Identification of Francisella tularensis genes affected by iron limitation

Cells of an attenuated live vaccine strain (LVS) of F. tularensis grown under iron-restricted conditions were found to contain increased quantities of several proteins relative to cells of this same strain grown under iron-replete conditions. Mass spectrometric analysis identified two of these proteins as IglC and PdpB, both of which are encoded by genes located in a previously identified pathogenicity island in F. tularensis LVS. Regions with homology to the consensus Fur box sequence were located immediately in front of the iglC and pdpB open reading frames (ORFs), and in silico analysis of the F. tularensis Schu4 genome detected a number of predicted 5' untranslated regions that contained putative Fur boxes. The putative Fur box preceding Francisella iron-regulated gene A (figA) had the highest degree of identity with the consensus Fur box sequence. DNA microarray analysis showed that nearly 80 of the genes in the F. tularensis LVS genome were up- or down-regulated at least twofold under iron-restricted growth conditions. When tested for possible siderophore production by means of the Chrome Azurol S assay, a wild-type F. novicida strain produced a large reaction zone whereas its figA mutant produced very little reactivity in this assay. In addition, a cross-feeding experiment demonstrated that this siderophore-like activity produced by the wild-type F. novicida strain could enhance the ability of the F. novicida figA mutant to grow under iron-restricted conditions. This study provides the first identification of iron-regulated genes in F. tularensis LVS and evidence for the production of a siderophore-like molecule by F. novicida.

Haemophilus ducreyi requires the flp gene cluster for microcolony formation in vitro

Haemophilus ducreyi, the etiologic agent of chancroid, has been shown to form microcolonies when cultured in the presence of human foreskin fibroblasts. We identified a 15-gene cluster in H. ducreyi that encoded predicted protein products with significant homology to those encoded by the tad (for tight adhesion) locus in Actinobacillus actinomycetemcomitans that is involved in the production of fimbriae by this periodontal pathogen. The first three open reading frames in this H. ducreyi gene cluster encoded predicted proteins with a high degree of identity to the Flp (fimbria-like protein) encoded by the first open reading frame of the tad locus; this 15-gene cluster in H. ducreyi was designated flp. RT-PCR analysis indicated that the H. ducreyi flp gene cluster was likely to be a polycistronic operon. Mutations within the flp gene cluster resulted in an inability to form microcolonies in the presence of human foreskin fibroblasts. In addition, the same mutants were defective in the ability to attach to both plastic and human foreskin fibroblasts in vitro. An H. ducreyi mutant with an inactivated tadA gene exhibited a small decrease in virulence in the temperature-dependent rabbit model for experimental chancroid, whereas another H. ducreyi mutant with inactivated flp-1 and flp-2 genes was as virulent as the wild-type parent strain. These results indicate that the flp gene cluster is essential for microcolony formation by H. ducreyi, whereas this phenotypic trait is not linked to the virulence potential of the pathogen, at least in this animal model of infection.

X-ray-Based Techniques to Study the Nano-Bio Interface

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

Role of the C-terminal domain of the alpha subunit of RNA polymerase in LuxR-dependent transcriptional activation of the lux operon during quorum sensing

During quorum sensing in Vibrio fischeri, the luminescence, or lux, operon is regulated in a cell density-dependent manner by the activator LuxR in the presence of an acylated homoserine lactone autoinducer molecule [N-(3-oxohexanoyl) homoserine lactone]. LuxR, which binds to the lux operon promoter at a position centered at -42.5 relative to the transcription initiation site, is thought to function as an ambidextrous activator making multiple contacts with RNA polymerase (RNAP). The specific role of the alpha-subunit C-terminal domain (alphaCTD) of RNAP in LuxR-dependent transcriptional activation of the lux operon promoter has been investigated. The effects of 70 alanine substitution variants of the alpha subunit were determined in vivo by measuring the rate of transcription of the lux operon via luciferase assays in recombinant Escherichia coli. The mutant RNAPs from strains exhibiting at least twofold-increased or -decreased activity in comparison to the wild type were further examined by in vitro assays. Since full-length LuxR has not been purified, an autoinducer-independent N-terminally truncated form of LuxR, LuxRDeltaN, was used for in vitro studies. Single-round transcription assays were performed using reconstituted mutant RNAPs in the presence of LuxRDeltaN, and 14 alanine substitutions in the alphaCTD were identified as having negative effects on the rate of transcription from the lux operon promoter. Five of these 14 alpha variants were also involved in the mechanisms of both LuxR- and LuxRDeltaN-dependent activation in vivo. The positions of these residues lie roughly within the 265 and 287 determinants in alpha that have been identified through studies of the cyclic AMP receptor protein and its interactions with RNAP. This suggests a model where residues 262, 265, and 296 in alpha play roles in DNA recognition and residues 290 and 314 play roles in alpha-LuxR interactions at the lux operon promoter during quorum sensing.

