A design-build-test-learn tool for synthetic biology

Modern synthetic gene regulatory networks emerge from iterative design-build-test cycles that encompass the decisions and actions necessary to design, build, and test target genetic systems. Historically, such cycles have been performed manually, with limited formal problem-definition and progress-tracking. In recent years, researchers have devoted substantial effort to define and automate many sub-problems of these cycles and create systems for data management and documentation that result in useful tools for solving portions of certain workflows. However, biologists generally must still manually transfer information between tools, a process that frequently results in information loss. Furthermore, since each tool applies to a different workflow, tools often will not fit together in a closed-loop and, typically, additional outstanding sub-problems still require manual solutions. This thesis describes an attempt to create a tool that harnesses many smaller tools to automate a fully closed-loop decision-making process to design, build, and test synthetic biology networks and use the outcomes to inform redesigns. This tool, called Phoenix, inputs a performance-constrained signal-temporal-logic (STL) equation and an abstract genetic-element structural description to specify a design and then returns iterative sets of building and testing instructions. The user executes the instructions and returns the data to Phoenix, which then processes it and uses it to parameterize models for simulation of the behavior of compositional designs. A model-checking algorithm then evaluates these simulations, and returns to the user a new set of instructions for building and testing the next set of constructs. In cases where experimental results disagree with simulations, Phoenix uses grammars to determine where likely points of design failure might have occurred and instructs the building and testing of an intermediate composition to test where failures occurred. A design tree represents the design hierarchy displayed in the user interface where progress can be tracked and electronic datasheets generated to review results. Users can validate the computations performed by Phoenix by using them to create sets of classic and novel temporal synthetic genetic regulatory functions in E. coli.2016-12-31T00:00:00

BBF RFC 94: Type IIS Assembly for Bacterial Transcriptional Units: A Standardized Assembly Method for Building Bacterial Transcriptional Units Using the Type IIS Restriction Enzymes BsaI and BbsI

This RFC94 describes an assembly standard based on the Type IIS restriction enzymes BsaI and BbsI (also called BpiI). This assembly standard is based upon the Modular Cloning (MoClo) assembly strategy, which was introduced in 2011 by Weber et al. [1] and is based upon Golden Gate cloning [2]. In this RFC, we describe our proposed MoClo standard for generating a library of bacterial DNA parts for generating four-part transcriptional units (promoter : 5’UTR : CDS : 3’UTR). In this work, we define 5’UTRs as including ribosomal binding sites (RBS) and bi-cistronic design elements (BCDs) [3], and 3’UTRs as transcriptional terminators. The 2012-2014 BostonU iGEM teams completed this work and a more compact library has also been created based on this work [4]

The ACS Nearby Galaxy Survey Treasury IV. The Star Formation History of NGC 2976

We present resolved stellar photometry of NGC 2976 obtained with the Advanced Camera for Surveys (ACS) as part of the ACS Nearby Galaxy Survey Treasury (ANGST) program. The data cover the radial extent of the major axis of the disk out to 6 kpc, or ~6 scale lengths. The outer disk was imaged to a depth of M_F606W ~ 1, and an inner field was imaged to the crowding limit at a depth of M_F606W ~ -1. Through detailed analysis and modeling of these CMDs we have reconstructed the star formation history of the stellar populations currently residing in these portions of the galaxy, finding similar ancient populations at all radii but significantly different young populations at increasing radii. In particular, outside of the well-measured break in the disk surface brightness profile, the age of the youngest population increases with distance from the galaxy center, suggesting that star formation is shutting down from the outside-in. We use our measured star formation history, along with H I surface density measurements, to reconstruct the surface density profile of the disk during previous epochs. Comparisons between the recovered star formation rates and reconstructed gas densities at previous epochs are consistent with star formation following the Schmidt law during the past 0.5 Gyrs, but with a drop in star formation efficiency at low gas densities, as seen in local galaxies at the present day. The current rate and gas density suggest that rapid star formation in NGC 2976 is currently in the process of ceasing from the outside-in due to gas depletion. This process of outer disk gas depletion and inner disk star formation was likely triggered by an interaction with the core of the M81 group >~1 Gyr ago that stripped the gas from the galaxy halo and/or triggered gas inflow from the outer disk toward the galaxy center.Comment: 22 pages, 14 figures, 2 tables, accepted for publication by Ap

Building biosecurity for synthetic biology.

The fast-paced field of synthetic biology is fundamentally changing the global biosecurity framework. Current biosecurity regulations and strategies are based on previous governance paradigms for pathogen-oriented security, recombinant DNA research, and broader concerns related to genetically modified organisms (GMOs). Many scholarly discussions and biosecurity practitioners are therefore concerned that synthetic biology outpaces established biosafety and biosecurity measures to prevent deliberate and malicious or inadvertent and accidental misuse of synthetic biology's processes or products. This commentary proposes three strategies to improve biosecurity: Security must be treated as an investment in the future applicability of the technology; social scientists and policy makers should be engaged early in technology development and forecasting; and coordination among global stakeholders is necessary to ensure acceptable levels of risk

The Recent Evolution of the Dwarf Starburst Galaxy NGC 625 from Hubble Space Telescope Imaging

