Antimony doping of Si layers grown by solid-phase epitaxy

We report here that layers of Si formed by solid-phase epitaxial growth (SPEG) can be doped intentionally. The sample consists initially of an upper layer of amorphous Si (~1 µm thick), a very thin intermediate layer of Sb (nominally 5 Å), and a thin lower layer of Pd (~500 Å), all electron-gun deposited on top of a single-crystal substrate (1–10 Ω cm, p type, orientation). After a heating cycle which induces epitaxial growth, electrically active Sb atoms are incorporated into the SPEG layer, as shown by the following facts: (a) the SPEG layer forms a p-n junction against the p-type substrate, (b) the Hall effect indicates strong n-type conduction of the layer, and (c) Auger electron spectra reveal the presence of Sb in the layer

Interaction of Al layers with polycrystalline Si

Auger electron spectroscopy, MeV 4He + backscattering spectrometry and scanning electron microscopy have been used to investigate interactions between Al films and polycrystalline layers of CVD Si deposited on SiO2. Depth profiling techniques showed that intermixing of the Al and Si occurred in the 400–560 °C temperature range (i.e., below the eutectic). Dissolution of the poly Si into the Al film occurs followed by nucleation and growth of Si crystallites in the Al film. The morphology of the final structure depends on the relative thicknesses of the as-deposited Al and Si layers. In the case of the original Al thickness being greater than that of the Si, the Si forms large precipitates in the Al matrix. For Al layers thinner than those of the Si, a nearly continuous Si film is formed on the outer surface. The thickness of this final Si film is approximately that of the original Al layer. The remaining Si and the Al form a two-phase layer between the outer Si film and the SiO2 substrate

Solid-phase crystallization of Si films in contact with Al layers

Low-temperature (400–540 °C) crystallization of amorphous and polycrystalline Si films deposited on SiO2 and covered with an evaporated Al layer has been studied using SEM, TEM, electron diffraction, electron channeling, and MeV 4He + backscattering. Silicon deposited by evaporation and chemical vapor deposition (CVD) at 640 °C (both amorphous) was found to crystallize into islands of polycrystalline aggregates. Silicon deposited by CVD at 900 °C (polycrystalline with ~2000-Å grains) produced relatively large (~10 µm) single-crystal islands. In both cases island size increased with annealing time, and the rate of crystallization increased with temperature. Crystallization rates were observed to be the same for both sources of amorphous Si, while 900 °C CVD Si was noticeably slower, consistent with the postulate that the driving force for the reaction is the free-energy difference between initial and final states. The crystallization rate for 900 °C CVD Si decreased when the Al layer thickness was reduced to a value less than the initial Si grain size. The inclusion of a native oxide layer between the deposited Si and Al layers greatly retarded the crystallization process

Promoter analysis by saturation mutagenesis

Gene expression and regulation are mediated by DNA sequences, in most instances, directly upstream to the coding sequences by recruiting transcription factors, regulators, and a RNA polymerase in a spatially defined fashion. Few nucleotides within a promoter make contact with the bound proteins. The minimal set of nucleotides that can recruit a protein factor is called a cis-acting element. This article addresses a powerful mutagenesis strategy that can be employed to define cis-acting elements at a molecular level. Technical details including primer design, saturation mutagenesis, construction of promoter libraries, phenotypic analysis, data analysis, and interpretation are discussed

Gene Function Classification Using Bayesian Models with Hierarchy-Based Priors

We investigate the application of hierarchical classification schemes to the annotation of gene function based on several characteristics of protein sequences including phylogenic descriptors, sequence based attributes, and predicted secondary structure. We discuss three Bayesian models and compare their performance in terms of predictive accuracy. These models are the ordinary multinomial logit (MNL) model, a hierarchical model based on a set of nested MNL models, and a MNL model with a prior that introduces correlations between the parameters for classes that are nearby in the hierarchy. We also provide a new scheme for combining different sources of information. We use these models to predict the functional class of Open Reading Frames (ORFs) from the E. coli genome. The results from all three models show substantial improvement over previous methods, which were based on the C5 algorithm. The MNL model using a prior based on the hierarchy outperforms both the non-hierarchical MNL model and the nested MNL model. In contrast to previous attempts at combining these sources of information, our approach results in a higher accuracy rate when compared to models that use each data source alone. Together, these results show that gene function can be predicted with higher accuracy than previously achieved, using Bayesian models that incorporate suitable prior information

Quantitative Metabolomics Reveals an Epigenetic Blueprint for Iron Acquisition in Uropathogenic Escherichia coli

Bacterial pathogens are frequently distinguished by the presence of acquired genes associated with iron acquisition. The presence of specific siderophore receptor genes, however, does not reliably predict activity of the complex protein assemblies involved in synthesis and transport of these secondary metabolites. Here, we have developed a novel quantitative metabolomic approach based on stable isotope dilution to compare the complement of siderophores produced by Escherichia coli strains associated with intestinal colonization or urinary tract disease. Because uropathogenic E. coli are believed to reside in the gut microbiome prior to infection, we compared siderophore production between urinary and rectal isolates within individual patients with recurrent UTI. While all strains produced enterobactin, strong preferential expression of the siderophores yersiniabactin and salmochelin was observed among urinary strains. Conventional PCR genotyping of siderophore receptors was often insensitive to these differences. A linearized enterobactin siderophore was also identified as a product of strains with an active salmochelin gene cluster. These findings argue that qualitative and quantitative epi-genetic optimization occurs in the E. coli secondary metabolome among human uropathogens. Because the virulence-associated biosynthetic pathways are distinct from those associated with rectal colonization, these results suggest strategies for virulence-targeted therapies