Metabolic analysis of Moraxella catarrhalis and the effect of selected in vitro growth conditions on global gene expression

The nucleotide sequence from the genome of Moraxella catarrhalis ATCC 43617 was annotated and used both to assess the metabolic capabilities and limitations of this bacterium and to design probes for a DNA microarray. An absence of gene products for utilization of exogenous carbohydrates was noteworthy and could be correlated with published phenotypic data. Gene products necessary for aerobic energy generation were present, as were a few gene products generally ascribed to anaerobic systems. Enzymes for synthesis of all amino acids except proline and arginine were present. M. catarrhalis DNA microarrays containing 70-mer oligonucleotide probes were designed from the genome-derived nucleotide sequence data. Analysis of total RNA extracted from M. catarrhalis ATCC 43617 cells grown under iron-replete and iron-restricted conditions was used to establish the utility of these DNA microarrays. These DNA microarrays were then used to analyze total RNA from M. catarrhalis cells grown in a continuous-flow biofilm system and in the planktonic state. The genes whose expression was most dramatically increased by growth in the biofilm state included those encoding a nitrate reductase, a nitrite reductase, and a nitric oxide reductase. Real-time reverse transcriptase PCR analysis was used to validate these DNA microarray results. These results indicate that growth of M. catarrhalis in a biofilm results in increased expression of gene products which can function not only in energy generation but also in resisting certain elements of the innate immune response.

Characterization of Haemophilus ducreyi cdtA, cdtB, and cdtC mutants in in vitro and in vivo systems

Haemophilus ducreyi expresses a soluble cytolethal distending toxin (CDT) that is encoded by the cdtABC gene cluster and can be detected in culture supernatant fluid by its ability to kill HeLa cells. The cdtA, cdtB, and cdtC genes of H. ducreyi were cloned independently into plasmid vectors, and their encoded proteins expressed singly or in various combinations in an Escherichia coli background. All three gene products had to be expressed in order for E. coli-derived culture supernatant fluids to demonstrate cytotoxicity for HeLa cells. Isogenic H. ducreyi cdtA and cdtB mutants were constructed and used in combination with the wild-type parent strain and a previously described H. ducreyi cdtC mutant (M. K. Stevens, J. L. Latimer, S. R. Lumbley, C. K. Ward, L. D. Cope, T. Lagergard, and E. J. Hansen, Infect. Immun. 67:3900-3908, 1999) to determine the relative contributions of the CdtA, CdtB, and CdtC proteins to CDT activity. Expression of CdtA, CdtB, and CdtC appeared necessary for H. ducreyi-derived culture supernatant fluid to exhibit cytotoxicity for HeLa cells. Whole-cell sonicates and periplasmic extracts from the cdtB and cdtC mutants had no effect on HeLa cells, whereas these same fractions from a cdtA mutant had a very modest cytotoxic effect on these same human cells. CdtA appeared to be primarily associated with the H. ducreyi cell envelope, whereas both CdtB and CdtC were present primarily in the soluble fraction from sonicated cells. Both the cdtA mutant and the cdtB mutant were found to be fully virulent in the temperature-dependent rabbit model for experimental chancroid.

Mutations in the lspA1 and lspA2 genes of Haemophilus ducreyi affect the virulence of this pathogen in an animal model system

