Understanding the Evolutionary Relationships and Major Traits of \u3cem\u3eBacillus\u3c/em\u3e through Comparative Genomics

Background: The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus. Results: Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches. Conclusions: The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches

Phylogenetic Distribution and Evolutionary History of Bacterial DEAD-Box Proteins

DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation

Anodic aluminum oxide processing, characterization and application to DNA hybridization electrical detection

Metal oxides have recently come under study thanks to their physical and electrical properties for different applications such as MOS devices, i.e. substituting the silicon oxide with a high-k material, or as MIM (Metal Insulator Metal) capacitors, to increase capacitance per unit area and circuit integration. One oxide of interest in this field is aluminum oxide since it features good electrical insulation and high dielectric constant. In-depth studies are presented here on the use of non-porous anodic Al2O3. Major physical and electrical parameters have been obtained, i.e. dielectric constant, stress, deformation, resistance, surface quality. Constant, low anodizing current density results in a denser oxide, with a thickness of around 100 nm. Performances such as capacitance, breakdown voltage, etc. can be improved when compared to other Al2O3 obtained by other methods. Results are also comparable to other high-k oxides. Fair performance is maintained for temperature raised up to 200°C, which opens new possible applications. Its mechanical and physical properties make it candidate in biological and MEMS devices. DNA re-association or hybridization is the underlining principle of DNA sensors. Different electrical Al structures protected by a thin anodic Al2O3 are tested. Interdigitated capacitors, the most promising electrical structure, were selected and process characterization performed. Three electrical extraction procedures are performed on the same device lying on a passivated silicon substrate: inter-electrodes capacitance, the self-resonance frequency, and the equivalent MOS capacitance between the short-circuited electrodes and the substrate. This study is the first of its kind to open the way for correlation studies and noise reduction techniques based on multiple electrical measurements of the same DNA hybridization event. The hybridization of concentrations as low as 50 pM target DNA has been successfully electrically detected using silver enhancement over gold nano-particles labeled DNA.(FSA 3)--UCL, 200

Insulated substrate impedance transducers

The present invention provides an electronic transducer (10) and a method for detecting and/or characterizing target materials or physico-chemical stimuli in an external medium (8) using the electronic transducer (10). The electronic transducer (10) comprises a sensing element (3) featuring a variable conductance when exposed to a stimulus from the external medium and a first and second electrode (5a, 5b) spaced apart on or in a sensing material surface of a substrate, the sensing element being provided in or on the substrate and being located between the first and the second electrodes (5a, 5b) forming a pair of sensing electrodes for sensing a change in conductance of the sensing element (3) in a direction substantially parallel to the sensing material surface, at least one of the sensing electrodes (5a, 5b) being electrically insulated from the sensing element (3) by a dielectric layer (4), so as to be capacitively coupled to the sensing element (3). An insulating layer or target specific layer (7) may optionally be provided covering the sensing element (3) and optionally the sensing electrodes and being adapted for contact with the external medium (8). Electrical measurements made between the pair of sensing electrodes (5a, 5b) are influenced by the impedance of the channel (3) which is affected by the presence of the medium (8) to be tested

Method and device for high sensitivity detection of the presence of DNA and other probes

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High-Voltage High-Current DMOS Transistor Compatible with High-Temperature Thin-Film SOI CMOS Applications

The goal of this work is to explore different ways for co-integrating a power DMOS device in the bulk Si-substrate which underlies the SOI buried oxide and thin Si overlayer, providing optimal performance and isolation of both kinds of devices. A first phase has consisted of the design and fabrication of a power DMOS, defining and optimising 3 mixed DMOS/SOI-CMOS process based on existing power VDMOS and FD SOI CMOS technologies. 150V power VDMOS have been fabricated. One of these process clearly gives better results than the other two proposed technologies. The compatibility of both power VDMOS devices and SOI circuitry is then demonstrated

Sensitive DNA electrical detection based on interdigitated Al/Al2O3 microelectrodes

The detection of DNA by electrical based methods still faces the challenge of the low amounts of genetic material to be analyzed in order to make the assay useful for biological applications. In this work we present the possibility of detecting DNA strands by measuring a change of capacitance between interdigitated electrodes, of 1, 2 and 3 mum widths and spacing, made of aluminum fingers, coated with a thin alumina layer and constructed over an oxidized silicon wafer, reducing the non-specific precipitation of silver that occurs when using noble metal electrodes like gold. Labeling of DNA was performed by incorporation of biotinylated nucleotides and reaction with anti-biotin antibodies coupled to gold nanoparticles, whose size was increased by silver crystal precipitation. We observed a change in capacitance by a factor of at least two, using DNA solutions down to 0.2 nM, spotted on the electrodes. This method of detection thus appears compatible with the requirements of microarray technology and paves the way for further use in biological applications. (C) 2003 Elsevier B.V. All rights reserved