: a final leap to the grocery shelf?
  - Nat Biotechnol 29(8):706-710 (2011)
  Nature Biotechnology | Opinion and Comment | Commentary Transgenic salmon: a final leap to the grocery shelf? * Alison L Van Eenennaam1 * William M Muir2 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:706–710Year published:(2011)DOI:doi:10.1038/nbt.1938Published online05 August 2011 Despite being caught up in regulatory proceedings for 15 years or more, AquAdvantage salmon, the first animal genetically engineered (GE) for food purposes, continues to raise concerns. Are any of these concerns scientifically justified? 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 * Alison L. Van Eenennaam is at the University of California, Davis, Department of Animal Science, Davis, California, USA * William M. Muir is at Purdue University, Department of Animal Sciences, W. Lafayette, Indiana, USA Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Alison L Van Eenennaam Author Details * Alison L Van Eenennaam Contact Alison L Van Eenennaam Search for this author in: * NPG journals * PubMed * Google Scholar * William M Muir Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Human DNA patent renewals on the decline
  - Nat Biotechnol 29(8):711-713 (2011)
  Nature Biotechnology | Feature | Patents Human DNA patent renewals on the decline * Ann E Mills1 * Patti Tereskerz1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:711–713Year published:(2011)DOI:doi:10.1038/nbt.1930Published online05 August 2011 The universe of human DNA patents may not be as large as previously anticipated if patent holders are not renewing their patents. 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 * Ann E. Mills and Patti Tereskerz are at the University of Virginia Center for Biomedical Ethics, Charlottesville, Virginia, USA. Competing financial interests The Biotechnology Industry Organization supported this project but data was collected by the U.S.P.T.O. Corresponding author Correspondence to: * Ann E Mills Author Details * Ann E Mills Contact Ann E Mills Search for this author in: * NPG journals * PubMed * Google Scholar * Patti Tereskerz Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (272K) Supplementary Methods Additional data
• Recent patent applications in microbial diagnostics
  - Nat Biotechnol 29(8):714 (2011)
  Article preview View full access options Nature Biotechnology | Feature | Patents Recent patent applications in microbial diagnostics Journal name:Nature BiotechnologyVolume: 29,Page:714Year published:(2011)DOI:doi:10.1038/nbt.1949Published online05 August 2011 Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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 infrared fluorescent protein for deeper imaging
  - Nat Biotechnol 29(8):715-716 (2011)
  Article preview View full access options Nature Biotechnology | News and Views An infrared fluorescent protein for deeper imaging * Jérôme Lecoq1 * Mark J Schnitzer1, 2 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:715–716Year published:(2011)DOI:doi:10.1038/nbt.1941Published online05 August 2011 A newly engineered infrared fluorescent protein will allow microscopists to peer more deeply into living animals. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * 日本語要約 * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Jérôme Lecoq and Mark J. Schnitzer are at the James H. Clark Center, Stanford University, Stanford, California, USA * Mark J. Schnitzer is at the Howard Hughes Medical Institute and the CNC Program, Stanford University, Stanford, California, USA. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Mark J Schnitzer Author Details * Jérôme Lecoq Search for this author in: * NPG journals * PubMed * Google Scholar * Mark J Schnitzer Contact Mark J Schnitzer Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Linkage illuminates a complex genome
  - Nat Biotechnol 29(8):717-718 (2011)
  Article preview View full access options Nature Biotechnology | News and Views Linkage illuminates a complex genome * John K McKay1 * Jan E Leach1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:717–718Year published:(2011)DOI:doi:10.1038/nbt.1945Published online05 August 2011 High-resolution linkage analysis enabled by transcriptome sequencing brings order to the genome of a polyploid crop. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * 日本語要約 * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * John K. McKay and Jan E. Leach are at Colorado State University, Fort Collins, Colorado, USA. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * John K McKay Author Details * John K McKay Contact John K McKay Search for this author in: * NPG journals * PubMed * Google Scholar * Jan E Leach Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• First CHO genome
  - Nat Biotechnol 29(8):718-720 (2011)
  Article preview View full access options Nature Biotechnology | News and Views First CHO genome * Florian M Wurm1 * David Hacker1 * Affiliations * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:718–720Year published:(2011)DOI:doi:10.1038/nbt.1943Published online05 August 2011 An ancestor of the Chinese hamster ovary cell lines used for production of recombinant therapeutics has been sequenced. Article preview Read the full article * Instant access to this article: US$18 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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. Author information Article tools * 日本語要約 * Print * Email * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Affiliations * Florian M. Wurm and David Hacker are at the Swiss Federal Institute of Technology Lausanne (EPFL), Faculty of Life Sciences and Faculty of Basic Sciences, Laboratory of Cellular Biotechnology, Lausanne, Switzerland. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Florian M Wurm Author Details * Florian M Wurm Contact Florian M Wurm Search for this author in: * NPG journals * PubMed * Google Scholar * David Hacker Search for this author in: * NPG journals * PubMed * Google Scholar Additional data
• Research highlights
  - Nat Biotechnol 29(8):721 (2011)
  Article preview View full access options Nature Biotechnology | Research Highlights Research highlights Journal name:Nature BiotechnologyVolume: 29,Page:721Year published:(2011)DOI:doi:10.1038/nbt.1954Published online05 August 2011 Synthetic enhancers Although enhancers are found in most genomes, their utility for synthetic biology applications has been limited by the lack of a quantitative understanding of their regulatory behavior. Enhancers are genetic elements that influence gene expression at distances of anywhere from hundreds of bases to hundreds of kilobases from the gene promoter. Using extensive quantification of gene transcription from artificial bacterial enhancer constructs, Amit et al. now describe predictive mathematical models for simple enhancer elements. Their enhancers consist of a promoter that uses a sigma factor (σ54) that is unable to initiate transcription without an additional activator (NRI~P), which binds upstream of the promoter. The authors introduce spacers of varying lengths, containing different binding sites for tetracycline-responsive TetR or TraR DNA-binding proteins, between promoter and activator sequences. Both the length of the spacer and the number of bound proteins influence the p! ropensity of the DNA to form a loop that brings sigma factor and activator in contact to start transcription. The authors find that enhancers can be engineered to show stepwise dose-response curves and that quantitative behavior can be predicted by their models when correctly parameterized in experiments. (Cell, 105–118, 2011) ME Shotgun cancer vaccination Until now, broad and effective use of cancer immunotherapy has been thwarted by two main challenges: the identification of one or two tumor-specific antigens that avoid the stimulation of immune response against normal cells; and countering the emergence of cancer cells resistant to the acquired antitumor immune response. Kottke et al. show that a less targeted strategy, which affords the immune system more comprehensive exposure to tumor-associated antigens, has the potential to address both challenges. In mice, intravenous delivery of highly immunogenic vesicular stomatitis viruses expressing a library of cDNAs derived from healthy human prostate tissue cures >80% of established prostate tumors without triggering autoimmunity. The key to their success apparently lies in the use of altered-self epitopes encoded by cDNA prepared from the same organ as that from which the tumor was derived. Although use of a virally delivered library avoided the need to individualize vaccines! for particular patients, it remains to be established whether the results are generalizable to other tumor models and whether the vesicular stomatitis virus vector can be used safely in humans. (Nat. Med.17, 854–859, 2011) PH Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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
• Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly
  - Nat Biotechnol 29(8):723-730 (2011)
