Nature Biotechnology Research Articles

A Novel Method of Mobilizing Leukemia Initiating Cells by a Small Molecule Cdc42 Activity-Specific Inhibitor (CASIN) for Acute Myeloid Leukemia Therapy.

Abstract 13A large body of studies has proposed that leukemia initiating cells (LICs) are the culprit of leukemia relapse from conventional therapies. Like normal hematopoietic stem/progenitor cells (HSPCs), LICs are thought to reside in the bone marrow (BM) endothelial and/or endosteal niche. Although the full nature of LIC-niche interaction remains elusive, it has been postulated as a useful target for leukemia therapy based on a dual rationale: on one hand, the survival of LICs may depend upon interactions with specific niche, while on the other hand, chasing LICs out of the BM niche may drive quiescent LICs into active cell cycle, sensitizing them for conventional chemotherapy. Recent progresses in studying the PML tumor suppressor and the CXCR4-antagonist AMD3100 have provided strong support for such a rationale (Blood 113, 6215; Nature 453, 1072). The Rho GTPase family member Cdc42 is a central regulator of cell proliferation, adhesion, and migration by integrating signals from multiple cell surface receptors. Ablation of Cdc42 in HSPCs in a conditional knockout mouse model leads to massive egress of HSPCs from BM to the peripheral blood (PB), a phenotype attributable to deficiencies in HSPC adhesion, migration, and F-actin polymerization. We recently demonstrated that pharmacological targeting of Cdc42 by a small molecule Cdc42 activity-specific inhibitor (CASIN) transiently and specifically inhibits Cdc42 activity and mimics the Cdc42 knockout mobilization phenotype by suppressing HSPC adhesion, migration, and F-actin polymerization. CASIN appears to be active in this regard on both murine and human blood progenitors in vitro and in xenografted mice (Blood 112: 68a, Nature Biotechnology under revision). In the present studies, we hypothesize that pharmacological targeting of Cdc42 by CASIN is effective in mobilizing LICs from the BM niche, thus providing a new method for combinatory therapy against LICs. To test this hypothesis, we used MLL-AF9/N-Ras human AML cells (MA9/N-Ras), whereby the N-Ras G12D oncogene was introduced into MLL-AF9 transduced human CD34+ umbilical cord blood (HCB) cells. These cells grow vigorously in vitro independent of cytokine supplementation and induce AML readily in humanized NOD/SCID-SGM3 (SGM3) mice. Xenotransplant experiments confirmed that MA9/N-Ras cells are clonal inducers of leukemia with the property of LICs, as animals transplanted with either bulk cultures or with single cell derived cultures succumbed to AML with similar latencies. In MA9/N-Ras cells CASIN effectively inhibited downstream effectors of Cdc42 such as p-PAK, p-MLC and p-FAK in a dose-dependent manner. In the SGM3 mouse xenograft, we found CASIN administration (1.2 mg/kg, IV) transiently elicited mobilization of LICs from BM to PB by 20 minutes post injection. This was correlated with in vitro suppression of SDF-1α induced F-actin polymerization detected by FACS analysis and directional migration detected by a transwell assay upon CASIN treatment of the LICs (5-10 μM). Similar observations were made using Cdc42-specific shRNA knockdown of endogenous Cdc42 in the LICs. Continuous CASIN infusion into the xenografted mice for 5 days (1.2 mg/kg, IV, once daily) led to a potent induction of apoptosis of LICs detected by AnnexinV/7AAD staining. Significantly, the CASIN infusion showed no effects on the survival of HCB cells in xenografted SGM3 mice. In addition to a potential niche-dependent survival mechanism, the LICs, not normal HCB cells, appear to directly depend on Cdc42 for survival signals as further in vitro culture studies found that a 24-hour CASIN treatment resulted in a dose-dependent apoptosis of MA9/N-Ras cells, but not of normal HCBs. Finally, mouse genetic studies using MA9 transduced Mx-cre;Cdc42lox/lox BM cells transplanted into congenic BoyJ recipients showed that none of the mice with deleted Cdc42 upon pIpC injection developed AML while all mock-injected mice die from leukemia with less than 4 weeks latency, providing genetic evidence that Cdc42 is required for MA9-induced initiation of AML. Whether CASIN is effective in sensitizing the LICs to conventional chemotherapy in a combinatory regiment is currently under investigation. Our studies present a novel concept that pharmacological targeting of the intracellular signal transducer Cdc42 may have therapeutic value in eradicating LICs. Disclosures:No relevant conflicts of interest to declare.

