Biotechnology Journal

Cover image for Vol. 7 Issue 3

Special Issue: Frontiers in Biochemical Engineering

March 2012

Volume 7, Issue 3

Pages 313–462, A1–A8

  1. Cover Picture

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    4. Editorial Board
    5. Editorial
    6. In this issue
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    8. BiotecVisions
    9. Forum
    10. Commentaries
    11. Reviews
    12. Rapid Communication
    13. Research Articles
    14. Meetings
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      Frontiers in Biochemical Engineering

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201290011

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      Frontiers in Biochemical Engineering. This issue of Biotechnology Journal is dedicated to Professor Michael Shuler of Cornell University in honor of his seminal research contributions and his pivotal role in the establishment and growth of biochemical engineering.

      The cover image is an artist's depiction of a Saccharomyces cerevisiae cell consuming cellobiose and xylose (center) and cellulase enzymes catalyzing the hydrolysis of cellulose (lower left). In a scenario in which cellulose hydrolysis is carried out alongside hexose and pentose co-fermentation, the engineered yeast strain may prevent cellobiose inhibition of cellulase enzymes while reducing glucose inhibition of xylose uptake.

      Image by: Jerome Fox

      Read the article by Fox et al. http://dx.doi.org/10.1002/biot.201100209

  2. Inside Cover

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    4. Editorial Board
    5. Editorial
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    11. Reviews
    12. Rapid Communication
    13. Research Articles
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      Inside Cover: Biotechnology Journal 3/2012

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201290017

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      Metabolic network modeling and simulation present an effective approach for drug targeting and discovery. The cover image shows a bacterial cell in the center of its metabolic network in a circular layout. Surrounding molecules are possible target drugs.

      Read the article by Kim et al. http://dx.doi.org/10.1002/biot.201100159.

      Image by: Hyun Uk Kim

  3. Editorial Board

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    4. Editorial Board
    5. Editorial
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    11. Reviews
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    14. Meetings
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  4. Editorial

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      Editorial: Michael Shuler's legacy in biochemical engineering (pages 314–316)

      Prof. George Georgiou and Prof. Sang Yup Lee

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201290012

  5. In this issue

    1. Top of page
    2. Cover Picture
    3. Inside Cover
    4. Editorial Board
    5. Editorial
    6. In this issue
    7. Contents
    8. BiotecVisions
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    11. Reviews
    12. Rapid Communication
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      In this issue (page 318)

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201290013

  6. Contents

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    2. Cover Picture
    3. Inside Cover
    4. Editorial Board
    5. Editorial
    6. In this issue
    7. Contents
    8. BiotecVisions
    9. Forum
    10. Commentaries
    11. Reviews
    12. Rapid Communication
    13. Research Articles
    14. Meetings
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  7. BiotecVisions

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    5. Editorial
    6. In this issue
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    8. BiotecVisions
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  8. Forum

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  9. Commentaries

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      A ribosomal surprise (pages 326–327)

      Prof. François Baneyx

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201100488

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      Ribosomes not only decode mRNAs and stitch amino acids together, they also control early protein folding events. This commentary discusses the work of Contreras-Martin et al. (DOI: 10.1002/biot.201100198), which shows that the ribosomal tunnel exit protein L29 exerts a pronounced influence on the production of T7-transcribed gene products.

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      Model-guided strain improvement: Simultaneous hydrolysis and co-fermentation of cellulosic sugars (pages 328–329)

      Dr. Yong-Su Jin and Dr. Jamie H. D. Cate

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201100489

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      Despite tremendous effort, no economical production of ethanol from the abundant plant biomass in plant cell walls has yet been implemented. Two factors are needed for this to become a reality: the economic saccharification of recalcitrant plant cell walls and the efficient fermentation of mixed sugars (glucose and xylose) that are prevalent in cellulosic hydrolysates. Yong-Su Jin and Jamie Cate comment on the latest study from Doug Clark's group, which provides a comprehensive model of cellulose hydrolysis and fermentation of prevalent sugars in lignocellulosic hydrolysates.

  10. Reviews

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    1. Metabolic network modeling and simulation for drug targeting and discovery (pages 330–342)

      Hyun Uk Kim, Seung Bum Sohn and Prof. Sang Yup Lee

      Version of Record online: 29 NOV 2011 | DOI: 10.1002/biot.201100159

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      Metabolic network modeling and simulation have emerged as an effective approach for drug targeting and discovery: this review focuses on specific applications of genome-scale metabolic networks in drug targeting for both microbial pathogens and several human diseases, and discusses future research directions.