  Nature Biotechnology | Computational Biology | Analysis Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly * Yingrui Li1, 10 * Hancheng Zheng1, 10 * Ruibang Luo1, 2, 3, 10 * Honglong Wu1, 4, 10 * Hongmei Zhu1 * Ruiqiang Li1 * Hongzhi Cao1, 4 * Boxin Wu1 * Shujia Huang1, 2 * Haojing Shao1, 2 * Hanzhou Ma1, 2 * Fan Zhang1, 2 * Shuijian Feng1 * Wei Zhang1 * Hongli Du2 * Geng Tian1 * Jingxiang Li1 * Xiuqing Zhang1 * Songgang Li1 * Lars Bolund1, 5 * Karsten Kristiansen1, 6 * Adam J de Smith7 * Alexandra I F Blakemore7 * Lachlan J M Coin8 * Huanming Yang1 * Jian Wang1 * Jun Wang1, 6, 9 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:723–730Year published:(2011)DOI:doi:10.1038/nbt.1904Received04 March 2011Accepted03 June 2011Published online24 July 2011 Abstract * Abstract * Accession codes * Author information * Supplementary information Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1–50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1–23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approac! h to deriving more comprehensive maps of genetic variation. View full text Figures at a glance * Figure 1: Mapping structural variation using whole-genome de novo assembly. () Homozygous structural variations 1–50 kb in length were identified by gapped alignment of de novo assemblies with build 36 of the NCBI reference genome. False positives are identified by comparing the ratio of aligned single-end reads to paired-end reads (S/P ratio) for each structural variation locus in the assembly and the reference. SPR, S/P ratio; RD, read depth; SR, split read. (,) Circular maps showing the genomic distribution of different classes of structural variations for YH () and NA18507 (). Chromosomes are shown color-coded in the outermost circle. The innermost circle shows green lines connecting the origin and the new location of identified intra- or interchromosomal duplications, and blue lines connecting copies of a fragment. Histograms represent the number of insertions (cyan) and deletion (red) in 5 Mb bins. () Overall distribution of the lengths of structural variations. () Distribution of structural variations between 100 bp and 1 kb in length. Peak! at ~300 bp is due to the enrichment of Alu element insertions and deletions. () Distribution of structural variations between 1 bp and 15 bp in length in coding sequences. Peaks at multiples of 3 bp can be explained by the fact that they are under weaker negative selection than are frame-shift indels with length not evenly divided by three47. * Figure 2: Simulation details. Structural variations were clustered into three parts to evaluate the sensitivity of different length ranges. Identified structural variations (blue) are comparatively higher than those structural variations with sequence assembled but not identified (violet). Most of the missing structural variations are due to the loss of the sequences (not assembled, red) and >10% of them contain repetitive sequences (green). The false-positive rate (orange) is very low for short (≤10) but for intermediate structural variations (>10 and ≤50) and long (>50) structural variations, it is higher due to increased complexity in gapped alignment and statistical analysis respectively. * Figure 3: Canonical structural variation profiles of genes and Alu elements in YH (red) and NA18507 (blue) genomes. () The canonical gene structure is defined by nine different features, denoted by the following on the x axis: i, upstream; ii, 5′ UTR; iii, first exon; iv, first intron; v, internal exon; vi, internal intron; vii, last exon; viii, 3′ UTR; ix, downstream. Y-axis represents the possibility of occurrence of structural variation event per base. Each feature of various length of coding genes was analyzed separately and fitted into equal numbers of bins. Each dot in the respective lines denotes the moving average of 5 bins. Structural variations are classified as 1–10 bp (YH, yellow; NA18507, green) and >10 bp (YH, violet; NA18507, orange). TSS (green dashed line), transcript start site. () Alu transposons with 2 kbp upstream and downstream region. The total probability of structural variation occurrence within Alu element is higher than upstream and downstream for both YH (red) and NA18507 (blue). * Figure 4: Selection pattern of structural variations. () Conservation level of structural variation-containing genes of YH (red) and NA18507 (blue) genome. Structural variation-containing genes were categorized by dN/dS ratio according to a comparison between the gene sets of human and mouse genomes from UCSC browser. Two sets were aligned by BLAST. Results with e-value < 1e-20 and identity >90 were included. To avoid double counting, the best results were selected from every aligned region for synonymous and nonsynonymous mutation detection. () A comparison between the frequency spectrums of identified structural variations and published 1000 Genomes SNP set revealed the excess of very low frequency structural variations. A higher proportion of structural variation (blue) than SNPs (red) is observed at very low frequency. Accession codes * Abstract * Accession codes * Author information * Supplementary information Referenced accessions GenBank * SRA000271 * ADDF000000000 * DAAB000000000 (NA18507) * ADDF010000000 * DAAB010000000 (NA18507) Sequence Read Archive * SRA009271 Author information * Abstract * Accession codes * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Yingrui Li, * Hancheng Zheng, * Ruibang Luo & * Honglong Wu Affiliations * BGI-Shenzhen, Shenzhen, China. * Yingrui Li, * Hancheng Zheng, * Ruibang Luo, * Honglong Wu, * Hongmei Zhu, * Ruiqiang Li, * Hongzhi Cao, * Boxin Wu, * Shujia Huang, * Haojing Shao, * Hanzhou Ma, * Fan Zhang, * Shuijian Feng, * Wei Zhang, * Geng Tian, * Jingxiang Li, * Xiuqing Zhang, * Songgang Li, * Lars Bolund, * Karsten Kristiansen, * Huanming Yang, * Jian Wang & * Jun Wang * School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China. * Ruibang Luo, * Shujia Huang, * Haojing Shao, * Hanzhou Ma, * Fan Zhang & * Hongli Du * Department of Computer Science, The University of Hong Kong, Hong Kong, China. * Ruibang Luo * Genome Research Institute, Shenzhen University Medical School, Shenzhen, China. * Honglong Wu & * Hongzhi Cao * Institute of Human Genetics, University of Aarhus, Aarhus, Denmark. * Lars Bolund * Department of Biology, University of Copenhagen, Copenhagen, Denmark. * Karsten Kristiansen & * Jun Wang * Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, UK. * Adam J de Smith & * Alexandra I F Blakemore * Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK. * Lachlan J M Coin * The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. * Jun Wang Contributions Jun W., Jian W. and H.Y. managed the project. Jun W., Y.L., R. Luo designed the analyses. Y.L., R. Luo, R. Li, H. Zheng, H. Zhu, H.W., H.C., B.W., S.H., H.S., F.Z., H.M., S.F., A.J.d.S., A.I.F.B., W.Z., H.D., L.J.M.C., S.L., L.B. and K.K. performed the data analyses. G.T., J.L. and X.Z. performed the sequencing. Jun W., Y.L. and R. Luo wrote the paper. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Jun Wang Author Details * Yingrui Li Search for this author in: * NPG journals * PubMed * Google Scholar * Hancheng Zheng Search for this author in: * NPG journals * PubMed * Google Scholar * Ruibang Luo Search for this author in: * NPG journals * PubMed * Google Scholar * Honglong Wu Search for this author in: * NPG journals * PubMed * Google Scholar * Hongmei Zhu Search for this author in: * NPG journals * PubMed * Google Scholar * Ruiqiang Li Search for this author in: * NPG journals * PubMed * Google Scholar * Hongzhi Cao Search for this author in: * NPG journals * PubMed * Google Scholar * Boxin Wu Search for this author in: * NPG journals * PubMed * Google Scholar * Shujia Huang Search for this author in: * NPG journals * PubMed * Google Scholar * Haojing Shao Search for this author in: * NPG journals * PubMed * Google Scholar * Hanzhou Ma Search for this author in: * NPG journals * PubMed * Google Scholar * Fan Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Shuijian Feng Search for this author in: * NPG journals * PubMed * Google Scholar * Wei Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Hongli Du Search for this author in: * NPG journals * PubMed * Google Scholar * Geng Tian Search for this author in: * NPG journals * PubMed * Google Scholar * Jingxiang Li Search for this author in: * NPG journals * PubMed * Google Scholar * Xiuqing Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Songgang Li Search for this author in: * NPG journals * PubMed * Google Scholar * Lars Bolund Search for this author in: * NPG journals * PubMed * Google Scholar * Karsten Kristiansen Search for this author in: * NPG journals * PubMed * Google Scholar * Adam J de Smith Search for this author in: * NPG journals * PubMed * Google Scholar * Alexandra I F Blakemore Search for this author in: * NPG journals * PubMed * Google Scholar * Lachlan J M Coin Search for this author in: * NPG journals * PubMed * Google Scholar * Huanming Yang Search for this author in: * NPG journals * PubMed * Google Scholar * Jian Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Jun Wang Contact Jun Wang Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Accession codes * Author information * Supplementary information Excel files * Supplementary Table 1 (115K) Primers, sequences of randomly selected structural variations and Sanger capillary sequencing results for PCR validation. * Supplementary Table 2 (152K) Summary of Fosmid sequences validation results. * Supplementary Table 3 (20K) Structural variations predicted on the YH and NA18507 genome were, respectively, compared to sets of variants discovered by alternative approaches. * Supplementary Table 4 (45K) Comparison between SVs detected in YH genome, Levy et al.6 and Pang et al.7 * Supplementary Table 5 (39K) Classification of those strongly conserved (dN/dS 0.1) genes containing SVs. Text files * Supplementary Data Set 2 (39K) Supplementary array CGH results Zip files * Supplementary Data Set 1 (5.8M) Souce code PDF files * Supplementary Text and Figures (913K) Supplementary Figures 1–8 and Supplementary Notes Additional data
