Hot off the presses! Jul 01 Nat Biotechnol

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Latest Articles Include:

• Credit where credit is overdue
  - Nat Biotechnol 27(7):579 (2009)
  A universal tagging system that links data sets with the author(s) that generated them is essential to promote data sharing within the proteomics and other research communities.
• Sanofi Aventis grooms its ranks for biotech partnering
  - Nat Biotechnol 27(7):581-582 (2009)
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• Governments fiddle while biotech burns
  - Nat Biotechnol 27(7):583-585 (2009)
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• Lilly's free web screening
  - Nat Biotechnol 27(7):584 (2009)
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• GE animal SBIR break
  - Nat Biotechnol 27(7):585 (2009)
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• Chavez own brand
  - Nat Biotechnol 27(7):585 (2009)
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• Ontario's $100 million draw
  - Nat Biotechnol 27(7):586 (2009)
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• Algae trailblazer shuts
  - Nat Biotechnol 27(7):586 (2009)
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• Diagnostics firms face new patent claim worries
  - Nat Biotechnol 27(7):586-587 (2009)
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• Budget winners
  - Nat Biotechnol 27(7):587 (2009)
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• Report claims no yield advantage for Bt crops
  - Nat Biotechnol 27(7):588-589 (2009)
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• iZumi's plans to capitalize on iPS cells
  - Nat Biotechnol 27(7):590-591 (2009)
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• Up in arms
  - Nat Biotechnol 27(7):592-594 (2009)
  Several European countries continue to defy EU law and ban genetically modified maize. Will the stalemate ever be resolved? Gunjan Sinha investigates.
• Six secrets to success—how to build a sustainable biotech business
  - Nat Biotechnol 27(7):595-597 (2009)
  
• PRIDE Converter: making proteomics data-sharing easy
  - Nat Biotechnol 27(7):598-599 (2009)
  Introduction To the Editor: Your editorial on 'Democratizing Proteomics Data'1 correctly addressed the increasing importance of making proteomics data publicly available so that it can be audited, reanalyzed or reused. To make global data-sharing in the field work, however, it is important to minimize the burden of uploading data into publicly available databases, such as PRIDE2. To this end, we have written a freely available, open source tool called PRIDE Converter that makes it straightforward to submit proteomics data to PRIDE from most common data formats. Public availability of data is the standard modus operandi for most of the life sciences, ranging from genome sequences, over microarray data, to protein information. Some of the best known examples in the field of proteomics include protein sequences in UniProt (http://www.uniprot.org/), protein structures in the Protein Databank (http://www.rcsb.org/) and protein modifications in UniMod and RESID (http://www.unimod.org/ and http://www.ebi.ac.uk/RESID). As highlighted in your 2007 editorial1, making data publicly available in a standardized and structured way enables other researchers to access and reanalyze the data, and to use the collected results in novel ways. Indeed, much of the progress over the past years in emerging fields, such as mass spectrometry (MS)-based proteomics, is directly related to the public availability of data obtained in earlier efforts3, specifically the genome sequencing projects. Not surprisingly, the need for data-sharing in the field of proteomics itself was quickly pointed out4. Several proteomics MS data repositories have since been established, with GPMDB, PRIDE, PeptideAtlas and Proteinpedia among the most prominent5. With this infrastructure in place, journals have followed suit by starting to request deposition of MS-related data in these databases1, 6. The PRIDE repository at the European Bioinformatics Institute (http://www.ebi.ac.uk/pride/) occupies a special place in the list of proteomics databases, in that it constitutes an actual data repository and does not assume editorial control over submitted data1. Additionally, it provides a simple yet powerful infrastructure to support anonymous peer review of submitted data while maintaining the submission as private in the system1. The PRIDE database has so far accumulated data on more than 9,500 experiments, collectively containing more than 40 million mass spectra, identifying well over 1.4 million unique peptide sequences, which in turn infer more than 100,000 unique Ensembl proteins across all species. Submitting an MS-based proteomics