Accreditation and attribution in data sharing

This is the author's final draft of the letter to the editor published as Nature Biotechnology, 2009, 27, pp. 984 - 985. The final version is available from http://www.nature.com/nbt/journal/v27/n11/full/nbt1109-984b.html

Japanese Biotech Patenting Strategies in the Era of Follow-On Biologics

Biotechnology Law ReportVol. 28, No. 4 ORIGINAL ARTICLEJapanese Biotech Patenting Strategies in the Era of Follow-On BiologicsJohn A. Tessensohn and Shusaku YamamotoJohn A. TessensohnSearch for more papers by this author and Shusaku YamamotoSearch for more papers by this authorPublished Online:30 Oct 2009https://doi.org/10.1089/blr.2009.9928AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetailsCited byPatent term extensions for biologic innovators in Japan1 January 2011 | Nature Biotechnology, Vol. 29, No. 1 Volume 28Issue 4Aug 2009 Information© 2009 Mary Ann Liebert, Inc.To cite this article:John A. Tessensohn and Shusaku Yamamoto.Japanese Biotech Patenting Strategies in the Era of Follow-On Biologics.Biotechnology Law Report.Aug 2009.483-496.http://doi.org/10.1089/blr.2009.9928Published in Volume: 28 Issue 4: October 30, 2009PDF download

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Masters of their universe

Nature Biotechnology talks to some of the leading characters behind the Genentech legend.

Standards and infrastructure for managing experimental metadata

Abstract*See also "related poster":http://precedings.nature.com/documents/3144/version/1*Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the "MIBBI":http://www.mibbi.org project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development^1^. More than 60 groups participate in the "OBO Foundry":http://www.obofoundry.org ^2^, which coordinates the orthogonal development of ontologies such as "OBI":http://obi-ontology.org for describing experimental (meta)data. And several groups participate in the development of "ISA-Tab":http://isatab.sf.net, a tabular framework for presenting experimental metadata^3^ (analogous to "FuGE":http://fuge.sf.net, a generic data model to underpin various XML file formats^4^).We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.View the "public instance":http://www.ebi.ac.uk/bioinvindex of our ISA-based infrastructure, running at EBI, and/or "download the components":http://isatab.sf.net for your local use.*References*1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.net

Standards and infrastructure for managing experimental metadata

Abstract*See also the "related presentation":http://precedings.nature.com/documents/3145/version/1*We present an infrastructure that leverages synergistic reporting standards and ontologies^1,2,3,4,5^ to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.The infrastructure’s components include: a data capture and editing tool (ISAcreator); validator (ISAvalidator); database (BioInvestigation Index); and converter (ISAconverter); and a BioConductor analysis package (R-ISApackage). The components are designed for local installation, and can work independently, or as unified system.View the "public instance":http://www.ebi.ac.uk/bioinvindex running at EBI and/or "download the components":http://isatab.sf.net for your local use.*References*1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org3. Ontology for Biomedical Investigations (OBI) "http://obi-ontology.org":http://obi-ontology.org4. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net5. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.net

