Design and Evolution of Engineered Biological Systems

Poster presented at the 2005 ICSB meeting, held at Harvard Medical School in Boston, MA.To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. We are interested in exploring how existing forward engineering approaches might be combined with directed evolution to make routine the construction of engineered biological systems. We have specified a procedure for construction of biological systems via screening of subcomponent libraries and rational re-assembly. We have begun development of tools to enable this approach, including a FACS-based screening system to rapidly measure the input/output function of a genetic circuit. Additionally, we have designed a microfluidic system that enables more sophisticated screening and selection functions. Specifically, a microfluidic chemostat integrated with a cell sorter (i.e., a sortostat). This microscope-based system will enable us to evaluate whether or not more complicated screens and selections will be of practical use in service of evolving engineered biological systems

Alternatives for Navigating Small Unmanned Air Vehicles without GPS

Considering the increased reliance on GPS navigation for the Army’s Unmanned Aircraft Systems, adversaries have invested in capabilities to deny our systems access to genuine GPS signals. Although significant effort has been put forth in the areas of anti-jamming and anti-spoofing in GPS receivers, a need for alternative navigation methods in a GPS denied environment has grown in importance. This report outlines the recommendation and analysis completed for Mr. Lars Ericsson of the Army Project Manager Unmanned Aircraft Systems (PM-UAS).  The report includes background research in the domain space, comprehensive stakeholder analysis, derived system requirements and functional requirements, ending with alternative generation, value scoring, costing, and provided findings for a recommended alternative for future consideration. 

A Plasmid-Transposon Hybrid Mutagenesis System Effective in a Broad Range of Enterobacteria.

Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rodentium, Serratia sp. ATCC39006, Serratia plymuthica, Dickeya dadantii, and many more. Transposon mutagenesis was optimized in each of these strains and three studies are presented to show the efficacy of this system. Firstly, the important agricultural pathogen D. dadantii was mutagenized. Two mutants that showed reduced protease production and one mutant producing the previously cryptic pigment, indigoidine, were identified and characterized. Secondly, the enterobacterium, Serratia sp. ATCC39006 was mutagenized and mutants incapable of producing gas vesicles, proteinaceous intracellular organelles, were identified. One of these contained a β-galactosidase transcriptional fusion within the gene gvpA1, essential for gas vesicle production. Finally, the system was used to mutate the biosynthetic gene clusters of the antifungal, anti-oomycete and anticancer polyketide, oocydin A, in the plant-associated enterobacterium, Dickeya solani MK10. The mutagenesis system was developed to allow easy identification of transposon insertion sites by sequencing, after facile generation of a replicon encompassing the transposon and adjacent DNA, post-excision. Furthermore, the system can also create transcriptional fusions with either β-galactosidase or β-glucuronidase as reporters, and exploits a variety of drug resistance markers so that multiple selectable fusions can be generated in a single strain. This system of various transposons has wide utility and can be combined in many different ways.The authors would like to acknowledge several funding sources. D. Smith was supported by a PhD studentship from the BBSRC. Work in the MW lab is supported by the BBSRC (grants BB/G015171/1 and BB/M019411/1). K. Roberts was funded by an MRC studentship. R. Monson and the Salmond lab were supported by grants from the BBSRC (Grant No Provisional BB/K001833/1). M.A. Matilla was supported by the EU Marie-Curie Intra-European Fellowship for Career Development (FP7-PEOPLE-2011-IEF), grant number 298003. B. Richardson was supported by a Harry Smith vacation studentship from the SGM, UK. The authors would also like to thank Ray Chai for careful reading and comments on this manuscript. Alison Drew provided technical support. Work with plant pathogens was carried out under DEFRA licence No. 50864/197900/1.This is the final version of the article. It was first available from Frontiers via http://dx.doi.org/10.3389/fmicb.2015.0144

Engagement Effects of Player Rating System-Based Matchmaking for Level Ordering in Human Computation Games

Human computation games lack established ways of balancing the difficulty of tasks or levels served to players, potentially contributing to their low engagement rates. Traditional player rating systems have been suggested as a potential solution: using them to rate both players and tasks could estimate player skill and task difficulty and fuel player-task matchmaking. However, neither the effect of difficulty balancing on engagement in human computation games nor the use of player rating systems for this purpose has been empirically tested. We therefore examined the engagement effects of using the Glicko-2 player rating system to order tasks in the human computation game Paradox. An online experiment (n=294) found that both matchmaking-based and pure difficulty-based ordering of tasks led to significantly more attempted and completed levels than random ordering. Additionally, both matchmaking and random ordering led to significantly more di cult tasks being completed than pure difficulty-based ordering. We conclude that poor balancing contributes to poor engagement in human computation games, and that player rating system-based difficulty rating may be a viable and efficient way of improving both

