Interface dynamics and crystal phase switching in GaAs nanowires.

Controlled formation of non-equilibrium crystal structures is one of the most important challenges in crystal growth. Catalytically grown nanowires are ideal systems for studying the fundamental physics of phase selection, and could lead to new electronic applications based on the engineering of crystal phases. Here we image gallium arsenide (GaAs) nanowires during growth as they switch between phases as a result of varying growth conditions. We find clear differences between the growth dynamics of the phases, including differences in interface morphology, step flow and catalyst geometry. We explain these differences, and the phase selection, using a model that relates the catalyst volume, the contact angle at the trijunction (the point at which solid, liquid and vapour meet) and the nucleation site of each new layer of GaAs. This model allows us to predict the conditions under which each phase should be observed, and use these predictions to design GaAs heterostructures. These results could apply to phase selection in other nanowire systems.

Strain and stability of ultrathin Ge layers in Si/Ge/Si axial heterojunction nanowires.

The formation of abrupt Si/Ge heterointerfaces in nanowires presents useful possibilities for bandgap engineering. We grow Si nanowires containing thick Ge layers and sub-1 nm thick Ge "quantum wells" and measure the interfacial strain fields using geometric phase analysis. Narrow Ge layers show radial compressive strains of several percent, while stress at the Si/Ge interface causes lattice rotation. High strains can be achieved in these heterostructures, but we show that they are unstable to interdiffusion.

Control of Electron Beam-Induced Au Nanocrystal Growth Kinetics through Solution Chemistry.

Measurements of solution-phase crystal growth provide mechanistic information that is helpful in designing and synthesizing nanostructures. Here, we examine the model system of individual Au nanocrystal formation within a defined liquid geometry during electron beam irradiation of gold chloride solution, where radiolytically formed hydrated electrons reduce Au ions to solid Au. By selecting conditions that favor the growth of well-faceted Au nanoprisms, we measure growth rates of individual crystals. The volume of each crystal increases linearly with irradiation time at a rate unaffected by its shape or proximity to neighboring crystals, implying a growth process that is controlled by the arrival of atoms from solution. Furthermore, growth requires a threshold dose rate, suggesting competition between reduction and oxidation processes in the solution. Above this threshold, the growth rate follows a power law with dose rate. To explain the observed dose rate dependence, we demonstrate that a reaction-diffusion model is required that explicitly accounts for the species H(+) and Cl(-). The model highlights the necessity of considering all species present when interpreting kinetic data obtained from beam-induced processes, and suggest conditions under which growth rates can be controlled with higher precision.

PerR controls oxidative stress defence and aerotolerance but not motility-associated phenotypes of Campylobacter jejuni.

The foodborne bacterial pathogen Campylobacter jejuni is an obligate microaerophile that is exposed to atmospheric oxygen during transmission through the food chain. Survival under aerobic conditions requires the concerted control of oxidative stress systems, which in C. jejuni are intimately connected with iron metabolism via the PerR and Fur regulatory proteins. Here, we have characterized the roles of C. jejuni PerR in oxidative stress and motility phenotypes, and its regulon at the level of transcription, protein expression and promoter interactions. Insertional inactivation of perR in the C. jejuni reference strains NCTC 11168, 81-176 and 81116 did not result in any growth deficiencies, but strongly increased survival in atmospheric oxygen conditions, and allowed growth around filter discs infused with up to 30 % H2O2 (8.8 M). Expression of catalase, alkyl hydroperoxide reductase, thioredoxin reductase and the Rrc desulforubrerythrin was increased in the perR mutant, and this was mediated at the transcriptional level as shown by electrophoretic mobility shift assays of the katA, ahpC and trxB promoters using purified PerR. Differential RNA-sequencing analysis of a fur perR mutant allowed the identification of eight previously unknown transcription start sites of genes controlled by Fur and/or PerR. Finally, inactivation of perR in C. jejuni did not result in reduced motility, and did not reduce killing of Galleria melonella wax moth larvae. In conclusion, PerR plays an important role in controlling oxidative stress resistance and aerobic survival of C. jejuni, but this role does not extend into control of motility and associated phenotypes.

Chicken juice enhances surface attachment and biofilm formation of Campylobacter jejuni.