Standards and infrastructure for managing experimental metadata

*See also "related poster":http://precedings.nature.com/documents/3144/version/1*Today’s researchers can perform biological and biomedical studies where the same material is run through a wide range of assays, comprising several technologies such as genomics, transcriptomics, proteomics and metabol/nomics (hereafter referred as ‘omics’). To enable others to correctly interpret the complex data sets that result, and the conclusions drawn, it is necessary to provide contextualizing experimental metadata at an appropriate level of granularity.Standards initiatives normally cater to particular domains. However, several synergistic standards activities foster cross-domain harmonization of the three kinds of reporting standard (minimum information checklists, ontologies and file formats). Some 29 groups participate in the "MIBBI":http://www.mibbi.org project, which offers a one-stop shop for those exploring the range of extant ‘minimum information’ checklists, and which fosters integrative development^1^. More than 60 groups participate in the "OBO Foundry":http://www.obofoundry.org ^2^, which coordinates the orthogonal development of ontologies such as "OBI":http://obi-ontology.org for describing experimental (meta)data. And several groups participate in the development of "ISA-Tab":http://isatab.sf.net, a tabular framework for presenting experimental metadata^3^ (analogous to "FuGE":http://fuge.sf.net, a generic data model to underpin various XML file formats^4^).We have developed an infrastructure that leverages the aforementioned synergistic reporting standards to create a common structured representation and storage mechanism for experimental metadata from biological and biomedical investigations ranging from simple single-assay studies to complex, methodologically diverse multi-assay studies.View the "public instance":http://www.ebi.ac.uk/bioinvindex of our ISA-based infrastructure, running at EBI, and/or "download the components":http://isatab.sf.net for your local use.*References*1. Taylor CF, Field D, Sansone SA,… Rocca-Serra P et al. (2008) The MIBBI Project. Nature Biotechnology Aug;26(8):889-896. "http://www.mibbi.org":http://www.mibbi.org2. Smith B, Ashburner M, Rosse C,… Rocca-Serra P, …Sansone SA et al. (2007) The OBO Foundry. Nature Biotechnology Nov;25(11):1251-5. "http://www.obofoundry.org":http://www.obofoundry.org3. Sansone SA, Rocca-Serra P, Brandizi M,… Taylor CF et al. (2008) The First MGED RSBI (ISA-TAB) Workshop. OMICS. Jun;12(2):143-9. "http://isatab.sf.net":http://isatab.sf.net4. Jones AR, Miller M, Aebersold R,… Sansone SA et al. (2007) The Functional Genomics Experiment model (FuGE). Nature Biotechnology Oct;25(10):1127-1133. "http://fuge.sf.net":http://fuge.sf.net

Flurogen Activating Peptides for Single Molecule Localization based Superresolution

Fluorgen Activating Peptides (FAPs) operate using an expressible dye binding peptide and a concentration of dye molecules that, upon binding to the receptor, have increased fluorescence excitation cross-sections by factors of hundreds to thousands [1] (see abstract by Qi Yan etal. for single-molecule characterization.) Depending on dye/receptor combination, affinities range from nanomolar to micromolar, corresponding to bound lifetimes up to 10s. The same receptor can repeatedly bind and activate new dye molecules, resulting in resistance to photobleaching when suitable concentration of unbleached dye remains and the FAP module hasn't been photodamaged. Binding rates can be controlled by dye concentration whereas fluorescent to dark state transitions can occur from unbinding and photobleaching. Adjusting dye concentration and excitation intensity allows tuning to maximize dyes localized per second per area. The following combined properties make the FAP system ideal for localization-based superresolution: 1)Expressible binding regions allow live cell studies; 2)Dye replenishment allows unlimited receptor position measurements, therefore arbitrary localization accuracy; 3)Only one excitation wavelength required; 4)Dye specific receptors allow multi-color superresolution.We demonstrate FAP superresolution by imaging live and fixed cells expressing beta-2 adrenergic receptor labeled with an extra-cellular FAP. Cell treatments show protein clustering details not apparent in diffraction limited images. Superresolution images are generated by placing Gaussian blobs at the found location of each activated dye molecule. Dye locations are found using a recently developed, iterative method that performs a maximum likelihood parameter estimation of the background count rate, dye location and dye emission rate. The blob widths are calculated from the Cramer-Rao Lower Bound (CRLB) corresponding to combined estimation of background, position and emission rate. Localization and CRLB are performed on GPU hardware using NVIDIA's CUDA architecture, achieving up to 10^5 combined fits and CRLB calculations per second.1. Szent-Gyorgyi et al, Nature Biotechnology, 2008. 26(2):p235-p240.