• Genetic engineering of human pluripotent cells using TALE nucleases
  - Nat Biotechnol 29(8):731-734 (2011)
  Nature Biotechnology | Brief Communication Genetic engineering of human pluripotent cells using TALE nucleases * Dirk Hockemeyer1, 4 * Haoyi Wang1, 4 * Samira Kiani1 * Christine S Lai1, 2 * Qing Gao1 * John P Cassady1, 2 * Gregory J Cost3 * Lei Zhang3 * Yolanda Santiago3 * Jeffrey C Miller3 * Bryan Zeitler3 * Jennifer M Cherone3 * Xiangdong Meng3 * Sarah J Hinkley3 * Edward J Rebar3 * Philip D Gregory3 * Fyodor D Urnov3 * Rudolf Jaenisch1, 2 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:731–734Year published:(2011)DOI:doi:10.1038/nbt.1927Received11 March 2011Accepted28 June 2011Published online07 July 2011 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Targeted genetic engineering of human pluripotent cells is a prerequisite for exploiting their full potential. Such genetic manipulations can be achieved using site-specific nucleases. Here we engineered transcription activator–like effector nucleases (TALENs) for five distinct genomic loci. At all loci tested we obtained human embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC) clones carrying transgenic cassettes solely at the TALEN-specified location. Our data suggest that TALENs employing the specific architectures described here mediate site-specific genome modification in human pluripotent cells with similar efficiency and precision as do zinc-finger nucleases (ZFNs). View full text Author information * Abstract * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Dirk Hockemeyer & * Haoyi Wang Affiliations * The Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA. * Dirk Hockemeyer, * Haoyi Wang, * Samira Kiani, * Christine S Lai, * Qing Gao, * John P Cassady & * Rudolf Jaenisch * Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. * Christine S Lai, * John P Cassady & * Rudolf Jaenisch * Sangamo BioSciences, Inc., Richmond, California, USA. * Gregory J Cost, * Lei Zhang, * Yolanda Santiago, * Jeffrey C Miller, * Bryan Zeitler, * Jennifer M Cherone, * Xiangdong Meng, * Sarah J Hinkley, * Edward J Rebar, * Philip D Gregory & * Fyodor D Urnov Contributions D.H., H.W. and R.J. designed the targeting experiments and wrote the manuscript. H.W. and D.H. generated donor plasmids. D.H. preformed targeting experiments. S.K., C.S.L. and H.W. assisted with Southern blot analysis. Q.G. analyzed teratomas. J.P.C. and D.H. performed FACS analysis of targeted cells. L.Z. and J.C.M. designed the TALENs, S.J.H. assembled the TALENs, G.J.C. and Y.S. tested the TALENs, and B.Z., J.M.C. and X.M. performed the off-target analysis. D.H., R.J., L.Z., G.J.C., J.C.M., B.Z., X.M. and F.D.U. analyzed the data. E.J.R., P.D.G. and F.D.U. designed and supervised the design of the TALENs and contributed to writing the manuscript. Competing financial interests R.J. is an adviser to Stemgent and a cofounder of Fate Therapeutics. G.J.C., L.Z., Y.S., J.C.M., B.Z., J.M.C., X.M., S.J.H., E.J.R., P.D.G. and F.D.U. are full-time employees of Sangamo BioSciences. Corresponding author Correspondence to: * Rudolf Jaenisch Author Details * Dirk Hockemeyer Search for this author in: * NPG journals * PubMed * Google Scholar * Haoyi Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Samira Kiani Search for this author in: * NPG journals * PubMed * Google Scholar * Christine S Lai Search for this author in: * NPG journals * PubMed * Google Scholar * Qing Gao Search for this author in: * NPG journals * PubMed * Google Scholar * John P Cassady Search for this author in: * NPG journals * PubMed * Google Scholar * Gregory J Cost Search for this author in: * NPG journals * PubMed * Google Scholar * Lei Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Yolanda Santiago Search for this author in: * NPG journals * PubMed * Google Scholar * Jeffrey C Miller Search for this author in: * NPG journals * PubMed * Google Scholar * Bryan Zeitler Search for this author in: * NPG journals * PubMed * Google Scholar * Jennifer M Cherone Search for this author in: * NPG journals * PubMed * Google Scholar * Xiangdong Meng Search for this author in: * NPG journals * PubMed * Google Scholar * Sarah J Hinkley Search for this author in: * NPG journals * PubMed * Google Scholar * Edward J Rebar Search for this author in: * NPG journals * PubMed * Google Scholar * Philip D Gregory Search for this author in: * NPG journals * PubMed * Google Scholar * Fyodor D Urnov Search for this author in: * NPG journals * PubMed * Google Scholar * Rudolf Jaenisch Contact Rudolf Jaenisch Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary Text and Figures (8.3M) Supplementary Tables 1–4, Supplementary Notes and Supplementary Figures 1–10 Additional data
• The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
  - Nat Biotechnol 29(8):735-741 (2011)
  Nature Biotechnology | Research | Article Open The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line * Xun Xu1, 11 * Harish Nagarajan2, 11 * Nathan E Lewis2, 11 * Shengkai Pan1, 11 * Zhiming Cai3, 11 * Xin Liu1 * Wenbin Chen1 * Min Xie1 * Wenliang Wang1 * Stephanie Hammond4 * Mikael R Andersen5 * Norma Neff6 * Benedetto Passarelli6 * Winston Koh6 * H Christina Fan6 * Jianbin Wang6 * Yaoting Gui3 * Kelvin H Lee4 * Michael J Betenbaugh7, 8 * Stephen R Quake6 * Iman Famili2 * Bernhard O Palsson2, 8 * Jun Wang1, 9, 10 * Affiliations * Contributions * Corresponding authorsJournal name:Nature BiotechnologyVolume: 29,Pages:735–741Year published:(2011)DOI:doi:10.1038/nbt.1932Received23 February 2011Accepted05 July 2011Published online31 July 2011 Abstract * Abstract * Accession codes * Author information * Supplementary information Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Chinese hamster ovary (CHO)–derived cell lines are the preferred host cells for the production of therapeutic proteins. Here we present a draft genomic sequence of the CHO-K1 ancestral cell line. The assembly comprises 2.45 Gb of genomic sequence, with 24,383 predicted genes. We associate most of the assembled scaffolds with 21 chromosomes isolated by microfluidics to identify chromosomal locations of genes. Furthermore, we investigate genes involved in glycosylation, which affect therapeutic protein quality, and viral susceptibility genes, which are relevant to cell engineering and regulatory concerns. Homologs of most human glycosylation-associated genes are present in the CHO-K1 genome, although 141 of these homologs are not expressed under exponential growth conditions. Many important viral entry genes are also present in the genome but not expressed, which may explain the unusual viral resistance property of CHO cell lines. We discuss how the availability of this geno! me sequence may facilitate genome-scale science for the optimization of biopharmaceutical protein production. View full text Figures at a glance * Figure 1: Chromosomal assignment to scaffolds. () Chromosomal preparations from CHO-K1 were sequenced and the reads were aligned to the scaffolds. For each of the N50 scaffolds, a vector was used to represent the read alignments in the 22 preparations. Using this metric, a correlation matrix was generated between all the N50 scaffolds. Upon clustering the matrix, 21 clusters of highly correlated scaffolds emerged, suggesting that the scaffolds are associated with 21 chromosomes in CHO-K1. () Classical karyotyping of CHO-K1 reveals 21 chromosomes. * Figure 2: Comparative analysis of functional categories and gene content. For each GOslim biological process category, the fraction of all GO terms in that category is shown for human, mouse, rat and CHO genomes. GOslim classes that are significantly enriched and show the highest and lowest coverage of human and mouse genes in the CHO genome are highlighted in red (*) and green (**), respectively. P value cutoff and coverage in human and mouse were used to determine significance. * Figure 3: A global view of the expression of CHO-K1 glycosylation genes. () While homologs were identified for 99% of the human glycosylation-associated transcripts, only 53% had detectable expression. Glycosylation gene classes enriched in expressed genes (denoted with **) include hyaluronoglucosaminidases, sugar-nucleotide synthesis, mannosyltransferases and lysozomal enzymes. Significantly depleted classes (P < 0.06) in expressed genes (denoted with *) include the sulfotransferases, fucosyltransferases and GalNAc transferases. () A selection of CHO N-linked glycosylation pathways are detailed to demonstrate the effects of CHO glycosylation gene expression on the possible glycoforms. (i) A difference between human and CHO glycosylation is seen in the lack of expression of MGAT3, which is responsible for the bisecting β(1,4) GlcNAc that occurs on ~10% of human antibodies. (ii) The only N-glycan-modifying fucosyltransferase expressed in CHO-K1 is FUT8, which adds fucose to the core glycan by an α(1,6) linkage. (iii) Sialylation of a terminal ga! lactose can occur through α(2,3) or α(2,6) linkages in human. However, CHO ST6Gal genes are not expressed, so CHO glycans primarily have α(2,3) linkages. (iv) The two most abundant sialic acids are Neu5Ac and Neu5Gc. Neu5Gc is immunogenic in humans. Thus, the lack of CMAH expression in the CHO-K1 sample minimizes this response by limiting the conversion of Neu5Ac to Neu5Gc. Pathways are adapted loosely from ref. 55. Abbreviations are defined in Supplementary Table 18. * Figure 4: An assessment of the expression state of viral susceptibility genes in CHO-K1. () A global view of viral susceptibility genes in CHO-K1 demonstrates no measurable expression for 158 of these genes. The enriched GO cell compartment terms among the nonexpressed