Haemophilus ducreyi 35000HP contains two genes, lspA1 and lspA2, whose predicted protein products have molecular weights of 456,000 and 543,000, respectively (C. K. Ward, S. R. Lumbley, J. L. Latimer, L. D. Cope, and E. J. Hansen, J. Bacteriol. 180:6013-6022, 1998). We have constructed three H. ducreyi 35000HP mutants containing antibiotic resistance cartridges in one or both of the lspA1 and lspA2 open reading frames. Western blot analysis using LspA1- and LspA2-specific monoclonal antibodies indicated that the wild-type parent strain 35000HP expressed LspA1 protein that was readily detectable in culture supernatant fluid together with a barely detectable amount of LspA2 protein. The lspA2 mutant 35000HP.2 expressed LspA1 protein that was detectable in culture supernatant fluid and no LspA2 protein. In contrast, the H. ducreyi lspA1 mutant 35000HP.1, which did not express the LspA1 protein, expressed a greater quantity of the LspA2 protein than did the wild-type parent strain. The lspA1 lspA2 double mutant 35000HP.12 expressed neither LspA1 nor LspA2. The three mutant strains adhered to human foreskin fibroblasts and to a human keratinocyte cell line in vitro at a level that was not significantly different from that of the wild-type strain 35000HP. Lack of expression of the LspA1 protein by both the lspA1 mutant and the lspA1 lspA2 double mutant was associated with an increased tendency to autoagglutinate. When evaluated in the temperature-dependent rabbit model for chancroid, the lspA1 lspA2 double mutant was substantially less virulent than the wild-type strain 35000HP. The results of these studies indicated that H. ducreyi requires both the LspA1 and LspA2 proteins to be fully virulent in this animal model for experimental chancroid.

Inactivation of the Haemophilus ducreyi luxS gene affects the virulence of this pathogen in human subjects

Haemophilus ducreyi 35000HP contains a homologue of the luxS gene, which encodes an enzyme that synthesizes autoinducer 2 (AI-2) in other gram-negative bacteria. H. ducreyi 35000HP produced AI-2 that functioned in a Vibrio harveyi-based reporter system. A H. ducreyi luxS mutant was constructed by insertional inactivation of the luxS gene and lost the ability to produce AI-2. Provision of the H. ducreyi luxS gene in trans partially restored AI-2 production by the mutant. The luxS mutant was compared with its parent for virulence in the human challenge model of experimental chancroid. The pustule-formation rate in 5 volunteers was 93.3% (95% confidence interval, 81.7%-99.9%) at 15 parent sites and 60.0% (95% confidence interval, 48.3%-71.7%) at 15 mutant sites (1-tailed P < .001). Thus, the luxS mutant was partially attenuated for virulence. This is the first report of AI-2 production contributing to the pathogenesis of a genital ulcer disease.

A UspA2H-negative variant of Moraxella catarrhalis strain O46E has a deletion in a homopolymeric nucleotide repeat common to uspA2H genes

Moraxella catarrhalis strains can express either a UspA2 protein or a UspA2H protein. The latter protein is encoded by a gene that possesses a homopolymeric nucleotide tract containing eight adenine (A) residues [i.e., a poly(A) tract] which is located near the 5' end. A spontaneous UspA2H-negative variant of M. catarrhalis strain O46E, designated O46E.U2V, was found to have a uspA2H poly(A) tract that contained seven A residues. Northern blot analysis of total RNA from the O46E parent strain revealed a readily detectable uspA2H mRNA transcript, whereas little or no uspA2H transcript was detectable in total RNA from the UspA2H-negative variant O46E.U2V. The 5' end of the uspA2H genes from both the O46E parent strain and the O46E.U2V variant were ligated to a promoterless lacZ gene to prepare translational fusions for use as reporter constructs. The level of beta-galactosidase activity expressed by the fusion construct containing eight A residues in its poly(A) tract was 200-fold greater than that obtained with the construct that had seven A residues. Site-directed mutagenesis of the 5' end of the uspA2H gene confirmed that translation was initiated at a GTG codon located 21 nucleotides (nt) upstream of the poly(A) tract. Primer extension analysis determined that the transcriptional start site of the uspA2H gene was located 291 nt upstream from the GTG translational start codon. This poly(A) tract was also found to be present in the uspA2H genes of other M. catarrhalis strains.

FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis

FindGDPs is a program that uses a greedy algorithm to quickly identify a set of genome-directed primers that specifically anneal to all of the open reading frames ina genome and that do not exhibit full-length complementarity to the members of another user-supplied set of nucleotide sequences.

Direct writing of colloidal suspensions onto inclined surfaces: Optimizing dispense volume for homogeneous structures

HYPOTHESIS

A process to fabricate structures on inclined substrates has the potential to yield novel applications for colloidal-based structures. However, for conventional techniques, besides the coffee ring effect (CRE), anisotropic particle deposition along the inclination direction (IE) is expected to occur. We hypothesize that both effects can be inhibited by reducing the dispense volume during printing by direct writing.

EXPERIMENTS

We combined an additive manufacturing technique, namely direct writing, with colloidal assembly (AMCA) for an automated and localized drop-cast of polystyrene and silica suspensions onto inclined surfaces. Herein, we investigated the influence of the substrate tilting angle and the dispense volume on the printing of colloids and the resulting structures' morphology.

