16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleotide similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates. The EzTaxon server is freely accessible over the Internet at http://www.eztaxon.org/

We report an electrochemical study of the collisions of single droplets in an emulsion by two methods. In the first method, an electroactive redox species, for example, ferrocene, inside a toluene-in-water emulsion droplet (but not in the continuous phase) is measured by chronoamperometry during a collision with an ultramicroelectrode (UME). Here, a blip or spike type of collision signal is observed, representing electrolysis of the droplet contents. In the second method, electrochemical oxidation of an electroactive redox species in the continuous aqueous phase is hindered by a droplet blocking collision. In this case, a staircase current decrease is observed. From an analysis of single soft particle collision data, one can find the emulsion droplet size distribution and the droplet contents.

In Helicobacter predominant patients, the microbial compositions of gastric mucosa from gastric cancer patients are significantly different to chronic gastritis and intestinal metaplasia patients. These alterations of gastric microbial composition may play an important, as-yet-undetermined role in gastric carcinogenesis of Helicobacter predominant patients.

We report here the electrochemistry of emulsion droplets by observing single emulsion droplet collisions with selective electrochemical reduction on an ultramicroelectrode (UME). With appropriately applied potentials at an UME, we can observe the electrochemical effects of single collision signals from the complete electrolysis of single emulsion droplets, or selective electrolysis of redox species in single emulsion droplets. This was observed with nitrobenzene (NB), 7,7,8,8-tetracyanoquinodimethane (TCNQ), and ionic liquid. The NB, TCNQ, and ionic liquid act as emulsion material, redox specie, and emulsifier (and electrolyte), respectively. NB emulsions and NB (TCNQ) emulsions were made by ultrasonic processing. During the amperometric current-time (i-t) curve measurement with NB/water emulsion at -0.65 V, reduction of NB emulsion droplets was measured. In the case of less negative potentials, e.g., at -0.45 V with a NB (TCNQ) emulsion, selective reduction of TCNQ in NB droplet was measured. Spike-like responses from electrolysis of NB or TCNQ in each experiment were observed. From these single-particle collision results of NB and NB (TCNQ) emulsions, the collision frequency, size distribution, i-t decay behavior of emulsion droplets, and possible mechanisms are discussed.

We describe the fabrication of a nanometer-size electrode based on an insulating TiO2 film and a metal nanoparticle (NP). The TiO2 film is deposited on the conducting Pt surface of an ultramicroelectrode (UME) to block electron transfer (ET) to solution species. The film thickness is, however, thin enough to enable tunneling to Pt NPs; thus, the subsequent contact of metal NP to the TiO2 film restores the ET to solution species solely on the NP surface via facile electron tunneling. Consequently, the composite of UME/metal oxide film/NP offers nm-scale active area. The TiO2 film is electrochemically deposited on the Pt UME (Pt UME/TiO2), monitoring the cyclic voltammetry (CV) of ferrocenemethanol until the oxidation wave just disappears. A single Pt NP is captured in a collision experiment by observing the current increase upon contact of the Pt NP with the Pt UME/TiO2 by means of Pt NP-mediated electrochemical reduction of Fe(CN)6(3-). The resultant Pt UME/TiO2/Pt NP (or tunneling UME, T-UME) showed long-term stability and robustness with well-defined electrochemical response, suggesting applicability as a novel nm-size electrode for CV and steady-state measurements such as those with scanning electrochemical microscopy (SECM). Here, we employed the T-UME to measure SECM approach curves and showed remarkable approach capability for a nm-size SECM probe.

We provide evidence of single attoliter oil droplet collisions at the surface of an ultra-microelectrode (UME) by the observation of simultaneous electrochemical current transients (i-t curves) and electrogenerated chemiluminescent (ECL) transients in an oil/water emulsion. An emulsion system based on droplets of toluene and tri-n-propylamine (2:1 v/v) emulsified with an ionic liquid and suspended in an aqueous continuous phase was formed by ultrasonification. When an ECL luminophore, such as rubrene, is added to the emulsion droplet, stochastic events can be tracked by observing both the current blips from oxidation at the electrode surface and the ECL blips from the follow-up ECL reaction, which produces light. This report provides a means of studying fundamental aspects of electrochemistry using the attoliter oil droplet and offers complementary analytical techniques for analyzing discrete collision events, size distribution of emulsion systems, and individual droplet electroactivity.

Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, “ Candidatus Nitrosopumilus koreensis” MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.

We describe a method to produce electrogenerated chemiluminescence (ECL) in water using a family of highly hydrophobic polycyclic aromatic hydrocarbon (PAH) luminophores and boron dipyrromethene (BODIPY). This method is based on an oil-in-water emulsion system. Various PAHs (rubrene, 9,10-diphenylanthracene, pyrene, or perylene) and BODIPY were trapped in a toluene and tri-n-propylamine mixed oil-in-water emulsion using an ionic liquid as the supporting electrolyte and emulsifier. ECL was observed for all the aforementioned PAHs and BODIPY, and the rubrene and BODIPY emulsion systems showed adequate light to record an ECL spectrum. ECL was also observed using oxalate as the co-reactant, which was dissolved in the aqueous continuous phase. The emulsions were stable for hours and showed a droplet size distribution that ranged from 275 to 764 nm, in accordance with dynamic light scattering data.