susceptibility genes shows that membrane proteins and DNA binding proteins are primarily not expressed. The expression state of all members of the "external side of plasma membrane" GO class is shown (blue and red for expressed and not expressed, respectively). () A schematic of entry mechanisms used by HSV-1. Viral entry receptors that are not expressed in CHO are shown by their gene names in red, and missing receptors are shown with a dashed outline. WT, wild type; Mut, mutant; Bov, bovine. * Figure 5: The CHO-K1 genome will aid in cell line engineering, generate hypotheses for biological discovery, and serve as a context to facilitate sequencing efforts and sequence analysis for additional cell lines. Although significant advances in CHO biology have occurred over the past decades, the accessibility of the CHO-K1 genome will have an impact on at least three major areas. () The CHO genome will aid cell line engineering by facilitating the application of experimental and computational sequence-based tools for genetic manipulation and genome analysis. For example, BLAST can be used to identify the CHO sequence of a desired gene, whereas siRNA and site-directed mutagenesis methods can be used to directly modulate gene expression levels and protein activities. Moreover, the genome sequence can be used to reconstruct models of CHO-K1 metabolism, which allow the assessment of how genetic manipulations affect other pathways and can predict nonintuitive genetic changes to improve product yield or quality. () The biomolecular mechanisms underlying many phenotypic properties of CHO are poorly characterized (e.g., viral susceptibility). The components underlying these phenotypes can ! be identified through the comparison of CHO gene content and gene expression with other organisms or cell lines. () Although large genomic changes can occur in immortalized and engineered cell lines such as CHO, the CHO-K1 genome can serve as a context for the assembly and analysis of genome sequences from additional CHO cell lines. Accession codes * Abstract * Accession codes * Author information * Supplementary information Referenced accessions DNA Data Bank of Japan * AFTD00000000 * AFTD01000000 Sequence Read Archive * SRA040022.1 * SRA040045.1 Author information * Abstract * Accession codes * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * Xun Xu, * Harish Nagarajan, * Nathan E Lewis, * Shengkai Pan & * Zhiming Cai Affiliations * BGI-Shenzhen, Shenzhen, People's Republic of China. * Xun Xu, * Shengkai Pan, * Xin Liu, * Wenbin Chen, * Min Xie, * Wenliang Wang & * Jun Wang * GT Life Sciences, San Diego, California, USA. * Harish Nagarajan, * Nathan E Lewis, * Iman Famili & * Bernhard O Palsson * Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, People's Republic of China. * Zhiming Cai & * Yaoting Gui * Department of Chemical Engineering and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA. * Stephanie Hammond & * Kelvin H Lee * Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark. * Mikael R Andersen * Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California, USA. * Norma Neff, * Benedetto Passarelli, * Winston Koh, * H Christina Fan, * Jianbin Wang & * Stephen R Quake * Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA. * Michael J Betenbaugh * Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark. * Michael J Betenbaugh & * Bernhard O Palsson * The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark. * Jun Wang * Department of Biology, University of Copenhagen, Copenhagen, Denmark. * Jun Wang Contributions B.O.P., J.W., I.F., X.X. and Z.C. conceived and designed the study. Z.C., Y.G., S.H. and K.H.L. performed sample preparation and sequencing. X.X., S.P. and W.C. performed the genome assembly. X.X., S.P., X.L., M.X., W.W., H.N. and N.E.L. performed genome annotation and evolutionary analysis. H.C.F., J.W., B.P., W.K., N.N. and S.R.Q. generated data and performed the microfluidic chromosomal analysis. The method and data for chromosome analysis was conceived and generated at Stanford. H.N., N.E.L., M.J.B., W.K. and M.R.A. performed the genomic and transcriptomic analysis of the glycosylation and viral susceptibility genes. H.N., N.E.L. and B.O.P. wrote the paper and coordinated research efforts between authors. All authors read and approved the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding authors Correspondence to: * Jun Wang or * Bernhard O Palsson Author Details * Xun Xu Search for this author in: * NPG journals * PubMed * Google Scholar * Harish Nagarajan Search for this author in: * NPG journals * PubMed * Google Scholar * Nathan E Lewis Search for this author in: * NPG journals * PubMed * Google Scholar * Shengkai Pan Search for this author in: * NPG journals * PubMed * Google Scholar * Zhiming Cai Search for this author in: * NPG journals * PubMed * Google Scholar * Xin Liu Search for this author in: * NPG journals * PubMed * Google Scholar * Wenbin Chen Search for this author in: * NPG journals * PubMed * Google Scholar * Min Xie Search for this author in: * NPG journals * PubMed * Google Scholar * Wenliang Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Stephanie Hammond Search for this author in: * NPG journals * PubMed * Google Scholar * Mikael R Andersen Search for this author in: * NPG journals * PubMed * Google Scholar * Norma Neff Search for this author in: * NPG journals * PubMed * Google Scholar * Benedetto Passarelli Search for this author in: * NPG journals * PubMed * Google Scholar * Winston Koh Search for this author in: * NPG journals * PubMed * Google Scholar * H Christina Fan Search for this author in: * NPG journals * PubMed * Google Scholar * Jianbin Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Yaoting Gui Search for this author in: * NPG journals * PubMed * Google Scholar * Kelvin H Lee Search for this author in: * NPG journals * PubMed * Google Scholar * Michael J Betenbaugh Search for this author in: * NPG journals * PubMed * Google Scholar * Stephen R Quake Search for this author in: * NPG journals * PubMed * Google Scholar * Iman Famili Search for this author in: * NPG journals * PubMed * Google Scholar * Bernhard O Palsson Contact Bernhard O Palsson Search for this author in: * NPG journals * PubMed * Google Scholar * Jun Wang Contact Jun Wang Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Accession codes * Author information * Supplementary information Excel files * Supplementary Table (791K) Supplementary Tables 1–20 PDF files * Supplementary Text and Figures (2M) Supplementary Figures 1–6 and Supplementary Notes Creative Commons Attribution-Noncommercial-Share Alike license This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar license. Additional data
• Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
  - Nat Biotechnol 29(8):742-749 (2011)
  Nature Biotechnology | Research | Article Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression * John R Prensner1, 8 * Matthew K Iyer1, 8 * O Alejandro Balbin1 * Saravana M Dhanasekaran1, 2 * Qi Cao1 * J Chad Brenner1 * Bharathi Laxman3 * Irfan A Asangani1 * Catherine S Grasso1 * Hal D Kominsky1 * Xuhong Cao1 * Xiaojun Jing1 * Xiaoju Wang1 * Javed Siddiqui1 * John T Wei4 * Daniel Robinson1 * Hari K Iyer5 * Nallasivam Palanisamy1, 2, 6 * Christopher A Maher1, 2 * Arul M Chinnaiyan1, 2, 4, 6, 7 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:742–749Year published:(2011)DOI:doi:10.1038/nbt.1914Received11 January 2011Accepted10 June 2011Published online31 July 2011 Abstract * Abstract * Accession codes * Author information * Supplementary information Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve ! the stratification of cancer subtypes. View full text Figures at a glance * Figure 1: Analysis of transcriptome data for the detection of unannotated transcripts. () Schematic overview of the methodology employed in this study. () Graphical representation of the bioinformatics filters used to merge individual transcriptome libraries into a single consensus transcriptome. The merged consensus transcriptome was generated by compiling all individual transcriptome libraries and using individual decision tree classifiers for each chromosome to define high-confidence 'expressed' transcripts and low-confidence 'background' transcripts, which were discarded. The example decision tree on the left was trained on transcripts on chromosome 1. The graphics on the right illustrate the application of the informatics filtration pipeline to sample assembled transcripts. () After informatic processing and filtration of the sequencing data, transcripts were categorized to identify unannotated ncRNAs. Transcribed pseudogenes were isolated, and the remaining transcripts were categorized based on overlap with an aggregated set of known gene annotations int! o annotated protein coding, noncoding and unannotated. Both annotated and unannotated ncRNA transcripts were then separated into intronic, intergenic and antisense categories based on their relationship to protein-coding genes. * Figure 2: Prostate cancer transcriptome sequencing reveals dysregulation of unannotated transcripts. () Global overview of transcription in prostate cancer. The pie chart on the left displays transcript distribution in prostate cancer. The pie charts on the right display unannotated (upper) or annotated (lower) ncRNAs categorized as sense transcripts (intergenic and intronic) and antisense transcripts, respectively. () Line graph showing that unannotated transcripts are more highly expressed (reads per kilobase of transcript per million mapped reads; RPKM) than control regions. Negative control intervals were generated by randomly permuting the