BiotecVisions 2012, October

Abstract

Biotechnology JournalVolume 7, Issue 10 p. A1-A8 BiotecVisionsFree Access BiotecVisions 2012, October Special Edition: High-throughput First published: 02 October 2012 https://doi.org/10.1002/biot.201200057AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Editors: Judy Peng /jp; Uta Göbel /ug; Lucie Kalvodova /lk E-mail: biotecvisions@wiley.com www.biotecvisions.com Contributors: Anja Gaugel /ag; Bill Mullen /bm; Danny Asling /da; Fran Harding /fh; Frédérique Belliard /fb; Joanna Cipolla /jc; Kerstin Brachhold /kb; Lotte Nielsen /ln; Meghana Hemphill /mh; Melissa McCulloch /mmc; Mia Ricci /mr; Peter W. Bass /pwb; Sarah Andrus /sa; Sarah Brett /sb; Susan Vice /sv; Vera Köster /vk; Erwin Ripmeester /er; Allison Goldstein /ago October 2012 BiotecNews BTJ and AFOB sign a collaboration agreement Biotechnology Journal (BTJ), Wiley, and the Asian Federation of Biotechnology (AFOB) are pleased to announce the signing of a collaboration agreement. The agreement was signed in Taiwan in June 2012 by Prof. Toshiomi Yoshida (outgoing AFOB president), representing the AFOB, and Dr. Carol Bacchus (VP and Publishing Director, Wiley), representing Wiley and witnessed by around 20 AFOB board members. The collaboration makes BTJ the official journal of the AFOB and aims to foster biotechnology research and development in Asia, and to bring the best of Asian research to the international community. Prior to this, the AFOB and BTJ published two special issues in 2010 and 2011. BTJ is pleased that the AFOB chose to continue this successful collaboration and confident that the journal will further boost biotechnology research in the area and further promote and strengthen the federation. BTJ will publish two AFOB special issues per year and include coverage of AFOB news items in the forum section as well as BiotecVisions. To celebrate this landmark signing, BTJ and the AFOB hosted a champagne reception at the IBS 2012 in Daegu, Korea in September 2012. The reception was attended by more than 20 AFOB and Wiley representatives, including Prof. Ho Nam Chang (incoming President of the AFOB), Prof. Sang Yup Lee (co-editor-in-Chief, BTJ), Prof. Alois Jungbauer (co-editor-in-Chief, BTJ), and Dr. Judy Peng (Managing Editor, BTJ). In addition to this new allience, BTJ continues its collaboration with the EFB Section on Biochemical Engineering (ESBES), making it a unique bridge between Asian and European biotechnologists. /jp http://www.afob.org/ Previous AFOB-related special issues: http://onlinelibrary.wiley.com/doi/10.1002/biot.v5:5/issuetoc http://onlinelibrary.wiley.com/doi/10.1002/biot.v6.11/issuetoc Getting published Cytometry Part A As the Editor-in-Chief of an interdisciplinary biological journal with not only a strong emphasis on cutting-edge technology and methods but also a keen interest in novel biomedical findings, I always face the challenge to get the top technology papers with the top results achieved by new technologies. My Journal has the publication criteria that manuscripts must contain data obtained under strict quality control and present results on single-cell analysis that help to understand the behavior of cells and cell systems under normal and perturbed conditions (disease; activation). The key words for this are image and flow cytometry, but we also embrace new technologies such as single-cell mass spectrometry, genomics and proteomics, just to name a few. The main criteria for getting published are submitting exciting new findings in conjunction with experiments performed under high quality criteria. To this end, a task force of the International Society for Advancement of Cytometry (ISAC) developed the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard that Cytometry Part A has adopted for submissions that contain flow cytometry (FCM) data. To the best of my knowledge, we are presently the only journal that expects this high quality criterion. Adhering to a minimum data standard allows, in principal, any result to be independently validated, even with the often highly complex technology used to perform an FCM experiment. However, in combination with making the original data openly accessible in FlowRepository.org the readership can repeat the experiments perfectly in vitro and in silico. Also, we have a unique manuscript type, OMIP ((Optimized Multicolor Immunofluorescence Panels), that describe how highly complex (and expensive) multiplexed experiments can be done anywhere on the globe. In about half of all cases, authors' submissions do not fulfill the above criteria and are not further considered for publication. We continue to encourage authors to share their new biomedical results with us and to publish their (often exciting) technology findings, too. Attila Tárnok