Synthetic gene design - The rationale for codon optimization and implications for molecular pharming in plants.

Degeneracy in the genetic code allows multiple codon sequences to encode the same protein. Codon usage bias in genes is the term given to the preferred use of particular synonymous codons. Synonymous codon substitutions had been regarded as "silent" as the primary structure of the protein was not affected; however, it is now accepted that synonymous substitutions can have a significant effect on heterologous protein expression. Codon optimization, the process of altering codons within the gene sequence to improve recombinant protein expression, has become widely practised. Multiple inter-linked factors affecting protein expression need to be taken into consideration when optimizing a gene sequence. Over the years, various computer programmes have been developed to aid in the gene sequence optimization process. However, as the rulebook for altering codon usage to affect protein expression is still not completely understood, it is difficult to predict which strategy, if any, will design the 'optimal' gene sequence. In this review, codon usage bias and factors affecting codon selection will be discussed and the evidence for codon optimization impact will be reviewed for recombinant protein expression using plants as a case study. These developments will be relevant to all recombinant expression systems, however, molecular pharming in plants is an area which has consistently encountered difficulties with low levels of recombinant protein expression, and should benefit from an evidence based rational approach to synthetic gene design

The Role of International Service-Learning in Facilitating Undergraduate Students’ Self-Exploration

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Oakleaf: an S locus-linked mutation of Primula vulgaris that affects leaf and flower development

•In Primula vulgaris outcrossing is promoted through reciprocal herkogamy with insect-mediated cross-pollination between pin and thrum form flowers. Development of heteromorphic flowers is coordinated by genes at the S locus. To underpin construction of a genetic map facilitating isolation of these S locus genes, we have characterised Oakleaf, a novel S locus-linked mutant phenotype. •We combine phenotypic observation of flower and leaf development, with classical genetic analysis and next-generation sequencing to address the molecular basis of Oakleaf. •Oakleaf is a dominant mutation that affects both leaf and flower development; plants produce distinctive lobed leaves, with occasional ectopic meristems on the veins. This phenotype is reminiscent of overexpression of Class I KNOX-homeodomain transcription factors. We describe the structure and expression of all eight P. vulgaris PvKNOX genes in both wild-type and Oakleaf plants, and present comparative transcriptome analysis of leaves and flowers from Oakleaf and wild-type plants. •Oakleaf provides a new phenotypic marker for genetic analysis of the Primula S locus. We show that none of the Class I PvKNOX genes are strongly upregulated in Oakleaf leaves and flowers, and identify cohorts of 507 upregulated and 314 downregulated genes in the Oakleaf mutant

Argo real-time quality control intercomparison

The real-time quality control (RTQC) methods applied to Argo profiling float data by the United Kingdom (UK) Met Office, the United States (US) Fleet Numerical Meteorology and Oceanography Centre, the Australian Bureau of Meteorology and the Coriolis Centre are compared and contrasted. Data are taken from the period 2007 to 2011 inclusive and RTQC performance is assessed with respect to Argo delayed-mode quality control (DMQC). An intercomparison of RTQC techniques is performed using a common data set of profiles from 2010 and 2011. The RTQC systems are found to have similar power in identifying faulty Argo profiles but to vary widely in the number of good profiles incorrectly rejected. The efficacy of individual QC tests are inferred from the results of the intercomparison. Techniques to increase QC performance are discussed

Long-distance remote comparison of ultrastable optical frequencies with 1e-15 instability in fractions of a second

We demonstrate a fully optical, long-distance remote comparison of independent ultrastable optical frequencies reaching a short term stability that is superior to any reported remote comparison of optical frequencies. We use two ultrastable lasers, which are separated by a geographical distance of more than 50 km, and compare them via a 73 km long phase-stabilized fiber in a commercial telecommunication network. The remote characterization spans more than one optical octave and reaches a fractional frequency instability between the independent ultrastable laser systems of 3e-15 in 0.1 s. The achieved performance at 100 ms represents an improvement by one order of magnitude to any previously reported remote comparison of optical frequencies and enables future remote dissemination of the stability of 100 mHz linewidth lasers within seconds.Comment: 7 pages, 4 figure

Effects of Policies Designed to Keep Firearms from High-Risk Individuals

This article summarizes and critiques available evidence from studies published between 1999 and August 2014 on the effects of policies designed to keep firearms from high-risk individuals in the United States. Some prohibitions for high-risk individuals (e.g., those under domestic violence restraining orders, violent misdemeanants) and procedures for checking for more types of prohibiting conditions are associated with lower rates of violence. Certain laws intended to prevent prohibited persons from accessing firearms -- rigorous permit-to-purchase, comprehensive background checks, strong regulation and oversight of gun dealers, and requiring gun owners to promptly report lost or stolen firearms -- are negatively associated with the diversion of guns to criminals. Future research is needed to examine whether these laws curtail nonlethal gun violence and whether the effects of expanding prohibiting conditions for firearm possession are modified by the presence of policies to prevent diversion

Field-test of a robust, portable, frequency-stable laser

We operate a frequency-stable laser in a non-laboratory environment where the test platform is a passenger vehicle. We measure the acceleration experienced by the laser and actively correct for it to achieve a system acceleration sensitivity of $\Delta f / f$ = $11(2) \times 10^{-12}$/g, $6(2) \times 10^{-12}$/g, and $4(1) \times 10^{-12}$/g for accelerations in three orthogonal directions at 1 Hz. The acceleration spectrum and laser performance are evaluated with the vehicle both stationary and moving. The laser linewidth in the stationary vehicle with engine idling is 1.7(1) Hz

Making optical atomic clocks more stable with 10−1610^{-16} level laser stabilization

The superb precision of an atomic clock is derived from its stability. Atomic clocks based on optical (rather than microwave) frequencies are attractive because of their potential for high stability, which scales with operational frequency. Nevertheless, optical clocks have not yet realized this vast potential, due in large part to limitations of the laser used to excite the atomic resonance. To address this problem, we demonstrate a cavity-stabilized laser system with a reduced thermal noise floor, exhibiting a fractional frequency instability of $2 \times 10^{-16}$. We use this laser as a stable optical source in a Yb optical lattice clock to resolve an ultranarrow 1 Hz transition linewidth. With the stable laser source and the signal to noise ratio (S/N) afforded by the Yb optical clock, we dramatically reduce key stability limitations of the clock, and make measurements consistent with a clock instability of $5 \times 10^{-16} / \sqrt{\tau}$

Demonstration of a Transportable 1 Hz-Linewidth Laser

We present the setup and test of a transportable clock laser at 698 nm for a strontium lattice clock. A master-slave diode laser system is stabilized to a rigidly mounted optical reference cavity. The setup was transported by truck over 400 km from Braunschweig to D\"usseldorf, where the cavity-stabilized laser was compared to a stationary clock laser for the interrogation of ytterbium (578 nm). Only minor realignments were necessary after the transport. The lasers were compared by a Ti:Sapphire frequency comb used as a transfer oscillator. The thus generated virtual beat showed a combined linewidth below 1 Hz (at 1156 nm). The transport back to Braunschweig did not degrade the laser performance, as was shown by interrogating the strontium clock transition.Comment: 3 pages, 4 figure