genomic positions of the transcripts. () Conservation analysis comparing unannotated transcripts to known genes and intronic controls shows a subtle degree of purifying selection among unannotated transcripts. The inset on the right shows an enlarged view. (–) Intersection plots displaying the fraction of unannotated transcripts enriched for H3K4me2 (), H3K4me3 (), acetyl-H3 () or RNA polymerase II () at their transcriptional start! site (TSS) using ChIP-Seq and RNA-Seq data for the VCaP prostate cancer cell line. The legend applies to plots in –. () A pie chart displaying the distribution of differentially expressed transcripts in prostate cancer (FDR < 0.01). * Figure 3: Unannotated intergenic transcripts differentiate prostate cancer and benign prostate samples. () Unsupervised clustering analyses of differentially expressed or outlier unannotated intergenic transcripts clusters benign samples, localized tumors and metastatic cancers. Expression is plotted as log2 fold-change relative to the median of the benign samples. The four transcripts detailed in this study are indicated on the side. () Cancer outlier expression analysis for the prostate cancer transcriptome ranks unannotated transcripts prominently. (–) qPCR on an independent cohort of prostate and nonprostate samples (benign (n = 19), PCA (n = 35), metastatic (MET) (n = 31), prostate cell lines (n = 7), breast cell lines (n = 14), lung cell lines (n = 16), other normal samples (n = 19); Supplementary Table 8)) measures expression levels of four nominated ncRNAs—PCAT-14 (), PCAT-43 (), PCAT-114 (), PCAT-1 ()—and upregulated in prostate cancer. Inset tables on the right quantify 'positive' and 'negative' expressing samples using the cut-off value (shown as a black dashe! d lines). Statistical significance was determined using a Fisher's exact test. qPCR analysis was performed by normalizing to GAPDH and the median expression of the benign samples. * Figure 4: PCAT-1 is a marker of aggressive cancer and a PRC2-repressed ncRNA. () The genomic location of PCAT-1 determined by 5′ and 3′ RACE, with DNA sequence features indicated by the colored boxes. () qPCR for PCAT-1 (y axis) and EZH2 (x axis) on a cohort of benign (n = 19), localized tumor (n = 35) and metastatic cancer (n = 31) samples. The inset table quantifies patient subsets demarcated by the gray dashed lines. () Knockdown of EZH2 in VCaP resulted in upregulation of PCAT-1. Data were normalized to GAPDH and represented as fold-change. ERG and B-actin serve as negative controls. The inset western blot indicates EZH2 knockdown. () Treatment of VCaP cells with 0.1 μM of the EZH2 inhibitor DZNep or vehicle control (DMSO) shows increased expression of PCAT-1 transcript after EZH2 inhibition. () PCAT-1 expression is increased upon treatment of VCaP cells with the demethylating agent 5′azacytidine (5′Aza), the histone deacetylase inhibitor SAHA or a combination of both. qPCR data were normalized to the average of (GAPDH + β-actin) and rep! resented as fold-change. GSTP1 and FKBP5 are positive and negative controls, respectively. () ChIP assays for SUZ12 demonstrated direct binding of SUZ12 to the PCAT-1 promoter. Primer locations are indicated (boxed numbers) in the PCAT-1 schematic. * Figure 5: PCAT-1 promotes cell proliferation. () Cell proliferation assays for RWPE benign immortalized prostate cells stably infected with PCAT-1 lentivirus or RFP and LacZ control lentiviruses. An asterisk (*) indicates P ≤ 0.02 by a two-tailed Student's t-test. () Cell proliferation assays in LNCaP using PCAT-1 siRNAs. An asterisk (*) indicates P ≤ 0.005 by a two-tailed Student's t-test. () Gene ontology analysis of PCAT-1 knockdown microarray data using the DAVID program. Blue bars represent the top hits for upregulated genes. Red bars represent the top hits for downregulated genes. DAVID enrichment scores are represented with Benjamini-Hochberg-adjusted P values. All error bars in this figure are mean ± s.e.m. * Figure 6: Prostate cancer tissues recapitulate PCAT-1 signaling. () qPCR expression of three PCAT-1 target genes after PCAT-1 knockdown in VCaP and LNCaP cells, as well as following EZH2 knockdown or dual EZH2 and PCAT-1 knockdown in VCaP cells. qPCR data were normalized to the average of (GAPDH + β-actin) and represented as fold change. Error bars represent mean ± s.e.m. () Standardized log2-transformed qPCR expression of a set of tumors and metastases with outlier expression of either PCAT-1 or EZH2. The shaded squares in the lower left show Spearman correlation values between the indicated genes (* indicates P < 0.05). Blue and red indicate negative or positive correlation, respectively. The upper squares show the scatter plot matrix and fitted trend lines for the same comparisons. () A heatmap of PCAT-1 target genes (BRCA2, CENPF, CENPE) in EZH2-outlier and PCAT-1-outlier patient samples (see Fig. 4b). Expression was determined by qPCR and normalized as in . () A predicted network generated by the HefaLMP program for 7 of 20 top upr! egulated genes following PCAT-1 knockdown in LNCaP cells. Gray nodes are genes found following PCAT-1 knockdown. Red edges indicate co-expressed genes; black edges indicate predicted protein-protein interactions; and purple edges indicate verified protein-protein interactions. () A proposed schematic representing PCAT-1 upregulation, function and relationship to PRC2. Accession codes * Abstract * Accession codes * Author information * Supplementary information Referenced accessions GenBank * HQ605084 * HQ605085 Gene Expression Omnibus * GSE25183 Author information * Abstract * Accession codes * Author information * Supplementary information Primary authors * These authors contributed equally to this work. * John R Prensner & * Matthew K Iyer Affiliations * Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA. * John R Prensner, * Matthew K Iyer, * O Alejandro Balbin, * Saravana M Dhanasekaran, * Qi Cao, * J Chad Brenner, * Irfan A Asangani, * Catherine S Grasso, * Hal D Kominsky, * Xuhong Cao, * Xiaojun Jing, * Xiaoju Wang, * Javed Siddiqui, * Daniel Robinson, * Nallasivam Palanisamy, * Christopher A Maher & * Arul M Chinnaiyan * Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA. * Saravana M Dhanasekaran, * Nallasivam Palanisamy, * Christopher A Maher & * Arul M Chinnaiyan * Department of Medicine, University of Chicago, Chicago, Illinois, USA. * Bharathi Laxman * Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan, USA. * John T Wei & * Arul M Chinnaiyan * Department of Statistics, Colorado State University, Fort Collins, Colorado, USA. * Hari K Iyer * Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA. * Nallasivam Palanisamy & * Arul M Chinnaiyan * Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan, USA. * Arul M Chinnaiyan Contributions M.K.I., J.R.P. and A.M.C. designed the project and directed experimental studies. M.K.I., O.A.B., C.S.G. and C.A.M. developed computational platforms and performed sequencing data analysis. M.K.I., O.A.B. and H.K.I. performed statistical analyses. J.R.P., S.M.D., J.C.B., Q.C., N.P., H.D.K., B.L., X.W., I.A.A., X.C., X.J. and D.R. performed experimental studies. J.S. and J.T.W. coordinated biospecimens. M.K.I., J.R.P. and A.M.C. interpreted data and wrote the manuscript. Competing financial interests The University of Michigan has filed for a patent on the detection of gene fusions in prostate cancer, on which A.M.C. is a co-inventor. The diagnostic field of use for ETS gene fusions has been licensed to GenProbe Inc. The University of Michigan has a sponsored research agreement with GenProbe, which is unrelated to this study. GenProbe has had no role in the design or experimentation of this study, nor has it participated in the writing of the manuscript. Corresponding author Correspondence to: * Arul M Chinnaiyan Author Details * John R Prensner Search for this author in: * NPG journals * PubMed * Google Scholar * Matthew K Iyer Search for this author in: * NPG journals * PubMed * Google Scholar * O Alejandro Balbin Search for this author in: * NPG journals * PubMed * Google Scholar * Saravana M Dhanasekaran Search for this author in: * NPG journals * PubMed * Google Scholar * Qi Cao Search for this author in: * NPG journals * PubMed * Google Scholar * J Chad Brenner Search for this author in: * NPG journals * PubMed * Google Scholar * Bharathi Laxman Search for this author in: * NPG journals * PubMed * Google Scholar * Irfan A Asangani Search for this author in: * NPG journals * PubMed * Google Scholar * Catherine S Grasso Search for this author in: * NPG journals * PubMed * Google Scholar * Hal D Kominsky Search for this author in: * NPG journals * PubMed * Google Scholar * Xuhong Cao Search for this author in: * NPG journals * PubMed * Google Scholar * Xiaojun Jing Search for this author in: * NPG journals * PubMed * Google Scholar * Xiaoju Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Javed Siddiqui Search for this author in: * NPG journals * PubMed * Google Scholar * John T Wei Search for this author in: * NPG journals * PubMed * Google Scholar * Daniel Robinson Search for this author in: * NPG journals * PubMed * Google Scholar * Hari K Iyer Search for this author in: * NPG journals * PubMed * Google Scholar * Nallasivam Palanisamy Search for this author in: * NPG journals * PubMed * Google Scholar * Christopher A Maher Search for this author in: * NPG journals * PubMed * Google Scholar * Arul M Chinnaiyan Contact Arul M Chinnaiyan Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Accession codes * Author information * Supplementary information PDF files * Supplementary Text and Figures (10M) Supplementary Tables 1–11, Supplementary Figures 1–28, Supplementary Methods and Supplementary Discussion Additional data