is Editor-in-Chief of Cytometry Part A, the journal of the International Society for Advancement of Cytometry (ISAC) http://isac-net.org http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1552-4930 Statistics: Choosing the test High throughput technologies generate large datasets. To make all the data useful and convert them to meaningful results, the data need to be analyzed and statistically processed. The initial experimental hypothesis needs to be translated into a mathematical hypothesis which is then validated using an appropriate statistical test. But how to choose the right test? Jean-Fran�ois Martin, statistical engineer at INRA/Clermont University, France, explains the steps involved in choosing the right test in the August issue of European Journal of Lipid Science and Technology. /lk [1] http://doi.wiley.com/10.1002/ejlt.201200260 Stepping stones in DNA sequencing In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. Recent technological advances related to massively parallel sequencing has enabled a significant cost reduction and a constantly increasing number of sequencing applications. This technical progress shows no signs of slowing down and will make sequencing even more accessible and important to genetics and biology in the future. This review in Biotechnology Journal by Henrik Stranneheim and Joakim Lundeberg (Stockholm, Sweden) covers some of the technical advances in sequencing that have enabled new frontiers in genomics. /ug [2] http://dx.doi.org/10.1002/biot.201200153 DNA fingerprinting of methanogens Understanding the ecology of methanogens (microorganisms that produce methane as a metabolic byproduct in anoxic conditions) in natural and engineered environments is a prerequisite to predicting or managing methane emissions. In this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. The method described in this article from FEMS Microbiology Letters designated amplicon length heterogeneity PCR of the mcrA gene (LH-mcrA), is based on the natural length variation in the mcrA gene. This gene encodes the alpha-subunit of the methyl-coenzyme M reductase involved in the terminal step of methane production by methanogens. LH-mcrA method was found to be a reliable, fast and cost-effective alternative for diversity assessment of methanogenic communities in microbial systems. /er [3] http://dx.doi.org/10.1111/j.1574-6968.2011.02418.x Pyrosequencing of foodborne pathogen Campylobacter is an important foodborne human pathogen, which has traditionally been studied using a variety of selective cultivation methods. In this article in FEMS Microbiology Ecology the authors show that high-throughput sequencing using 16S rRNA tagged-pyrosequencing provides an efficient and powerful alternative. /ln [4] http://dx.doi.org/10.1111/j.1574-6941.2011.01219.x High-throughput sequencing in plant molecular breeding High-throughput sequencing is a revolutionary technological innovation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. It has advanced research methods and solutions in genomics and post-genomics. This article in Journal of Integrative plant biology (JIPB) focuses on how high-throughput sequencing has led to a revolution in molecular breeding and enables us to launch multi-level, multi-faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. /jc [5] http://dx.doi.org/10.1111/j.1744-7909.2012.01115.x Plant. Biotechnol. J. Special issue: Next generation sequencing technologies The last 5 years have seen a revolution in next-generation DNA sequencing, with plant researchers readily adopting the technology to decipher the structure and function of plant genomes. This special issue in Plant Biotechnology Journal aims to capture the latest developments in plant biotechnology driven by advances in DNA sequencing technology. The use of this technology varies, with applications in genome sequencing, molecular genetic marker discovery, transcriptomics, candidate gene identification and plant taxonomy. /jc http://onlinelibrary.wiley.com/doi/10.1111/pbi.2012.10.issue-6/issuetoc Evolutionary engineering of Saccharomyces cerevisiae Evolutionary engineering is a powerful approach with widespread use in improving industrially important and genetically complex properties of S. cerevisiae and other microorganisms. It is expected that emerging high-throughput technologies in biological research, such as microfluidics, will change evolutionary engineering experiments by decreasing their costs and increasing their precision and allowing high-throughput continuous and batch processing of multiple samples. Development in high-throughput screening and analytical technologies will further increase the utilization frequencies of evolutionary engineering and genetic-driven selection strategies, which are both based on