Multivariable Parameter Optimization Of Microfluidic Post Arrays For DNA Fractionation

Length-based fractionation of long DNA is a fundamental process in genomic analysis. Traditional methods, such as pulsed-field gel electrophoresis or capillary electrophoresis, are slow and not easily coupled to downstream analytical processes. Microfluidic devices containing arrays of micron-scale posts have previously been described for length-based fractionation of kilobase length DNA. [1] Here, we present experimental and computational studies defining and optimizing a broad array of parameters in order to maximize mass throughput and isolation of DNA > 150 kb. Parameters explored include post field geometry, electric field intensity, and field oscillation timing. Experimental studies were performed by analyzing of the mobility of single YOYO-1 intercalated DNA molecules in PDMS post arrays. Computational studies simulated kilobase length DNA as a worm-like chain model and investigated the interaction of such molecules with post arrays of various geometries. Optimization of our system results in the ability to isolate 165 kb DNA from 125 kb DNA and process 5 ng of DNA within 30 minutes of operation. This research was supported by the Department of Homeland Security, Science and Technology Directorate.[1] Huang et al.., Nature Biotechnology, 2002, 20, 1048.

Controlling HIV infection: HIV co‐receptor gets the finger

Controlling HIV infection: HIV co‐receptor gets the finger

Guidelines for reporting the use of gel electrophoresis in proteomics

the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. Developed through a joint effort between the gel-based analysis working group of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; this http URL) and the wider proteomics community, they constitute one part of the overall Minimum Information about a Proteomics Experiment (MIAPE) documentation system published last August in Nature Biotechnology

Beyond Equal: From Same But Different to the Doctrine of Substantial Equivalence

A same-but-different dichotomy has recently been encapsulated within the ill-defined concept of “substantial equivalence”. By invoking this concept the genetically modified organism (GMO) industry has escaped the rigors of safety testing that might otherwise apply. The curious concept of “substantial equivalence” grants a presumption of safety to GMO food. This presumption has yet to be earned, and has been used to constrain labelling of both GMO and non-GMO food. It is an idea that well serves corporatism. It enables the claim of difference to secure patent protection, while upholding the contrary claim of sameness to avoid labelling and safety scrutiny. It offers the best of both worlds for corporate food entrepreneurs, and delivers the worst of both worlds to consumers. The term “substantial equivalence” has established its currency within the GMO discourse. As the opportunities for patenting food technologies expand, the GMO recruitment of this concept will likely be a dress rehearsal for the developing debates on the labelling and testing of other techno-foods - including nano-foods and clone-foods.

Building Better Beta Cells

Type 1 diabetes represents an attractive target for human embryonic stem cell (hESC)-based cell replacement therapies. Recently, in Nature Biotechnology, Kroon et al. (2008) reported encouraging progress toward this goal with the development of functional islet-like structures in mice transplanted with hESC-derived pancreatic endoderm.

