Biotechnology and Bioengineering

Cover image for Vol. 109 Issue 4

April 2012

Volume 109, Issue 4

Pages C1–C1, fmi–fmvi, 853–1099

  1. Cover

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
    1. You have free access to this content
      Biotechnology and Bioengineering: Volume 109, Number 4, April 2012 (page C1)

      Version of Record online: 22 FEB 2012 | DOI: 10.1002/bit.24287

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      Cover Picture: “Confocal fluorescence image obtained by using the auto-fluorescence present in the intact plant cell walls of switchgrass. See related article by Singh et. al., Biotechnology and Bioengineering, Volume 104, Number 1 (September 1, 2009), pages 68–75.(Image courtesy of Dr. Seema Singh)”.

  2. Contents

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
  3. Spotlights

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
  4. Editors' Choices

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
    1. Editors' Choice

      Rational bioprocess design for human pluripotent stem cell expansion and endoderm differentiation based on cellular dynamics (pages 853–866)

      Mark D. Ungrin, Geoff Clarke, Ting Yin, Sylvia Niebrugge, M. Cristina Nostro, Farida Sarangi, Geoffrey Wood, Gordon Keller and Peter W. Zandstra

      Version of Record online: 2 DEC 2011 | DOI: 10.1002/bit.24375

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      The authors combine quantitative assessment of process inefficiencies during differentiation of pluripotent stem cells towards definitive endoderm fate with investigations of the underlying cellular mechanisms and new technologies for aggregate size control. This has resulted in an improved understanding of the biological foundations of this process, a thirty-six fold increase in yield of target cells, and a generalizable template for future study and optimization of pluripotent stem cell differentiation bioprocesses.

  5. Articles

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
    1. Biocatalysis, Protein Engineering, and Nanobiotechnology

      Development of thermostable Candida antarctica lipase B through novel in silico design of disulfide bridge (pages 867–876)

      Quang Anh Tuan Le, Jeong Chan Joo, Young Je Yoo and Yong Hwan Kim

      Version of Record online: 22 NOV 2011 | DOI: 10.1002/bit.24371

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      Two computational tools (MODIP; DbD) have been widely used to predict residue pairs for possible disulfide bonds. The authors proposed an effective and easy method to select promising residue pairs based on residue flexibility analysis to improve thermostability of a versatile biocatalyst, Candida antarctica lipase B (CalB) remarkably. Flexibility analysis includes the residue flexibility of CalB wild type and flexibility changes caused by newly introduced disulfide bonds in CalB mutants.

    2. Biofuels and Environmental Biotechnology

      Detection of biological uranium reduction using magnetic resonance (pages 877–883)

      Sarah J. Vogt, Brandy D. Stewart, Joseph D. Seymour, Brent M. Peyton and Sarah L. Codd

      Version of Record online: 24 NOV 2011 | DOI: 10.1002/bit.24369

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      The conversion of soluble uranyl ions (UOmath image) by bacterial reduction to sparingly soluble uraninite(UO2(s)) is being studied as a way of immobilizing subsurfaceuranium contamination. Experiments using a suspension of uraninite (UO2(s)) particles produced by Shewanella putrefaciens CN32 bacteria show a dependence of (MR) relaxation times on theoxidation state and solubility of the uranium. Gradientecho MR images (see figure) show image contrast due to increased presence of UO2(s) particles produced during bacterial reduction.

    3. Degradation of reactive dyes in a photocatalytic circulating-bed biofilm reactor (pages 884–893)

      Guozheng Li, Seongjun Park and Bruce E. Rittmann

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24366

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      Biorecalcitrant Reactive Black 5 was decolorized and mineralized by Intimately Coupled Photocatalysis and Biodegradation (ICPB) on TiO2-coated biofilm carriers in a Photocatalytic Circulating-Bed Biofilm Reactor (PCBBR). In ICPB, biofilm bacteria growing inside the macroporous carrier, protected from the harsh photocatalytic environment, mineralizes the biodegradable products generated by photocatalysis.

    4. Using FTIR spectroscopy to model alkaline pretreatment and enzymatic saccharification of six lignocellulosic biomasses (pages 894–903)

      Deborah L. Sills and James M. Gossett

      Version of Record online: 22 NOV 2011 | DOI: 10.1002/bit.24376

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      PLS regression models applied to FTIR spectra accurately predicted overall sugar conversions (g sugar per 100 g potential sugar) and yields (g sugar per 100 g dry solids) from pretreatment and enzymatic hydrolysis of six plant biomasses (two switchgrass cultivars, big bluestem grass, a mixture of prairie biomasses, mixed hardwood, and corn stover). The sugar yield models are noteworthy for their ability to predict overall saccharification per mass dry untreated solids without a priori knowledge of the composition of solids.