    2. Metabolic ensemble modeling for strain engineers (pages 343–353)

      Yikun Tan and Prof. James C. Liao

      Version of Record online: 21 OCT 2011 | DOI: 10.1002/biot.201100186

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      Previous mathematical modeling efforts have made significant contributions to the development of systems biology for predicting biological behavior quantitatively; however, dynamic metabolic model construction remains challenging due to uncertainties in mechanistic structures and parameters. In this review, the authors focus on approaches that utilize readily available fermentation data for parameter screening and model validation. This metabolic ensemble modeling approach, has been shown to be useful in designing Escherichia coli strains.

  11. Rapid Communication

    1. Top of page
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    1. You have full text access to this OnlineOpen article
      The ribosomal exit tunnel as a target for optimizing protein expression in Escherichia coli (pages 354–360)

      Lydia M. Contreras-Martinez, Jason T. Boock, Jan S. Kostecki and Prof. Matthew P. DeLisa

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201100198

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      Production of recombinant proteins has broad implications in various disciplines, including biotechnology and biopharmaceuticals. The current study provides support for the notion that the ribosomal exit tunnel is not simply a static conduit for newly made proteins but rather a dynamic channel that is intimately involved in the production of cellular proteins. The improved knowledge of how exit tunnel proteins contribute to protein expression and folding could be key in the context of rationally engineering bacterial translation for efficient production of active, structurally complex proteins.

  12. Research Articles

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    1. An evaluation of cellulose saccharification and fermentation with an engineered Saccharomyces cerevisiae capable of cellobiose and xylose utilization (pages 361–373)

      Jerome M. Fox, Seth E. Levine, Dr. Harvey W. Blanch and Prof. Douglas S. Clark

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201100209

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      Commercial-scale cellulosic ethanol production has been hindered by high costs associated with cellulose-to-glucose conversion and hexose/pentose co-fermentation. Simultaneous saccharification and fermentation (SSF) with a yeast strain capable of co-utilizing xylose and cellobiose has been proposed as a possible avenue to reduce these costs. In this study, we investigated the ability of cellobiose-consuming strains to obviate the need for exogenously added β-glucosidase in the cellulose hydrolysis step, and to assess the impact of cellobiose utilization on SSF and separate hydrolysis and fermentation (SHF) processes where xylose is additionally present.

    2. You have full text access to this OnlineOpen article
      Querying quantitative logic models (Q2LM) to study intracellular signaling networks and cell-cytokine interactions (pages 374–386)

      Melody K. Morris, Zachary Shriver, Ram Sasisekharan and Dr. Douglas A. Lauffenburger

      Version of Record online: 10 JAN 2012 | DOI: 10.1002/biot.201100222

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      Querying Quantitative Logic Models (Q2LM) to study intracellular signaling networks and cell/cytokine interactions: The authors present a framework for building and asking questions of constrained fuzzy logic (cFL) models constructed based on prior knowledge. We demonstrate the utility of this framework for generating testable hypotheses in an intracellular signaling network model and a model for pharmacokinetics and pharmacodynamics of G-CSF.

    3. Screening of cell-penetrating peptides using mRNA display (pages 387–396)

      Jae-Hun Lee, Hyun Seok Song, Sun-Gu Lee, Tae Hyun Park and Prof. Byung-Gee Kim

      Version of Record online: 16 DEC 2011 | DOI: 10.1002/biot.201100220

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      Drug delivery into the cell has been a major challenge for researchers in both academia and the pharmaceutical industry. Cell-penetrating peptides (CPPs) offer an attractive solution to this problem. In this article, the authors demonstrate that CPPs can be screened by mRNA display using a model cell line and also how this process can be applied to other target cell lines.