• Cell-surface markers for the isolation of pancreatic cell types derived from human embryonic stem cells
  - Nat Biotechnol 29(8):750-756 (2011)
  Nature Biotechnology | Research | Article Cell-surface markers for the isolation of pancreatic cell types derived from human embryonic stem cells * Olivia G Kelly1 * Man Yin Chan1 * Laura A Martinson1 * Kuniko Kadoya1 * Traci M Ostertag1 * Kelly G Ross1 * Mike Richardson1 * Melissa K Carpenter1 * Kevin A D'Amour1 * Evert Kroon1 * Mark Moorman1 * Emmanuel E Baetge1 * Anne G Bang1 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:750–756Year published:(2011)DOI:doi:10.1038/nbt.1931Received17 May 2011Accepted05 July 2011Published online31 July 2011 Abstract * Abstract * Author information * Supplementary information Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Using a flow cytometry–based screen of commercial antibodies, we have identified cell-surface markers for the separation of pancreatic cell types derived from human embryonic stem (hES) cells. We show enrichment of pancreatic endoderm cells using CD142 and of endocrine cells using CD200 and CD318. After transplantation into mice, enriched pancreatic endoderm cells give rise to all the pancreatic lineages, including functional insulin-producing cells, demonstrating that they are pancreatic progenitors. In contrast, implanted, enriched polyhormonal endocrine cells principally give rise to glucagon cells. These antibodies will aid investigations that use pancreatic cells generated from pluripotent stem cells to study diabetes and pancreas biology. View full text Figures at a glance * Figure 1: Cell-surface markers for endocrine and PE cells in hES cell–derived pancreatic cultures. (–) Flow cytometric analyses of CyT49 pancreatic cultures co-stained with anti-CHGA and anti-CD200 (), anti-CD318 (), or anti-CD142 (), or co-stained with anti-CD142 and anti-CD200 (). () Flow cytometric analyses of CyT49 pancreatic cultures co-stained with anti-CD142, anti-NKX6.1 and anti-CHGA. () Immunofluorescence analyses of intact CyT49 pancreatic cultures with anti-PDX1 (green), anti-CHGA (blue), anti-CD142 (red) and anti-CD200 (red). Scale bar, 100 μm. () Immunofluorescence analyses of adult human pancreas with anti-CD318 (red), anti-CD200 (red), anti-SST (green), anti-GCG (green) and anti-INS (blue). Scale bar, 100 μm. CHGA, chromogranin A; INS, insulin; GCG, glucagon; SST, somatostatin. * Figure 2: FACS isolation of CD142 and CD200 cell subsets from hES cell–derived pancreatic cultures. (,) Representative CD142 () and CD200 () FACS experiments of CyT49 differentiated cultures showing cellular compositions in the pre-sort population and isolated fractions as assessed by anti-CHGA and anti-NKX6.1 co-staining. Cellular compositions are represented as pie charts with CHGA+ endocrine cells (EN, blue), CHGA−/NKX6.1+ PE cells (red) and CHGA−/NKX6.1− cells (gray). CHGA, chromogranin A; SSC, side scatter. * Figure 3: CD142, CD200 and CD318 immuno-magnetic cell separations from hES cell–derived pancreatic cultures. () Flow cytometry analyses of anti-CHGA, anti-CD142 and anti-NKX6.1 co-staining in the pre-sort population and the isolated bound fraction from a representative CD142 cell separation of a CyT49 differentiated culture. Additional experiments are shown in Table 1. () Flow cytometry analyses of anti-CD200 and anti-CHGA co-staining of the pre-sort population, the isolated bound fraction and aggregates of bound-fraction cells from a representative CD200 cell separation of a CyT49 differentiated culture. In this experiment the bound aggregate was not restained with CD200 (FL2). Additional experiments are shown in Supplementary Table 1. () Flow cytometry analyses of anti-CD318 and anti-CHGA co-staining of the pre-sort population, the isolated bound fraction and aggregates of bound-fraction cells from a representative CD318 cell separation of a CyT49 differentiated culture. Additional experiments are shown in Supplementary Table 1. Cellular compositions are represented as pie charts! with CHGA+ endocrine cells (EN, blue), CHGA−/NKX6.1+ PE cells (red), and CHGA−/NKX6.1− cells (gray) or CHGA− cells (gray). CHGA, chromogranin A; SSC, side scatter. * Figure 4: Immunofluorescence analyses of transplants of unenriched or CD318-enriched endocrine cells. (–) Grafts at 3 weeks after transplant. Unenriched (,,,) and CD318-enriched (,,,) explants stained with (–) anti-GCG (red), anti-SST (green), anti-INS (blue) or (–) anti-NKX6.1 (red), anti-PDX1 (green) and anti-INS (blue). (–) Grafts at 5 weeks after transplant. Unenriched (,,) or CD318-enriched (,,) explants stained with (–) anti-GCG (red), anti-SST (green), anti-INS (blue) or (,) anti-NKX6.1 (red), anti-PDX1 (green), anti-INS (blue). (,) Unenriched graft at 19 weeks after transplant () or CD318-enriched graft at 9 weeks after transplant () stained with anti-GCG (red), anti-SST (green) and anti-INS (blue). The CD318-enriched transplanted cells were enriched in endocrine cells and depleted in PE cells (Supplementary Table 1, experiment 7). Scale bars, 100 μm. INS, insulin; GCG, glucagon; SST, somatostatin. * Figure 5: Immunofluorescence and functional analyses of transplants of unenriched or CD142-enriched PE cells. () CD142-enriched cellular aggregates cultured in the presence of Y-27632 (10 μM) were stained with anti-NKX6.1 (green), anti-PDX1 (red, blue), anti-CD142 (red, blue), anti-CHGA (blue) and anti-PTF1A (red). Scale bar, 50 μm. () Analyses of human C-peptide levels in mouse sera after fasting and 60 min after glucose injection 10 weeks after transplant. Mice were transplanted with CD142-enriched cells and nonsorted cells that were aggregated with Y-27632 (10 μM). The transplanted CD142-enriched cells were enriched in PE cells and depleted in endocrine cells (Table 1 and Supplementary Fig. 7). () Grafts at 13 weeks after transplant. Unenriched (,,,) and CD142-enriched grafts (,,,) stained with (,) anti-GCG (red), anti-SST (green), anti-INS (blue) (,) anti-NKX6.1 (red), anti-PDX1 (green), anti-INS (blue) (,) anti-PTF1A (red), anti-TRY (green), DAPI (blue) (,) anti-PDX1 (red), anti-SST (green) and anti-CK19 (blue). Scale bar, 100 μm. INS, insulin; GCG, glucagon; SST, somatosta! tin; TRY, trypsin; No., mouse number. Author information * Abstract * Author information * Supplementary information Affiliations * ViaCyte, Inc. (formerly Novocell, Inc.), San Diego, California, USA. * Olivia G Kelly, * Man Yin Chan, * Laura A Martinson, * Kuniko Kadoya, * Traci M Ostertag, * Kelly G Ross, * Mike Richardson, * Melissa K Carpenter, * Kevin A D'Amour, * Evert Kroon, * Mark Moorman, * Emmanuel E Baetge & * Anne G Bang Contributions O.G.K. and A.G.B. wrote the paper. O.G.K. and A.G.B. designed, directed and interpreted experiments with intellectual contributions from E.E.B., M.M., L.A.M., E.K., K.A.D., K.K. and M.K.C. The antibody screen was proposed by A.G.B. and carried out by O.G.K., M.Y.C. and M.M. K.A.D. suggested the Y-27632 compound. M.M. developed and performed the flow cytometry assays and analyses with assistance from M.Y.C. and K.G.R. O.G.K., A.G.B., M.Y.C. and T.M.O. performed the cell culture experiments and immuno-magnetic cell separations. M.Y.C. and O.G.K. performed qPCR and immunofluorescence analyses of in vitro material. L.A.M., E.K. and M.R. executed the in vivo experiments, including transplantations and C-peptide assays. K.K. performed the histological and immunofluorescence analyses of implanted grafts. Competing financial interests The authors are employees or former employees of ViaCyte (formerly Novocell). Corresponding author Correspondence to: * Olivia G Kelly Author Details * Olivia G Kelly Contact Olivia G Kelly Search for this author in: * NPG journals * PubMed * Google Scholar * Man Yin Chan Search for this author in: * NPG journals * PubMed * Google Scholar * Laura A Martinson Search for this author in: * NPG journals * PubMed * Google Scholar * Kuniko Kadoya Search for this author in: * NPG journals * PubMed * Google Scholar * Traci M Ostertag Search for this author in: * NPG journals * PubMed * Google Scholar * Kelly G Ross Search for this author in: * NPG journals * PubMed * Google Scholar * Mike Richardson Search for this author in: * NPG journals * PubMed * Google Scholar * Melissa K Carpenter Search for this author in: * NPG journals * PubMed * Google Scholar * Kevin A D'Amour Search for this author in: * NPG journals * PubMed * Google Scholar * Evert Kroon Search for this author in: * NPG journals * PubMed * Google Scholar * Mark Moorman Search for this author in: * NPG journals * PubMed * Google Scholar * Emmanuel E Baetge Search for this author in: * NPG journals * PubMed * Google Scholar * Anne G Bang Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Abstract * Author information * Supplementary information PDF files * Supplementary Text and Figures (3M) Supplementary Table 1 and Supplementary Figures 1–9 Additional data
• Bright and stable near-infrared fluorescent protein for in vivo imaging
  - Nat Biotechnol 29(8):757-761 (2011)
