The Sensitivity of PsbS to the Environment, Residue by Residue

Under strong sunlight, plants avoid photooxidation by quenching the excess absorbed energy. Quenching is triggered by PsbS, a membrane protein that is activated and deactivated by the light-dependent pH changes in the thylakoid lumen. The mechanism of action of this protein is unknown, but it was suggested that several glutamates act as pH sensors. However, the pK a of glutamate is several pH units below the physiological values in the lumen. Thus, how can PsbS sense the pH of the lumen, and how does it respond to it? By applying a nonstandard molecular dynamics method that treats pH explicitly, we show that the lumen-exposed glutamates of PsbS have strongly shifted pK a values and that such shifts are crucial for the pH sensitivity in physiological conditions. We also demonstrate that protonation drives a systematic unfolding of a region key for protein-protein interactions, indicating that PsbS response to pH is a functional conformational switch.publishersversionpublishe

Simple Dynamics on the Brane

We apply methods of dynamical systems to study the behaviour of the Randall-Sundrum models. We determine evolutionary paths for all possible initial conditions in a 2-dimensional phase space and we investigate the set of accelerated models. The simplicity of our formulation in comparison to some earlier studies is expressed in the following: our dynamical system is a 2-dimensional Hamiltonian system, and what is more advantageous, it is free from the degeneracy of critical points so that the system is structurally stable. The phase plane analysis of Randall-Sundrum models with isotropic Friedmann geometry clearly shows that qualitatively we deal with the same types of evolution as in general relativity, although quantitatively there are important differences.Comment: an improved version, 34 pages, 9 eps figure

Generation of entangled coherent states via cross phase modulation in a double electromagnetically induced transparency regime

The generation of an entangled coherent state is one of the most important ingredients of quantum information processing using coherent states. Recently, numerous schemes to achieve this task have been proposed. In order to generate travelling-wave entangled coherent states, cross phase modulation, optimized by optical Kerr effect enhancement in a dense medium in an electromagnetically induced transparency (EIT) regime, seems to be very promising. In this scenario, we propose a fully quantized model of a double-EIT scheme recently proposed [D. Petrosyan and G. Kurizki, {\sl Phys. Rev. A} {\bf 65}, 33833 (2002)]: the quantization step is performed adopting a fully Hamiltonian approach. This allows us to write effective equations of motion for two interacting quantum fields of light that show how the dynamics of one field depends on the photon-number operator of the other. The preparation of a Schr\"odinger cat state, which is a superposition of two distinct coherent states, is briefly exposed. This is based on non-linear interaction via double-EIT of two light fields (initially prepared in coherent states) and on a detection step performed using a $50:50$ beam splitter and two photodetectors. In order to show the entanglement of a generated entangled coherent state, we suggest to measure the joint quadrature variance of the field. We show that the entangled coherent states satisfy the sufficient condition for entanglement based on quadrature variance measurement. We also show how robust our scheme is against a low detection efficiency of homodyne detectors.Comment: 15 pages, 9 figures; extensively revised version; added Section

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus

Clupeiformes, such as sardines and herrings, represent an important share of worldwide fisheries. Among those, the European sardine (Sardina pilchardus, Walbaum 1792) exhibits significant commercial relevance. While the last decade showed a steady and sharp decline in capture levels, recent advances in culture husbandry represent promising research avenues. Yet, the complete absence of genomic resources from sardine imposes a severe bottleneck to understand its physiological and ecological requirements. We generated 69 Gbp of paired-end reads using Illumina HiSeq X Ten and assembled a draft genome assembly with an N50 scaffold length of 25,579 bp and BUSCO completeness of 82.1% (Actinopterygii). The estimated size of the genome ranges between 655 and 850 Mb. Additionally, we generated a relatively high-level liver transcriptome. To deliver a proof of principle of the value of this dataset, we established the presence and function of enzymes (Elovl2, Elovl5, and Fads2) that have pivotal roles in the biosynthesis of long chain polyunsaturated fatty acids, essential nutrients particularly abundant in oily fish such as sardines. Our study provides the first sustainableomics datasetexploitation.from a valuable economic marine teleost species, the European sardine, representing an essential resource for their effective conservation, management, and sustainable exploitation. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.Funding: We acknowledge the North Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) that supported this research through the Coral—Sustainable Ocean Exploitation (reference NORTE-01-0145-FEDER-000036). R.R.d.F. thanks the Danish National Research Foundation for its support of the Center for Macroecology, Evolution, and Climate (grant DNRF96). Acknowledgments: Some computational work was performed on the Abel Supercomputing Cluster (Norwegian metacenter for High Performance Computing (NOTUR) and the University of Oslo) operated by the Research Computing Services group at USIT, the University of Oslo IT-department (http://www.hpc.uio.no/). We would like to thank Jette Bornholdt, Amal Al-Chaer and George Pacheco for help with laboratory procedures, and the Bioinformatics Center of the University of Copenhagen for providing laboratory space. This work is part of the CIIMAR-lead initiative Portugal-Fishomics