http://www.jbioleng.org The latest research articles published by Journal of Biological Engineering 2012-05-15T00:00:00Z AC Biosusceptometry (ACB) was previously employed towards recording gastrointestinal motility. Our data show a reliable and successful evaluation of gastrointestinal transit of liquid and solid meals in rats, considering the methods scarcity and number of experiments needed to endorsement of drugs and medicinal plants. ACB permits real time and simultaneous experiments using the same animal, preserving the physiological conditions employing both meals with simplicity and accuracy. http://www.jbioleng.org/content/6/1/6 Caio Quini Madileine Americo Luciana Cora Marcos Calabresi Matheus Alvarez Ricardo Oliveira Jose Ricardo Miranda Journal of Biological Engineering 2012, null:6 2012-05-15T00:00:00Z doi:10.1186/1754-1611-6-6 /content/figures/1754-1611-6-6-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 6 2012-05-15T00:00:00Z PDF Background: Temperature-sensitive (Ts) plasmids are useful tools for genetic engineering, but there are currently none compatible with the gram positive, thermophilic, obligate anaerobe, Clostridium thermocellum. Traditional mutagenesis techniques yield Ts mutants at a low frequency, and therefore requires the development of high-throughput screening protocols, which are also not available for this organism. Recently there has been progress in the development of computer algorithms which can predict Ts mutants of a protein based solely on its amino acid sequence. Most plasmids currently used for genetic modification of C. thermocellum are based on the replicon of plasmid pNW33N, which replicates using the RepB replication protein. To address this problem, we set out to create a Ts plasmid by mutating the RepB replication protein using an algorithm designed by Varadarajan et al. (1996) for predicting Ts mutants based on the amino-acid sequence of the protein. Results: A library of 34 mutant plasmids was designed, synthesized and screened, resulting in 6 mutants which exhibited a Ts phenotype. Of these 6, the one with the most temperature-sensitive phenotype (M166A) was compared with the original plasmid. It exhibited lower stability at 48degreesC and was completely unable to replicate at 55degreesC. Conclusions: The plasmid described in this work could be useful in future efforts to genetically engineer C. thermocellum, and the method used to generate this plasmid may be useful for others trying to make Ts plasmids. http://www.jbioleng.org/content/6/1/5 Daniel Olson Lee Lynd Journal of Biological Engineering 2012, null:5 2012-05-11T00:00:00Z doi:10.1186/1754-1611-6-5 /content/figures/1754-1611-6-5-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 5 2012-05-11T00:00:00Z PDF Tumor shape and size effect on drug delivery to solid tumors are studied, based on the application of thegoverning equations for fluid flow, i.e., the conservation laws for mass and momentum, to physiological systemscontaining solid tumors. The discretized form of the governing equations, with appropriate boundary conditions,is developed for predefined tumor geometries. The governing equations are solved using a numerical method, theelement-based finite volume method. Interstitial fluid pressure and velocity are used to show the details of drugdelivery in a solid tumor, under an assumption that drug particles flow with the interstitial fluid. Drug deliveryproblems have been most extensively researched in spherical tumors, which have been the simplest to examinewith the analytical methods. With our numerical method, however, more complex shapes of the tumor can bestudied. The numerical model of fluid flow in solid tumors previously introduced by our group is furtherdeveloped to incorporate and investigate non-spherical tumors such as prolate and oblate ones. Also the effects ofthe surface area per unit volume of the tissue, vascular and interstitial hydraulic conductivity on drug delivery areinvestigated. http://www.jbioleng.org/content/6/1/4 M Soltani P Chen Journal of Biological Engineering 2012, null:4 2012-04-25T00:00:00Z doi:10.1186/1754-1611-6-4 /content/figures/1754-1611-6-4-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 4 2012-04-25T00:00:00Z PDF Background: Evolutionary dynamics of microbial organisms can now be visualized using the Visualizing Evolution in Real Time (VERT) system, in which several isogenic strains expressing different fluorescent proteins compete during adaptive evolution and are tracked using fluorescent cell sorting to construct a population history over time. Mutations conferring enhanced growth rates can be detected by observing changes in the fluorescent population proportions. Results: Using data obtained from several VERT experiments, we construct a hidden Markov-derived model to detect these adaptive events in VERT experiments without external intervention beyond initial training. Analysis of annotated data revealed that the model achieves consensus with human annotation for 85-93% of the data points when detecting adaptive events. A method to determine the optimal time point to isolate adaptive mutants is also introduced. Conclusions: The developed model offers a new way to monitor adaptive evolution experiments without the need for external intervention, thereby simplifying adaptive evolution efforts relying on population tracking. Future efforts to construct a fully automated system to isolate adaptive mutants may find the algorithm a useful tool. http://www.jbioleng.org/content/6/1/3 James Winkler Katy Kao Journal of Biological Engineering 2012, null:3 2012-04-02T00:00:00Z doi:10.1186/1754-1611-6-3 /content/figures/1754-1611-6-3-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 3 2012-04-02T00:00:00Z XML Background: Recombinant protein production is a process of great industrial interest, with products that range from pharmaceuticals to biofuels. Since high level production of recombinant protein imposes significant stress in the host organism, several methods have been developed over the years to optimize protein production. So far, these trial-and-error techniques have proved laborious and sensitive to process parameters, while there has been no attempt to address the problem by applying Synthetic Biology principles and methods, such as integration of standardized parts in novel synthetic circuits. Results: We present a novel self-regulatory protein production system that couples the control of recombinant protein production with a stress-induced, negative feedback mechanism. The synthetic circuit allows the down-regulation of recombinant protein expression through a stress-induced promoter. We used E. coli as the host organism, since it is widely used in recombinant processes. Our results show that the introduction of the self-regulatory circuit increases the soluble/insoluble ratio of recombinant protein at the expense of total protein yield. To further elucidate the dynamics of the system, we developed a computational model that is in agreement with the observed experimental data, and provides insight on the interplay between protein solubility and yield. Conclusion: Our work introduces the idea of a self-regulatory circuit for recombinant protein products, and paves the way for processes with reduced external control or monitoring needs. It demonstrates that the library of standard biological parts serves as a valuable resource for initial synthetic blocks that needs to be further refined to be successfully applied in practical problems of biotechnological significance. Finally, the development of a predictive model in conjunction with experimental validation facilitates a better understanding of the underlying dynamics and can be used as a guide to experimental design. http://www.jbioleng.org/content/6/1/2 Martin Dragosits Daniel Nicklas Ilias Tagkopoulos Journal of Biological Engineering 2012, null:2 2012-03-30T00:00:00Z doi:10.1186/1754-1611-6-2 /content/figures/1754-1611-6-2-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 2 2012-03-30T00:00:00Z PDF Background: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results: We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions: DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. http://www.jbioleng.org/content/6/1/1 Joanna Chen Douglas Densmore Timothy Ham Jay Keasling Nathan Hillson Journal of Biological Engineering 2012, null:1 2012-02-28T00:00:00Z doi:10.1186/1754-1611-6-1 /content/figures/1754-1611-6-1-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 1 2012-02-28T00:00:00Z XML A modified BioBrick™ assembly method was developed with higher fidelity than current protocols. The method utilizes a PCR reaction with a standard primer set to amplify the inserted part. Background colonies are reduced by a combination of dephosphorylation and digestion with DpnI restriction endonuclease to reduce vector and insert background respectively. The molar ratio of the insert to vector in the ligation was also optimized, with the accuracy of the transformed construct approaching 100%. http://www.jbioleng.org/content/5/1/17 Michael Speer Tom Richard Journal of Biological Engineering 2011, null:17 2011-12-16T00:00:00Z doi:10.1186/1754-1611-5-17 /content/figures/1754-1611-5-17-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 17 2011-12-16T00:00:00Z XML Background: In a globalized word, prevention of infectious diseases is a major challenge. Rapid