  Nature Biotechnology | Research | Letter Bright and stable near-infrared fluorescent protein for in vivo imaging * Grigory S Filonov1 * Kiryl D Piatkevich1 * Li-Min Ting2 * Jinghang Zhang3 * Kami Kim2 * Vladislav V Verkhusha1 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:757–761Year published:(2011)DOI:doi:10.1038/nbt.1918Received28 February 2011Accepted15 June 2011Published online17 July 2011 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Imaging biological processes in mammalian tissues will be facilitated by fluorescent probes with excitation and emission bands within the near-infrared optical window of high transparency1. Here we report a phytochrome-based near-infrared fluorescent protein (iRFP) with excitation and emission maxima at 690 nm and 713 nm, respectively. iRFP does not require an exogenous supply of the chromophore biliverdin and has higher effective brightness, intracellular stability and photostability than earlier phytochrome-derived fluorescent probes. Compared with far-red GFP-like proteins, iRFP has a substantially higher signal-to-background ratio in a mouse model due to its infrared-shifted spectra. View full text Figures at a glance * Figure 1: In vitro properties of iRFP and IFP1.4. () Absorbance in arbitrary units (a.u.) with absorbance at 280 nm set to 100%. () Fluorescence excitation and emission spectra normalized to 100% for both proteins. () Fitted curves of the maturation kinetics in hours in bacteria at 37 °C. () Equilibrium pH dependence of fluorescence. (,) FACS dot-plots representing near-infrared fluorescence of iRFP and IFP1.4 (x axis) and green fluorescence from co-expressed EGFP (y axis) of transiently transfected HeLa cells not treated () or treated () with 25 μM of BV for 2 h before analysis. A 676 nm laser line for excitation (ex.) and a 700 nm long pass filter to collect emission (em.) from iRFP and IFP1.4 were used. () Mean near-infrared fluorescence intensity of the double-positive cells from and normalized to transfection efficiency (EGFP signal), absorbance of the respective protein at 676 nm and overlap of the fluorescence spectrum of the respective protein with the transmission of the emission filter. () Fluorescent images of ! the transiently transfected HeLa cells with and without addition of 25 μM BV for 2 h before imaging. Scale bar, 20 μm. () Photobleaching in HeLa cells. The curves were normalized to absorbance spectra and extinction coefficients of the proteins (calculated based on BV absorbance), spectrum of an arc lamp and transmission of a photobleaching filter. Plot represents the data obtained with endogenous BV but both proteins demonstrated no change in photostability after addition of exogenous BV. () Degradation of the proteins in HEK293 cells after treatment with 1 mM puromycin. Cells were incubated with 25 μM BV to achieve a higher fluorescent signal. Protein concentration was assessed by measuring fluorescence intensity of crude cell lysates. () BV binding to iRFP and IFP1.4 proteins in HeLa cells. Cells were incubated with the respective amounts of BV for 2 h before harvesting on the second day after adenovirus infection. Fluorescence intensity was measured in crude cell lys! ates and normalized to 100%. Lines are fitted based on the Sca! tchard equation. () Protein expression in HeLa cells 48 h after adenovirus infection. Data for the cells without exogenous BV, with 25 μM of BV added 2 h and 42 h before the analysis are shown. Fluorescence intensities were normalized to the total cell number, excitation wavelength, emission collection bandwidth and protein molecular brightness to represent the iRFP or IFP1.4 concentrations. * Figure 2: Expression of iRFP in living mouse. () Overlay of representative light and fluorescent images of iRFP or IFP1.4 adenovirus infected mice with and without injection of 250 nmol BV. A non-infected control mouse is shown on the right. The fluorescence images were acquired using IVIS Spectrum instrument equipped with 675/30 nm excitation and 720/20 nm emission filters. The color bar indicates the fluorescence radiant efficiency, multiplied by 109. () Near infrared fluorescence total radiant efficiency of the liver areas of the iRFP and IFP1.4 expressing mice in (), normalized to the bandwidth of the excitation and emission filters. () Time course of the near-infrared fluorescence total radiant efficiency of the liver areas of the iRFP and IFP1.4 expressing mice in () after BV injection. () Overlay of the photograph and fluorescent image of the isolated livers from the BV-injected infected and non-infected (control) mice. () Time course of the near-infrared fluorescence total radiant efficiency of the liver areas o! f the mice not being injected with BV. The fluorescence signals in and were also normalized to the bandwidth of the excitation and emission filters. * Figure 3: Comparison of iRFP with far-red GFP-like proteins in mouse phantom. (,) Samples consisting of equal amounts of the purified proteins of the same concentration were placed inside of the phantom mouse in bores located 7.0 mm () or 18.1 mm () deep from the mouse surface. Each protein sample was imaged using epifluorescence mode in several wavelength channels. A signal-to-background ratio in each channel was calculated as (ROI1 - ROI2) / ROI2, where ROI1 or ROI2 were total radiant efficiencies of the respective areas with and without the protein sample. Images for the highest signal-to-background ratio for each protein are shown. The color bar indicates the fluorescence radiant efficiency, multiplied by 108. (,) The highest signal-to-background ratio values, calculated for the respective images in and . Author information * Author information * Supplementary information Affiliations * Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA. * Grigory S Filonov, * Kiryl D Piatkevich & * Vladislav V Verkhusha * Department of Medicine and Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA. * Li-Min Ting & * Kami Kim * Flow Cytometry Core Facility, Albert Einstein College of Medicine, Bronx, New York, USA. * Jinghang Zhang Contributions G.S.F. developed the protein and together with K.D.P. characterized it in vitro. G.S.F. studied the protein in mammalian cells. G.S.F. and J.Z. analyzed and sorted cells using FACS. G.S.F., L.-M.T. and K.K. characterized protein expression in mice. V.V.V. designed and planned the project and together with G.S.F. wrote the manuscript. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Vladislav V Verkhusha Author Details * Grigory S Filonov Search for this author in: * NPG journals * PubMed * Google Scholar * Kiryl D Piatkevich Search for this author in: * NPG journals * PubMed * Google Scholar * Li-Min Ting Search for this author in: * NPG journals * PubMed * Google Scholar * Jinghang Zhang Search for this author in: * NPG journals * PubMed * Google Scholar * Kami Kim Search for this author in: * NPG journals * PubMed * Google Scholar * Vladislav V Verkhusha Contact Vladislav V Verkhusha Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Author information * Supplementary information PDF files * Supplementary Text and Figures (2M) Supplementary Table 1 and Supplementary Figures 1–10 Additional data
• Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing
  - Nat Biotechnol 29(8):762-766 (2011)
  Nature Biotechnology | Research | Letter Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing * Ian Bancroft1 * Colin Morgan1 * Fiona Fraser1 * Janet Higgins1 * Rachel Wells1 * Leah Clissold1 * David Baker2 * Yan Long3 * Jinling Meng3 * Xiaowu Wang4 * Shengyi Liu5 * Martin Trick1 * Affiliations * Contributions * Corresponding authorJournal name:Nature BiotechnologyVolume: 29,Pages:762–766Year published:(2011)DOI:doi:10.1038/nbt.1926Received10 May 2011Accepted27 June 2011Published online31 July 2011 Article tools * Full text * 日本語要約 * Print * Email * Download PDF * Download citation * Order reprints * Rights and permissions * Share/bookmark * Connotea * CiteULike * Facebook * Twitter * Delicious * Digg Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation1 and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the e! fficiency of predictive breeding even in the absence of a complete genome sequence. View full text Figures at a glance * Figure 1: Schematic representation of sequence polymorphism types in homozygous lines. The positions of sequence polymorphisms are highlighted using bold text. The two types of allelic SNPs are indicated by solid boxes (interhomoeolog polymorphisms are not allelic SNPs). International Union of Biochemistry ambiguity codes: Y = C or T, S = C or G. Reproduced from ref. 1, with permission from John Wiley & Sons. * Figure 2: Transcript abundance and comparative analysis of linkage group A1. () Bin map for the 37 scored DH lines, indicating the number of SNP markers mapped within each recombination bin. Colored tracks represent the 37 individual lines of the TNDH population that were used for linkage map construction; pink, alleles inherited from maternal parent (Tapidor); blue, alleles inherited from paternal parent (Ningyou 7). () Quantification of transcript abundance, expressed as reads per kb per million aligned reads (RPKM), for each unigene mapped to the linkage group, displayed in inferred order along the linkage group. () Alignment to A. thaliana AGI gene models for each unigene mapped to the linkage group, displayed in inferred order along the linkage group. Light blue, chromosome 1 (At1g prefix); orange, chromosome 2 (At2g prefix); dark blue, chromosome 3 (At3g prefix); green, chromosome 4 (At4g prefix); red, chromosome 5 (At5g prefix). * Figure 3: Origins of alleles of loci mapped to linkage group A1. () Assignment of markers to likely progenitor species genome of origin. Blue, marker assigned to A genome; orange, marker assigned to C genome; vertical red bar indicates region of likely homoeologous exchange. () Origins of Tapidor alleles from four ancestral cultivars. Tap, Tapidor; Bie, Bienvenu; Reg, Regent; Bro, Bronowski; Lih, Liho. Blue-green horizontal lines, match to Tapidor allele scored in the population; gray horizontal lines, allele not determined; no horizontal lines, allele scored and does not match