Meet The Guest Editors

Christian Buchholz studied microbiology at the University of Munich. He obtained his Ph.D. at the Max-Planck-Institute for Biochemistry in 1993, where he worked on the molecular mechanism of viral RNA-dependent RNA polymerases under supervision of Prof. Wolfgang Neubert. He then became a postdoctoral fellow in the Institute for Molecular Biology in Zurich where he elucidated the role of the measles virus receptor in membrane fusion in Prof. Roberto Cattaneos laboratory. As an EMBO fellow he joined the Centre for Protein Engineering in Cambridge (UK) and established the retrovirus based screening and display library technology together with Prof. Stephen J. Russell. Since 1999 he is head of the Section “Viral Gene Transfer Medicinal Products” at the Paul-Ehrlich-Institut, and later on became Associate Professor for Biochemistry at the University of Frankfurt. SELECTED PUBLICATIONS [1] Buchholz, C.J., Peng, K.W., Morling, F.J., Zhang, J., Cosset, F.L., and Russell, S.J. (1998) In vivo selection of protease cleavage sites from retrovirus display libraries. Nature Biotechnology 16: 951-954. [2] Schneider, R.M., Medvedovska, Y., Hartl, I., Voelker, B., Chadwick, M., Russell, S.J., Cichutek, K., and Buchholz, C.J. (2003) Directed evolution of retroviruses activatable by tumour associated matrix metalloproteases. Gene Therapy 10: 1370-1380. [3] Merten, C.A., Stitz, J., Braun, G., Poeschla, E.M., Cichutek, K. and Buchholz, C.J. (2005) Directed evolution of retrovirus envelope protein cytoplasmic tails guided by functional incorporation into lentivirus particles. Journal of Virology 79: 834-840. [4] Hartl, I., Schneider, R.M., Sun, Y., Medvedovska, J., Chadwick, M.P., Russell, S.J., Cichutek, K. and Buchholz, C.J. (2005) Library-based selection of retroviruses selectively spreading through matrix metalloprotease-positive cells. Gene Therapy 12: 918-926. [5] Urban, J.H., Schneider, R.M., Compte, M., Finger, C., Cichutek, K., Álvarez-Vallina, L., and Buchholz, C.J. (2005) Selection of functional human antibodies from retroviral display libraries. Nucleic Acids Research 33: e35. [6] Merten, C.A., Stitz, J., Braun, G., Medvedovska, J., Cichutek, K., Buchholz, C.J. (2006) Fusoselect: cell-cell fusion activity engineered by directed evolution of a retroviral glycoprotein. Nucleic Acids Research 34: e41. Hildegard Büning studied biology at the Universities of Münster and Munich. She received her Ph.D. at the Institute for Biochemistry of the University of Munich in 1997, where she worked on protein-DNA interaction under supervision of Prof. Haralabos Zorbas and Prof. Ernst-Ludwig Winnacker. She then worked as a postdoctoral fellow and later as Principal Investigator at the Gene Center in Munich on AAV vector development in the laboratory of Prof. Michael Hallek. In 2004 she started her own research group at the Clinic I for Internal Medicine of the University of Cologne. One year later, she became a member of the Center for Molecular Medicine Cologne, and is currently the Scientific Secretary of the German Society of Gene Therapy. Her work focuses on AAV vector targeting and on the study of AAV biology. SELECTED PUBLICATIONS [1] Nicklin, S.A., Buning, H., Dishart, K.L., de Alwis, M., Girod, A., Hacker, U., Thrasher, A.J., Ali, R.R., Hallek, M. and Baker, A.H. (2001) Efficient and selected AAV2-mediated gene transfer directed to human vascular endothelial cells. Molecular Therapy 4, 174-181. [2] Seisenberger, G., Ried, M.U., Endress, T., Buning, H., Hallek, M., Brauchle, C. (2001) Real-time single-molecule imaging of the infection pathway of an adeno-associated virus. Science. 294, 1929-1932. [3] Perabo, L., Buning, H., Kofler, D.M., Ried, M.U., Girod, A., Wendtner, C.M., Enssle, J., Hallek, M. (2003) In vitro selection of viral vectors with modified tropism: the adeno-associated virus display. Molecular Therapy 8, 151-157. [4] Lux, K., Goerlitz, N., Schlemminger, S., Perabo, L., Goldnau, D., Endell, J., Leike, K., Kofler, D.M., Finke, S., Hallek, M., Buning, H. (2005) Green Fluorescent protein-tagged adeno-associated virus particles allow the study of cytosolic and nuclear trafficking. Journal of Virology 79: 11776-11787. [5] Perabo, L., Endell, J., King S., Lux, K., Goldnau, D., Hallek, M., Buning, H. (2006) Combinatorial engineering of a gene therapy vector: directed evolution of adeno-associated virus. The Journal of Gene Medicine 8: 155-162. [6] Work, L.M., Buning, H., Hunt, E., Nicklin, S.A., Denby, L., Britton, N., Leike, K, Odenthal, M., Drebber, U., Hallek, M, Baker, A.H. (2006) Vascular bed-targeted in vivo gene delivery using tropism-modified adeno-associated viruses. Molecular Therapy 13: 683-693. [7] Perabo, L., Goldnau, D., White, K., Endell, J., Boucas, J., Humme, S., Work, L.M., Janicki, H., Hallek, M., Baker, A.H., Buning, H. (2006) Heparan sulfate proteoglycan binding properties of adeno-associated virus retargeting mutants and consequences for their in vivo tropism. Journal of Virology 80: 7265-7269.