FINDINGS

The results demonstrate that a reduction in the dispense volume hinders the CRE and IE for both particles' systems, even though the evaporation mode is different. For polystyrene, the droplets evaporated solely in stick-mode, enabling a "surface capturing effect", while for silica, droplets evaporated in mixed stick-slip mode and a "confinement effect" was observed, which improved uniformity of the deposition. These findings were used to generate a model of the critical droplet radius needed to print homogeneous colloidal-based structures onto inclined substrates.

Plasmonic hot carrier injection from single gold nanoparticles into topological insulator Bi2Se3 nanoribbons

Plasmonic gold nanoparticles injecting hot carriers into the topological insulator (TI) interface of Bi₂Se₃ nanoribbons are studied by resonant Raman spectroscopy. We resolve the impact of individual gold particles with sizes ranging from 140 nm down to less than 40 nm on the topological surface states of the nanoribbons. In resonance at 1.96 eV (633 nm), we find distinct phonon renormalization in the E_g²- and A_1g²-modes that can be associated with plasmonic hot carrier injection. The phonon modes are strongly enhanced by a factor of 350 when tuning the excitation wavelengths into interband transition and in resonance with the surface plasmon of gold nanoparticles. At 633 nm wavelength, a plasmonic enhancement factor of 18 is observed indicating a contribution of hot carriers injected from the gold nanoparticles into the TI interface. Raman studies as a function of gold nanoparticle size reveal the strongest hot carrier injection for particles with size of 108 nm in agreement with the resonance energy of its surface plasmon. Hot carrier injection opens the opportunity to locally control the electronic properties of the TI by metal nanoparticles attached to the surface of nanoribbons.

Carrier Injection Observed by Interface-Enhanced Raman Scattering from Topological Insulators on Gold Substrates

The electron-phonon interaction at the interface between topological insulator (TI), namely, Bi₂Se₃ and Bi₂Te₃ two-dimensional (2D) nanoflakes, to a gold substrate as a function of TI flake thickness is studied by means of Raman scattering. We reveal the presence of interface-enhanced Raman scattering and a strong phonon renormalization induced by carriers injected from the gold substrate to the topological surface in contact. We derive the change of the electron-phonon coupling showing a nearly linear behavior as a function of layer thickness. The strongly nonlinear change of the Raman scattering cross section as a function of flake thickness can be associated with band bending effects at the metal-TI interface. Our results provide spectroscopic evidence for a strongly modified band structure in the first few quintuple layers of Bi₂Se₃ and Bi₂Te₃ in contact with gold.

Dataset of ptychographic X-ray computed tomography of inverse opal photonic crystals produced by atomic layer deposition

This data article describes the detailed parameters for synthesizing mullite inverse opal photonic crystals via Atomic Layer Deposition (ALD), as well as the detailed image analysis routine used to interpret the data obtained by the measurement of such photonic crystals, before and after the heat treatment, via Ptychographic X-ray Computed Tomography (PXCT). The data presented in this article are related to the research article by Furlan and co-authors entitled “Photonic materials for high-temperature applications: Synthesis and characterization by X-ray ptychographic tomography” (Furlan et al., 2018). The data include detailed information about the ALD super-cycle process to generate the ternary oxides inside a photonic crystal template, the raw data from supporting characterization techniques, as well as the full dataset obtained from PXCT. All the data herein described is publicly available in a Mendeley Data archive “Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals” located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes.

Dynamic control for nanostructures through slowly ramping parameters

We propose a nanostructure control method which uses slowly ramping parameters. We demonstrate the dynamics of this method in both a nonlinear classical system and a quantum system. When a quantum mechanical two-level atom (quantum dot) is irradiated by an electric field with a slowly increasing frequency, there exists a sudden transition from ground (excited) to excited (ground) state. This occurs when the ramping rate is smaller than the square of the Rabi frequency. The transition arises when its "instant frequency"-the time derivative of the driving field phase-matches the resonance frequency, satisfying the Fermi golden rule. We also find that the parameter ramping is an efficient control manner for classical nanomechanical shuttles. For ramping of driving amplitudes, the shuttle's mechanical oscillation is amplified and even survives when the ramping is stopped outside the original oscillation region. This strange oscillation is due to the entrance into a multistable dynamic region in phase space. For ramping of driving frequencies, an onset of oscillation arises when the instant frequency enters the oscillation region. Thus, regardless of being classical or quantum, the instant frequency is physically relevant. We discuss in which conditions the dynamic control is efficient.