Biotechnology and Bioengineering

Cover image for Vol. 109 Issue 10

October 2012

Volume 109, Issue 10

Pages C1–C1, fmi–fmvi, 2417–2698

  1. Cover

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
    1. You have free access to this content
      Biotechnology and Bioengineering: Volume 109, Number 10, October 2012 (page C1)

      Article first published online: 21 AUG 2012 | DOI: 10.1002/bit.24323

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      Cover Picture: Chemicals and materials currently derived from fossil oil through petroleum refineries can be produced through biorefineries by employing high-performance metabolically engineered microorganisms from various renewable biomass. (Image courtesy of Sang Yup Lee and Yu-Sin Jang at KAIST, Korea.)

  2. Contents

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
  3. Spotlights

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
  4. Editorial

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
    1. Elmer L. Gaden, Jr. Tribute (pages 2417–2421)

      Douglas S. Clark, Harvey W. Blanch, Daniel I.C. Wang, Arnold L. Demain, Christian Wandrey, Wei-Shou Hu, Jerome S. Schultz, Michael L. Shuler, Mike Hoare, Edwin N. Lightfoot, Arthur E. Humphrey, Jonathan S. Dordick and Juan A. Asenjo

      Article first published online: 21 AUG 2012 | DOI: 10.1002/bit.24610

  5. Reviews

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
    1. Biologically produced nanosilver: Current state and future perspectives (pages 2422–2436)

      Liesje Sintubin, Willy Verstraete and Nico Boon

      Article first published online: 27 JUN 2012 | DOI: 10.1002/bit.24570

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      The biological production of nanosilver is not only an eco-friendly process; it also creates nanoparticles with unique characteristics. Depending on the microorganism or plant used for the manufacturing process, nanoparticles can be designed such that they have properties which are suitable for specific applications. However, the implementation of biological nanoparticles is mainly an unexplored field due to the complicated large scale production. Therefore, the true challenge for biogenic silver is finding a balance between scalability, price and applicability.

    2. Bio-based production of C2–C6 platform chemicals (pages 2437–2459)

      Yu-Sin Jang, Byoungjin Kim, Jae Ho Shin, Yong Jun Choi, Sol Choi, Chan Woo Song, Joungmin Lee, Hye Gwon Park and Sang Yup Lee

      Article first published online: 13 JUL 2012 | DOI: 10.1002/bit.24599

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      Platform chemicals composed of 2–6 carbons derived from fossil resources are used as important precursors for making a variety of chemicals and materials. The techniques and strategies for developing microbial strains for these chemicals' production have advanced rapidly. In this study, the authors review the current status of the bio-based production of major C2–C6 platform chemicals, focusing on the microbial production of platform chemicals that have been used for the production of chemical intermediates, building block compounds, and polymers.

  6. Articles

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editorial
    6. Reviews
    7. Articles
    1. Biocatalysis, Protein Engineering, and Nanobiotechnology

      Chip-based protein–protein interaction studied by atomic force microscopy (pages 2460–2467)

      Feng-Sheng Kao, Waylon Ger, Yun-Ru Pan, Hui-Chen Yu, Ray-Quen Hsu and Hueih-Min Chen

      Article first published online: 26 APR 2012 | DOI: 10.1002/bit.24521

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      Efficient and targetable drug screening is established by protein-immobilization on chip via AFM detection. For example, unbinding force can directly be quantified (q1-q2) to indicate when candidate component (a blocker between CD28 and CD80) is captured by imm-CD28 and measured by afm-CD80. This set-up can be widely applied to other drugs' discovery.

    2. Biofuels and Environmental Biotechnology

      Continuous microalgae cultivation in a photobioreactor (pages 2468–2474)

      Haiying Tang, Meng Chen, K.Y. Simon Ng and Steven O. Salley

      Article first published online: 4 MAY 2012 | DOI: 10.1002/bit.24516

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      Chlorella minutissima continuous cultivation in a 3L photobioreactor was performed with continuous light of 50 µE/(m2 s) initial light intensity using white LEDs, and 4% CO2, at a temperature of 25°C. The maximum biomass and total FAME productivity were 137 mg/L/day and 6 mg/L/day at an optimal dilution rate of 0.328 day−1.

    3. The design of long-term effective uranium bioremediation strategy using a community metabolic model (pages 2475–2483)

      K. Zhuang, E. Ma, Derek R. Lovley and Radhakrishnan Mahadevan

      Article first published online: 26 APR 2012 | DOI: 10.1002/bit.24528

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      Previously, it has been shown that in situ uranium bioremediation is limited by the availability of Fe(III). Using a computational model of the subsurface community, which consist of Geobacter and sulfate-reducing bacteria, the authors demonstrate that the simultaneous addition of acetate and Fe(III) may be an effective strategy for uranium bioremediation. By connecting the model with an optimization framework, the authors were able to recommend a strategy that minimizes the cost of chemical addition.