screening of a large number of samples for a desirable trait. Recent developments in functional genomics methods allow rapid identification of the molecular basis of the desired phenotypes obtained by evolutionary engineering. This review in FEMS Yeast Research reviews evolutionary engineering of S. cerevisiae. /fb [6] http://dx.doi.org/10.1111/j.1567-1364.2011.00775.x High-throughput electroporation protocol design Electroporation, the reversible or irreversible permeabilization of the cell membrane with electric fields, is important in biotechnology, medicine, and food industries. Electroporation protocols depend on numerous parameters such as cell type, solution composition, and in particular electric field strength. Conventional electroporation protocol designs seek optimal parameters by performing numerous experiments in which one single electric field is tested each time in a Cartesian system experimental setup. The research from Fernand and co-workers in micro- and nanoelectroporation suggests that using more complex electric field topologies than the conventional Cartesian should facilitate high-throughput electroporation protocol design. In this article in Biotechnology and Bioengineering, the authors demonstrate the concept and show how the use of a cylindrical coordinate system topology identifies reversible/irreversible electroporation interface parameters in a single experiment rather than from numerous experiments in the conventional Cartesian systems. The concept can, of course, be used for other high-throughput applications of electroporation such as identifying optimal transfection parameters in single experiments. /mr [7] http://dx.doi.org/10.1002/bit.24479 High-throughput cellobiose dehydrogenase screening Extracellular fungal flavocytochrome cellobiose dehydrogenase (CDH) is a promising enzyme for both bioelectronics and lignocellulose bioconversion. Neutral CDHs from ascomycetes are of particular interest because of their possible application in the physiologically compatible nanobiodevices. In this article in Biotechnology Journal, authors from Moskow, Russia and Vienna, Austria present a new selective and high-throughput screening assay for these enzymes based on in situ Prussian Blue formation. The assay can be applied on active growing cultures on agar plates or on fungal culture supernatants in 96-well plates under aerobic conditions. Neither other carbohydrate oxidoreductases nor laccase interfered with CDH activity in this assay. The developed assay is applicable for selection of new ascomycetous CDH producers as well as controlled synthesis of new Prussian Blue nanocomposites by CDH. /ug [8] http://dx.doi.org/10.1002/biot.201100480 Lectin-based gold nanoparticle assay for glycan differentiation In this Spotlight article in Biotechnology and Bioengineering, Sánchez-Pomales and co-workers demonstrate a rapid glycoanalysis method by lectin binding to glycoprotein-modified gold nanoparticles detected using either simple instrumentation (e.g., DLS or spectrophotometry) or by visual inspection. The assay is applied to a model protein, RNase B and a therapeutic monoclonal antibody, rituximab. The versatility of this method is great due to the breadth of the assay design space and may prove useful for rapid, high-throughput detection of changes in glycan profiles of therapeutic glycoproteins in process development or process monitoring. /mr [9] http://dx.doi.org/10.1002/bit.24513 Reverse phase protein detection with aptamers Many previous studies have investigated the application of aptamers in forward phase protein microarray assays. In Engineering in Life Sciences authors from Hannover, Germany, present the reverse phase format utilizing aptamers for the first time. Aptamers are promising tools for capturing and detection of proteins, with many advantages over antibodies, such as their higher stability. This new system is a simple and fast way to detect proteins in cell lysates, as demonstreated by Cy3-labeled aptamers directed against the histidine-tag. Purified his-tagged PFEI (Pseudomonas fluorescence esterase I) could be detected at a concentration as low as 30 nM. This new technique may therefore be applicable to monitor protein production and purification processes in high-throughput applications. [10] http://dx.doi.org/10.1002/elsc.201100100 High-throughput antibody purification In the last decade, high-throughput downstream process development techniques have entered the biopharmaceutical industry. As chromatography is the standard downstream purification method, several high-throughput chromatographic methods have been developed and applied including miniaturized chromatographic columns for utilization on liquid handling stations. These columns were used to setup a complete downstream