data set to a structured repository, such as PRIDE, has many advantages over alternative ways of making peptide and protein identifications publicly available, such as uploading raw data files on a web page7 or submitting text or PDF files as supplementary information to a journal2. Furthermore, centralized repositories can also offer additional services and tools to the scientific community, based on uploaded data. PRIDE for instance includes tools for (i) visualizing protein coverage, peptide modifications and spectrum annotations, (ii) automatic mapping of protein accession numbers to identifiers from all other commonly used proteomics databases using the PICR service8 and (iii) comprehensive protein list comparisons (through Venn diagrams)9. Submitting data to PRIDE could be challenging for some users, however. PRIDE relies on an XML-based data format for submissions, which is built around the Proteomics Standards Initiative mzData standard for mass spectrometry (http://www.ebi.ac.uk/pride/schemaXmlspyDocumentation.do)10. And although the PRIDE XML format is well documented, converting proteomics data to PRIDE XML could present difficulties, especially for wet-lab scientists without a strong bioinformatics background or informatics support. To alleviate this problem, two tools for converting data into PRIDE XML have already been developed: the ProteomeHarvest PRIDE Submission Spreadsheet, which is Microsoft Excel-based (http://www.ebi.ac.uk/pride/proteomeharvest/), and the PRIDE Wizard for Mascot result files (http://www.mcisb.org/resources/PrideWizard/). Both tools come with important limitations, however, ProteomeHarvest can not accommodate peak lists easily and requires substantial manual effort from the user! , whereas the PRIDE Wizard only accepts Mascot result files as input. In addition, both of them were developed for dealing with relatively small volumes of data. We therefore developed PRIDE Converter, a tool that dramatically improves on the existing ones in three crucial aspects: (i) it can accommodate a large variety of input formats, (ii) it is suitable for both small and large data submissions and (iii) having a wizard-like graphical user interface, it is very intuitive and easy to use. PRIDE Converter is platform independent, is written in Java and is open source under the permissive Apache2 license. At the time of writing, PRIDE Converter supports the conversion of fifteen different input formats into PRIDE XML (Fig. 1). The conversion process is divided into eight simple steps using a wizard-like graphical-user interface. In each of these steps, the user is requested to provide appropriate metadata using controlled vocabulary terms that are retrieved through an online connection to the Ontology Lookup Service11 (Fig. 2). Like the PRIDE repository itself, PRIDE Converter can fully accommodate Minimum Information About A Proteo! mics Experiment (MIAPE)-compliant data reporting, although it does not rigorously enforce it. The PRIDE Converter application is freely available (http://code.google.com/p/pride-converter/), and further support is available through the PRIDE support team (pride-support@ebi.ac.uk). Even though PRIDE Converter has only been available for a few months, it has already been successfully used by a variety of people to submit their data to PRIDE, so far resulting in 557 distinct submissions, containing >230,000 identified proteins, close to 1.5 million peptides and well over 23 million spectra. From these numbers, it is clear that PRIDE Converter already plays a substantial role in easing the burden of data submission to PRIDE. Interestingly, PRIDE Converter has also been used to make one of the most discussed proteomics data sets published to date publicly available12. As such, we are confident that PRIDE Converter will be a key asset in allowing authors to efficiently comply with the data submission guidelines proposed by Nature journals1, 6 and others (http://www3.interscience.wiley.com/homepages/76510741/2120_instruc.pdf). And although the completion of ongoing efforts to develop community standards will eventually result in the replacement of PRIDE XML ! by these standard formats, it will take some time before the new standards are in daily use in the laboratory. In addition, the ability of PRIDE Converter to act as an annotation tool will remain important even when the new standards enjoy widespread adoption, as important high-level metadata will remain outside the scope of these data formats. We therefore envision that future versions of PRIDE Converter will continue to be a key part of the efficient dissemination of mass spectrometry–based proteomics data for quite some time to come, especially with regard to empowering those labs that lack a strong informatics support.