    4. You have free access to this content
      Novel renewable ionic liquids as highly effective solvents for pretreatment of rice straw biomass by selective removal of lignin (pages 2484–2493)

      Xue-Dan Hou, Thomas J. Smith, Ning Li and Min-Hua Zong

      Article first published online: 25 APR 2012 | DOI: 10.1002/bit.24522

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      A series of renewable bio-ionic liquids (cholinium amino acids) have proven to be highly effective solvents for pretreatment of rice straw.

    5. Butyrate production enhancement by Clostridium tyrobutyricum using electron mediators and a cathodic electron donor (pages 2494–2502)

      Okkyoung Choi, Youngsoon Um and Byoung-In Sang

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24520

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      The electron flow altered NADH formation by electron mediators and by the cathodic electron donor, increasing the yield and selectivity of reduced end-products like butyrate. This is the first report to show the increase of butyric acid production by electrically driven acidogenesis.

    6. Multiplex fluorometric assessment of nutrient limitation as a strategy for enhanced lipid enrichment and harvesting of Neochloris oleoabundans (pages 2503–2512)

      Ryan W. Davis, Joanne V. Volponi, Howland D.T. Jones, Benjamin J. Carvalho, Huawen Wu and Seema Singh

      Article first published online: 30 APR 2012 | DOI: 10.1002/bit.24517

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      The combination of single-cell and population-based fluorometric studies revealed correlated dynamics among changes in lipid accumulation, lipid speciation, and cellular morphology as a result of nitrate limitation. The results suggest that actively imposed nitrate limitation during log-phase growth maximizes total lipid and elicits a membrane recycling mechanism involving direct exchange of membrane components between plastids and the endoplasmic reticulum. Furthermore, changes in cell size corresponding to lipid-enriched states may be exploited for selective and reduced energy harvesting.

    7. Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae (pages 2513–2522)

      Timothy C.R. Brennan, Christopher D. Turner, Jens O. Krömer and Lars K. Nielsen

      Article first published online: 28 MAY 2012 | DOI: 10.1002/bit.24536

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      Monoterpenes are olefins that can be used as immediate precursors for drop-in jet fuels. Microbial synthesis of monoterpenes is currently limited by product toxicity, as monoterpene compounds severely inhibit growth in E. coli and baker's yeast. This work provides an excellent strategy to alleviate monoterpene toxicity burdens by using a two-phase extraction system in-situ during fermentation. In particular, employing farnesene as the extractant, one can provide a terpene jet fuel blend that simplifies downstream processing steps and product recovery.

    8. Bioprocess Engineering and Supporting Technologies

      Controlling trisulfide modification in recombinant monoclonal antibody produced in fed-batch cell culture (pages 2523–2532)

      Rashmi Kshirsagar, Kyle McElearney, Alan Gilbert, Marty Sinacore and Thomas Ryll

      Article first published online: 9 APR 2012 | DOI: 10.1002/bit.24511

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      Trisulfide modification, insertion of a sulfur atom in the disulfide bonds at heavy-heavy and heavy-light junctions of a mAb, during fed-batch cell culture was investigated. Optimizing culture duration and feeding strategy resulted in more consistent trisulfide levels. Cysteine feeding correlated with trisulfide levels as it contributed hydrogen sulfide which reacted with the mAb in the supernatant forming a trisulfide bond. Optimizing the cysteine feeding strategy enabled consistent and low trisulfide modification.

    9. High-yield export of a native heterologous protein to the periplasm by the tat translocation pathway in Escherichia coli (pages 2533–2542)

      Cristina F.R.O. Matos, Steven D. Branston, Anna Albiniak, Arjun Dhanoya, Robert B. Freedman, Eli Keshavarz-Moore and Colin Robinson

      Article first published online: 11 MAY 2012 | DOI: 10.1002/bit.24535

    10. Different mechanisms of action of poly(ethylene glycol) and arginine on thermal inactivation of lysozyme and ribonuclease A (pages 2543–2552)

      Shunsuke Tomita, Yukio Nagasaki and Kentaro Shiraki

      Article first published online: 11 MAY 2012 | DOI: 10.1002/bit.24531

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      Poly(ethylene glycol) (PEG) with molecular weight 1,000 suppressed thermal inactivation of lysozyme and ribonuclease A, especially at higher protein concentrations, while arginine (Arg) suppressed, especially at lower protein concentrations. This difference suggests that PEG, but not Arg, effectively inhibited intermolecular disulfide exchange among thermally denatured proteins, indicating that the molecular mechanism of action of PEG is different from that of Arg.