New HST/WFPC2 imaging of the dwarf starburst galaxy NGC 625 is presented. These data, 80% complete to V and I magnitudes of 26.0 and 25.3, respectively, allow us to study the recent star formation history of NGC 625. We derive a tip of the red giant branch (TRGB) distance modulus of 27.95+/-0.07, corresponding to a distance of 3.89+/-0.22 Mpc, and a location on the far side of the Sculptor Group. NGC 625 has a well-defined radial stellar population gradient, evidenced by a central concentration of young MS stars and an RGB/AGB ratio that increases with galactocentric distance. The prominent AGB is very red, and RGB stars are detected far from the central star forming regions. Using H Alpha and H Beta narrow band imaging and previous optical spectroscopy we identify substantial and varying internal extinction (A_V = 0.0 to 0.6 mag) associated with the central active star formation regions. To better understand the effects of internal extinction on the analysis of young stellar populations, synthetic models are presented which, for the first time, examine and account for this effect. Using the luminous blue helium burning stars, we construct a simple model of the recent (< 100 Myr) star formation in which an elevated but declining star formation rate has been present over this entire period. This is at odds with the presence of spectroscopic W-R features in the major star formation region which imply a short duration (<= 5 Myr) for the recent starburst. This suggests that starbursts displaying W-R features are not necessarily all of a short duration. Finally, we speculate on the possible causes of the present burst of star formation in this apparently isolated galaxy, and compare it to other nearby, well-studied dwarf starburst systems.Comment: 56 pages, including 15 figures (2 in color). Scheduled to appear in AJ, December, 2003. Full-resolution version may be obtained at http://www.astro.umn.edu/~Cannon/n625.p

A computer-guided design tool to increase the efficiency of cellular conversions

Human cell conversion technology has become an important tool for devising new cell transplantation therapies, generating disease models and testing gene therapies. However, while transcription factor over-expression-based methods have shown great promise in generating cell types in vitro, they often endure low conversion efficiency. In this context, great effort has been devoted to increasing the efficiency of current protocols and the development of computational approaches can be of great help in this endeavor. Here we introduce a computer-guided design tool that combines a computational framework for prioritizing more efficient combinations of instructive factors (IFs) of cellular conversions, called IRENE, with a transposon-based genomic integration system for efficient delivery. Particularly, IRENE relies on a stochastic gene regulatory network model that systematically prioritizes more efficient IFs by maximizing the agreement of the transcriptional and epigenetic landscapes between the converted and target cells. Our predictions substantially increased the efficiency of two established iPSC-differentiation protocols (natural killer cells and melanocytes) and established the first protocol for iPSC-derived mammary epithelial cells with high efficiency. Transcription factor over-expression-based cellular conversion methods often endure low conversion efficiency. Here the authors show how to increase conversion efficiency by combining a computational method for prioritizing more efficient TF combinations with a transposon-based genomic integration system for delivery

Magnesium intake and sleep disorder symptoms : findings from the Jiangsu Nutrition Study of Chinese adults at five-year follow-up

(1) Background: In clinical trials, dietary magnesium use can improve insomnia symptoms. However, little is known about the association between dietary magnesium consumption and sleep disorder symptoms including daytime falling asleep, sleepiness and snoring at the population level. (2) Methods: We used data from 1487 adults aged 20 and above attending the Jiangsu Nutrition Study. At baseline in 2002, dietary magnesium was assessed by 3-day weighed food records. At follow-up in 2007, sleep disorder symptoms, including daytime falling asleep, sleepiness and snoring at night, were gathered using a sleep questionnaire. (3) Results: The mean intake of magnesium was 332.5 mg/day. In total, 5.3%, 13.2% and 35.7% of the subjects reported daytime falling asleep, daytime sleepiness, and snoring during sleep, respectively. Compared with the lowest quartile of magnesium intake, the highest quartile was associated with decreased likelihood of falling asleep (odds ratio (OR) 0.12 (0.02, 0.57)) in women but not in men after adjusting for demographic, anthropometric, lifestyle factors, hypertension, and overall dietary patterns. No associations were found between dietary magnesium intake and daytime sleepiness nor night snoring in either gender. (4) Conclusions: Dietary magnesium intake may have long-term benefits in reducing the likelihood of daytime falling asleep in women

SSRI antidepressant use potentiates weight gain in the context of unhealthy lifestyles : results from a 4-year Australian follow-up study

Objective: To examine the association between antidepressant use and weight gain, as well as the interaction with lifestyle factors. Design: Longitudinal study. Setting and participants: We used data from 2334 adults from two stages (4.4 years apart) of the North West Adelaide Health Study, including validated diet and lifestyle questionnaires, measured body weight and linked pharmaceutical prescription data. Main outcome measures: Body weight change. Results 188 (8.1%) participants had a mean annual number of 1–2 antidepressant prescriptions, and 212 (9.1%) had over two prescriptions. The mean annual weight gain was 0.12, 0.18 and 0.28 kg in non-users, low (1–2 prescriptions/year) and high (>2 prescriptions/ year) antidepressant users, respectively. In multivariable regression models, antidepressant use was positively associated with weight gain: high antidepressant users gained an extra 0.22 (95% CI 0.00 to 0.44) kg per year. This association was mainly due to selective serotonin reuptake inhibitor (SSRI) use. High SSRI users gained 0.48 (95% CI 0.20 to 0.76) kg more than non-users. There was no association between tricyclic or other antidepressant use and weight gain. The association between SSRI use and weight gain was stronger among those with high intake of Western diet, greater sedentary activity, and who smoked. Conclusions: SSRIs use was associated with weight gain in the presence of unhealthy behaviours including Western diet, sedentarism and smoking