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Bioengineering, Volume 3, Issue 1 (March 2016) – 10 articles

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1571 KiB  
Article
Construction and Experimental Validation of a Quantitative Kinetic Model of Nitric Oxide Stress in Enterohemorrhagic Escherichia coli O157:H7
by Jonathan L. Robinson and Mark P. Brynildsen
Bioengineering 2016, 3(1), 9; https://doi.org/10.3390/bioengineering3010009 - 06 Feb 2016
Cited by 259 | Viewed by 6285
Abstract
Enterohemorrhagic Escherichia coli (EHEC) are responsible for large outbreaks of hemorrhagic colitis, which can progress to life-threatening hemolytic uremic syndrome (HUS) due to the release of Shiga-like toxins (Stx). The presence of a functional nitric oxide (NO·) reductase (NorV), which protects EHEC from [...] Read more.
Enterohemorrhagic Escherichia coli (EHEC) are responsible for large outbreaks of hemorrhagic colitis, which can progress to life-threatening hemolytic uremic syndrome (HUS) due to the release of Shiga-like toxins (Stx). The presence of a functional nitric oxide (NO·) reductase (NorV), which protects EHEC from NO· produced by immune cells, was previously found to correlate with high HUS incidence, and it was shown that NorV activity enabled prolonged EHEC survival and increased Stx production within macrophages. To enable quantitative study of EHEC NO· defenses and facilitate the development of NO·-potentiating therapeutics, we translated an existing kinetic model of the E. coli K-12 NO· response to an EHEC O157:H7 strain. To do this, we trained uncertain model parameters on measurements of [NO·] and [O2] in EHEC cultures, assessed parametric and prediction uncertainty with the use of a Markov chain Monte Carlo approach, and confirmed the predictive accuracy of the model with experimental data from genetic mutants lacking NorV or Hmp (NO· dioxygenase). Collectively, these results establish a methodology for the translation of quantitative models of NO· stress in model organisms to pathogenic sub-species, which is a critical step toward the application of these models for the study of infectious disease. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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680 KiB  
Review
Metabolic Engineering Strategies for Co-Utilization of Carbon Sources in Microbes
by Yifei Wu, Xiaolin Shen, Qipeng Yuan and Yajun Yan
Bioengineering 2016, 3(1), 10; https://doi.org/10.3390/bioengineering3010010 - 06 Feb 2016
Cited by 259 | Viewed by 9201
Abstract
Co-utilization of carbon sources in microbes is an important topic in metabolic engineering research. It is not only a way to reduce microbial production costs but also an attempt for either improving the yields of target products or decreasing the formation of byproducts. [...] Read more.
Co-utilization of carbon sources in microbes is an important topic in metabolic engineering research. It is not only a way to reduce microbial production costs but also an attempt for either improving the yields of target products or decreasing the formation of byproducts. However, there are barriers in co-utilization of carbon sources in microbes, such as carbon catabolite repression. To overcome the barriers, different metabolic engineering strategies have been developed, such as inactivation of the phosphotransferase system and rewiring carbon assimilation pathways. This review summarizes the most recent developments of different strategies that support microbes to utilize two or more carbon sources simultaneously. The main content focuses on the co-utilization of glucose and pentoses, major sugars in lignocellulose. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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628 KiB  
Editorial
Acknowledgement to Reviewers of Bioenginering in 2015
by Bioengineering Editorial Office
Bioengineering 2016, 3(1), 8; https://doi.org/10.3390/bioengineering3010008 - 28 Jan 2016
Cited by 27 | Viewed by 3489
Abstract
The editors of Bioengineering would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2015. [...] Full article
3080 KiB  
Article
DNA and RNA Extraction and Quantitative Real-Time PCR-Based Assays for Biogas Biocenoses in an Interlaboratory Comparison
by Michael Lebuhn, Jaqueline Derenkó, Antje Rademacher, Susanne Helbig, Bernhard Munk, Alexander Pechtl, Yvonne Stolze, Steffen Prowe, Wolfgang H. Schwarz, Andreas Schlüter, Wolfgang Liebl and Michael Klocke
Bioengineering 2016, 3(1), 7; https://doi.org/10.3390/bioengineering3010007 - 13 Jan 2016
Cited by 56 | Viewed by 13079
Abstract
Five institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on [...] Read more.