Signature-Tagged Mutagenesis in a Chicken Infection Model Leads to the Identification of a Novel Avian Pathogenic Escherichia coli Fimbrial Adhesin

The extraintestinal pathogen, avian pathogenic E. coli (APEC), known to cause systemic infections in chickens, is responsible for large economic losses in the poultry industry worldwide. In order to identify genes involved in the early essential stages of pathogenesis, namely adhesion and colonization, Signature-tagged mutagenesis (STM) was applied to a previously established lung colonization model of infection by generating and screening a total of 1,800 mutants of an APEC strain IMT5155 (O2:K1:H5; Sequence type complex 95). The study led to the identification of new genes of interest, including two adhesins, one of which coded for a novel APEC fimbrial adhesin (Yqi) not described for its role in APEC pathogenesis to date. Its gene product has been temporarily designated ExPEC Adhesin I (EA/I) until the adhesin-specific receptor is identified. Deletion of the ExPEC adhesin I gene resulted in reduced colonization ability by APEC strain IMT5155 both in vitro and in vivo. Furthermore, complementation of the adhesin gene restored its ability to colonize epithelial cells in vitro. The ExPEC adhesin I protein was successfully expressed in vitro. Electron microscopy of an afimbriate strain E. coli AAEC189 over-expressed with the putative EA/I gene cluster revealed short fimbrial-like appendages protruding out of the bacterial outer membrane. We observed that this adhesin coding gene yqi is prevalent among extraintestinal pathogenic E. coli (ExPEC) isolates, including APEC (54.4%), uropathogenic E. coli (UPEC) (65.9%) and newborn meningitic E. coli (NMEC) (60.0%), and absent in all of the 153 intestinal pathogenic E. coli strains tested, thereby validating the designation of the adhesin as ExPEC Adhesin I. In addition, prevalence of EA/I was most frequently associated with the B2 group of the EcoR classification and ST95 complex of the multi locus sequence typing (MLST) scheme, with evidence of a positive selection within this highly pathogenic complex. This is the first report of the newly identified and functionally characterized ExPEC adhesin I and its significant role during APEC infection in chickens

A survey of assistive technologies and applications for blind users on mobile platforms: a review and foundation for research

This paper summarizes recent developments in audio and tactile feedback based assistive technologies targeting the blind community. Current technology allows applications to be efficiently distributed and run on mobile and handheld devices, even in cases where computational requirements are significant. As a result, electronic travel aids, navigational assistance modules, text-to-speech applications, as well as virtual audio displays which combine audio with haptic channels are becoming integrated into standard mobile devices. This trend, combined with the appearance of increasingly user- friendly interfaces and modes of interaction has opened a variety of new perspectives for the rehabilitation and training of users with visual impairments. The goal of this paper is to provide an overview of these developments based on recent advances in basic research and application development. Using this overview as a foundation, an agenda is outlined for future research in mobile interaction design with respect to users with special needs, as well as ultimately in relation to sensor-bridging applications in genera

HIV-1 Epidemic in the Caribbean Is Dominated by Subtype B

The molecular epidemiology of HIV-1 in the Caribbean has been described using partial genome sequencing; subtype B is the most common subtype in multiple countries. To expand our knowledge of this, nearly full genome amplification, sequencing and analysis was conducted.Virion RNA from sera collected in Haiti, Dominican Republic, Jamaica and Trinidad and Tobago were reverse transcribed, PCR amplified, sequenced and phylogenetically analyzed. Nearly full genomes were completed for 15 strains; partial pol was done for 67 strains. All but one of the 67 strains analyzed in pol were subtype B; the exception was a unique recombinant of subtypes B and C collected in the Dominican Republic. Of the nearly full genomes of 14 strains that were subtype B in pol, all were subtype B from one end of the genome to the other and not inter-subtype recombinants. Surprisingly, the Caribbean subtype B strains clustered significantly with each other and separate from subtype B from other parts of the pandemic.The more complete analysis of HIV-1 from 4 Caribbean countries confirms previous research using partial genome analysis that the predominant subtype in circulation was subtype B. The Caribbean strains are phylogenetically distinct from other subtype B strains although the biological meaning of this finding is unclear

Characterisation of a 3-hydroxypropionic acid-inducible system from Pseudomonas putida for orthogonal gene expression control in Escherichia coli and Cupriavidus necator

3-hydroxypropionic acid (3-HP) is an important platform chemical used as a precursor for production of added-value compounds such as acrylic acid. Metabolically engineered yeast, Escherichia coli, cyanobacteria and other microorganisms have been developed for the biosynthesis of 3-HP. Attempts to overproduce this compound in recombinant Pseudomonas denitrificans revealed that 3-HP is consumed by this microorganism using the catabolic enzymes encoded by genes hpdH, hbdH and mmsA. 3-HP-inducible systems controlling the expression of these genes have been predicted in proteobacteria and actinobacteria. In this study, we identify and characterise 3-HP-inducible promoters and their corresponding LysR-type transcriptional regulators from Pseudomonas putida KT2440. A newly-developed modular reporter system proved possible to demonstrate that PpMmsR/PmmsA and PpHpdR/PhpdH are orthogonal and highly inducible by 3-HP in E. coli (12.3- and 23.3-fold, respectively) and Cupriavidus necator (51.5- and 516.6-fold, respectively). Bioinformatics and mutagenesis analyses revealed a conserved 40-nucleotide sequence in the hpdH promoter, which plays a key role in HpdR-mediated transcription activation. We investigate the kinetics and dynamics of the PpHpdR/PhpdH switchable system in response to 3-HP and show that it is also induced by both enantiomers of 3-hydroxybutyrate. These findings pave the way for use of the 3-HP-inducible system in synthetic biology and biotechnology applications