• NCBI Peptidome: a new public repository for mass spectrometry peptide identifications
  - Nat Biotechnol 27(7):600-601 (2009)
  Introduction To the Editor: Peptidome (available at http://www.ncbi.nlm.nih.gov/peptidome/) is a new public resource that archives and freely distributes tandem mass spectrometry (MS) peptide and protein identification data generated by the scientific community (Fig. 1). The database is administered by the National Center for Biotechnology Information (NCBI; Bethesda, MD, USA) at the National Institutes of Health. The core structure of the Peptidome database is based on NCBI's Gene Expression Omnibus (GEO1, 2), and uses much of the same source code for handling submissions and accessing the database. Peptidome, like GEO, was constructed to promote sharing and dissemination of experimental data at a level of detail that is useful to both the specialized community and to the general biological community. Great emphasis has been placed on making the deposit procedures as simple as possible, yet still supporting a high level of experimental annotation. Although data from all stages of the experiment are captured, the burden of submission is minimized by accepting standard file formats and using spreadsheet templates for metadata. This method was chosen to allow submissions to be generated either programmatically or by hand, using tools familiar to everyone, without the delay of waiting for the perfect file format and slick graphical user interface to be developed. As the field matures, so will the data submission process. A Peptidome submission includes the following components: * Biological and methodological metadata. This information gives context to the experimental data and facilitates understanding of the goals of the study, the material under investigation, the instrumentation employed and the protocols used to generate and analyze the data. * The original raw spectra data, converted to open format. Raw data includes all of the original MS1 and MS2 data before any post-processing, regardless of whether it was identified or not. The availability of raw data is critical for independent verification and validation of the reported study results. Furthermore, collections of raw data greatly benefit the MS community in wider applications, such as preparing custom spectral libraries, conducting large-scale statistical studies of peptide fragmentation and developing new peptide-matching algorithms. * Peptide identification output files. These files contain matched peptide sequence information derived from the observed spectra using any search algorithm. * Conclusion-level results. These include the final, filtered list of identified proteins, and the peptides leading to those assignments, as determined by the submitter. This finalized list has much flexibility in that it allows inclusion of identifications from new algorithms or de novo identifications. It also allows the submitter to provide complete results independent of the methodology used, for example, cutoff scores, reverse database searches for false positives or agreement between multiple search engines. Peptidome processing procedures augment these lists with auxiliary information extracted from the peptide identification files, including scores and post-translational modifications. This augmented and enriched list is a convenient mechanism to access the relevant data discussed in an associated manuscript. Submissions are organized into studies and samples. A sample includes all results from the same biological source, regardless of the number of instrument runs required to collect the data. A study is a collection of samples related in some fashion, for example, one sample may be the control and another the diseased state, or each sample may be one slice of a time series. Each sample has its own list of identified proteins, peptides and spectra. All studies and samples are assigned unique and stable accession numbers that may be used to cite and retrieve the records. Data may remain private for a limited time, typically pending manuscript publication, and during this period submitters may grant journal reviewers anonymous access to their data. Public data may be browsed by studies or by samples, and each sample may be viewed either protein-centric or peptide-centric. The evidence for each peptide may also be explored down to the level of individual spectra. The current focus ! is on providing a complete view of all the data; additional functionality will be added in the future to aid in the analysis of the data, such as annotating spectra displays with theoretical fragment ions. In addition to displaying results through the website, all originally submitted files may be downloaded for offline analysis. Peptidome incorporates several measures to increase the quality, value and utility of submitted data. One of the distinguishing features of Peptidome is the high level of human support and curation in the submission process intended to ensure sufficient metadata and completeness of the submission. In addition, an attempt is made to match submitted identified protein names to NCBI protein designations, which improves accessibility to the larger biological community; this allows the experimental results to be retrieved by an independent search for a given protein or gene locus, without a priori knowledge of the pertinent experiment. Users can locate studies and proteins of interest by querying NCBI's powerful Entrez search system with relevant keywords, protein names, accessions and more. Data navigation is further enhanced through inter-database links that reciprocally connect Peptidome to other NCBI resources such as PubMed, GenBank and Gene. In the spirit of collaborative data-sharing, Peptidome is entering into data exchange agreements with established MS resources including PRIDE3, PeptideAtlas4, Tranche5 and other ProteomExchange members. We hope to expand this network in the future by collaborating with other, more specialized proteomic resources, such as Human ProteinPedia6. In spite of any apparent duplication of effort and design of these resources, we believe the community will benefit from alternative analysis or presentation styles and the cooperation of disparate repositories in data deposits and dissemination options. The initial exemplar submissions in Peptidome have been culled from selected submissions to PeptideAtlas, with the metadata enriched from papers associated with the experiments. Sharing and linking between resources will maximize the visibility and utility of public MS peptide identification data. We invite the proteomics community to support and participate in these data-sharing endeavors7 by contributing to the Peptidome resource, and we welcome input and suggestions.
• More eyeballs on AERS
  - Nat Biotechnol 27(7):601-602 (2009)
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• Lessons in biopolitics
  - Nat Biotechnol 27(7):602-604 (2009)
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• Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response
  - Nat Biotechnol 27(7):604-605 (2009)
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• Developing safe therapies from human pluripotent stem cells
  - Nat Biotechnol 27(7):606-613 (2009)
  Translation of human pluripotent stem cells into cell therapies will require the development of standardized tests for product consistency, stability, tumorigenicity, toxicity and immunogenicity.