Five institutional partners participated in an interlaboratory comparison of nucleic acid extraction, RNA preservation and quantitative Real-Time PCR (qPCR) based assays for biogas biocenoses derived from different grass silage digesting laboratory and pilot scale fermenters. A kit format DNA extraction system based on physical and chemical lysis with excellent extraction efficiency yielded highly reproducible results among the partners and clearly outperformed a traditional CTAB/chloroform/isoamylalcohol based method. Analytical purpose, sample texture, consistency and upstream pretreatment steps determine the modifications that should be applied to achieve maximum efficiency in the trade-off between extract purity and nucleic acid recovery rate. RNA extraction was much more variable, and the destination of the extract determines the method to be used. RNA stabilization with quaternary ammonium salts was an as satisfactory approach as flash freezing in liquid N2. Due to co-eluted impurities, spectrophotometry proved to be of limited value for nucleic acid qualification and quantification in extracts obtained with the kit, and picoGreen® based quantification was more trustworthy. Absorbance at 230 nm can be extremely high in the presence of certain chaotropic guanidine salts, but guanidinium isothiocyanate does not affect (q)PCR. Absolute quantification by qPCR requires application of a reliable internal standard for which correct PCR efficiency and Y-intercept values are important and must be reported. Full article
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703 KiB  
Review
Controlling Arteriogenesis and Mast Cells Are Central to Bioengineering Solutions for Critical Bone Defect Repair Using Allografts
by Ben Antebi, Longze Zhang, Dmitriy Sheyn, Gadi Pelled, Xinping Zhang, Zulma Gazit, Edward M. Schwarz and Dan Gazit
Bioengineering 2016, 3(1), 6; https://doi.org/10.3390/bioengineering3010006 - 11 Jan 2016
Cited by 14 | Viewed by 7098
Abstract
Although most fractures heal, critical defects in bone fail due to aberrant differentiation of mesenchymal stem cells towards fibrosis rather than osteogenesis. While conventional bioengineering solutions to this problem have focused on enhancing angiogenesis, which is required for bone formation, recent studies have [...] Read more.
Although most fractures heal, critical defects in bone fail due to aberrant differentiation of mesenchymal stem cells towards fibrosis rather than osteogenesis. While conventional bioengineering solutions to this problem have focused on enhancing angiogenesis, which is required for bone formation, recent studies have shown that fibrotic non-unions are associated with arteriogenesis in the center of the defect and accumulation of mast cells around large blood vessels. Recently, recombinant parathyroid hormone (rPTH; teriparatide; Forteo) therapy have shown to have anti-fibrotic effects on non-unions and critical bone defects due to inhibition of arteriogenesis and mast cell numbers within the healing bone. As this new direction holds great promise towards a solution for significant clinical hurdles in craniofacial reconstruction and limb salvage procedures, this work reviews the current state of the field, and provides insights as to how teriparatide therapy could be used as an adjuvant for healing critical defects in bone. Finally, as teriparatide therapy is contraindicated in the setting of cancer, which constitutes a large subset of these patients, we describe early findings of adjuvant therapies that may present future promise by directly inhibiting arteriogenesis and mast cell accumulation at the defect site. Full article
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3965 KiB  
Article
Metabolic Control in Mammalian Fed-Batch Cell Cultures for Reduced Lactic Acid Accumulation and Improved Process Robustness
by Viktor Konakovsky, Christoph Clemens, Markus Michael Müller, Jan Bechmann, Martina Berger, Stefan Schlatter and Christoph Herwig
Bioengineering 2016, 3(1), 5; https://doi.org/10.3390/bioengineering3010005 - 11 Jan 2016
Cited by 35 | Viewed by 14979
Abstract
Biomass and cell-specific metabolic rates usually change dynamically over time, making the “feed according to need” strategy difficult to realize in a commercial fed-batch process. We here demonstrate a novel feeding strategy which is designed to hold a particular metabolic state in a [...] Read more.