process on a liquid handling station for the first time. In Biotechnology Progress, Treier and co-workers report on the establishment of a monoclonal antibody process in lab-scale and scale-down. Liquid handling in miniaturized single and multicolumn processes was improved and applicability was demonstrated by volume balances. The challenges of absorption measurement are discussed and strategies were shown to improve volume balances and mass balances in 96-well microtiter plates. The feasibility of miniaturizing a complete downstream process was shown. In the future, analytical bottlenecks should be addressed to gain the full benefit from miniaturized complete process development. /mr [11] http://dx.doi.org/10.1002/btpr.1533 Therapeutic antibody targets multiple chemokines In chronic inflammatory diseases, tissue damage is caused by excessive numbers of immune cells travelling to a specific site. Blocking the trafficking of these cells by interfering with chemokine signaling has been proposed as a therapeutic strategy. However, blocking single chemokine signaling pathways has not been successful in controlling inflammation. To overcome this, an academic-industry partnership based in Seattle has developed a therapeutic antibody targeted against multiple human chemokines. Inspired by pox and herpes viruses, which secret a protein able to block several chemokines, antibodies cross reactive against CCL3, CCL 4 and CCL5 were created by sequentially immunizing mice. Phage display affinity maturation was used to improve the efficacy of selected antibody clone against all three targets, resulting in more than 1000-fold enhancement of chemotaxis compared to the original clone. /fh [12] http://dx.doi.org/10.1371/journal.pone.0043332 Breast cancer cells adapt glucose metabolism Anti-cancer drug therapies can produce excellent initial tumor suppression, only to lose effectiveness as treatment progresses. Results published in Molecular Systems Biology reveal a newly discovered strategy by which breast cancer cells are able to counter the efficacy of the drug lapatinib. Researchers from Houston, TX, used microarrays to compare gene expression in breast cancer cells sensitive and resistant to lapatinib. Computational analysis of more than 15 000 gene interactions revealed an increased expression of genes involved in the response to glucose deprivation. Analysis of gene expression networks in breast cancer patients confirmed that the glucose deprivation network is associated with high relapse rates. Bioinformatics mining based on upregulation of this gene network in lapatinib resistant cells has identified several drug candidates with promise for treating drug-resistance in breast cancer patients. /fh [13] http://dx.doi.org/10.1038/msb.2012.25 Lessons from yeast: Mining high-throughput screens for cancer drug targets The recent decrease in the rate that new cancer therapies are being translated into clinical use is mainly due to the lack of therapeutic efficacy and clinical safety or toxicology. High-throughput screening is increasingly being used to test new drug compounds and to infer their cellular targets, but these quantitative screens result in high-dimensional datasets with many inherent sources of noise. This article in WIREs Data Mining and Knowledge Discovery reviews the state-of-the-art statistical scoring approaches used in the prediction of drug-target interactions, and illustrates their operation using publicly available data from yeast chemical-genomic profiling studies. The real data examples, such as personalized cancer therapies, underscore the need for developing more advanced data mining approaches for extracting the full information from the high-throughput screens. /mh [14] http://dx.doi.org/10.1002/widm.1055 Current protocols Embryoid body differentiation of stem cells Serum-free human pluripotent stem cell media offer the potential to develop reproducible clinically applicable differentiation strategies and protocols. The vast array of possible growth factor and cytokine combinations for media formulations makes differentiation protocol optimization both labor- and cost-intensive. One high-throughput assay uses 96-well plate, 4-color flow cytometry-based screening to optimize pluripotent stem cell differentiation protocols. The authors provide conditions both to differentiate human embryonic stem cells (hESCs) into the three primary germ layers, ectoderm, endoderm, and mesoderm, and to utilize flow cytometry to distinguish between them. This assay exhibits low inter-well variability and can be utilized to efficiently screen a variety of media formulations. /bm [15] http://www.currentprotocols.com/WileyCDA/CPUnit/refId-sc01d06.html RT-PCR for small-molecule screening Quantitative measurement of the levels of mRNA