Uneven distribution of the luxS gene within the genus Campylobacter

Polymerase chain reaction (PCR) amplification was performed on 20 isolates of five Campylobacter species using a degenerate primer pair designed in silico to generate a product of the luxS gene or its homologue from Campylobacter organisms. Although the primer pair successfully amplified products of approximately 500 base pairs (bp) with the eight isolates of C. jejuni and C. coli and some of C. upsaliensis and C. fetus, it failed to amplify fragments with all four isolates of C. lari (two urease-negative C. lari; two urease-positive thermophilic campylobacters). When Southern blot hybridisation analysis was carried using the mixed luxS gene fragments prepared from the C. jejuni, C. coli, C. upsaliensis and C. fetus strains as a probe, all C. jejuni, C. coli, C. upsaliensis and C. fetus isolates gave positive signals, but no positive signal was detected with any C. lari isolate. These results clearly indicate that C. jejuni, C. coli, C. upsaliensis and C. fetus carry the luxS gene or its homologue. However, no luxS gene or its homologue was identified to occur in the C. lari genome. Although autoinducer-2 assays were positive in C. jejuni, C. coli, C. upsaliensis and C. fetus isolates, it was negative with all the C. lari isolates examined. In addition, a biofilm formation assay demonstrated that biofilm formation in the C. lari species does not appear to correlate with the occurrence of the luxS gene because biofilm formation occurred among some isolates of C. lari.

Non-coding small (micro) RNAs of Pseudomonas aeruginosa isolated from clinical isolates from adult patients with cystic fibrosis

MicroRNAs are a class of small non-coding RNAs widely reported in eukaryotic multicellular organisms. In this study, a number of small non-coding micro (mi)RNA species in clinical isolates of prokaryote Pseudomonas aeruginosa were obtained from the sputum of adult patients with cystic fibrosis (CF) utilising a DynaExpress miRNA cloning kit, and five miRNAs of 16-47 nucleotides that were smaller than those encountered or described (80-100 nucleotides) previously in bacterial systems were described. This report presents data on these unknown cellular miRNAs cloned from P. aeruginosa isolates from CF patients. Adapting a computational miRNA prediction model that takes advantage of the highly conserved known miRNA hair pin stems regions, the results revealed that the fold structure of the microRNAs had a high homology to the recently reported human bacterial infection response (BiR)-related microRNA, mi-146, associated with the Toll-like receptor (TLR) family, which is the primary evolutionarily conserved sensors of pathogen-associated molecular patterns (PAMPs), and known to trigger host inflammatory and immune responses.

Campylobacter lari: molecular and comparative analyses of the virulence-associated chromosome locus J (vacJ) gene homologue, including the promoter region

Following TA cloning and sequencing with a novel in silico-designed polymerase chain reaction (PCR) primer pair (f-ClvacJ/r-ClvacJ), approximately 750 base pairs (bp) of promoter and structural gene regions for vacJ and its adjacent genetic loci (approximately 1.14 kbp) were identified in 20 isolates of Campylobacter lari (urease-negative C. lari [n=7]; urease-positive thermophilic Campylobacter [n=13]). The nucleotide sequences of an approximately 70-bp non-coding region, including the typical promoter structure, showed sequence differences at 12 loci among 21 isolates including C. lari RM2100. The putative sigma70 promoter region upstream of the putative open reading frame (ORF), a start codon TTG and a probable ribosome binding site, AGGA, for the vacJ gene were also identified in all 21 C. lari isolates examined. Each ORF for the vacJ terminated with a TAA stop codon. No hypothetical transcriptional terminators were identified within the amplicons. The putative ORFs of the vacJ gene from 21 C. lari isolates consisted of 684 bases, similarly differing from those of the other thermophilic campylobacters (696 bases for C. jejuni RM1221 and NCTC11168 and C. coli RM2228; 690 for C. upsaliensis RM3195). Reverse transcription PCR analysis confirmed the transcription of the vacJ gene in the C. lari cells. A neighbour joining tree suggested a strong molecular discrimination efficacy between UPTC and UN C. lari employing vacJ nucleotide sequence information. The vacJ gene homologue from C. lari organisms appears not to be a lipoprotein signal peptide or a signal peptide in silico.