    11. A novel environmental chamber for neuronal network multisite recordings (pages 2553–2566)

      E. Biffi, G. Regalia, D. Ghezzi, R. De Ceglia, A. Menegon, G. Ferrigno, G.B. Fiore and A. Pedrocchi

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24526

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      The authors describe the development and the experimental verification of a closed chamber for multisite electrophysiology and optical monitoring. The chamber provides stable temperature, pH, and humidity and guarantees cell viability comparable to standard incubators. It also integrates the electronics for long-term neuronal activity recording. This device is a solution for long-term electrophysiology, for dual network experiments and for coupled optical and electrical measurements.

    12. Photosynthetic efficiency of Chlamydomonas reinhardtii in attenuated, flashing light (pages 2567–2574)

      Carsten Vejrazka, Marcel Janssen, Mathieu Streefland and René H. Wijffels

      Article first published online: 1 MAY 2012 | DOI: 10.1002/bit.24525

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      The interaction of L/D cycle frequency, culture density and incident PFD play a role in overall PBR productivity. Appropriate L/D cycle setting by mixing strategy appears as a possible way to reduce the effect that dark zone exposure impinges on biomass yield in microalgae cultivation. The results may find application in optimization of outdoor PBR design to maximize biomass yields.

    13. Predictive models for transient protein expression in tobacco (Nicotiana tabacum L.) can optimize process time, yield, and downstream costs (pages 2575–2588)

      J.F. Buyel and R. Fischer

      Article first published online: 1 MAY 2012 | DOI: 10.1002/bit.24523

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      Predictive models for biomass production and recombinant protein expression in Nicotiana tabacum were generated using statistical experiment planning (design of experiments, DoE). The models were used to optimize cultivation conditions and to evaluate economic impact of these conditions on the production costs of a recombinant monoclonal antibody.

    14. Bioseparations and Downstream Processing

      Caprylic acid precipitation method for impurity reduction: An alternative to conventional chromatography for monoclonal antibody purification (pages 2589–2598)

      Yan Brodsky, Cheng Zhang, Yinges Yigzaw and Ganesh Vedantham

      Article first published online: 16 MAY 2012 | DOI: 10.1002/bit.24539

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      Precipitation of impurities with caprylic acid provides an alternative to a polishing chromatography step in mAb purification processes. It can be implemented in a bioreactor prior to cell separation or used to precipitate impurities after a protein A capture column. High throughput of the precipitation step along with complete xMuLV virus clearance and comparable host cell protein reduction to a polishing chromatography make this purification technique desirable for high titer cell culture processes.

    15. Cellular and Metabolic Engineering

      Development of a novel ER stress based selection system for the isolation of highly productive clones (pages 2599–2611)

      Lars Kober, Christoph Zehe and Juergen Bode

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24527

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      The novel selection system based on ER stress works as follows: Overexpression of secretory recombinant proteins (Step 1) causes GRP78 dissociation from various ER stress sensors (Step 2). Transcription factors (TF) are formed (simplified pathway shown in Step 3), the natural GRP78 promoter (Step 4) as well as an artificial d2eGFP Reporter construct (Step 5) is upregulated and high expressing clones can be identify and isolated by FACS.

    16. Engineering glyceraldehyde-3-phosphate dehydrogenase for switching control of glycolysis in Escherichia coli (pages 2612–2619)

      Han-Saem Cho, Sang Woo Seo, Young Mi Kim, Gyoo Yeol Jung and Jong Moon Park

      Article first published online: 17 MAY 2012 | DOI: 10.1002/bit.24532

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      Switching control of glycolysis is presented in response to a change in temperature. The directed evolution of gapA ensured the sensitive regulation of glycolysis. This system can help redirect carbon flux to achieve a desired phenotype.

    17. In silico assessment of cell-free systems (pages 2620–2629)

      Matthias Bujara and Sven Panke

      Article first published online: 2 MAY 2012 | DOI: 10.1002/bit.24534

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      The paper describes the adaptation of a genome-scale metabolic network to an in vitro batch reaction in order to analyze and propose insulation strategies for cascade reactions recruited from cell-free extracts. The scope of the method is illustrated by applying it to the production of dihydroxyacetone phosphate, an important building block for diasteroselective aldol reactions.