expression via real-time reverse transcription polymerase chain reaction (RT-PCR) has long been used for analyzing expression differences in tissue or cell lines of interest. This method has been used somewhat less frequently to measure the changes in gene expression due to perturbagens such as small molecules or siRNA. The availability of new instrumentation for liquid handling and real-time PCR analysis, as well as the commercial availability of start-to-finish kits for RT-PCR, has enabled the use of this method for high-throughput small-molecule screening on a scale comparable to traditional high-throughput screening (HTS) assays. This protocol focuses on the special considerations necessary for using quantitative RT-PCR as a primary small-molecule screening assay, including the different methods available for mRNA isolation and analysis. [16] http://www.currentprotocols.com/WileyCDA/CPUnit/refId-ch110204.html BiotecBooks Fundamentals of light microscopy and electronic imaging (2nd Edition) Douglas B. Murphy, Michael W. Davidson; ISBN: 978-0-471-69214-0 Providing a coherent introduction to the principles and applications of the integrated electron microscope system, this revised version of the bestselling first edition includes new chapters on live cell imaging, measurement of protein dynamics, deconvolution microscopy, and interference microscopy. /ago www.wiley.com/buy/9780471692140 Essentials of pharmaceutical preformulation Simon Gaisford, Mark Saunders; ISBN: 978-0-470-97635-7 A study guide describing the basic principles of pharmaceutical physicochemical characterization. Perfect for undergraduate-level pharmacy students and R&D / analytical scientists working in the pharmaceutical sector. /ago www.wiley.com/buy/9780470976364 Biocatalysts and enzyme technology (2nd Edition) Klaus Buchholz, Volker Kasche, Uwe Theo Bornscheuer; ISBN: 978-3-527-32989-2 This updated and revised second edition offers 40% more printed content covering the current knowledge of biocatalysis and enzyme technology. /ago www.wiley.com/buy/9783527329892 Biochemical pathwaysAn atlas of biochemistry and molecular biology (2nd Edition) Gerhard Michal and Dietmar Schomburg; ISBN: 978-0-470-14684-2 Covering a wide range of subject matter, including biochemistry, molecular and cell biology, medicine, chemistry, and allied health, Biochemical Pathways is a full-color, easy-to-use resource for students and professionals. This information-packed reference features a unique summary of biochemical pathways based on the well-known Biochemical Pathways chart. Included is descriptive information about properties such as enzymes, chemicals, proteins, and DNA, all of which act together to create an elaborate chain that drives all biological functions. Completely updated, this new edition continues to play a valuable role in this important scientific field. /as www.wiley.com/buy/9780470146842 Chemical sensors and biosensorsFundamentals and applications Florinel-Gabriel Banica; ISBN: 978-0-470-71067-8 This is a modern introductory book on sensors, combining underlying theory with bang up to date topics such as nanotechnology and electronic noses. The text is suitable for graduate students and research scientists with little background in analytical chemistry. It is user-friendly, with accessible theoretical approach of the basic principles, and adequate references to further reading. The book covers up-to-date advances in the sensor field, e.g. nanotechnology, microfluidics, lab-on-a-chip, and quantum dots. It includes calculation exercises and solutions, and contains a guide to Laboratory Exercises essential for course instructors and for experimental projects. An accompanying website contains colour illustrations and Powerpoint slides. /as www.wiley.com/buy/9780470710678 Special issue High-throughput process development High-throughput process development (HTPD) combines high-throughput experimentation, adequate analytical methods and advanced experimental design and/or data analysis. This Special issue of Biotechnology Journal is edited by Jürgen Hubbuch (Karlsruhe Institute of Technology, KIT, Karlsruhe, Germany). www.biotechnology-journal.com BiotecAwards Charles Thom Award Editor-in-Chief of Biotechnology Journal wins the 2012 Charles Thom Award from the Society for Industrial Microbiology and Biotechnology, his award lecture was on: “Microbial production of natural and non-natural chemicals through inherent, noninherent, and created pathways”. The Charles Thom Award recognizes individuals who have made one or more outstanding research contributions in industrial microbiology and/or biotechnology. These contributions should be of exceptional merit, reflecting an independence of thought and originality that adds appreciably to scientific