The bacterial pathogen Campylobacter jejuni is primarily transmitted via the consumption of contaminated foodstuffs, especially poultry meat. In food processing environments, C. jejuni is required to survive a multitude of stresses and requires the use of specific survival mechanisms, such as biofilms. An initial step in biofilm formation is bacterial attachment to a surface. Here, we investigated the effects of a chicken meat exudate (chicken juice) on C. jejuni surface attachment and biofilm formation. Supplementation of brucella broth with ≥5% chicken juice resulted in increased biofilm formation on glass, polystyrene, and stainless steel surfaces with four C. jejuni isolates and one C. coli isolate in both microaerobic and aerobic conditions. When incubated with chicken juice, C. jejuni was both able to grow and form biofilms in static cultures in aerobic conditions. Electron microscopy showed that C. jejuni cells were associated with chicken juice particulates attached to the abiotic surface rather than the surface itself. This suggests that chicken juice contributes to C. jejuni biofilm formation by covering and conditioning the abiotic surface and is a source of nutrients. Chicken juice was able to complement the reduction in biofilm formation of an aflagellated mutant of C. jejuni, indicating that chicken juice may support food chain transmission of isolates with lowered motility. We provide here a useful model for studying the interaction of C. jejuni biofilms in food chain-relevant conditions and also show a possible mechanism for C. jejuni cell attachment and biofilm initiation on abiotic surfaces within the food chain.

Strategies to control morphology in hybrid group III-V/group IV heterostructure nanowires.

By combining in situ and ex situ transmission electron microscopy measurements, we examine the factors that control the morphology of "hybrid" nanowires that include group III-V and group IV materials. We focus on one materials pair, GaP/Si, for which we use a wide range of growth parameters. We show through video imaging that nanowire morphology depends on growth conditions, but that a general pattern emerges where either single kinks or inclined defects form some distance after the heterointerface. We show that pure Si nanowires can be made to exhibit the same kinks and defects by changing their droplet volume. From this we derive a model where droplet geometry drives growth morphology and discuss optimization strategies. We finally discuss morphology control for material pairs where the second material kinks immediately at the heterointerface and show that an interlayer between segments can enable the growth of unkinked hybrid nanowires.

Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria.

BACKGROUND: Gene reshuffling, point mutations and horizontal gene transfer contribute to bacterial genome variation, but require the genome to rewire its transcriptional circuitry to ensure that inserted, mutated or reshuffled genes are transcribed at appropriate levels. The genomes of Epsilonproteobacteria display very low synteny, due to high levels of reshuffling and reorganisation of gene order, but still share a significant number of gene orthologs allowing comparison. Here we present the primary transcriptome of the pathogenic Epsilonproteobacterium Campylobacter jejuni, and have used this for comparative and predictive transcriptomics in the Epsilonproteobacteria. RESULTS: Differential RNA-sequencing using 454 sequencing technology was used to determine the primary transcriptome of C. jejuni NCTC 11168, which consists of 992 transcription start sites (TSS), which included 29 putative non-coding and stable RNAs, 266 intragenic (internal) TSS, and 206 antisense TSS. Several previously unknown features were identified in the C. jejuni transcriptional landscape, like leaderless mRNAs and potential leader peptides upstream of amino acid biosynthesis genes. A cross-species comparison of the primary transcriptomes of C. jejuni and the related Epsilonproteobacterium Helicobacter pylori highlighted a lack of conservation of operon organisation, position of intragenic and antisense promoters or leaderless mRNAs. Predictive comparisons using 40 other Epsilonproteobacterial genomes suggests that this lack of conservation of transcriptional features is common to all Epsilonproteobacterial genomes, and is associated with the absence of genome synteny in this subdivision of the Proteobacteria. CONCLUSIONS: Both the genomes and transcriptomes of Epsilonproteobacteria are highly variable, both at the genome level by combining and division of multicistronic operons, but also on the gene level by generation or deletion of promoter sequences and 5' untranslated regions. Regulatory features may have evolved after these species split from a common ancestor, with transcriptome rewiring compensating for changes introduced by genomic reshuffling and horizontal gene transfer.

Nanoscale chemical templating of Si nanowires seeded with Al.

