Performance of Solid-State Sensors for Continuous, Real-Time Measurement of Soil CO\u3csub\u3e2\u3c/sub\u3e Concentrations

Recent advances in sensor technology provide a robust capability for continuous measurement of soil gases. The performance of solid-state CO2 sensors (Model GMM220 series, Vaisala, Inc., Helsinki, Finland) was evaluated in laboratory, greenhouse, and irrigated winter wheat (Triticum aestivum L.). In ambient CO2 concentration, the GMM222 sensor averaged 427 ± 8.3 μL L−1. Under variable CO2 concentrations, the sensor was slightly lower than concentrations measured with an infrared gas analyzer (IRGA). In greenhouse pots planted with triticale (Triticale hexaploide Lart.) and an agricultural field of irrigated winter wheat, soil CO2 concentration exceeded the 10,000 μL L−1 limit of the GMM222. Alternatively, the GMM221 sensor, designed to measure between 0 and 20,000 μL L−1, showed soil CO2 concentrations were between 14,000 and 16,000 μL L−1. The GMM222 accurately measures real-time soil CO2 concentrations under field conditions that were within the sensor detection limit. However, periods of high biological soil activity require the GMM221 sensor with a higher detection limit

AnnoTALE : bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities

Mechanics of extended masses in general relativity

The "external" or "bulk" motion of extended bodies is studied in general relativity. Compact material objects of essentially arbitrary shape, spin, internal composition, and velocity are allowed as long as there is no direct (non-gravitational) contact with other sources of stress-energy. Physically reasonable linear and angular momenta are proposed for such bodies and exact equations describing their evolution are derived. Changes in the momenta depend on a certain "effective metric" that is closely related to a non-perturbative generalization of the Detweiler-Whiting R-field originally introduced in the self-force literature. If the effective metric inside a self-gravitating body can be adequately approximated by an appropriate power series, the instantaneous gravitational force and torque exerted on it is shown to be identical to the force and torque exerted on an appropriate test body moving in the effective metric. This result holds to all multipole orders. The only instantaneous effect of a body's self-field is to finitely renormalize the "bare" multipole moments of its stress-energy tensor. The MiSaTaQuWa expression for the gravitational self-force is recovered as a simple application. A gravitational self-torque is obtained as well. Lastly, it is shown that the effective metric in which objects appear to move is approximately a solution to the vacuum Einstein equation if the physical metric is an approximate solution to Einstein's equation linearized about a vacuum background.Comment: 39 pages, 2 figures; fixed equation satisfied by the Green function used to construct the effective metri

On Global Conservation Laws at Null Infinity

The ``standard'' expressions for total energy, linear momentum and also angular momentum of asymptotically flat Bondi metrics at null infinity are also obtained from differential conservation laws on asymptotically flat backgrounds, derived from a quadratic Lagrangian density by methods currently used in classical field theory. It is thus a matter of taste and commodity to use or not to use a reference spacetime in defining these globally conserved quantities. Backgrounds lead to N\oe ther conserved currents; the use of backgrounds is in line with classical views on conservation laws. Moreover, the conserved quantities are in principle explicitly related to the sources of gravity through Einstein's equations, while standard definitions are not. The relations depend, however, on a rule for mapping spacetimes on backgrounds

Quasi-Local Gravitational Energy

A dynamically preferred quasi-local definition of gravitational energy is given in terms of the Hamiltonian of a `2+2' formulation of general relativity. The energy is well-defined for any compact orientable spatial 2-surface, and depends on the fundamental forms only. The energy is zero for any surface in flat spacetime, and reduces to the Hawking mass in the absence of shear and twist. For asymptotically flat spacetimes, the energy tends to the Bondi mass at null infinity and the \ADM mass at spatial infinity, taking the limit along a foliation parametrised by area radius. The energy is calculated for the Schwarzschild, Reissner-Nordstr\"om and Robertson-Walker solutions, and for plane waves and colliding plane waves. Energy inequalities are discussed, and for static black holes the irreducible mass is obtained on the horizon. Criteria for an adequate definition of quasi-local energy are discussed.Comment: 16 page

Post-Newtonian Gravitational Radiation

1 Introduction 2 Multipole Decomposition 3 Source Multipole Moments 4 Post-Minkowskian Approximation 5 Radiative Multipole Moments 6 Post-Newtonian Approximation 7 Point-Particles 8 ConclusionComment: 46 pages, in Einstein's Field Equations and Their Physical Implications, B. Schmidt (Ed.), Lecture Notes in Physics, Springe

Spontaneous fluctuations in a magnetic Fe/Gd skyrmion lattice

Magnetic skyrmions are topological spin textures that exhibit classical or quantum quasiparticle behavior. A substantial amount of research has occurred in this field, both because of their unique electromagnetic properties and potential application for future nonvolatile memory storage applications, as well as fundamental questions on their topology and unique magnetic phases. Here, we investigate the fluctuation properties of a magnetic Fe/Gd skyrmion lattice, using short-pulsed x rays. We first measure spontaneous fluctuations of the skyrmion lattice phase and find an inherent, collective mode showing an underdamped oscillation with a relaxation of a couple of nanoseconds. Further observations track the response towards the continuous phase transition and a critical-like slowing down of fluctuations is observed well before the critical point. These results suggest that the skyrmion lattice phase never fully freezes into a static crystal. This constant state of fluctuation indicates that the physics of topological magnetic phases may have more in common with high-temperature superconductors with disorder

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

Prokaryotic type II CRISPR-Cas systems can be adapted to enable targeted genome modifications across a range of eukaryotes.1–7. Here we engineer this system to enable RNA-guided genome regulation in human cells by tethering transcriptional activation domains either directly to a nuclease-null Cas9 protein or to an aptamer-modified single guide RNA (sgRNA). Using this functionality we developed a novel transcriptional activation–based assay to determine the landscape of off-target binding of sgRNA:Cas9 complexes and compared it with the off-target activity of transcription activator–like (TAL) effector proteins8, 9. Our results reveal that specificity profiles are sgRNA dependent, and that sgRNA:Cas9 complexes and 18-mer TAL effector proteins can potentially tolerate 1–3 and 1–2 target mismatches, respectively. By engineering a requirement for cooperativity through offset nicking for genome editing or through multiple synergistic sgRNAs for robust transcriptional activation, we suggest methods to mitigate off-target phenomena. Our results expand the versatility of the sgRNA:Cas9 tool and highlight the critical need to engineer improved specificity