Research data supporting "Interchange of Weyl Points in the Phonon Bands of a Half-Metal Alloy"

The dataset contains output files (*.check format) from CASTEP calculations of phonons in tetragonally distorted NiMnSb. These files are not human-readable, but we also supply input files (*.cell and *.param format) that would prompt a new CASTEP run to open and make use of the *.check files. The *.cell files, in particular, may be altered to cause CASTEP to output *.phonon files (containing frequencies and eigendisplacements) at any desired wavevector. Further instructions are provided in the README_Data file

Determination of yielding point by means a probabilistic method on acoustic emission signals for application to health monitoring of reinforced concrete structures

Reinforced concrete (RC) flanged beam specimens were tested under incremental cyclic load till failure in flexure, and simultaneously, the acoustic emission (AE) signals released by the specimens were recorded. To assess damage in RC structures, a previously published index of damage (ID) based on AE signals was used. This index, however, needs to know the yielding point of the specimen. In the present study, yielding point was identified with a probabilistic method known as Gaussian mixture modeling (GMM) applied to the AE signals, as compared with that obtained by means of the plastic strain energy. It was observed that yielding load obtained with both methodologies was almost same, thus validating the GMM method. This result permits to use the ID index for damage monitoring of RC structure in practical scenarios, by using only information hidden in the AE signals. The influence of loading rate, failure type (tensile and shear), RC beam depth, concrete compressive strength, and percentage of tensile steel reinforcement on ID were studied in this work

Rhizobium sp. IRBG74 Alters Arabidopsis Root Development by Affecting Auxin Signaling

Rhizobium sp. IRBG74 not only nodulates Sesbania cannabina but also can enhance rice growth; however, the underlying molecular mechanisms are not clear. Here, we show that Rhizobium sp. IRBG74 colonizes the roots of Arabidopsis thaliana, which leads to inhibition in the growth of main root but enhancement in the formation of lateral roots. The promotion of lateral root formation by Rhizobium sp. IRBG74 in the fls2-1 mutant, which is insensitive to flagellin, is similar to the wild-type plant, while the auxin response deficient mutant tir1-1 is significantly less sensitive to Rhizobium sp. IRBG74 than the wild type in terms of the inhibition of main root elongation and the promotion of lateral root formation. Further transcriptome analysis of Arabidopsis roots inoculated with Rhizobium sp. IRBG74 revealed differential expression of 50 and 211 genes at 24 and 48 h, respectively, and a majority of these genes are involved in auxin signaling. Consistent with the transcriptome analysis results, Rhizobium sp. IRBG74 treatment induces expression of the auxin responsive reporter DR5:GUS in roots. Our results suggest that in Arabidopsis Rhizobium sp. IRBG74 colonizes roots and promotes the lateral root formation likely through modulating auxin signaling. Our work provides insight into the molecular mechanisms of interactions between legume-nodulating rhizobia and non-legume plants

Kustu S: Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. Proc Natl Acad Sci 2005