Koinonia

Best Practice FeaturesLife on Life Learning: Steps Towards Authentic Mentoring, Brian Jensen The Heart of the Honor Code: I am My Brother\u27s Keeper, Emily J. Darnell Spotlight FeaturesOld People are Whole Persons, Too: Why Understanding Heritage is a Foundational Component of College Student Development, Philip Byers Ministry and Learning in Residence Life, Josh Arnold Shepherding in an Age of Edupunks, Drew Moser The Gap in the Curtain: Seeing Pieces of a Residential Community\u27s Future, David Johnstone InterviewsA Conversation with Juana Bordas, conducted by Rob Pepper Looking Into the Future: Two Educators\u27 Perspectives on Christian Higher Education, by Kim Stave and Ken Heffner (edited by Kirstin Vander Giessen-Reitsma) Book ReviewsThe Unlikely Disciple (by Kevin Roose), reviewed by Christopher Bohle ReflectionsSeven Greek Words that Mean the World to Me, Bob Crow FeaturesThe President\u27s Corner Editor\u27s Deskhttps://pillars.taylor.edu/acsd_koinonia/1013/thumbnail.jp

Additions to Philippine Slender Skinks of the <i>Brachymeles bonitae </i>Complex (Reptilia: Squamata: Scincidae) III:a new species from Tablas Island

Davis, Drew R., Geheber, Aaron D., Watters, Jessa L., Penrod, Michelle L., Feller, Kathryn D., Ashford, Alissa, Kouri, Josh, Nguyen, Daniel, Shauberger, Kathryn, Sheatsley, Kyra, Winfrey, Claire, Wong, Rachel, Sanguila, Marites B., Brown, Rafe M., Siler, Cameron D. (2016): Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) III: a new species from Tablas Island. Zootaxa 4132 (1), DOI: http://doi.org/10.11646/zootaxa.4132.1.

DUF2285 is a novel helix-turn-helix domain variant that orchestrates both activation and antiactivation of conjugative element transfer in proteobacteria.

Horizontal gene transfer is tightly regulated in bacteria. Often only a fraction of cells become donors even when regulation of horizontal transfer is coordinated at the cell population level by quorum sensing. Here, we reveal the widespread 'domain of unknown function' DUF2285 represents an 'extended-turn' variant of the helix-turn-helix domain that participates in both transcriptional activation and antiactivation to initiate or inhibit horizontal gene transfer. Transfer of the integrative and conjugative element ICEMlSymR7A is controlled by the DUF2285-containing transcriptional activator FseA. One side of the DUF2285 domain of FseA has a positively charged surface which is required for DNA binding, while the opposite side makes critical interdomain contacts with the N-terminal FseA DUF6499 domain. The QseM protein is an antiactivator of FseA and is composed of a DUF2285 domain with a negative surface charge. While QseM lacks the DUF6499 domain, it can bind the FseA DUF6499 domain and prevent transcriptional activation by FseA. DUF2285-domain proteins are encoded on mobile elements throughout the proteobacteria, suggesting regulation of gene transfer by DUF2285 domains is a widespread phenomenon. These findings provide a striking example of how antagonistic domain paralogues have evolved to provide robust molecular control over the initiation of horizontal gene transfer

Astrometry with the Keck-Interferometer: the ASTRA project and its science

The sensitivity and astrometry upgrade ASTRA of the Keck Interferometer is introduced. After a brief overview of the underlying interferometric principles, the technology and concepts of the upgrade are presented. The interferometric dual-field technology of ASTRA will provide the KI with the means to observe two objects simultaneously, and measure the distance between them with a precision eventually better than 100 uas. This astrometric functionality of ASTRA will add a unique observing tool to fields of astrophysical research as diverse as exo-planetary kinematics, binary astrometry, and the investigation of stars accelerated by the massive black hole in the center of the Milky Way as discussed in this contribution.Comment: 22 pages, 10 figures (low resolution), contribution to the summerschool "Astrometry and Imaging with the Very Large Telescope Interferometer", 2 - 13 June, 2008, Keszthely, Hungary, corrected authorlis