Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants

Alsophis rufiventris

Number of Pages: 4Integrative BiologyGeological Science

Beyond transcoherent states: Field states for effecting optimal coherent rotations on single or multiple qubits

Semiclassically, laser pulses can be used to implement arbitrary transformations on atomic systems; quantum mechanically, residual atom-field entanglement spoils this promise. Transcoherent states are field states that fix this problem in the fully quantized regime by generating perfect coherence in an atom initially in its ground or excited state. We extend this fully quantized paradigm in four directions: First, we introduce field states that transform an atom from its ground or excited state to any point on the Bloch sphere without residual atom-field entanglement. The best strong pulses for carrying out rotations by angle $\theta$ are are squeezed in photon-number variance by a factor of $\rm{sinc}\theta$. Next, we investigate implementing rotation gates, showing that the optimal Gaussian field state for enacting a $\theta$ pulse on an atom in an arbitrary, unknown initial state is number squeezed by less: $\rm{sinc}\tfrac{\theta}{2}$. Third, we extend these investigations to fields interacting with multiple atoms simultaneously, discovering once again that number squeezing by $\tfrac{\pi}{2}$ is optimal for enacting $\tfrac{\pi}{2}$ pulses on all of the atoms simultaneously, with small corrections on the order of the ratio of the number of atoms to the average number of photons. Finally, we find field states that best perform arbitrary rotations by $\theta$ through nonlinear interactions involving $m$-photon absorption, where the same optimal squeezing factor is found to be $\rm{sinc}\theta$. Backaction in a wide variety of atom-field interactions can thus be mitigated by squeezing the control fields by optimal amounts.Comment: Updated formatting following acceptance in Quantu

Prospects for Mirage Mediation

Mirage mediation reduces the fine-tuning in the minimal supersymmetric standard model by dynamically arranging a cancellation between anomaly-mediated and modulus-mediated supersymmetry breaking. We explore the conditions under which a mirage "messenger scale" is generated near the weak scale and the little hierarchy problem is solved. We do this by explicitly including the dynamics of the SUSY-breaking sector needed to cancel the cosmological constant. The most plausible scenario for generating a low mirage scale does not readily admit an extra-dimensional interpretation. We also review the possibilities for solving the mu/Bmu problem in such theories, a potential hidden source of fine-tuning.Comment: 14 page

Purely Four-dimensional Viable Anomaly Mediation

Anomaly mediation of supersymmetry breaking solves the supersymmetric flavor problem thanks to its ultraviolet-insensitivity. However, it suffers from two problems: sleptons have negative masses-squared, and there are likely bulk moduli that spoil the framework. Here, we present the first fully ultraviolet-insensitive model of anomaly mediation with positive slepton masses-squared in a purely four-dimensional framework. Our model is based on the additional D-term contributions to the sparticle masses, and the conformal sequestering mechanism.Comment: 7 pages, Uses RevTex4 (included). References modifie

Mini-chromosome maintenance complexes form a filament to remodel DNA structure and topology.

Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins during G1 and S phases. Here, we report an unusually wide left-handed filament structure for an archaeal MCM, as determined by X-ray and electron microscopy. The crystal structure reveals that an α-helix bundle formed between two neighboring subunits plays a critical role in filament formation. The filament has a remarkably strong electro-positive surface spiraling along the inner filament channel for DNA binding. We show that this MCM filament binding to DNA causes dramatic DNA topology change. This newly identified function of MCM to change DNA topology may imply a wider functional role for MCM in DNA metabolisms beyond helicase function. Finally, using yeast genetics, we show that the inter-subunit interactions, important for MCM filament formation, play a role for cell growth and survival

On the rate of black hole binary mergers in galactic nuclei due to dynamical hardening

We assess the contribution of dynamical hardening by direct three-body scattering interactions to the rate of stellar-mass black hole binary (BHB) mergers in galactic nuclei. We derive an analytic model for the single-binary encounter rate in a nucleus with spherical and disk components hosting a super-massive black hole (SMBH). We determine the total number of encounters $N_{\rm GW}$ needed to harden a BHB to the point that inspiral due to gravitational wave emission occurs before the next three-body scattering event. This is done independently for both the spherical and disk components. Using a Monte Carlo approach, we refine our calculations for $N_{\rm GW}$ to include gravitational wave emission between scattering events. For astrophysically plausible models we find that typically $N_{\rm GW} \lesssim$ 10. We find two separate regimes for the efficient dynamical hardening of BHBs: (1) spherical star clusters with high central densities, low velocity dispersions and no significant Keplerian component; and (2) migration traps in disks around SMBHs lacking any significant spherical stellar component in the vicinity of the migration trap, which is expected due to effective orbital inclination reduction of any spherical population by the disk. We also find a weak correlation between the ratio of the second-order velocity moment to velocity dispersion in galactic nuclei and the rate of BHB mergers, where this ratio is a proxy for the ratio between the rotation- and dispersion-supported components. Because disks enforce planar interactions that are efficient in hardening BHBs, particularly in migration traps, they have high merger rates that can contribute significantly to the rate of BHB mergers detected by the advanced Laser Interferometer Gravitational-Wave Observatory.Comment: 13 pages, 9 figures, accepted for publication in MNRA

Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion

The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants. © 2018, The Author(s)

Phonon-Assisted Ballistic Current From First Principles Calculations

The bulk photovoltaic effect (BPVE) refers to current generation due to illumination by light in a homogeneous bulk material lacking inversion symmetry. In addition to the intensively studied shift current, the ballistic current, which originates from asymmetric carrier generation due to scattering processes, also constitutes an important contribution to the overall kinetic model of the BPVE. In this letter, we use a perturbative approach to derive a formula for the ballistic current resulting from the intrinsic electron-phonon scattering in a form amenable to first-principles calculation. We then implement the theory and calculate the ballistic current of the prototypical BPVE material \ch{BaTiO3} using quantum-mechanical density functional theory. The magnitude of the ballistic current is comparable to that of shift current, and the total spectrum (shift plus ballistic) agrees well with the experimentally measured photocurrents. Furthermore, we show that the ballistic current is sensitive to structural change, which could benefit future photovoltaic materials design