knowledge. Activities such as journal editing, organizing and chairing conferences, and serving scientific societies in official capacities also may be considered when judging research contributions. However, the most important factor in selecting nominees for this Award is research accomplishments. /jp http://www.simhq.org/annual/awardwinners/ GIT Innovations Award 2012 GIT proudly present the winners of the GIT Innovations Award 2012. Our readers, customers and many visitors of Analytica 2012 in Munich and of Achema 2012 in Frankfurt selected their favorites. Our congratulations go to the companies Postnova Analytics, Nanotemper Technologies, Carl Zeiss Microscopy and Thermo Fisher Scientific. /ag Read more on the award and the placing of other companies with their products within each category at http://goo.gl/WcxpZ Rita and John Cornforth Award 2012 The Rita and John Cornforth award 2012 recognizes Prof. Stefan Przyborski's (CSO and founder of Reinnverate) leadership and inter-disciplinary work at the boundaries of physical chemistry and biology, developing Alvetex Scaffold for three dimensional (3D) cell culture. /ag www.reinnervate.com Read the latest R&D and business specific news at http://www.laboratory-journal.com WIREs Postgenomics for Wnt signaling While sequencing projects have been extremely successful in identifying key genes/components of many biological processes, such as signal transduction cascades, the function(s) of the majority of genes in the genome remains a mystery. This article discusses the use of a variety of high-throughput postgenomic tools, including functional genomics, proteomics, and chemical genetics, that are being implemented in an exhaustive molecular dissection of the Wnt signal transduction pathway. /mh http://onlinelibrary.wiley.com/doi/10.1002/wsbm.140/full Viruses and microRNAs: A toolbox for systematic analysis A comprehensive analysis of microRNA functions focusing on herpes virus not only requires systematic approaches employing high-throughput technologies, but also calls for the development of improved experimental technologies and a profound bioinformatic analysis. /mh http://onlinelibrary.wiley.com/doi/10.1002/wrna.92/full Molecular diagnostics for personal medicine using a nanopore Semiconductor nanotechnology has created the ultimate analytical tool: a nanopore with single molecule sensitivity. This tool offers the intriguing possibility of high-throughput, low cost sequencing of DNA with the absolute minimum of material and preprocessing. /mh http://onlinelibrary.wiley.com/doi/10.1002/wnan.86/full BiotecCareers PhD and then? Interview with a technology transfer specialist After her postdoctoral training in cancer research, Kerstin Papenfuss joined a technology transfer organization and became a “Therapeutics Review Team Manager” Q: Please tell us about what you do. A: I am a member of the Therapeutics review team at MRC Technology. We have our own drug discovery division at MRCT and we are trying to bridge the gap between research in academic institutions and the pharma industry. By producing chemical leads or humanized antibodies we try to produce a data package that would be attractive to pharmaceutical companies. My job is to review the ideas for new drug targets by academics with regards to scientific background, potential partnering, competition and IP landscape. I also build up relationship with academics and manage the whole review process. Q: What do you enjoy most about the job? A: The diversity and the challenge. Our company has no disease focus as the expertise in the specific disease area usually comes from the academic we are collaborating with. For me it is a big challenge to understand the molecular mechanisms of different diseases working on several projects at the same time. Q: Are there any aspects that could be different? A: Nothing that I can think of at the moment. Q: Why/how did you decide to move from academia to this sector/job? A: I got a good insight into the drug development process when I was working as a postdoc. I found that quite fascinating and wanted to move into this direction but was also looking for a job where I could use my strengths such as presentation, communication more. Q: What aspects of your PhD/postdoc experience have been most useful in getting the job, and doing the job? A: Having to write reviews and learning how to impartially review and present scientific data. Q: What is your one tip for PhD students or postdocs who might be considering a move to this sector? A: Don't underestimate yourself, you will have gained a lot of skills working as a PhD student or Postdoc that you are probably not aware of. Take some time to figure out what these skills are and don't be shy to mention them in your application. BiotecEvents Advertori