Genomic Organization, Molecular Diversification, and Evolution of Antimicrobial Peptide Myticin-C Genes in the Mussel (Mytilus galloprovincialis)

Myticin-C is a highly variable antimicrobial peptide associated to immune response in Mediterranean mussel (Mytilus galloprovincialis). In this study, we tried to ascertain the genetic organization and the mechanisms underlying myticin-C variation and evolution of this gene family. We took advantage of the large intron size variation to find out the number of myticin-C genes. Using fragment analysis a maximum of four alleles was detected per individual at both introns in a large mussel sample suggesting a minimum of two myticin-C genes. The transmission pattern of size variants in two full-sib families was also used to ascertain the number of myticin-C genes underlying the variability observed. Results in both families were in accordance with two myticin-C genes organized in tandem. A more detailed analysis of myticin-C variation was carried out by sequencing a large sample of complementary (cDNA) and genomic DNA (gDNA) in 10 individuals. Two basic sequences were detected at most individuals and several sequences were constituted by combination of two different basic sequences, strongly suggesting somatic recombination or gene conversion. Slight within-basic sequence variation detected in all individuals was attributed to somatic mutation. Such mutations were more frequently at the C-terminal domain and mostly determined non-synonymous substitutions. The mature peptide domain showed the highest variation both in the whole cDNA and in the basic-sequence samples, which is in accordance with the pathogen recognition function associated to this domain. Although most tests suggested neutrality for myticin-C variation, evidence indicated positive selection in the mature peptide and C-terminal region. Three main highly supported clusters were observed when reconstructing phylogeny on basic sequences, meiotic recombination playing a relevant role on myticin-C evolution. This study demonstrates that mechanisms to generate molecular variation similar to that observed in vertebrates are also operating in molluscs

Arabidopsis CULLIN3 Genes Regulate Primary Root Growth and Patterning by Ethylene-Dependent and -Independent Mechanisms

CULLIN3 (CUL3) together with BTB-domain proteins form a class of Cullin-RING ubiquitin ligases (called CRL3s) that control the rapid and selective degradation of important regulatory proteins in all eukaryotes. Here, we report that in the model plant Arabidopsis thaliana, CUL3 regulates plant growth and development, not only during embryogenesis but also at post-embryonic stages. First, we show that CUL3 modulates the emission of ethylene, a gaseous plant hormone that is an important growth regulator. A CUL3 hypomorphic mutant accumulates ACS5, the rate-limiting enzyme in ethylene biosynthesis and as a consequence exhibits a constitutive ethylene response. Second, we provide evidence that CUL3 regulates primary root growth by a novel ethylene-dependant pathway. In particular, we show that CUL3 knockdown inhibits primary root growth by reducing root meristem size and cell number. This phenotype is suppressed by ethylene-insensitive or resistant mutations. Finally, we identify a function of CUL3 in distal root patterning, by a mechanism that is independent of ethylene. Thus, our work highlights that CUL3 is essential for the normal division and organisation of the root stem cell niche and columella root cap cells

Outer membrane protein folding from an energy landscape perspective

The cell envelope is essential for the survival of Gram-negative bacteria. This specialised membrane is densely packed with outer membrane proteins (OMPs), which perform a variety of functions. How OMPs fold into this crowded environment remains an open question. Here, we review current knowledge about OFMP folding mechanisms in vitro and discuss how the need to fold to a stable native state has shaped their folding energy landscapes. We also highlight the role of chaperones and the β-barrel assembly machinery (BAM) in assisting OMP folding in vivo and discuss proposed mechanisms by which this fascinating machinery may catalyse OMP folding

An ant colony-based matheuristic approach for solving a class of vehicle routing problems

We propose a matheuristic approach to solve several types of vehicle routing problems (VRP). In the VRP, a fleet of capacitated vehicles visits a set of customers exactly once to satisfy their demands while obeying problem specific characteristics and constraints such as homogeneous or heterogeneous fleet, customer service time windows, single or multiple depots. The proposed matheuristic is based on an ant colony optimization (ACO) algorithm which constructs good feasible solutions. The routes obtained in the ACO procedure are accumulated in a pool as columns which are then fed to an integer programming (IP) optimizer that solves the set-partitioning (-covering) formulation of the particular VRP. The (near-)optimal solution found by the solver is used to reinforce the pheromone trails in ACO. This feedback mechanism between the ACO and IP procedures helps the matheuristic better converge to high quality solutions. We test the performance of the proposed matheuristic on different VRP variants using the well-known benchmark instances from the literature. Our computational experiments reveal competitive results: we report 6 new best solutions and meet the best-known solution in 120 instances out of 193

An ant colony-based matheuristic approach for solving a class of vehicle routing problems

We propose a matheuristic approach to solve several types of vehicle routing problems (VRP). In the VRP, a fleet of capacitated vehicles visits a set of customers exactly once to satisfy their demands while obeying problem specific characteristics and constraints such as homogeneous or heterogeneous fleet, customer service time windows, single or multiple depots. The proposed matheuristic is based on an ant colony optimization (ACO) algorithm which constructs good feasible solutions. The routes obtained in the ACO procedure are accumulated in a pool as columns which are then fed to an integer programming (IP) optimizer that solves the set-partitioning (-covering) formulation of the particular VRP. The (near-)optimal solution found by the solver is used to reinforce the pheromone trails in ACO. This feedback mechanism between the ACO and IP procedures helps the matheuristic better converge to high quality solutions. We test the performance of the proposed matheuristic on different VRP variants using well-known benchmark instances from the literature. Our computational experiments reveal competitive results: we report six new best solutions and meet the best-known solution in 120 instances out of 193

A scalable multi-photon coincidence detector based on superconducting nanowires

© 2018 The Author(s). Coincidence detection of single photons is crucial in numerous quantum technologies and usually requires multiple time-resolved single-photon detectors. However, the electronic readout becomes a major challenge when the measurement basis scales to large numbers of spatial modes. Here, we address this problem by introducing a two-terminal coincidence detector that enables scalable readout of an array of detector segments based on superconducting nanowire microstrip transmission line. Exploiting timing logic, we demonstrate a sixteen-element detector that resolves all 136 possible single-photon and two-photon coincidence events. We further explore the pulse shapes of the detector output and resolve up to four-photon events in a four-element device, giving the detector photon-number-resolving capability. This new detector architecture and operating scheme will be particularly useful for multi-photon coincidence detection in large-scale photonic integrated circuits