CloneQC: lightweight sequence verification for synthetic biology

Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source

Precision neutron interferometric measurement of the nd coherent neutron scattering length and consequences for models of three-nucleon forces

We have performed the first high precision measurement of the coherent neutron scattering length of deuterium in a pure sample using neutron interferometry. We find b_nd = (6.665 +/- 0.004) fm in agreement with the world average of previous measurements using different techniques, b_nd = (6.6730 +/- 0.0045) fm. We compare the new world average for the nd coherent scattering length b_nd = (6.669 +/- 0.003) fm to calculations of the doublet and quartet scattering lengths from several modern nucleon-nucleon potential models with three-nucleon force (3NF) additions and show that almost all theories are in serious disagreement with experiment. This comparison is a more stringent test of the models than past comparisons with the less precisely-determined nuclear doublet scattering length of a_nd = (0.65 +/- 0.04) fm.Comment: 4 pages, 4 figure

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p

Titan's lakes chemical composition: sources of uncertainties and variability

Between 2004 and 2007 the instruments of the CASSINI spacecraft discovered hydrocarbon lakes in the polar regions of Titan. We have developed a lake-atmosphere equilibrium model allowing the determination of the chemical composition of these liquid areas. The model is based on uncertain thermodynamic data and precipitation rates of organic species predicted to be present in the lakes and seas that are subject to spatial and temporal variations. Here we explore and discuss the influence of these uncertainties and variations. The errors and uncertainties relevant to thermodynamic data are simulated via Monte-Carlo simulations. Global Circulation Models (GCM) are also employed in order to investigate the possibility of chemical asymmetry between the south and the north poles, due to differences in precipitation rates. We find that mole fractions of compounds in the liquid phase have a high sensitivity to thermodynamic data used as inputs, in particular molar volumes and enthalpies of vaporization. When we combine all considered uncertainties, the ranges of obtained mole fractions are rather large (up to ~8500%) but the distributions of values are narrow. The relative standard deviations remain between 10% and ~300% depending on the compound considered. Compared to other sources of uncertainties and variability, deviation caused by surface pressure variations are clearly negligible, remaining of the order of a few percent up to ~20%. Moreover no significant difference is found between the composition of lakes located in north and south poles. Because the theory of regular solutions employed here is sensitive to thermodynamic data and is not suitable for polar molecules such as HCN and CH3CN, our work strongly underlines the need for experimental simulations and the improvement of Titan's atmospheric models.Comment: Accepted in Planetary and Space Scienc

What is going on around here? Intolerance of uncertainty predicts threat generalization

Attending to stimuli that share perceptual similarity to learned threats is an adaptive strategy. However, prolonged threat generalization to cues signalling safety is considered a core feature of pathological anxiety. One potential factor that may sustain over-generalization is sensitivity to future threat uncertainty. To assess the extent to which Intolerance of Uncertainty (IU) predicts threat generalization, we recorded skin conductance in 54 healthy participants during an associative learning paradigm, where threat and safety cues varied in perceptual similarity. Lower IU was associated with stronger discrimination between threat and safety cues during acquisition and extinction. Higher IU, however, was associated with generalized responding to threat and safety cues during acquisition, and delayed discrimination between threat and safety cues during extinction. These results were specific to IU, over and above other measures of anxious disposition. These findings highlight: (1) a critical role of uncertainty-based mechanisms in threat generalization, and (2) IU as a potential risk factor for anxiety disorder development

Refractive Index of Humid Air in the Infrared: Model Fits

The theory of summation of electromagnetic line transitions is used to tabulate the Taylor expansion of the refractive index of humid air over the basic independent parameters (temperature, pressure, humidity, wavelength) in five separate infrared regions from the H to the Q band at a fixed percentage of Carbon Dioxide. These are least-squares fits to raw, highly resolved spectra for a set of temperatures from 10 to 25 C, a set of pressures from 500 to 1023 hPa, and a set of relative humidities from 5 to 60%. These choices reflect the prospective application to characterize ambient air at mountain altitudes of astronomical telescopes.Comment: Corrected exponents of c0ref, c1ref and c1p in Table

Efficiency Analysis of a Hall Thruster Operating with Krypton and Xenon

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/76560/1/AIAA-19613-425.pd

SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes

Synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE) generates combinatorial genomic diversity through rearrangements at designed recombinase sites. We applied SCRaMbLE to yeast synthetic chromosome arm synIXR (43 recombinase sites) and then used a computational pipeline to infer or unscramble the sequence of recombinations that created the observed genomes. Deep sequencing of 64 synIXR SCRaMbLE strains revealed 156 deletions, 89 inversions, 94 duplications, and 55 additional complex rearrangements; several duplications are consistent with a double rolling circle mechanism. Every SCRaMbLE strain was unique, validating the capability of SCRaMbLE to explore a diverse space of genomes. Rearrangements occurred exclusively at designed loxPsym sites, with no significant evidence for ectopic rearrangements or mutations involving synthetic regions, the 99% nonsynthetic nuclear genome, or the mitochondrial genome. Deletion frequencies identified genes required for viability or fast growth. Replacement of 3′ UTR by non-UTR sequence had surprisingly little effect on fitness. SCRaMbLE generates genome diversity in designated regions, reveals fitness constraints, and should scale to simultaneous evolution of multiple synthetic chromosomes.</jats:p

Ultraviolet Spectroscopy of Comet 9P/Tempel 1 with Alice/Rosetta during the Deep Impact Encounter

We report on spectroscopic observations of periodic comet 9P/Tempel 1 by the Alice ultraviolet spectrograph on the Rosetta spacecraft in conjunction with NASA's Deep Impact mission. Our objectives were to measure an increase in atomic and molecular emissions produced by the excavation of volatile sub-surface material. We unambiguously detected atomic oxygen emission from the quiescent coma but no enhancement at the 10% (1-sigma) level following the impact. We derive a quiescent water production rate of 9 x 10^27 molecules per second with an estimated uncertainty of 30%. Our upper limits to the volatiles produced by the impact are consistent with other estimates.Comment: 11 pages, 4 postscript figures. Accepted for publication in Icarus special issue on Deep Impac