    5. Gallionella spp. in trickling filtration of subsurface aerated and natural groundwater (pages 904–912)

      W.W.J.M. de Vet, I.J.T. Dinkla, B.A. Abbas, L.C. Rietveld and M.C.M. van Loosdrecht

      Version of Record online: 2 DEC 2011 | DOI: 10.1002/bit.24378

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      Strong Gallionella growth during subsurface aeration and groundwater trickling filtration for drinking water production is presented. Inhibition of Gallionella occurs in the filter treating subsurface aerated groundwater.

    6. You have free access to this content
      Prolonged conversion of n-butyrate to n-butanol with Clostridium saccharoperbutylacetonicum in a two-stage continuous culture with in-situ product removal (pages 913–921)

      Hanno Richter, Nasib Qureshi, Sebastian Heger, Bruce Dien, Michael A. Cotta and Largus T. Angenent

      Version of Record online: 7 DEC 2011 | DOI: 10.1002/bit.24380

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      This study illustrates that efficient conversion of n-butyrate into n-butanol by solventogenic Clostridium species is feasible in a continuous system operating for longer than one month. However, a relatively large amount of glucose is required to supply electrons and ATP for this conversion and for cell growth in continuous culture.

    7. Scale-up and integration of alkaline hydrogen peroxide pretreatment, enzymatic hydrolysis, and ethanolic fermentation (pages 922–931)

      Goutami Banerjee, Suzana Car, Tongjun Liu, Daniel L. Williams, Sarynna López Meza, Jonathan D. Walton and David B. Hodge

      Version of Record online: 13 DEC 2011 | DOI: 10.1002/bit.24385

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      Alkaline hydrogen peroxide (AHP) pretreatment is performed in an inexpensive plastic container at room temperature and atmospheric pressure. On the left is shown corn stover at 15% solids loading after 48 h treatment with 12.5% hydrogen peroxide at pH 11.5. After AHP, enzyme hydrolysis is performed in the same container with no biomass washing or transfer. On the right is shown the appearance of the material after 48-h enzymatic hydrolysis.

    8. Bioprocess Engineering and Supporting Technologies

      Airlift column photobioreactors for Porphyridium sp. culturing: Part I. effects of hydrodynamics and reactor geometry (pages 932–941)

      Hu-Ping Luo and Muthanna H. Al-Dahhan

      Version of Record online: 23 NOV 2011 | DOI: 10.1002/bit.24361

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      The research by Luo and Al-Dahhan discovered that Porphyridium sp. effectively turned the culture medium (a dilute aqueous solution) into a shear thinning fluid and significantly affected the flow dynamics in photobioreactors resulting in a larger static wall region and considerably higher turbulent and gas holdup in the reactor. Consequently, the spiral flow pattern in the split column photobioreactor is able to enhance the reactor performance by moving cells in and out of the highly illuminated wall region more frequently.

    9. Airlift column photobioreactors for Porphyridium sp. culturing: Part II. verification of dynamic growth rate model for reactor performance evaluation (pages 942–949)

      Hu-Ping Luo and Muthanna H. Al-Dahhan

      Version of Record online: 23 NOV 2011 | DOI: 10.1002/bit.24362

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      The authors used data from the literature and part I of this work to rigorously verify the dynamic growth rate model developed in earlier studies for photobioreactor performance evaluation based on first principles of photosynthesis. This model successfully predicted the algae's growth in both low and high irradiance regimes when reliable hydrodynamic, irradiance, and photosynthesis kinetic data were used. The simulation results also revealed the significant difference in hydrodynamics between real culturing systems and air-water systems.

    10. Evaluation of the energy efficiency of enzyme fermentation by mechanistic modeling (pages 950–961)

      Mads O. Albaek, Krist V. Gernaey, Morten S. Hansen and Stuart M. Stocks

      Version of Record online: 21 DEC 2011 | DOI: 10.1002/bit.24364

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      A mechanistic model is used to evaluate the energy efficiency of cellulase production by Trichoderma reesei in pilot plant stirred tank reactors. The central part of the model is an oxygen mass transfer correlation, which is coupled to fungal growth by a viscosity prediction. The simulations confirm the inverse relationship between productivity and efficiency of the process.