We describe a new approach for achieving controlled spatial placement of VLS-grown nanowires that uses an oxygen-reactive seed material and an oxygen-containing mask. Oxygen-reactive seed materials are of great interest for electronic applications, yet they cannot be patterned using the approaches developed for noble metal seed materials such as Au. This new process, nanoscale chemical templating, takes advantage of the reactivity of the blanket seed layer by depositing it over a patterned oxide that reacts with the seed material to prevent nanowire growth in undesired locations. Here we demonstrate this technique using Al as the seed material and SiO2 as the mask, and we propose that this methodology will be applicable to other reactive metals that are of interest for nanowire growth. The method has other advantages over conventional patterning approaches for certain applications including reducing patterning steps, flexibility in lithographic techniques, and high growth yields. We demonstrate its application with standard and microsphere lithography. We show a high growth yield and fidelity, with no NWs between openings and a majority of openings occupied by a single vertical nanowire, and discuss the dependence of yield on parameters.

Contactless measurement of surface dominated recombination in gold- and aluminum-catalyzed silicon vapor-liquid-solid wires.

Carrier lifetimes of Si micro/nanowires grown by the vapor-liquid-solid method are measured using an extension of the classic contactless photoconductivity decay method. The samples measured consist of a thin aggregated film of oxide passivated wires on a fused silica carrier. Au catalyzed wires in the 392-730 nm diameter range are studied. Recombination in these wires is controlled by the surface or near surface effects, not bulk Au impurities. The lifetimes of Au- and Al-catalyzed wires of comparable diameter are measured. The Al wires are found to have slightly longer lifetimes than those grown with Au at a comparable diameter. Across all samples, the lifetimes measured range was from 0.2 to 1.0 ns. The surface controlled nature of the recombination measured implies larger diameter wires will offer better performance in devices that rely on minority carrier transport.

In vivo and in silico determination of essential genes of Campylobacter jejuni.

BACKGROUND: In the United Kingdom, the thermophilic Campylobacter species C. jejuni and C. coli are the most frequent causes of food-borne gastroenteritis in humans. While campylobacteriosis is usually a relatively mild infection, it has a significant public health and economic impact, and possible complications include reactive arthritis and the autoimmune diseases Guillain-Barré syndrome. The rapid developments in "omics" technologies have resulted in the availability of diverse datasets allowing predictions of metabolism and physiology of pathogenic micro-organisms. When combined, these datasets may allow for the identification of potential weaknesses that can be used for development of new antimicrobials to reduce or eliminate C. jejuni and C. coli from the food chain. RESULTS: A metabolic model of C. jejuni was constructed using the annotation of the NCTC 11168 genome sequence, a published model of the related bacterium Helicobacter pylori, and extensive literature mining. Using this model, we have used in silico Flux Balance Analysis (FBA) to determine key metabolic routes that are essential for generating energy and biomass, thus creating a list of genes potentially essential for growth under laboratory conditions. To complement this in silico approach, candidate essential genes have been determined using a whole genome transposon mutagenesis method. FBA and transposon mutagenesis (both this study and a published study) predict a similar number of essential genes (around 200). The analysis of the intersection between the three approaches highlights the shikimate pathway where genes are predicted to be essential by one or more method, and tend to be network hubs, based on a previously published Campylobacter protein-protein interaction network, and could therefore be targets for novel antimicrobial therapy. CONCLUSIONS: We have constructed the first curated metabolic model for the food-borne pathogen Campylobacter jejuni and have presented the resulting metabolic insights. We have shown that the combination of in silico and in vivo approaches could point to non-redundant, indispensable genes associated with the well characterised shikimate pathway, and also genes of unknown function specific to C. jejuni, which are all potential novel Campylobacter intervention targets.

Biofilm formation by Campylobacter jejuni is increased under aerobic conditions.