    18. Engineering Science of Biological Systems

      Rapid micropatterning of cell lines and human pluripotent stem cells on elastomeric membranes (pages 2630–2641)

      Isha Paik, David J. Scurr, Bryan Morris, Graham Hall, Chris Denning, Morgan R. Alexander, Kevin M. Shakesheff and James E. Dixon

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24529

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      Paik and coworkers describe a rapid method for patterning mammalian cells including human embryonic stem cells (HESCs) and induced pluripotent stem cells (iPSCs) on elastomeric membranes such that micron-scale control of cell position can be achieved over centimetre-length scales. Their method employs polymer surface engineering and aerosol deposition of extracellular matrix (ECM) proteins. The ability to rapidly pattern cells at high resolution over macro scales should aid future tissue engineering efforts for regenerative medicine applications.

    19. Correlation of thrombosis growth rate to pathological wall shear rate during platelet accumulation (pages 2642–2650)

      David L. Bark Jr., Andrea N. Para and David N. Ku

      Article first published online: 16 MAY 2012 | DOI: 10.1002/bit.24537

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      Local hemodynamics around platelet accumulation was studied to determine the relationship between wall shear rates (WSR) and platelet accumulation rates in an in vitro system that is used to simulate a range of shear rates that are expected to exist in a stenosed artery. A positive correlation exists at shear rates below 6,000 s−1 (P < 0.0001), with growth rates that remain higher for pathological shear rates reaching 100,000 s−1, relative to physiological shear rates below 400 s−1.

    20. pH, redox potential and local biofilm potential microenvironments within Geobacter sulfurreducens biofilms and their roles in electron transfer (pages 2651–2662)

      Jerome T. Babauta, Hung Duc Nguyen, Timothy D. Harrington, Ryan Renslow and Haluk Beyenal

      Article first published online: 11 MAY 2012 | DOI: 10.1002/bit.24538

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      The pH continues to decrease in the biofilm through different growth phases, showing that the pH is not always a limiting factor in the biofilm. The local biofilm potential value corresponds to the open circuit potential of graphite electrodes with attached G. sulfurreducens biofilms. Limitations on pH are imposed at the counter electrode surface as current increases. For the first time, the authors measured pH variations at the counter electrode and showed this directly.

    21. Fluorescent silica particles for monitoring oxygen levels in three-dimensional heterogeneous cellular structures (pages 2663–2670)

      Miguel A. Acosta, Melissa Velasquez, Katelyn Williams, Julia M. Ross and Jennie B. Leach

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24530

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      Oxygen availability to bacterium has been implicated in biofilm formation and planktonic cell detachment; however, insufficient tools have been available to measure oxygen in complex structures with ∼1 µm resolution. Herein, oxygen-sensing microparticles were designed to measure oxygen inside bacterial biofilms. Two fluorophores, oxygen-sensitive Ru(Ph2phen3)Cl2 and the reference fluorophore Nile blue chloride were immobilized on the surface of the particles. The authors demonstrate application of the microparticles towards measuring the oxygen concentration profiles in a live S. aureus biofilm.

    22. Tissue Engineering and Delivery Systems

      Chondroitin sulfate and dynamic loading alter chondrogenesis of human MSCs in PEG hydrogels (pages 2671–2682)

      Neven J. Steinmetz and Stephanie J. Bryant

      Article first published online: 24 APR 2012 | DOI: 10.1002/bit.24519

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      This work demonstrates the combined effects of biochemical and biomechanical cues in the regulation of chondrogenesis of human marrow stromal cells (hMSCs) using PEG and PEG/chondroitin sulfate hydrogels combined with dynamic compressive loading. While the 3D hydrogel environment enhanced the terminal differentiation of hMSCs, the presence of charge may slow the terminal differentiation process particularly when dynamic loading is applied.

    23. Disorganized collagen scaffold interferes with fibroblast mediated deposition of organized extracellular matrix in vitro (pages 2683–2698)

      Nima Saeidi, Xiaoqing Guo, Audrey E.K. Hutcheon, Edward A. Sander, Shyam Sundar Bale, Suzanna A. Melotti, James D. Zieske, Vickery Trinkaus-Randall and Jeffrey W. Ruberti

      Article first published online: 4 MAY 2012 | DOI: 10.1002/bit.24533

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      Very little is known about how fibroblasts control the organization of the matrix they deposit during the remodeling of implantable scaffolds. Given the proliferation of engineering and regenerative medicine approaches to tissue replacement, it is important to determine how fibroblasts interact with and modify the scaffold into which they have been seeded. With this investigation, the authors show that seeding primary human cells onto a disorganized collagen gel disrupts the ability of the fibroblast culture system to produce organized matrix.

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