Editorial

Microbial activities and products have been employed in the service of Humankind since the dawn of civilization. Though microbial biotechnologies broadened in range over time, a quantum quantitative and qualitative increase was heralded in by the gene technology revolution in the 1970s. Over the current and coming decades, a further quantum increase will be catalysed by a combination of an acceleration in accessing new microbial diversity, particularly through intensified exploration of our biosphere, (meta)genomics approaches, new developments in instrumentation and miniaturization (e.g. micro-fluidics), analytical procedures, and increasing development and application of systems and synthetic biology, on one hand, and driven by commercial, medical and societal demands for new and improved products and processes, on the other. The vast range of unexplored microbial diversity, and the pervasiveness of microbial activities influencing biosphere functioning and human endeavours and well-being, have recently precipitated a major research expansion in environmental microbiology. Despite this intensification of effort, more than 90% of microbial diversity still remains to be discovered. It is this new biodiversity that will become the treasure chest of new and improved biotechnological developments and applications in the sectors of chemicals, pharmaceuticals, energy, mining, materials, agriculture, food, environmental protection, etc. As exploration of new microbial diversity will reveal novel underlying catalytic reactions, metabolic activities and products, many of the applications resulting from these discoveries will be highly original and innovative. Such applications merit publication in high profile journals. Currently, there exists only one high impact journal, Nature Biotechnology, which explicitly includes microbial biotechnology research, but this journal covers all types of biotechnological research (microbial, plant, animal), and has a small page budget, so is only able to accept a small fraction of top research papers in microbial biotechnology. All other journals focusing on microbial biotechnology are currently of modest impact. This means that there is not only a paucity of options for placing top work in top journals, but also that the field of microbial biotechnology has no dedicated high profile vehicle that provides leadership in setting high benchmarks of quality and originality, effectively disseminates top research, and stimulates and promotes the field. Microbial Biotechnology has been created to publish papers of original research reporting significant advances in any aspect of microbial applications. In selecting and publishing the best original, innovative research and enabling advances that may lead to new applications, it aims to rapidly become the high profile flagship of microbial biotechnology. To achieve this, it has appointed a sterling Editorial Board, composed of leaders in the various sectors of the field and associated fields, and a core of experienced and dedicated Editors who, together, will apply rigorous reviewing and quality selection to assure the highest quality, originality and actuality of the published material. A key selection criterion is that material considered for publication belongs to the upper 25% of research in the field. Much research in cutting edge microbial biotechnology is multidisciplinary in nature and, with new advances and creative exploratory science, the topics and component disciplines range over an ever-increasing spectrum of the life and non-life sciences. Thus an important feature of Microbial Biotechnology will be the inclusiveness of its scope, which will widen in response to all developments that can lead to significant new applications involving microbes or their activities or products. For this reason, the specified scope of the Journal is only a guideline and will expand to incorporate new advances. As part of its aim to promote the field, Microbial Biotechnology will feature both primary research papers and (mini)reviews, editorials and correspondence, as well as regular features, like ‘Web Alert’ and ‘Genomics Update’. Particularly topical themes will be the focus of Special Issues. As part of its aim to provide a greater focus for, and understanding of, microbial biotechnology and its societal benefits, and to achieve wider dissemination of the work it publishes, Reviewers and Editors will flag up research articles of particular interest to the general public and these will be the subject of press releases. Microbial Biotechnology joins the extremely successful stable of microbiology journals of Wiley-Blackwell. It benefits from the support of the Society for Applied Microbiology, which is one of the oldest learned societies dedicated to the promotion of applied microbiology, and a major global promoter of microbial biotechnology, and from the exceptional publishing experience of Wiley-Blackwell and its highly professional Production Office. So: enjoy reading this first issue of Microbial Biotechnology, anticipate the issues to come (free access for 2008!), and start to prepare your best material for submission for publication in a future issue!

New Tools for Genome Modification in Human Embryonic Stem Cells

Two recent papers outline improvements in gene editing technology that may facilitate the analysis of signaling networks important for development. The systems developed by both Thyagarajan and coworkers (Thyagarajan et al., 2007) in Nature Biotechnology, and Lombardo and colleagues (Lombardo et al., 2007) in Stem Cells, have the potential to advance our understanding of human embryonic stem cells.