The microaerophilic human pathogen Campylobacter jejuni is the leading cause of food-borne bacterial gastroenteritis in the developed world. During transmission through the food chain and the environment, the organism must survive stressful environmental conditions, particularly high oxygen levels. Biofilm formation has been suggested to play a role in the environmental survival of this organism. In this work we show that C. jejuni NCTC 11168 biofilms developed more rapidly under environmental and food-chain-relevant aerobic conditions (20% O(2)) than under microaerobic conditions (5% O(2), 10% CO(2)), although final levels of biofilms were comparable after 3 days. Staining of biofilms with Congo red gave results similar to those obtained with the commonly used crystal violet staining. The level of biofilm formation by nonmotile aflagellate strains was lower than that observed for the motile flagellated strain but nonetheless increased under aerobic conditions, suggesting the presence of flagellum-dependent and flagellum-independent mechanisms of biofilm formation in C. jejuni. Moreover, preformed biofilms shed high numbers of viable C. jejuni cells into the culture supernatant independently of the oxygen concentration, suggesting a continuous passive release of cells into the medium rather than a condition-specific active mechanism of dispersal. We conclude that under aerobic or stressful conditions, C. jejuni adapts to a biofilm lifestyle, allowing survival under detrimental conditions, and that such a biofilm can function as a reservoir of viable planktonic cells. The increased level of biofilm formation under aerobic conditions is likely to be an adaptation contributing to the zoonotic lifestyle of C. jejuni.

Growth system, structure, and doping of aluminum-seeded epitaxial silicon nanowires.

We have examined the formation of silicon nanowires grown by self-assembly from Si substrates with thin aluminum films. Postgrowth and in situ investigations using various Al deposition and annealing conditions suggest that nanowire growth takes place with a supercooled liquid droplet (i.e., the vapor-liquid-solid system), even though the growth temperatures are below the bulk Al/Si eutectic temperature. Wire morphology as a function of processing conditions is also described. It is shown that when Al environmental exposure is prevented before wire growth a wide process window for wire formation can be achieved. Under optimum growth conditions, it is possible to produce excellent crystal quality nanowires with rapid growth rates, high surface densities, low diameter dispersion, and controlled tapering. Photoelectron spectroscopy measurements indicate that the use of Al leads to active doping levels that depend on the growth temperature in as-grown nanowires and increase when annealed. We suggest that these structural and electronic properties will be relevant to photovoltaic and other applications, where the more common use of Au is believed to be detrimental to performance.

Inactivation of the core cheVAWY chemotaxis genes disrupts chemotactic motility and organised biofilm formation in Campylobacter jejuni.

Flagellar motility plays a central role in the bacterial foodborne pathogen Campylobacter jejuni, as flagellar motility is required for reaching the intestinal epithelium and subsequent colonisation or disease. Flagellar proteins also contribute strongly to biofilm formation during transmission. Chemotaxis is the process directing flagellar motility in response to attractant and repellent stimuli, but its role in biofilm formation of C. jejuni is not well understood. Here we show that inactivation of the core chemotaxis genes cheVAWY in C. jejuni strain NCTC 11168 affects both chemotactic motility and biofilm formation. Inactivation of any of the core chemotaxis genes (cheA, cheY, cheV or cheW) impaired chemotactic motility but did not affect flagellar assembly or growth. The ∆cheY mutant swam in clockwise loops, while complementation restored normal motility. Inactivation of the core chemotaxis genes interfered with the ability to form a discrete biofilm at the air-media interface, and the ∆cheY mutant displayed reduced dispersal/shedding of bacteria into the planktonic fraction. This suggests that while the chemotaxis system is not required for biofilm formation per se, it is necessary for organized biofilm formation. Hence interference with the Campylobacter chemotaxis system at any level disrupts optimal chemotactic motility and transmission modes such as biofilm formation.

Surface Crystallization of Liquid Au-Si and Its Impact on Catalysis.

In situ transmission electron microscopy reveals that an atomically thin crystalline phase at the surface of liquid Au-Si is stable over an unexpectedly wide range of conditions. By measuring the surface structure as a function of liquid temperature and composition, a simple thermodynamic model is developed to explain the stability of the ordered phase. The presence of surface ordering plays a key role in the pathway by which the Au-Si eutectic solidifies and also dramatically affects the catalytic properties of the liquid, explaining the anomalously slow growth kinetics of Si nanowires at low temperature. A strategy to control the presence of the surface phase is discussed, using it as a tool in designing strategies for nanostructure growth.

Directed Self-Assembly of Ge Quantum Dots Using Focused Si2+ Ion Beam Patterning.

