Role of PII proteins in nitrogen fixation control of Herbaspirillum seropedicae strain SmR1

<p>Abstract</p> <p>Background</p> <p>The PII protein family comprises homotrimeric proteins which act as transducers of the cellular nitrogen and carbon status in prokaryotes and plants. In <it>Herbaspirillum seropedicae</it>, two PII-like proteins (GlnB and GlnK), encoded by the genes <it>glnB </it>and <it>glnK</it>, were identified. The <it>glnB </it>gene is monocistronic and its expression is constitutive, while <it>glnK </it>is located in the <it>nlmAglnKamtB </it>operon and is expressed under nitrogen-limiting conditions.</p> <p>Results</p> <p>In order to determine the involvement of the <it>H. seropedicae glnB </it>and <it>glnK </it>gene products in nitrogen fixation, a series of mutant strains were constructed and characterized. The <it>glnK^-</it>mutants were deficient in nitrogen fixation and they were complemented by plasmids expressing the GlnK protein or an N-truncated form of NifA. The nitrogenase post-translational control by ammonium was studied and the results showed that the <it>glnK </it>mutant is partially defective in nitrogenase inactivation upon addition of ammonium while the <it>glnB </it>mutant has a wild-type phenotype.</p> <p>Conclusions</p> <p>Our results indicate that GlnK is mainly responsible for NifA activity regulation and ammonium-dependent post-translational regulation of nitrogenase in <it>H. seropedicae</it>.</p

Identification and characterization of PhbF: A DNA binding protein with regulatory role in the PHB metabolism of Herbaspirillum seropedicae SmR1

<p>Abstract</p> <p>Background</p> <p><it>Herbaspirillum seropedicae </it>SmR1 is a nitrogen fixing endophyte associated with important agricultural crops. It produces polyhydroxybutyrate (PHB) which is stored intracellularly as granules. However, PHB metabolism and regulatory control is not yet well studied in this organism.</p> <p>Results</p> <p>In this work we describe the characterization of the PhbF protein from <it>H. seropedicae </it>SmR1 which was purified and characterized after expression in <it>E. coli</it>. The purified PhbF protein was able to bind to eleven putative promoters of genes involved in PHB metabolism in <it>H. seropedicae </it>SmR1. <it>In silico </it>analyses indicated a probable DNA-binding sequence which was shown to be protected in DNA footprinting assays using purified PhbF. Analyses using <it>lacZ </it>fusions showed that PhbF can act as a repressor protein controlling the expression of PHB metabolism-related genes.</p> <p>Conclusions</p> <p>Our results indicate that <it>H. seropedicae </it>SmR1 PhbF regulates expression of <it>phb</it>-related genes by acting as a transcriptional repressor. The knowledge of the PHB metabolism of this plant-associated bacterium may contribute to the understanding of the plant-colonizing process and the organism's resistance and survival <it>in planta</it>.</p

A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana

The mycalesine butterfly Bicyclus anynana, the “Squinting bush brown,” is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).Peer reviewe

Attractor dynamics approach to joint transportation by autonomous robots: theory, implementation and validation on the factory floor

This paper shows how non-linear attractor dynamics can be used to control teams of two autonomous mobile robots that coordinate their motion in order to transport large payloads in unknown environments, which might change over time and may include narrow passages, corners and sharp U-turns. Each robot generates its collision-free motion online as the sensed information changes. The control architecture for each robot is formalized as a non-linear dynamical system, where by design attractor states, i.e. asymptotically stable states, dominate and evolve over time. Implementation details are provided, and it is further shown that odometry or calibration errors are of no significance. Results demonstrate flexible and stable behavior in different circumstances: when the payload is of different sizes; when the layout of the environment changes from one run to another; when the environment is dynamice.g. following moving targets and avoiding moving obstacles; and when abrupt disturbances challenge team behavior during the execution of the joint transportation task.- This work was supported by FCT-Fundacao para a Ciencia e Tecnologia within the scope of the Project PEst-UID/CEC/00319/2013 and by the Ph.D. Grants SFRH/BD/38885/2007 and SFRH/BPD/71874/2010, as well as funding from FP6-IST2 EU-IP Project JAST (Proj. Nr. 003747). We would like to thank the anonymous reviewers, whose comments have contributed to improve the paper

CHY representations for gauge theory and gravity amplitudes with up to three massive particles

We show that a wide class of tree-level scattering amplitudes involving scalars, gauge bosons, and gravitons, up to three of which may be massive, can be expressed in terms of a Cachazo-He-Yuan representation as a sum over solutions of the scattering equations. These amplitudes, when expressed in terms of the appropriate kinematic invariants, are independent of the masses and therefore identical to the corresponding massless amplitudes.Comment: 20 pages, 1 figure; v2: minor typos corrected, published versio