• Dynamics of global disclosure through patent and journal publications for biopharmaceutical products
  - Nat Biotechnol 27(7):614-618 (2009)
  Examining the relationships between invention disclosure type in industry and academia and geographical disclosure trends, using plant-made pharmaceuticals as a single-sector model for the biopharmaceutical industry.
• Recent patent applications in stem cells
  - Nat Biotechnol 27(7):619 (2009)
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• Minicells overcome tumor drug-resistance
  - Nat Biotechnol 27(7):620-621 (2009)
  Bacterially derived minicells loaded with siRNA reverse drug resistance in tumor xenografts.
• Biomarker validation by targeted mass spectrometry
  - Nat Biotechnol 27(7):622-623 (2009)
  A multilaboratory study demonstrates the potential for establishing quantitative targeted proteomic assays for moderately to highly abundant plasma proteins.
• The importance of being red
  - Nat Biotechnol 27(7):624-625 (2009)
  A near-infrared fluorescent protein opens a window into the mammalian body.
• Research highlights
  - Nat Biotechnol 27(7):626 (2009)
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• Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream
  - Nat Biotechnol 27(7):627-632 (2009)
  As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise for far-reaching advancements in microbiology as well as in diverse, related sciences. But realizing that potential will require meeting the challenges that have accompanied the rapid development of the underlying technology and the exponential growth of data. New technologies provide unprecedented opportunities but also call for conceptual shifts. Experience gained in the first decade of genomics can guide the improved approaches now needed for the selection of genome sequencing projects and their funding, for genome publication and annotation, as well as for data analysis and access. Equipped with these new tools and policies, microbiologists will have a unique opportunity for unprecedented exploration of our microbial planet.
• Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
  - Nat Biotechnol 27(7):633-641 (2009)
  Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low g/ml protein concentrations ! in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
• Sequential treatment of drug-resistant tumors with targeted minicells containing siRNA or a cytotoxic drug
  - Nat Biotechnol 27(7):643-651 (2009)
  The dose-limiting toxicity of chemotherapeutics, heterogeneity and drug resistance of cancer cells, and difficulties of targeted delivery to tumors all pose daunting challenges to effective cancer therapy. We report that small interfering RNA (siRNA) duplexes readily penetrate intact bacterially derived minicells previously shown to cause tumor stabilization and regression when packaged with chemotherapeutics. When targeted via antibodies to tumor-cell-surface receptors, minicells can specifically and sequentially deliver to tumor xenografts first siRNAs or short hairpin RNA (shRNA)–encoding plasmids to compromise drug resistance by knocking down a multidrug resistance protein. Subsequent administration of targeted minicells containing cytotoxic drugs eliminate formerly drug-resistant tumors. The two waves of treatment, involving minicells loaded with both types of payload, enable complete survival without toxicity in mice with tumor xenografts, while involving sever! al thousandfold less drug, siRNA and antibody than needed for conventional systemic administration of cancer therapies.
• Quantification of the yeast transcriptome by single-molecule sequencing
  - Nat Biotechnol 27(7):652-658 (2009)
  We present single-molecule sequencing digital gene expression (smsDGE), a high-throughput, amplification-free method for accurate quantification of the full range of cellular polyadenylated RNA transcripts using a Helicos Genetic Analysis system. smsDGE involves a reverse-transcription and polyA-tailing sample preparation procedure followed by sequencing that generates a single read per transcript. We applied smsDGE to the transcriptome of Saccharomyces cerevisiae strain DBY746, using 6 of the available 50 channels in a single sequencing run, yielding on average 12 million aligned reads per channel. Using spiked-in RNA, accurate quantitative measurements were obtained over four orders of magnitude. High correlation was demonstrated across independent flow-cell channels, instrument runs and sample preparations. Transcript counting in smsDGE is highly efficient due to the representation of each transcript molecule by a single read. This efficiency, coupled with the high ! throughput enabled by the single-molecule sequencing platform, provides an alternative method for expression profiling.
• Synergistic drug combinations tend to improve therapeutically relevant selectivity
  - Nat Biotechnol 27(7):659-666 (2009)
  Drug combinations are a promising strategy to overcome the compensatory mechanisms and unwanted off-target effects that limit the utility of many potential drugs. However, enthusiasm for this approach is tempered by concerns that the therapeutic synergy of a combination will be accompanied by synergistic side effects. Using large scale simulations of bacterial metabolism and 94,110 multi-dose experiments relevant to diverse diseases, we provide evidence that synergistic drug combinations are generally more specific to particular cellular contexts than are single agent activities. We highlight six combinations whose selective synergy depends on multitarget drug activity. For one anti-inflammatory example, we show how such selectivity is achieved through differential expression of the drugs' targets in cell types associated with therapeutic, but not toxic, effects and validate its therapeutic relevance in a rat model of asthma. The context specificity of synergistic comb! inations creates many opportunities for therapeutically relevant selectivity and enables improved control of complex biological systems.
• Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
  - Nat Biotechnol 27(7):667-670 (2009)
  Metazoan genomes encode hundreds of RNA-binding proteins (RBPs) but RNA-binding preferences for relatively few RBPs have been well defined1. Current techniques for determining RNA targets, including in vitro selection and RNA co-immunoprecipitation2, 3, 4, 5, require significant time and labor investment. Here we introduce RNAcompete, a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. We tested RNAcompete by analyzing nine diverse RBPs (HuR, Vts1, FUSIP1, PTB, U1A, SF2/ASF, SLM2, RBM4 and YB1). RNAcompete identified expected and previously unknown RNA binding preferences. Using in vitro and in vivo binding data, we demonstrate that preferences for individual 7-mers identified by RNAcompete are a more accurate representation of binding activity than are conventional motif mode! ls. We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions.
• Corrigendum: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 6, 549–555 (2009); published online 24 May 2009; corrected after print 8 July 2009 In the version of this article initially published, Figure 2f is not referenced in the figure legend and is referenced as Figure 2e in the main text. Also, on p.5, right col., para. 1, line 8, miR-21 should be miR-122. The errors have been corrected in the HTML and PDF versions of the article.
• Erratum: Venture capital shifts strategies, startups suffer
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 27, 103–104 (2009); published online 9 February 2009; corrected after print 8 July 2009 In the version of this article initially published, "GSK Ventures" should have read "GlaxoSmithKline's SR One." The error has been corrected in the HTML and PDF versions of the article.
• Erratum: New relief for gout
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 27, 309–311 (2009); published online 7 April 2009; corrected after print 8 July 2009 In the version of this article initially published, the incidence of gout was incorrectly stated to be in the hundreds of millions worldwide and 300 million in the US (p. 309, para. 2). The incidence is known for industrialized countries, not worldwide. In the US, the number is 3 million. The last five lines of the paragraph should have read, "including about 1 in 100 adult men in industrialized countries (an estimated 3 million in the US according to the Centers for Disease Control)." The errors have been corrected in the HTML and PDF versions of the article.
• Erratum: Biotech hirings and firings
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 27, 395, 2009; published online 7 April 2009; corrected after print 8 July 2009 In the version of this article initially published, a company name was omitted from Table 2. GlaxoSmithKline should be listed in third place. The error has been corrected in the HTML and PDF versions of the article.
• Erratum: Wyeth preemption case ruling sparks labeling confusion
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 27, 399–400 (2009); published online 8 May 2009; corrected after print 8 July 2009 In the version of this article initially published, Phenergan is incorrectly mentioned in paragraph 2 as Merck's antinausea drug. Phenergan is made by Wyeth. The original version also states in paragraph 3 that Wyeth is located in Whitehouse Station, New Jersey. The company's correct location is Madison. The errors have been corrected in the HTML and PDF versions of the article.
• Erratum: Academia and the company coin
  - Nat Biotechnol 27(7):671 (2009)
  Introduction Nat. Biotechnol. 27, 411–414 (2009); published online 8 May 2009; corrected after print 8 July 2009 In the version of this article initially published, on p. 411, left column, last paragraph, one of the researchers' names was incorrectly given as "Martin Feller." It should have read Martin Keller. The error has been corrected in the HTML and PDF versions of the article.