    11. Bioseparations and Downstream Processing

      Single pass tangential flow filtration to debottleneck downstream processing for therapeutic antibody production (pages 962–970)

      Jemelle Dizon-Maspat, Justin Bourret, Anna D'Agostini and Feng Li

      Version of Record online: 7 DEC 2011 | DOI: 10.1002/bit.24377

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      Single Pass Tangential Flow Filtration (SPTFF) is an emerging technology, which is potentially useful in debottlenecking downstream capacity, especially when the pool tank size is a limiting factor. In this study, SPTFF technology was systematically evaluated for reducing process intermediate volumes from 2× to 10× with multiple mAbs and the impact of SPTFF on product quality, and process yield was analyzed.

    12. Host cell protein dynamics in the supernatant of a mAb producing CHO cell line (pages 971–982)

      A.S. Tait, C.E.M. Hogwood, C.M. Smales and D.G. Bracewell

      Version of Record online: 12 DEC 2011 | DOI: 10.1002/bit.24383

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      The dynamics of the host cell protein (HCP) profile towards the end of fed-batch culture are investigated and show how this is a dynamic process that changes with harvest time. The authors' data suggests that the majority of HCPs in the supernatant of the cell lines investigated here arise through lysis or breakage of cells, associated with loss in viability, and are not present due to the secretion of protein material from within the cell.

    13. Investigation of the impact of Tat export pathway enhancement on E. coli culture, protein production and early stage recovery (pages 983–991)

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

      Version of Record online: 12 DEC 2011 | DOI: 10.1002/bit.24384

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      The E. coli Tat pathway has the potential to export commercially useful proteins. Uniquely, it exports folded proteins, but its native capacity is low. This article studies the fermentation and downstream processing performances of E. coli strains engineered to over-express the Tat pathway to remove this bottleneck. Fermentation experimentation showed increased growth and periplasmic protein in engineered strains. An ultra scale-down approach used to predict robustness and clarification behavior showed this was achieved with no compromise in downstream processing performance.

    14. Cellular and Metabolic Engineering

      Metabolic oligosaccharide engineering with N-Acyl functionalized ManNAc analogs: Cytotoxicity, metabolic flux, and glycan-display considerations (pages 992–1006)

      Ruben T. Almaraz, Udayanath Aich, Hargun S. Khanna, Elaine Tan, Rahul Bhattacharya, Shivam Shah and Kevin J. Yarema

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24363

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      Per-acetylated N-azido-mannosamine (Ac4ManNAz) is a widely used metabolic substrate for labeling sialic acids in living cells and animals. In this work the authors show that n-butanoylated ManNAz can achieve higher flux through the sialic acid biosynthetic pathway and highlight structure-activity relationships where tributanoylated analog with the “3,4,6” pattern of butyrate derivation is highly toxic while the corresponding “1,3,4” analog has negligible toxicity and thus serves as an optimal molecular tool for incorporating azide groups into cellular sialoglycans.

    15. Improving the efficiency of CHO cell line generation using glutamine synthetase gene knockout cells (pages 1007–1015)

      Lianchun Fan, Ibrahim Kadura, Lara E. Krebs, Christopher C. Hatfield, Margaret M. Shaw and Christopher C. Frye

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24365

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      A more stringent selection condition has been achieved through knockout of the glutamine synthetase gene in CHO cells, which resulted in both significant improvement on bulk culture productivity (monoclonal antibody) and extremely high efficiency for the identification of highly productive clonal cell lines for clinical cell line development.

    16. Early prediction of instability of chinese hamster ovary cell lines expressing recombinant antibodies and antibody-fusion proteins (pages 1016–1030)

      Haimanti Dorai, Susanne Corisdeo, Dawn Ellis, Cherylann Kinney, Matt Chomo, Pam Hawley-Nelson, Gordon Moore, Michael J. Betenbaugh and Subinay Ganguly

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/bit.24367

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      A significant proportion of the GS-selected CHO production cell lines were observed to be unstable. Reduced antibody titers correlated with the gradual appearance of a secondary, less productive population of cells as detected with flow cytometric analysis of intracellular antibody content. Where tested, it was observed that the secondary population arose spontaneously from the parental population following multiple passages, which suggested inherent clonal instability. This knowledge has been used to develop screening protocols that identify unstable CHO production cell lines at an early stage of the cell line development process, potentially reducing the cost of biotherapeutic development.

    17. Engineering Science of Biological Systems

      The effect of biofilm permeability on bio-clogging of porous media (pages 1031–1042)

      Thomas R.R. Pintelon, Cristian Picioreanu, Mark C.M. van Loosdrecht and Michael L. Johns

      Version of Record online: 12 DEC 2011 | DOI: 10.1002/bit.24381

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      2D slices from a 3D lattice for simulations of biofilm (shown in green) growth on a random porous medium (shown in black). The LHS shows an impermeable biofilm, the RHS shows a permeable biofilm at the same time point grown under otherwise identical conditions. The effect of considering biofilm permeability on growth rate is stark. Color-scale indicates the local velocity field.