detection of viable virus particles in water and other environmental samples is essential to public health risk assessment, homeland security and environmental protection. Current virus detection methods, especially assessing viral infectivity, are complex and time-consuming, making point-of-care detection a challenge. Faster, more sensitive, highly specific methods are needed to quantify potentially hazardous viral pathogens and to determine if suspected materials contain viable viral particles. Fourier transform infrared (FTIR) spectroscopy combined with cellular-based sensing, may offer a precise way to detect specific viruses. This approach utilizes infrared light to monitor changes in molecular components of cells by tracking changes in absorbance patterns produced following virus infection. In this work poliovirus (PV1) was used to evaluate the utility of FTIR spectroscopy with cell culture for rapid detection of infective virus particles. Results: Buffalo green monkey kidney (BGMK) cells infected with different virus titers were studied at 1 - 12 hours post-infection (h.p.i.). A partial least squares (PLS) regression method was used to analyze and model cellular responses to different infection titers and times post-infection. The model performs best at 8 h.p.i., resulting in an estimated root mean square error of cross validation (RMSECV) of 17 plaque forming units (PFU)/ml when using low titers of infection of 10 and 100 PFU/ml. Higher titers, from 103 to 106 PFU/ml, could also be reliably detected. Conclusions: This approach to poliovirus detection and quantification using FTIR spectroscopy and cell culture could potentially be extended to compare biochemical cell responses to infection with different viruses. This virus detection method could feasibly be adapted to an automated scheme for use in areas such as water safety monitoring and medical diagnostics. http://www.jbioleng.org/content/5/1/16 Felipe Lee-Montiel Kelly Reynolds Mark Riley Journal of Biological Engineering 2011, null:16 2011-12-05T00:00:00Z doi:10.1186/1754-1611-5-16 /content/figures/1754-1611-5-16-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 16 2011-12-05T00:00:00Z XML CD-ELISA uses the microfluidic ranking method and centrifugal force to control the testing solution as it flows into the reaction region. The most challenging part of CD-ELISA is controlling the flow process for different biological testing solutions, i.e. the controlling sequence for the microfluidic channel valves. The microfluidic channel valve is therefore the most important fluid channel structure for CD-ELISA. In this study, we propose a valve design suitable for a wide range rotational speeds which can be applied for mass production (molding). Together with supporting experiments, simulation based on two-phase flow theory is used in this study, and the feasibility of this novel valve design is confirmed. Influencing design factors for the microfluidic channel valves in CD-ELISA are investigated, including various shapes of the arc, distance d, radius r, the location of the center of the circle, and the contact angle. From both the experimental results and the simulated results, it is evident that the narrowest channel width and the contact angle are the primary factors influencing valve burst frequency. These can be used as the main controlling factors during the design. http://www.jbioleng.org/content/5/1/15 Samuel I En Lin Journal of Biological Engineering 2011, null:15 2011-11-07T00:00:00Z doi:10.1186/1754-1611-5-15 /content/figures/1754-1611-5-15-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 15 2011-11-07T00:00:00Z XML On February 15, 2008, the National Academy of Engineering unveiled their list of 14 Grand Challenges for Engineering. Building off of tremendous advancements in the past century, these challenges were selected for their role in assuring a sustainable existence for the rapidly increasing global community. It is no accident that the first five Challenges on the list involve the development of sustainable energy sources and management of environmental resources. While the focus of this review is to address the single Grand Challenge of "develop carbon sequestration methods", is will soon be clear that several other Challenges are intrinsically tied to it through the principles of sustainability. How does the realm of biological engineering play a role in addressing these Grand Challenges? http://www.jbioleng.org/content/5/1/14 Ben Stuart Journal of Biological Engineering 2011, null:14 2011-11-02T00:00:00Z doi:10.1186/1754-1611-5-14 /content/figures/1754-1611-5-14-toc.gif Journal of Biological Engineering 1754-1611 ${item.volume} 14 2011-11-02T00:00:00Z XML