Tapidor allele; vertical blue bar, region inherited by Tapidor from Bienvenu; vertical red bar, segment likely originating from Liho, inherited via Regent. () Assignment of Chuanyou 2 alleles of hemi-SNP markers, as represented in Ningyou 7, to parent of origin. Chu, Chuanyou 2; She, Shengliyoucai; Che, Chengduaiyoucai. Yellow-green horizontal lines, match to Chuanyou 2 allele; no horizontal lines, allele scored and does not match Chuanyou 2 allele; vertical red ba! rs, regions in which the Chuanyou 2 alleles generally matches those of the B. rapa parent Chengduaiyoucai, but not that of the B. napus parent Shengliyoucai (loci with one or more alleles not determined are not shown). Accession codes * Accession codes * Author information * Supplementary information Referenced accessions Sequence Read Archive * ERA036824 Author information * Accession codes * Author information * Supplementary information Affiliations * John Innes Centre, Norwich Research Park, Norwich, Norfolk, UK. * Ian Bancroft, * Colin Morgan, * Fiona Fraser, * Janet Higgins, * Rachel Wells, * Leah Clissold & * Martin Trick * Biotechnology and Biological Sciences Research Council Genome Analysis Centre, Norwich Research Park, Norwich, Norfolk, UK. * David Baker * National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China. * Yan Long & * Jinling Meng * Key Laboratory of Horticultural Crop Genetic Improvement, Ministry of Agriculture; Sino-Dutch Joint Lab of Horticultural Genomics Technology; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China. * Xiaowu Wang * Key Laboratory of Oil Crops Biology, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China. * Shengyi Liu Contributions I.B. and M.T. conceived and planned the project. F.F., L.C. and D.B. carried out the experiments. I.B., C.M., J.H., R.W. and M.T. performed data analysis. Y.L. and J.M. provided materials and scoring data for conventional markers on the population. X.W. and S.L. provided access to unpublished genome sequence scaffolds. I.B. and M.T. wrote the manuscript and all authors reviewed it. Competing financial interests The authors declare no competing financial interests. Corresponding author Correspondence to: * Ian Bancroft Author Details * Ian Bancroft Contact Ian Bancroft Search for this author in: * NPG journals * PubMed * Google Scholar * Colin Morgan Search for this author in: * NPG journals * PubMed * Google Scholar * Fiona Fraser Search for this author in: * NPG journals * PubMed * Google Scholar * Janet Higgins Search for this author in: * NPG journals * PubMed * Google Scholar * Rachel Wells Search for this author in: * NPG journals * PubMed * Google Scholar * Leah Clissold Search for this author in: * NPG journals * PubMed * Google Scholar * David Baker Search for this author in: * NPG journals * PubMed * Google Scholar * Yan Long Search for this author in: * NPG journals * PubMed * Google Scholar * Jinling Meng Search for this author in: * NPG journals * PubMed * Google Scholar * Xiaowu Wang Search for this author in: * NPG journals * PubMed * Google Scholar * Shengyi Liu Search for this author in: * NPG journals * PubMed * Google Scholar * Martin Trick Search for this author in: * NPG journals * PubMed * Google Scholar Supplementary information * Accession codes * Author information * Supplementary information Excel files * Supplementary Data Set 1 (18M) Marker details for the cognate linkage map * Supplementary Data Set 2 (1M) Marker details for the non-cognate linkage map * Supplementary Data Set 3 (10M) Base counts at IHP positions in Tapidor and Ningyou 7 * Supplementary Data Set 4 (16K) Coordinates for splitting of Brassica rapa and Brassica oleracea genome assembly scaffolds * Supplementary Data Set 5 (803K) B. rapa and B. oleracea genome scaffolds anchored to the B. napus * Supplementary Data Set 6 (4M) Marker alleles scored in ancestors of Tapidor and Ningyou 7 Text files * Supplementary Data Set 7 (25K) Perl script combiner.pl * Supplementary Data Set 8 (4K) Perl script cure_cycle.pl * Supplementary Data Set 9 (4K) Perl script cure_refseqs.pl * Supplementary Data Set 10 (12K) Perl script ihp.pl * Supplementary Data Set 11 (4K) Perl script tag_counter.pl * Supplementary Data Set 12 (8K) Perl script AC_count.pl PDF files * Supplementary Text and Figures (1M) Supplementary Tables 1, 2 and Supplementary Figures 1–6 Additional data
• People
  - Nat Biotechnol 29(8):768 (2011)
  Article preview View full access options Nature Biotechnology | Careers and Recruitment | People People Journal name:Nature BiotechnologyVolume: 29,Page:768Year published:(2011)DOI:doi:10.1038/nbt.1950Published online05 August 2011 Roche (Nutley, NJ, USA) has announced the appointment of (right) as head of translational medicine in the oncology discovery and translational area (DTA) in its Pharma Research and Early Development (pRED) section. Cassidy was previously professor of oncology, head of the department of cancer research and head of the division of cancer sciences and molecular pathology at the University of Glasgow, Scotland. "We are very fortunate to have Jim join Roche," says Mike Burgess, global head, oncology DTA and head, large molecule research in pRED at Roche. "With his rich and deep experience in oncology research, we believe he is the perfect fit for the translational medicine position. He brings new energy and inspiration to our group that will allow us to enhance our development of new, more effective treatments for cancer patients." ERA-NET PathoGenoMics, a project funded by the European Commission aimed at advancing transnational research in the field of pathogenomics, has announced the winners of the 2011 PhD Award for the outstanding PhD theses in the field of genome research on human-pathogenic microorganisms (bacteria and fungi). The three winners, from the Technical University of Munich, Germany; from the Universidad Autónoma of Madrid, Spain; and from the New University of Lisbon, Portugal, were awarded 2,000 ($2,876) each. has been elected co-chairperson of the board of directors of Repligen (Waltham, MA, USA) along with . Dawes has served as a director since September 2005. has joined Corning Life Science (Lowell, MA, USA) as vice president and general manager, succeeding , who will lead Corning's environmental technologies business segment. Eglen most recently worked for the biodiscovery business of PerkinElmer. has been appointed chief medical officer of Oncolytics Biotech (Calgary, Alberta, Canada). He has been senior vice president of clinical safety and regulatory affairs at Oncolytics since 2002. Previously, he held executive positions at Ligand Pharmaceuticals, ICI Pharmaceuticals and Bristol-Myers (now Bristol-Myers Squibb). EMD Serono (Rockland, MA, USA) has appointed as president. Hoyes will also serve as a member of the executive management board for Merck Serono, the global pharmaceuticals division of EMD Serono parent company Merck KGaA. He previously served as chief commercial officer for EMD Serono and also held positions at Elan, Sanofi and Sterling Drug. Cellectis Therapeutics (Paris) has named as CSO. Scharenberg is an attending physician in immunology at Seattle Children's Hospital and professor of pediatrics and immunology at the University of Washington. He is also a principal investigator and codirector of the Northwest Genome Engineering Consortium, and cofounder and a member of the board of directors of Pregenen. Boreal Genomics (Vancouver, BC, Canada) has named as CEO and a member of the board of directors. Sood joins Boreal from Agilent Technologies, where he most recently served as general manager in charge of the automation business. He has also held senior management positions at Applied Biosystems, now Life Technologies. The US Food and Drug Administration (FDA) has named as deputy commissioner for medical products & tobacco, a newly created position. Spielberg is an FDA advisory board member and currently serves as director of personalized medicine at Children's Mercy Hospital in Kansas City. He was formerly vice president for pediatric drug development at Johnson & Johnson and dean of Dartmouth Medical School. He will oversee the centers for drugs, medical devices, biological products and tobacco. In addition, has been promoted from director of FDA drug center's compliance office to deputy commissioner for global regulatory operations and policy; deputy commissioner for international programs was named senior adviser and representative for global issues; and acting principal deputy commissioner will stay on as a counselor in FDA commissioner Margaret Hamburg's office. has been named chairman of the California Institute for Regenerative Medicine (CIRM; Los Angeles), succeeding , who served as chairman since the institute's founding in 2004. Thomas, an investment banker who started Saybrook Capital in 1990, was elected by a 14-11 vote of the CIRM board over , a Los Angeles cardiologist and medical device entrepreneur. Genesis Biopharma (Los Angeles) has named to its board of directors. Voyticky is currently president of Miller Energy Resources. He previously served as a vice president at the investment banks Goldman Sachs & Co. and Houlihan Lokey Howard & Zukin and as a partner in Red Mountain Capital Partners and Chapman Capital. Article preview Read the full article * Instant access to this article: US$32 Buy now * Subscribe to Nature Biotechnology for full access: Subscribe * Personal subscribers: Log in Additional access options: * Login via Athens * Login via your Institution * Purchase a site license * Use a document delivery service * Rent this article from DeepDyve * 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