We previously characterized nutrient-specific transcriptional changes in Escherichia coli upon limitation of nitrogen (N) or sulfur (S). These global homeostatic responses presumably minimize the slowing of growth under a particular condition. Here, we characterize responses to slow growth per se that are not nutrientspecific. The latter help to coordinate the slowing of growth, and in the case of down-regulated genes, to conserve scarce N or S for other purposes. Three effects were particularly striking. First, although many genes under control of the stationary phase sigma factor RpoS were induced and were apparently required under S-limiting conditions, one or more was inhibitory under N-limiting conditions, or RpoS itself was inhibitory. RpoS was, however, universally required during nutrient downshifts. Second, limitation for N and S greatly decreased expression of genes required for synthesis of flagella and chemotaxis, and the motility of E. coli was decreased. Finally, unlike the response of all other met genes, transcription of metE was decreased under S-and N-limiting conditions. The metE product, a methionine synthase, is one of the most abundant proteins in E. coli grown aerobically in minimal medium. Responses of metE to S and N limitation pointed to an interesting physiological rationale for the regulatory subcircuit controlled by the methionine activator MetR. Escherichia coli genomics ͉ flagella ͉ methionine regulation ͉ nutrient metabolism ͉ RpoS W e have previously explored global responses of Escherichia coli K12 to limitation for the nutrients nitrogen (N) or sulfur (S) on glass-slide DNA microarrays (1). To determine responses of a wild-type strain, we compared its transcriptional profiles under nutrient-limiting and -excess conditions and under conditions of rapid transition between the two, magnifying transcriptional responses (2). Homeostatic responses to N or S limitation entail increased assimilation of preferred N or S sources, respectively, and scavenging of alternative N or S sources from the medium (1, 3). Common responses to N and S limitation apparently occur as a consequence of slow growth. Here, we characterize the latter responses, both increases and decreases in transcription, and explore several of them biologically. Materials and Methods Bacterial Strains. An rpoS::Tn10 allele (4) and a Tn10 insertion at an innocuous locus (zih-102::Tn10) were transferred to NCM3722 by P1-mediated transduction to generate NCM3890 and control strain NCM3964, respectively. The same lesions were also transferred to MG1655 (CGSC 6300) [also known as NCM3105 (5)] to generate NCM3962 and NCM3963, respectively. NCM3876 [glnL(Up)] has been described (1), and NCM4022 was isolated as a spontaneous motile derivative of NCM3722 on an arginine swim plate. Nutrient Shifts and Other Growth Experiments. For carbon (C) and N downshift experiments growth of rpoS and control strains was monitored at 37°C in N Ϫ C Ϫ minimal medium containing various C or N sources. For C downshift experiments, ammonium chloride (10 mM) was the N source, and the C sources were glucose (0.04%) plus glycerol (0.4%), or glucose (0.04%) plus lactose (0.2%). For N downshift experiments, glycerol (0.4%) was the C source, and the N sources were ammonium (1 mM) plus arginine (2.5 mM). For S downshift experiments, cells were grown in N -C -S -minimal medium with glycerol (0.4%) and ammonium (10 mM) as the C and N sources, respectively. The S sources were sulfate (0.02 mM) plus glutathione (0.25 mM). The glutathione stock (25 mM) was stored at Ϫ20°C, and each aliquot was thawed and used once. For C upshift experiments, growth was started on glycerol (0.4%) and shifted by addition of glucose (to 0.2%); for N upshift, growth was started on arginine (2.5 mM) and shifted by addition of ammonium chloride (to 10 mM); for S upshift, growth was started on glutathione (0.25 mM) and shifted by addition of sulfate (to 0.25 mM). Cultures used for inoculation were grown on the appropriate preshift medium and were inoculated at a ratio of 1:50 into large baffled tubes containing 5 ml of medium and incubated with rapid shaking. Experiments were performed at least three times each. Lanthionine and L-djenkolic acid were purchased from TCI America (Portland, OR). The doubling time of strain NCM3722 on djenkolate appeared to be similar to that on glutathione. However, when NCM3722 was inoculated on L-djenkolate, it initially grew rapidly on what we presume to be a contaminant and then shifted to the slower growth rate. We were unable to obtain L-djenkolic acid from another commercial source. Motility Tests. Motility was assessed by using swim agar plates (0.3% Difco agar) or by direct observation under the light microscope (Zeiss Axiophot). Details are provided in Supporting Methods, which is published as supporting information on the PNAS web site. Immunoblots. After adaptation to a particular medium, cells were grown to mid-exponential phase (OD 600 of 0.4-0.45) at 37°C in a tube roller. Whole-cell preparations were made by suspending cells (1 ml) grown with ammonium or arginine as the N source in 0.25 ml of SDS loading buffer [60 mM Tris⅐HCl, pH 6.8͞2% SDS͞0.7 mM 2-mercaptoethanol͞0.1 mM phenylmethylsulfonyl f luoride͞10% glycerol͞0.001% Bromophenol blue] supplemented with n-octyl ␤-D-glucopyranoside (Sigma), and disrupted by incubation at 37°C for 30 min. Samples (10 or 15 l) were run on acrylamide gels (12%) and blotted to nitrocellulose membranes (6). Polyclonal rabbit antibodies raised to the flagellin protein [prepared in the laboratory of the late R. MacNa

Physiological Studies of Escherichia coli Strain MG1655: Growth Defects and Apparent Cross-Regulation of Gene Expression

Escherichia coli strain MG1655 was chosen for sequencing because the few mutations it carries (ilvG rfb-50 rph-1) were considered innocuous. However, it has a number of growth defects. Internal pyrimidine starvation due to polarity of the rph-1 allele on pyrE was problematic in continuous culture. Moreover, the isolate of MG1655 obtained from the E. coli Genetic Stock Center also carries a large deletion around the fnr (fumarate-nitrate respiration) regulatory gene. Although studies on DNA microarrays revealed apparent cross-regulation of gene expression between galactose and lactose metabolism in the Stock Center isolate of MG1655, this was due to the occurrence of mutations that increased lacY expression and suppressed slow growth on galactose. The explanation for apparent cross-regulation between galactose and N-acetylglucosamine metabolism was similar. By contrast, cross-regulation between lactose and maltose metabolism appeared to be due to generation of internal maltosaccharides in lactose-grown cells and may be physiologically significant. Lactose is of restricted distribution: it is normally found together with maltosaccharides, which are starch degradation products, in the mammalian intestine. Strains designated MG1655 and obtained from other sources differed from the Stock Center isolate and each other in several respects. We confirmed that use of other E. coli strains with MG1655-based DNA microarrays works well, and hence these arrays can be used to study any strain of interest. The responses to nitrogen limitation of two urinary tract isolates and an intestinal commensal strain isolated recently from humans were remarkably similar to those of MG1655

Legume-Nodulating Betaproteobacteria: Diversity, Host Range, and Future Prospects

International audienceRhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkhold-eria and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteo-bacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of ge-nus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha-and betaproteobacteria