HUPO Plasma Proteome Project 2007 Workshop Report

The HUPO Plasma Proteome Project (PPP) held its annual workshop at the 6th HUPO World Congress in Seoul, Korea, October 7, 2007. The agenda was organized around the aims of the next phase of the PPP. The pilot phase accomplished its goals of providing reference specimens of serum and plasma to a large international network of collaborating laboratories, comparing protein identifications with various fractionation and analytical technology platforms, introducing new technologies from vendor partners, generating extensive submissions to open source databases (www.peptideatlas. org/hupo/hppp (ISB); www.ebi.ac.uk/pride (EBI)) and bioinformatics insights, and laying a foundation for integration of plasma studies with organ proteome and disease biomarker projects. Results were published in a special issue of Proteomics (1), a Wiley book (2), and a special analysis in Nature Biotechnology (3). The specimens and databases have been utilized for many other studies. Participants at the PPP workshop in Long Beach, California, in November 2006 agreed to develop the current plans. The 2007 workshop was organized with panels of leading scientists in proteomics describing their commitments. The overriding principle is the sharing of data to advance the field and facilitate much needed comparative analyses. The first panel comprised laboratory leaders with advanced technology platforms. Ruedi Aebersold described the N-glycosite Nx(S/T) proteotypic peptide library approach for targeted analyses. Christie Hunter presented applications of multiple reaction monitoring with multiple transitions for each labeled peptide. Denis Hochstrasser emphasized the preanalytical variables and the advantages of starting from tissue, followed by the multiplex analyses of plasma (or serum, if immunoassays). Bill Hancock introduced multilectin affinity chromatography for glycoproteins, including glycan characterization. Ole Jensen introduced microparticles and phosphoprotein analyses. Richard Smith explained powerful ion mobility separation mass spectrometry and electrospray emitter design. And Rong Zeng presented label-free, integrated analyses after ethanol precipitation and pH elution of plasma proteins from diabetics. The second panel presented highly complementary bioinformatics and database resources already impressively connected with the PPP. Henry Lam announced that PeptideAtlas at the Institute for Systems Biology now has a human PPPspecific subatlas (see above); as the total resource has grown, more and more of the newly reported multiobserved peptides are confirmatory. PeptideAtlas applies to submitted datasets its uniform data analysis pipeline, including MS/MS spectral library searches with SpectraST (joint with the National Institute of Standards and Technology), which are much faster than Sequest. Lennart Martens described typical pitfalls in the analysis of mass spectrometry data obtained from serum or plasma samples along with tools that help resolve these problems. He reported that the PPP datasets were the first external data submitted to PRIDE at the European Bioinformatics Institute (see above); PRIDE assists data dissemination and links to EBI resources. Ron Beavis noted that the PPP was also one of the first datasets in the Global Proteome Machine, GPMdb (with the distinctive prefix 101). Martin McIntosh emphasized statistical variables, starting with variability among individuals and populations to be studied and discussed that follow-up analysis of the same individual minimizes genetic variation. Akhilesh Pandey described the Proteinpedia portal for sharing protein data and annotations. Both PRIDE and Proteinpedia use Tranche at ProteomeCommons.org, created by Philip Andrews of the University of Michigan, for storage of large volume raw datasets. Tranche provides encrypted file sharing among collaborators as well as open access datasets when made available. Contributors to the PPP should submit complex datasets with full experimental annotation specified by the HUPO Protein Standards. Users can find unaltered submissions at PRIDE, X!Tandem analyses at Global Proteome Machine, and TransProteomic Pipeline-processed datasets at PeptideAtlas. The final panel, moderated by John Bergeron as chair of HUPO Initiatives, demonstrated that the PPP and all other HUPO initiatives are complementary. EDTA-plasma specimens should be collected as part of organ-based studies for analysis in the same laboratories, followed by sharing of data on plasma and tissue findings with the PPP through the informatics resources just described. Helmut E. Meyer (Brain Proteome Project) reinforced the priority for starting from From ‡Human Genetics and Public Health, Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, ¶Institute for Molecular Systems Biology, HPT E 76 ETH Honggerberg, CH-8093 ZAurich, Switzerland, and Department of Biochemistry, Yonsei Proteome Research Center & Biomedical Proteome Research Center, Room 423 Industry-University Building, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, Seoul, 120-749 Korea 1 The abbreviations used are: PPP, HUPO Plasma Proteome Project; PRIDE, Proteomics Identification Database. 2 This citation refers to just one of the articles used in this publication. HUPO Views

The Endosteum Region Keeps Human Leukemic Stem Cells Alive

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