    18. Synthetic Biology

      Multigene expression in vivo: Supremacy of large versus small terminators for T7 RNA polymerase (pages 1043–1050)

      Liping Du, Seth Villarreal and Anthony C. Forster

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/bit.24379

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      In vivo supremacy of large versus small terminators for T7 RNA polymerase revealed by insertion between two genes in a bicistron is described.

    19. Tissue Engineering and Delivery Systems

      Controlled release of IGF-I from a biodegradable matrix improves functional recovery of skeletal muscle from ischemia/reperfusion (pages 1051–1059)

      David W. Hammers, Apurva Sarathy, Chantal B. Pham, Charles T. Drinnan, Roger P. Farrar and Laura J. Suggs

      Version of Record online: 1 DEC 2011 | DOI: 10.1002/bit.24382

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      Polyethylene glycol (PEG)-ylated fibrin gel (PEG-Fib) is a biodegradable matrix capable of releasing covalently-bound growth factors in a controlled manner. In this study, IGF-I conjugated PEG-Fib (PEG-Fib-IGF) was evaluated as a therapeutic approach for the treatment of skeletal muscle ischemia/reperfusion (I/R) injury. The authors found that PEG-Fib-IGF greatly improves both the histological and functional recovery of skeletal muscle from I/R, and that this improvement is likely due to increased survival of affected muscle tissue.

    20. Tissue engineering of cartilage using a mechanobioreactor exerting simultaneous mechanical shear and compression to simulate the rolling action of articular joints (pages 1060–1073)

      Kifah Shahin and Pauline M. Doran

      Version of Record online: 22 DEC 2011 | DOI: 10.1002/bit.24372

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      A novel mechanobioreactor was used to apply simultaneous dynamic mechanical shear and compression during synthesis of human tissue-engineered cartilage in a mixed fluid environment. A treatment regime of 10 min loading per day improved the quality of the tissues substantially compared with control cultures. Synthesis of both major structural components of cartilage, glycosaminoglycan and collagen type II, was enhanced by up to an order of magnitude depending on the scaffold type and seeding cell density.

    21. Combinatorial insulin secretion dynamics of recombinant hepatic and enteroendocrine cells (pages 1074–1082)

      Kiranmai Durvasula, Peter M. Thulé and Athanassios Sambanis

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24373

  6. Communications to the Editor

    1. Top of page
    2. Cover
    3. Contents
    4. Spotlights
    5. Editors' Choices
    6. Articles
    7. Communications to the Editor
    1. Biofuels and Environmental Biotechnology

      The challenge of enzyme cost in the production of lignocellulosic biofuels (pages 1083–1087)

      Daniel Klein-Marcuschamer, Piotr Oleskowicz-Popiel, Blake A. Simmons and Harvey W. Blanch

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24370

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      The cost contribution of enzymes to the production of lignocellulosic biofuels has been widely debated. By modeling the production of cellulolytic enzymes and analyzing the technical and economic performance of the process, the authors estimated their cost. Furthermore, using information about enzyme use in typical biorefinery processes, the authors were able to determine the contribution of enzymes to the total cost of production of lignocellulosic ethanol. The authors concluded that this contribution is much higher than estimates given in the literature.

    2. Simultaneous hydrogen utilization and in situ biogas upgrading in an anaerobic reactor (pages 1088–1094)

      Gang Luo, Sara Johansson, Kanokwan Boe, Li Xie, Qi Zhou and Irini Angelidaki

      Version of Record online: 21 NOV 2011 | DOI: 10.1002/bit.24360

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      This paper proposes an innovative method for in-situ biogas upgrading by the addition of hydrogen to the anaerobic reactor. Hydrogen can be obtained by water electrolysis using the surplus electricity from a wind mill.

    3. Tissue Engineering and Delivery Systems

      Modeling and design of optimal flow perfusion bioreactors for tissue engineering applications (pages 1095–1099)

      L. Araida Hidalgo-Bastida, Sundaramoorthy Thirunavukkarasu, Sarah Griffiths, Sarah H. Cartmell and Shailesh Naire

      Version of Record online: 22 NOV 2011 | DOI: 10.1002/bit.24368

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      The focus of this communication is to design an optimized perfusion bioreactor system for tissue engineering applications using CFD. Fluid flow within a circular and a rectangular bioreactor system are compared. Fluid flow simulations within the rectangular bioreactor are shown to overcome the limitations in the circular design. This communication challenges the commonly used circular cross-section bioreactor configuration paradigm and provides proof of the advantages of the new design over the existing one.

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