      Corrected by:

      Correction: Correction to: Screening of cell-penetrating peptides using mRNA display

      Vol. 7, Issue 6, 823, Version of Record online: 1 JUN 2012

    4. Biochemical and mechanical extracellular matrix properties dictate mammary epithelial cell motility and assembly (pages 397–408)

      Olga Shebanova and Dr. Daniel A. Hammer

      Version of Record online: 16 DEC 2011 | DOI: 10.1002/biot.201100188

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      Understanding cell migration and cell-cell interactions are key to understanding cell invasion, a critical step in the progression of breast cancer. In this study, the authors show that the migration velocity and the assembly of breast cancer epithelial cells is optimal at intermediate concentrations of fibronectin concentration and substrate compliance. On low compliance polyacrylamide gels (400 Pa), cells assemble into clusters, whereas on stiffer gels, cells remain dispersed.

    5. You have full text access to this OnlineOpen article
      Optimization of endothelial cell growth in a murine in vitro blood–brain barrier model (pages 409–417)

      Diane M. Wuest and Prof. Kelvin H. Lee

      Version of Record online: 28 DEC 2011 | DOI: 10.1002/biot.201100189

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      In vitro cell culture models of the blood-brain barrier (BBB) are important tools used to study cellular physiology and brain disease therapeutics. While many models exist, it is not clear whether any of these have been effectively optimized. The current work presents a sequential-screening study to optimize the culture conditions of an in vitro model of the blood-brain barrier.

    6. Contribution of taxane biosynthetic pathway gene expression to observed variability in paclitaxel accumulation in Taxus suspension cultures (pages 418–427)

      Rohan A. Patil, Martin E. Kolewe, Jennifer Normanly, Elsbeth L. Walker and Dr. Susan C. Roberts

      Version of Record online: 10 JAN 2012 | DOI: 10.1002/biot.201100183

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      Paclitaxel is a chemotherapeutic agent used for the treatment of several cancer types. Although plant cells cultures have variable productivity, it has nevertheless become a sustainable source of paclitaxel supply. In this article, the authors correlate gene expression levels to accumulation of the compound – it is the first study to compare gene expression in cultures with variable levels of paclitaxel accumulation, providing valuable information regarding the regulation of paclitaxel synthesis.

    7. Integrated biofabrication for electro-addressed in-film bioprocessing (pages 428–439)

      Jessica L. Terrell, Tanya Gordonov, Yi Cheng, Hsuan-Chen Wu, Darryl Sampey, Xiaolong Luo, Chen-Yu Tsao, Reza Ghodssi, Gary W. Rubloff, Gregory F. Payne and Dr. William E. Bentley

      Version of Record online: 24 JAN 2012 | DOI: 10.1002/biot.201100181

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      Many recent advances in bioprocessing have been enabled by developments in miniaturization and microfluidics. A continuing challenge, however, is integrating multiple unit operations that require distinct spatial boundaries, especially with included labile biological components. In this article, the authors demonstrate “in-film” bioprocessing, which has diverse application potential such as in drug screening and biopsy analysis.

    8. Enhanced growth and hepatic differentiation of fetal liver epithelial cells through combinational and temporal adjustment of soluble factors (pages 440–448)

      Lichuan Qian, Diane S. Krause and Dr. W. Mark Saltzman

      Version of Record online: 26 OCT 2011 | DOI: 10.1002/biot.201100184

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      Fetal liver epithelial cells (FLEC) are valuable for liver cell therapy and tissue engineering, but there are major challenges in developing culture media that support concurrent growth and maturation. In this work, the authors explore the optimal media formulation to support FLEC proliferation and hepatic differentiation, with the long-term goal of developing an optimal culture system to generate functional liver tissue. Their findings serve to advance culture methods for liver progenitors in cell therapy and tissue engineering applications.

    9. Use of flux pre-analysis to enable 13C tracer studies in pyruvate kinase-deficient Escherichia coli (pages 449–460)

      Jonathan Meade, Saleem Khan, Mohammad Ataai and Michael Domach

      Version of Record online: 2 MAR 2012 | DOI: 10.1002/biot.201100338

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      Pyruvate kinase-deficient Escherichia coli (PB25) is a low by-product producing yet fast growing strain that has been shown to have technological potential. Flux bounding through finding the extreme point flux sets was previously reported to identify highly variable fluxes and thus alternate metabolite trafficking scenarios. In this study, the authors examine the utility of bounding the fluxes and predetermine the trafficking scenarios in the PB25 problem.

  13. Meetings

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    2. Cover Picture
    3. Inside Cover
    4. Editorial Board
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    7. Contents
    8. BiotecVisions
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    10. Commentaries
    11. Reviews
    12. Rapid Communication
    13. Research Articles
    14. Meetings
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