Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi.

Erwinia toletana was first reported in 2004 as a bacterial species isolated from olive knots caused by the plant bacterium Pseudomonas savastanoi pv. savastanoi. Recent studies have shown that the presence of this bacterium in the olive knot environment increases the virulence of the disease, indicating possible interspecies interactions with P. savastanoi pv. savastanoi. Here, we report the first draft genome sequence of an E. toletana strain.D.P.D.S. was the beneficiary of an ICGEB fellowship. The laboratory of V.V. was financed by Progetto AGER and ICGEB core funding

AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens

This is the final version. Available on open access from the Microbiology Society via the DOI in this recordAzelaic acid is a dicarboxylic acid that has recently been shown to play a role in plant-bacteria signalling and also occurs naturally in several cereals. Several bacteria have been reported to be able to utilize azelaic acid as a unique source of carbon and energy, including Pseudomonas nitroreducens. In this study, we utilize P. nitroreducens as a model organism to study bacterial degradation of and response to azelaic acid. We report genetic evidence of azelaic acid degradation and the identification of a transcriptional regulator that responds to azelaic acid in P. nitroreducens DSM 9128. Three mutants possessing transposons in genes of an acyl-CoA ligase, an acyl-CoA dehydrogenase and an isocitrate lyase display a deficient ability in growing in azelaic acid. Studies on transcriptional regulation of these genes resulted in the identification of an IclR family repressor that we designated as AzeR, which specifically responds to azelaic acid. A bioinformatics survey reveals that AzeR is confined to a few proteobacterial genera that are likely to be able to degrade and utilize azelaic acid as the sole source of carbon and energy

Transversality-Enforced Tight-Binding Model for 3D Photonic Crystals aided by Topological Quantum Chemistry

Tight-binding models can accurately predict the band structure and topology of crystalline systems and they have been heavily used in solid-state physics due to their versatility and low computational cost. It is quite straightforward to build an accurate tight-binding model of any crystalline system using the maximally localized Wannier functions of the crystal as a basis. In 1D and 2D photonic crystals, it is possible to express the wave equation as two decoupled scalar eigenproblems where finding a basis of maximally localized Wannier functions is feasible using standard Wannierization methods. Unfortunately, in 3D photonic crystals, the vectorial nature of the electromagnetic solutions cannot be avoided. This precludes the construction of a basis of maximally localized Wannier functions via usual techniques. In this work, we show how to overcome this problem by using topological quantum chemistry which will allow us to express the band structure of the photonic crystal as a difference of elementary band representations. This can be achieved by the introduction of a set of auxiliary modes, as recently proposed by Solja\v{c}i\'c et. al., which regularize the $\Gamma$-point obstruction arising from transversality constraint of the Maxwell equations. The decomposition into elementary band representations allows us to isolate a set of pseudo-orbitals that permit us to construct an accurate transversality-enforced tight-binding model (TETB) that matches the dispersion, symmetry content, and topology of the 3D photonic crystal under study. Moreover, we show how to introduce the effects of a gyrotropic bias in the framework, modeled via non-minimal coupling to a static magnetic field. Our work provides the first systematic method to analytically model the photonic bands of the lowest transverse modes over the entire BZ via a TETB model.Comment: 3 figure

New On Line Resource for Psycholinguistic

Picture naming is a widely used technique in psycholinguistic studies. Here, we describe new on-line resources that our project has compiled and made available to researchers on the world wide web at http://crl.ucsd.edu/~aszekely/ipnp/. The website provides access to a wide range of picture stimuli and related norms in seven languages. Picture naming norms, including indices of name agreement and latency, for 520 black-and-white drawings of common objects and 275 concrete transitive and intransitive actions are presented. Norms for age-of-acquisition, word-frequency, familiarity, goodness-of-depiction, and visual complexity are included. An on-line database query system can be used to select a specific range of stimuli, based on parameters of interest for a wide range of studies on healthy and clinical populations, as well as studies of language development

Genomic features of bacterial adaptation to plants

Author(s): Levy, A; Salas Gonzalez, I; Mittelviefhaus, M; Clingenpeel, S; Herrera Paredes, S; Miao, J; Wang, K; Devescovi, G; Stillman, K; Monteiro, F; Rangel Alvarez, B; Lundberg, DS; Lu, TY; Lebeis, S; Jin, Z; McDonald, M; Klein, AP; Feltcher, ME; Rio, TG; Grant, SR; Doty, SL; Ley, RE; Zhao, B; Venturi, V; Pelletier, DA; Vorholt, JA; Tringe, SG; Woyke, T; Dangl, JL | Abstract: © 2017 The Author(s). Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering

Decoding the Folding of Burkholderia glumae Lipase: Folding Intermediates En Route to Kinetic Stability

The lipase produced by Burkholderia glumae folds spontaneously into an inactive near-native state and requires a periplasmic chaperone to reach its final active and secretion-competent fold. The B. glumae lipase-specific foldase (Lif) is classified as a member of the steric-chaperone family of which the propeptides of α-lytic protease and subtilisin are the best known representatives. Steric chaperones play a key role in conferring kinetic stability to proteins. However, until present there was no solid experimental evidence that Lif-dependent lipases are kinetically trapped enzymes. By combining thermal denaturation studies with proteolytic resistance experiments and the description of distinct folding intermediates, we demonstrate that the native lipase has a kinetically stable conformation. We show that a newly discovered molten globule-like conformation has distinct properties that clearly differ from those of the near-native intermediate state. The folding fingerprint of Lif-dependent lipases is put in the context of the protease-prodomain system and the comparison reveals clear differences that render the lipase-Lif systems unique. Limited proteolysis unveils structural differences between the near-native intermediate and the native conformation and sets the stage to shed light onto the nature of the kinetic barrier

Theorising terminology development: Frames from language acquisition and the philosophy of science

The manner in which our conceptualisation and practice of terminology development can be informed by processes of knowledge change in child language development and a paradigm shift in disciplines, has been relatively underexplored. As a result, insights into what appears to be fundamental processes of knowledge change have not been employed to reflect on terminology development, its dynamics, requirements and relationship to related fields. In this article, frames of knowledge change in child language development and the philosophy of science are used to examine terminology development as knowledge growth that is signalled lexico-semantically through a range of transformations: addition, deletion, redefinition and reorganisation. The analysis is shown to have implications for work procedures, expertise types, critique, and for the relationships between terminology development and translating