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Journal of Biological Engineering

William J Hadden, Yu Suk Choi
Each cell forever interacts with its extracellular matrix (ECM); a stem cell relies on this interaction to guide differentiation. The stiffness, nanotopography, protein composition, stress and strain inherent to any given ECM influences stem cell lineage commitment. This interaction is dynamic, multidimensional and reciprocally evolving through time, and from this concerted exchange the macroscopic tissues that comprise living organisms are formed. Mesenchymal stem cells can give rise to bone, cartilage, tendon and muscle; thus attempts to manipulate their differentiation must heed the physical properties of incredibly complex native microenvironments to realize regenerative goals...
2016: Journal of Biological Engineering
Mathias Foo, Rucha Sawlekar, Declan G Bates
BACKGROUND: Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours - ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic. RESULTS: In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry...
2016: Journal of Biological Engineering
David Flitsch, Sebastian Krabbe, Tobias Ladner, Mario Beckers, Jana Schilling, Stefan Mahr, Uwe Conrath, Werner K Schomburg, Jochen Büchs
BACKGROUND: Small-scale micro-bioreactors have become the cultivation vessel of choice during the first steps of bioprocess development. They combine high cultivation throughput with enhanced cost efficiency per cultivation. To gain the most possible information in the early phases of process development, online monitoring of important process parameters is highly advantageous. One of these important process parameters is the oxygen transfer rate (OTR). Measurement of the OTR, however, is only available for small-scale fermentations in shake flasks via the established RAMOS technology until now...
2016: Journal of Biological Engineering
Yingfang Ma, Wei Shen, Xianzhong Chen, Long Liu, Zhemin Zhou, Fei Xu, Haiquan Yang
BACKGROUND: Alkaline amylase has significant potential for applications in the textile, paper and detergent industries, however, low yield of which cannot meet the requirement of industrial application. In this work, a novel ARTP mutagenesis-screening method and fermentation optimization strategies were used to significantly improve the expression level of recombinant alkaline amylase in B. subtilis 168. RESULTS: The activity of alkaline amylase in mutant B. subtilis 168 mut-16# strain was 1...
2016: Journal of Biological Engineering
Matthew L Paff, Scott L Nuismer, Andrew D Ellington, Ian J Molineux, Ryan H May, James J Bull
BACKGROUND: We propose, model, and implement a novel system of population-level intervention against a virus. One context is a treatment against a chronic infection such as HIV. The underlying principle is a form of virus 'wars' in which a benign, transmissible agent is engineered to protect against infection by and spread of a lethal virus. In our specific case, the protective agent consists of two entities, a benign virus and a gene therapy vector mobilized by the benign virus. RESULTS: Numerical analysis of a mathematical model identified parameter ranges in which adequate, population-wide protection is achieved...
2016: Journal of Biological Engineering
Georg Wandrey, Joel Wurzel, Kyra Hoffmann, Tobias Ladner, Jochen Büchs, Lorenz Meinel, Tessa Lühmann
BACKGROUND: Genetic code expansion has developed into an elegant tool to incorporate unnatural amino acids (uAA) at predefined sites in the protein backbone in response to an amber codon. However, recombinant production and yield of uAA comprising proteins are challenged due to the additional translation machinery required for uAA incorporation. RESULTS: We developed a microtiter plate-based high-throughput monitoring system (HTMS) to study and optimize uAA integration in the model protein enhanced green fluorescence protein (eGFP)...
2016: Journal of Biological Engineering
Ritu Raman, Marlon Mitchell, Pablo Perez-Pinera, Rashid Bashir, Lizanne DeStefano
BACKGROUND: The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method...
2016: Journal of Biological Engineering
N Salmanikhas, M Tizghadam, A Rashidi Mehrabadi
BACKGROUND: In this study, a hybrid treatment system (Fluidized Bed positioned in a biological reactor of an Activated Sludge process) was used to treat saline domestic wastewater. The performance of the mentioned hybrid system was compared with the conventional activated sludge. A pilot study was conducted, and Chemical Oxygen Demand (COD), Electrical Conductivity (EC), Total Dissolved Solids (TDS) and pH were measured to investigate treatment efficiency. Three saline wastewater samples with salt concentrations of 0...
2016: Journal of Biological Engineering
Shengli Yang, Hui Zhang
BACKGROUND: Cordyceps sobolifera (C. sobolifera) isolated from cicadae was used as the starting fungus to produce selenium-enriched C. sobolifera extracellular polysaccharide (Se-CEPS). An orthogonal experimental design based on a single-factor experiment was used to optimize the C. sobolifera fermentation conditions, including the potato juice, peptone, and KH2PO4 concentrations. Ultraviolet (UV) and infrared (IR) analyses of CEPS and Se-CEPS were conducted, as well as an in vivo anti-tumor analysis...
2016: Journal of Biological Engineering
Hendrik Laube, Frank-Michael Matysik, Andreas Schmidberger, Kerstin Mehlmann, Andreas Toursel, Jana Boden
BACKGROUND: During the downstream process of bio-based bulk chemicals, organic impurities, mostly residues from the fermentation process, must be separated to obtain a pure and ready-to-market chemical. In this study, capillary electrophoresis was investigated for the non-targeting downstream process monitoring of organic impurities and simultaneous quantitative detection of lactic acid during the purification process of fermentatively produced lactic acid. The downstream process incorporated 11 separation units, ranging from filtration, adsorption and ion exchange to electrodialysis and distillation, and 15 different second-generation renewable feedstocks were processed into lactic acid...