Biomass and cell-specific metabolic rates usually change dynamically over time, making the “feed according to need” strategy difficult to realize in a commercial fed-batch process. We here demonstrate a novel feeding strategy which is designed to hold a particular metabolic state in a fed-batch process by adaptive feeding in real time. The feed rate is calculated with a transferable biomass model based on capacitance, which changes the nutrient flow stoichiometrically in real time. A limited glucose environment was used to confine the cell in a particular metabolic state. In order to cope with uncertainty, two strategies were tested to change the adaptive feed rate and prevent starvation while in limitation: (i) inline pH and online glucose concentration measurement or (ii) inline pH alone, which was shown to be sufficient for the problem statement. In this contribution, we achieved metabolic control within a defined target range. The direct benefit was two-fold: the lactic acid profile was improved and pH could be kept stable. Multivariate Data Analysis (MVDA) has shown that pH influenced lactic acid production or consumption in historical data sets. We demonstrate that a low pH (around 6.8) is not required for our strategy, as glucose availability is already limiting the flux. On the contrary, we boosted glycolytic flux in glucose limitation by setting the pH to 7.4. This new approach led to a yield of lactic acid/glucose (Y L/G) around zero for the whole process time and high titers in our labs. We hypothesize that a higher carbon flux, resulting from a higher pH, may lead to more cells which produce more product. The relevance of this work aims at feeding mammalian cell cultures safely in limitation with a desired metabolic flux range. This resulted in extremely stable, low glucose levels, very robust pH profiles without acid/base interventions and a metabolic state in which lactic acid was consumed instead of being produced from day 1. With this contribution, we wish to extend the basic repertoire of available process control strategies, which will open up new avenues in automation technology and radically improve process robustness in both process development and manufacturing. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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6134 KiB  
Article
Transient Mechanical Response of Lung Airway Tissue during Mechanical Ventilation
by Israr Bin Muhammad Ibrahim, Parya Aghasafari and Ramana M. Pidaparti
Bioengineering 2016, 3(1), 4; https://doi.org/10.3390/bioengineering3010004 - 05 Jan 2016
Cited by 38 | Viewed by 6537
Abstract
Patients with acute lung injury, airway and other pulmonary diseases often require Mechanical Ventilation (MV). Knowledge of the stress/strain environment in lung airway tissues is very important in order to avoid lung injuries for patients undergoing MV. Airway tissue strains responsible for stressing [...] Read more.
Patients with acute lung injury, airway and other pulmonary diseases often require Mechanical Ventilation (MV). Knowledge of the stress/strain environment in lung airway tissues is very important in order to avoid lung injuries for patients undergoing MV. Airway tissue strains responsible for stressing the lung’s fiber network and rupturing the lung due to compliant airways are very difficult to measure experimentally. Multi-level modeling is adopted to investigate the transient mechanical response of the tissue under MV. First, airflow through a lung airway bifurcation (Generation 4–6) is modeled using Computational Fluid Dynamics (CFD) to obtain air pressure during 2 seconds of MV breathing. Next, the transient air pressure was used in structural analysis to obtain mechanical strain experienced by the airway tissue wall. Structural analysis showed that airway tissue from Generation 5 in one bifurcation can stretch eight times that of airway tissue of the same generation number but with different bifurcation. The results suggest sensitivity of load to geometrical features. Furthermore, the results of strain levels obtained from the tissue analysis are very important because these strains at the cellular-level can create inflammatory responses, thus damaging the airway tissues. Full article
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4124 KiB  
Review
13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production
by Weihua Guo, Jiayuan Sheng and Xueyang Feng
Bioengineering 2016, 3(1), 3; https://doi.org/10.3390/bioengineering3010003 - 25 Dec 2015
Cited by 67 | Viewed by 12720
Abstract
Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to [...] Read more.
Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to achieve a satisfactory yield, titer or productivity of the target chemicals for industrial commercialization. In order to overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, many 13C-MFA studies have been performed in academic labs and biotechnology industries to pinpoint key issues related to microbe-based chemical production. Insightful information about the metabolic rewiring has been provided to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this review, we will introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied via integration with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production for various host microorganisms Full article
(This article belongs to the Special Issue Metabolic Engineering)
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2514 KiB  
Article
Rebalancing Redox to Improve Biobutanol Production by Clostridium tyrobutyricum
by Chao Ma, Jianfa Ou, Ningning Xu, Janna L. Fierst, Shang-Tian Yang and Xiaoguang Liu
Bioengineering 2016, 3(1), 2; https://doi.org/10.3390/bioengineering3010002 - 24 Dec 2015
Cited by 30 | Viewed by 7735
Abstract
Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in Clostridium tyrobutyricum via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production. The objective of this [...] Read more.
Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in Clostridium tyrobutyricum via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production. The objective of this study was to improve butanol production by rebalancing redox. Firstly, a metabolically-engineered mutant CTC-fdh-adhE2 was constructed by introducing heterologous formate dehydrogenase (fdh) and bifunctional aldehyde/alcohol dehydrogenase (adhE2) simultaneously into wild-type C. tyrobutyricum. The mutant evaluation indicated that the fdh-catalyzed NADH-producing pathway improved butanol titer by 2.15-fold in the serum bottle and 2.72-fold in the bioreactor. Secondly, the medium supplements that could shift metabolic flux to improve the production of butyrate or butanol were identified, including vanadate, acetamide, sodium formate, vitamin B12 and methyl viologen hydrate. Finally, the free-cell fermentation produced 12.34 g/L of butanol from glucose using the mutant CTC-fdh-adhE2, which was 3.88-fold higher than that produced by the control mutant CTC-adhE2. This study demonstrated that the redox engineering in C. tyrobutyricum could greatly increase butanol production. Full article
(This article belongs to the Special Issue Metabolic Engineering)
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6924 KiB  
Article
Sustained Release of Antibacterial Agents from Doped Halloysite Nanotubes
by Shraddha Patel, Uday Jammalamadaka, Lin Sun, Karthik Tappa and David K. Mills
Bioengineering 2016, 3(1), 1; https://doi.org/10.3390/bioengineering3010001 - 23 Dec 2015
Cited by 90 | Viewed by 6447
Abstract
The use of nanomaterials for improving drug delivery methods has been shown to be advantageous technically and viable economically. This study employed the use of halloysite nanotubes (HNTs) as nanocontainers, as well as enhancers of structural integrity in electrospun poly-e-caprolactone (PCL) [...] Read more.
The use of nanomaterials for improving drug delivery methods has been shown to be advantageous technically and viable economically. This study employed the use of halloysite nanotubes (HNTs) as nanocontainers, as well as enhancers of structural integrity in electrospun poly-e-caprolactone (PCL) scaffolds. HNTs were loaded with amoxicillin, Brilliant Green, chlorhexidine, doxycycline, gentamicin sulfate, iodine, and potassium calvulanate and release profiles assessed. Selected doped halloysite nanotubes (containing either Brilliant Green, amoxicillin and potassium calvulanate) were then mixed with poly-e-caprolactone (PLC) using the electrospinning method and woven into random and oriented-fibered nanocomposite mats. The rate of drug release from HNTs, HNTs/PCL nanocomposites, and their effect on inhibiting bacterial growth was investigated. Release profiles from nanocomposite mats showed a pattern of sustained release for all bacterial agents. Nanocomposites were able to inhibit bacterial growth for up to one-month with only a slight decrease in bacterial growth inhibition. We propose that halloysite doped nanotubes have the potential for use in a variety of medical applications including sutures and surgical dressings, without compromising material properties. Full article
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