• Small-cap biotechs in dire straits
  - Nat Biotechnol 27(7):672-673 (2009)
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• People
  - Nat Biotechnol 27(7):674 (2009)
  Introduction OXiGENE (Waltham, MA, USA) has announced the appointment of Peter J. Langecker as executive vice president and chief development officer. Langecker has more than 20 years of experience developing both drugs and biological products. He joins the company from Durect Corp. where he served as chief medical officer after previous stints at Schering-Plough, Coulter Pharmaceuticals, SUGEN and Intarcia Therapeutics. "I am particularly excited to be joining OXiGENE," says Langecker. "Their leading position in the field of vascular disrupting agents (VDAs), which represent an exciting potential therapy in the field of oncology, as well as the breadth of their product pipeline and the promising results Zybrestat and OXi4503 have shown to date in a variety of tumor types make this role particularly attractive. I am looking forward to helping guide these product candidates through the development process as I believe they will be valuable additions to the oncology armamentarium." Laura Agensky has been appointed vice president of clinical operations of Transition Therapeutics (Toronto). Since joining the company in 2001, Agensky has managed the execution of all clinical trials across a diverse set of disease indications including Alzheimer's disease and diabetes. ViroPharma (Exton, PA, USA) has announced the appointment of Frank Baldino, Jr. to its board of directors. He previously served as a member of ViroPharma's board of directors from 1996 to 2006. Baldino is the founder, CEO and chairman of the board of directors of Cephalon. Anavex Life Sciences (Geneva) has announced the appointment of Hervé de Kergrohen as CEO and director. He has over 25 years in senior and executive management positions, having held CEO, chairman or director roles with more than 12 companies in the US and Europe. In 2000, de Kergrohen cofounded Global Biomedical Partners, the asset management firm of International Biomedicine Holdings, a $400-million fund based in Basel, Switzerland. Hemispherx Biopharma (Philadelphia) has appointed Robert Dickey IV as senior vice president, a newly created role that will bring together various activities relating to fundraising, strategic partnering and finance functions. Dickey combines over 12 years of experience in biotech senior management and an 18-year career as an investment banker. He has served as CFO, COO, CEO and board member at three biotech companies and as a managing director at Legg Mason. J. Melville Engle, CEO of ThermoGenesis Corp. (Rancho Cordova, CA, USA), has been appointed to the company's board of directors, bringing the total number of directors to six. Engle has more than 30 years of management experience in the healthcare industry. He joined ThermoGenesis as CEO in April. Stephen Fellows has been appointed vice president of finance of Generex Biotechnology (Worcester, MA, USA). He has approximately 20 years of experience in financial management and accounting reporting for both public and private companies, most recently at Sona Mobile Holdings where he served as CFO. Alexander R. Giaquinto has been named to the board of directors of Protox Therapeutics (Vancouver, BC, Canada). Giaquinto is currently senior vice president of regulatory affairs and quality assurance at Regado Biosciences and acts as an independent consultant to several pharmaceutical companies. He currently serves on the board of directors for SemBioSys Genetics, Endoceutics and Biothera, as well as a member of the scientific advisory boards for Allozyne and EndoCeutics. Leaving the Protox board is Nitin Kaushal, who has served as a director since 2004. Five Prime Therapeutics (San Francisco) has named Julia P. Gregory president, CEO and a member of the company's board of directors. From 2000 to 2008, she served as executive vice president and CFO of Lexicon Pharmaceuticals, and prior to that she was an investment banker for over 20 years, primarily as head of healthcare and investment banking at Punk, Ziegel & Company and at Dillon, Read & Co. She succeeds Gail Maderis, who is stepping down for health reasons. Lorianne Masuoka has been promoted to the position of chief medical officer at Nektar Therapeutics (San Carlos, CA, USA). She has over 15 years of experience in clinical R&D, most recently serving as vice president of clinical development at Five Prime Therapeutics. Masuoka joined Nektar in August 2008. Oncothyreon (Seattle) has named Scott Peterson as vice president, R&D. He joins Oncothyreon from Zymogenetics where he served as director and department head, oncology research, since 2007. From 1999 until 2007 he held a variety of positions at ICOS, most recently as a principal scientist in oncology drug discovery. H. Michael Shepard has joined Halozyme Therapeutics (San Diego) as vice president, discovery research. He brings over 25 years of experience in the biotech industry to Halozyme. At Genentech, Shepard led the team that discovered the breast cancer drug Herceptin (trastuzumab). He most recently founded and served as president of Receptor BioLogix. Joseph Stauffer has joined Durect Corp. (Cupertino, CA, USA) as chief medical officer and executive vice president, corporate strategy. He served as chief medical officer and senior vice president of clinical research & medical affairs at Alpharma until its acquisition by King Pharmaceuticals earlier this year. Synta Pharmaceuticals (Lexington, MA, USA) has named Vojo Vukovic senior vice president and chief medical officer, succeeding Eric Jacobson, who recently announced his resignation from the company. Vukovic was previously vice president, clinical research at Synta, a position he has held since January 2009. Daniel O. Wilds has been elected executive chairman of Calcionics' (Bellevue, WA, USA) board of directors. He recently retired as CEO of SCOLR Pharma and previously served as chairman and CEO at Northwest Biotherapeutics, as CEO of Shiloov Biotechnologies (USA), as CEO of Adeza BioMedical and as CEO of Medisense.