2016: Journal of Biological Engineering
Damien Biot-Pelletier, Vincent J J Martin
CRISPR assisted homology directed repair enables the introduction of virtually any modification to the Saccharomyces cerevisiae genome. Of obvious interest is the marker-free and seamless introduction of point mutations. To fulfill this promise, a strategy that effects single nucleotide changes while preventing repeated recognition and cutting by the gRNA/Cas9 complex is needed. We demonstrate a two-step method to introduce point mutations at 17 positions in the S. cerevisiae genome. We show the general applicability of the method, enabling the seamless introduction of single nucleotide changes at any location, including essential genes and non-coding regions...
2016: Journal of Biological Engineering
Toby P Call, M Kalim Akhtar, Frank Baganz, Chris Grant
BACKGROUND: In recent years, there have been intensive efforts to develop synthetic microbial platforms for the production, biosensing and bio-remediation of fossil fuel constituents such as alkanes. Building predictable engineered systems for these applications will require the ability to tightly control and modulate the rate of import of alkanes into the host cell. The native components responsible for the import of alkanes within these systems have yet to be elucidated. To shed further insights on this, we used the AlkBGT alkane monooxygenase complex from Pseudomonas putida GPo1 as a reporter system for assessing alkane import in Escherichia coli...
2016: Journal of Biological Engineering
Arthur T Johnson
Respiratory protective masks are used whenever it is too costly or impractical to remove airborne contamination from the atmosphere. Respirators are used in a wide range of occupations, form the military to medicine. Respirators have been found to interfere with many physiological and psychological aspects of task performance at levels from resting to maximum exertion. Many of these limitations have been investigated in order to determine quantitatively how much performance decrement can be expected from different levels of respirator properties...
2016: Journal of Biological Engineering
Gregory Linshiz, Erik Jensen, Nina Stawski, Changhao Bi, Nick Elsbree, Hong Jiao, Jungkyu Kim, Richard Mathies, Jay D Keasling, Nathan J Hillson
BACKGROUND: Synthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening. RESULTS: Herein, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform's capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation...
2016: Journal of Biological Engineering
Afnan Azizi, Wilson Lam, Hilary Phenix, Lioudmila Tepliakova, Ian J Roney, Daniel Jedrysiak, Alex Power, Vaibhav Gupta, Nada Elnour, Martin Hanzel, Alexandra C Tzahristos, Shihab Sarwar, Mads Kærn
[This corrects the article DOI: 10.1186/s13036-015-0006-z.].
2016: Journal of Biological Engineering
Nathan D Israelsen, Donald Wooley, Cynthia Hanson, Elizabeth Vargis
BACKGROUND: Surface-enhanced Raman scattering (SERS) is a powerful light scattering technique that can be used for sensitive immunoassay development and cell labeling. A major obstacle to using SERS is the complexity of fabricating SERS probes since they require nanoscale characterization and optical uniformity. The light scattering response of SERS probes may also be modulated by the substrate used for SERS analysis. A typical SERS substrate such as quartz can be expensive. Polystyrene is a cheaper substrate option but can decrease the SERS response due to interfering Raman emission peaks and high background fluorescence...
2016: Journal of Biological Engineering
Thiyagarajan Gnanasekaran, Konstantinos Vavitsas, Johan Andersen-Ranberg, Agnieszka Zygadlo Nielsen, Carl Erik Olsen, Björn Hamberger, Poul Erik Jensen
BACKGROUND: Plant terpenoids are known for their diversity, stereochemical complexity, and their commercial interest as pharmaceuticals, food additives, and cosmetics. Developing biotechnology approaches for the production of these compounds in heterologous hosts can increase their market availability, reduce their cost, and provide sustainable production platforms. In this context, we aimed at producing the antimicrobial diterpenoid isopimaric acid from Sitka spruce. Isopimaric acid is synthesized using geranylgeranyl diphosphate as a precursor molecule that is cyclized by a diterpene synthase in the chloroplast and subsequently oxidized by a cytochrome P450, CYP720B4...
2015: Journal of Biological Engineering
Shasha Zhang, Xuejin Zhao, Yong Tao, Chunbo Lou
BACKGROUND: Imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. Several targets were intensively investigated to balance the gene expression, such as promoter, ribosome binding site (RBS), the order of genes, as well as the species of the enzymes. However, the capability of simultaneous manipulation of multiple targets still needs to be explored. RESULTS: We reported a new DNA assembling method to vary all the above types of regulatory targets simultaneously, named oligo-linker mediated assembly (OLMA) method, which can incorporate up to 8 targets in a single assembly step...
2015: Journal of Biological Engineering
Yong Cheol Shin, Jong Ho Lee, Min Jeong Kim, Suck Won Hong, Bongju Kim, Jung Keun Hyun, Yu Suk Choi, Jong-Chul Park, Dong-Wook Han
BACKGROUND: In the field of biomedical engineering, many studies have focused on the possible applications of graphene and related nanomaterials due to their potential for use as scaffolds, coating materials and delivery carriers. On the other hand, electrospun nanofiber matrices composed of diverse biocompatible polymers have attracted tremendous attention for tissue engineering and regenerative medicine. However, their combination is intriguing and still challenging. RESULTS: In the present study, we fabricated nanofiber matrices composed of M13 bacteriophage with RGD peptide displayed on its surface (RGD-M13 phage) and poly(lactic-co-glycolic acid, PLGA) and characterized their physicochemical properties...
2015: Journal of Biological Engineering
Kathy Y Wei, Christina D Smolke
BACKGROUND: The cell cycle plays a key role in human health and disease, including development and cancer. The ability to easily and reversibly control the mammalian cell cycle could mean improved cellular reprogramming, better tools for studying cancer, more efficient gene therapy, and improved heterologous protein production for medical or industrial applications. RESULTS: We engineered RNA-based control devices to provide specific and modular control of gene expression in response to exogenous inputs in living cells...
2015: Journal of Biological Engineering
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