We show that templating a Si surface with a focused beam of Si2+ or Si+ ions can create suitable nucleation sites for the subsequent growth of self-assembled Ge quantum dots by chemical vapor deposition. To determine the mechanism of patterning we use atomic force microscopy to show that, similar to Ga+ patterning, the formation of a surface pit is required to enable control over Ge quantum dot locations. We find that relatively high implantation doses are required to achieve patterning, and these doses lead to amorphization of the substrate. We assess the degree to which the substrate crystallinity can be recovered by subsequent processing. Using in situ transmission electron microscopy heating experiments we find that recrystallization is possible at the growth temperature of the Ge quantum dots, but defects remain that follow the pattern of the initial implantation. We discuss the formation mechanism of the defects and the benefits of using Si ions for patterning both defects and quantum dots on Si substrates.

Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach.

BACKGROUND: Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge. RESULTS: A computing tool (ArrayLeaRNA) has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19), a published Bayesian approach also using predicted operon structure. The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements. ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at http://www.ifr.ac.uk/safety/ArrayLeaRNA/ CONCLUSION: We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where differentially regulated genes predominate.

Nanowire growth kinetics in aberration corrected environmental transmission electron microscopy.

We visualize atomic level dynamics during Si nanowire growth using aberration corrected environmental transmission electron microscopy, and compare with lower pressure results from ultra-high vacuum microscopy. We discuss the importance of higher pressure observations for understanding growth mechanisms and describe protocols to minimize effects of the higher pressure background gas.

A proposed essential gene discovery pipeline: a Campylobacter jejuni case study.

Genes required for an organism's growth and survival are termed essential and represent potential intervention targets. Following in the footsteps of the genomics era, the "next-gen" genomic era provides vast amounts of genetic information. Sequencing of a representative bacterial pathogen genome has been superseded by sequencing of whole strain collections, whether from environmental or clinical sources (Harris et al., Science 327:469-474, 2010; Lewis et al., J Hosp Infect 75:37-41, 2010; Beres et al., Proc Natl Acad Sci U S A 107:4371-4376, 2010; Qi et al., PLoS Pathog 5:e1000580, 2009; He et al., Proc Natl Acad Sci U S A 107:7527-7532, 2010; Barrick et al., Nature 461:1243-1247, 2009; Sheppard et al., Mol Ecol 22:1051-1064, 2013). However, the challenge of using this information to gain biological insight remains. Nonetheless, this information, in combination with experimental data from the literature, can serve as the framework for gaining a better understanding of an organism's biology. Generic metabolic pathways have long been known, and a number of websites (e.g., KEGG and BioCyc) attempt to map information from genome annotation to metabolic pathways (Kanehisa et al., Nucleic Acids Res 40:D109-D114, 2010; Karp et al., Nucleic Acids Res 33:6083-6089, 2005). Extending this analysis to incorporate metabolic flux models further allows in silico prediction of potential essential genes. Such efforts are of value, either to highlight novel generic antimicrobials or to seek novel treatments for non-paradigm organisms. Such in silico approaches are attractive as they can highlight pathways and genes that would otherwise only be identified by costly and time-consuming laboratory methods.

Campylobacter jejuni biofilms contain extracellular DNA and are sensitive to DNase I treatment.

Biofilms make an important contribution to survival and transmission of bacterial pathogens in the food chain. The human pathogen Campylobacter jejuni is known to form biofilms in vitro in food chain-relevant conditions, but the exact roles and composition of the extracellular matrix are still not clear. Extracellular DNA has been found in many bacterial biofilms and can be a major component of the extracellular matrix. Here we show that extracellular DNA is also an important component of the C. jejuni biofilm when attached to stainless steel surfaces, in aerobic conditions and on conditioned surfaces. Degradation of extracellular DNA by exogenous addition of DNase I led to rapid biofilm removal, without loss of C. jejuni viability. Following treatment of a surface with DNase I, C. jejuni was unable to re-establish a biofilm population within 48 h. Similar results were obtained by digesting extracellular DNA with restriction enzymes, suggesting the need for high molecular weight DNA. Addition of C. jejuni genomic DNA containing an antibiotic resistance marker resulted in transfer of the antibiotic resistance marker to susceptible cells in the biofilm, presumably by natural transformation. Taken together, this suggest that eDNA is not only an important component of C. jejuni biofilms and subsequent food chain survival of C. jejuni, but may also contribute to the spread of antimicrobial resistance in C. jejuni. The degradation of extracellular DNA with enzymes such as DNase I is a rapid method to remove C. jejuni biofilms, and is likely to potentiate the activity of antimicrobial treatments and thus synergistically aid disinfection treatments.