Simulation of a chain of collapsible contracting lymphangions with progressive valve closure

The aim of this investigation was to achieve the first step toward a comprehensive model of the lymphatic system. A numerical model has been constructed of a lymphatic vessel, consisting of a short series chain of contractile segments (lymphangions) and of intersegmental valves. The changing diameter of a segment governs the difference between the flows through inlet and outlet valves and is itself governed by a balance between transmural pressure and passive and active wall properties. The compliance of segments is maximal at intermediate diameters and decreases when the segments are subject to greatly positive or negative transmural pressure. Fluid flow is the result of time-varying active contraction causing diameter to reduce and is limited by segmental viscous and valvular resistance. The valves effect a smooth transition from low forward-flow resistance to high backflow resistance. Contraction occurs sequentially in successive lymphangions in the forward-flow direction. The behavior of chains of one to five lymphangions was investigated by means of pump function curves, with variation of valve opening parameters, maximum contractility, lymphangion size gradation, number of lymphangions, and phase delay between adjacent lymphangion contractions. The model was reasonably robust numerically, with mean flow-rate generally reducing as adverse pressure was increased. Sequential contraction was found to be much more efficient than synchronized contraction. At the highest adverse pressures, pumping failed by one of two mechanisms, depending on parameter settings: either mean leakback flow exceeded forward pumping or contraction failed to open the lymphangion outlet valve. Maximum pressure and maximum flow-rate were both sensitive to the contractile state; maximum pressure was also determined by the number of lymphangions in series. Maximum flow-rate was highly sensitive to the transmural pressure experienced by the most upstream lymphangions, suggesting that many feeding lymphatics would be needed to supply one downstream lymphangion chain pumping at optimal transmural pressure.

Molecular analysis and characterisation of the full-length flagellin C gene (flaC) from Campylobacter lari

A degenerate polymerase chain reaction (PCR) primer pair (f-ClflaC/r-ClflaC) was constructed in silico to amplify flaC and its adjacent genetic loci from Campylobacter lari isolates. Approximately 1.45 kbp amplicons, including the sequences encoding the flaC structural gene of 750 bp, putative promoter, rho-independent intrinsic terminator regions and partial sequences of two putative open reading frames (ORFs), immediately upstream and downstream of the gene, were identified in 16 C. lari isolates (four urease-negative [UN] C. lari; 12 urease-positive thermophilic campylobacters [UPTC)]). All 16 flaC structural genes commenced with an ATG start codon and terminated with a TAA stop codon and probable ribosome-binding sites were identified in all 16 isolates. These probably indicate a monocistronic operon structure for the flaC gene in C. lari isolates. In addition, the putative flaC gene ORFs were deduced to be similar in 747 bp among all 26 thermophilic Campylobacter isolates examined, resulting in a similar calculated molecular weight of approximately 26.6-26.9 kDa. The flaC from C. lari was different from the flaA-like sequence and the shorter flaA of UPTC isolates found previously. Reverse transcription PCR and Northern blot hybridisation analyses identified flaC transcription in C. lari cells. The transcription initiation site for the flaC gene was also determined by primer extension analysis. A dendrogram constructed, based on the nucleotide sequence information of flaC from 17 C. lari isolates, demonstrated that the C. lari isolates were genetically variable and formed two minor clusters for UN C. lari and UPTC.

Molecular analysis and characterization of a urease gene operon from Campylobacter sputorum biovar paraureolyticus

When recombinant plasmid DNA from a genomic DNA library and inverse PCR products of Campylobacter sputorum biovar paraureolyticus LMG17591 strain were analyzed, an approximate 6.5-kb pair region, encoding a urease gene operon, was identified. Within the operon, seven closely spaced and putative open reading frames for ureG, ureH(D), ureA, ureB, ureC, ureE, and ureF were detected in order. A possible overlap was detected between ureG and ureH(D), ureH(D) and ureA, and ureE and ureF. In addition, two putative promoter structures, probable ribosome-binding sites and a putative ρ-independent transcriptional terminator structure were identified. The urease gene operon transcription in the cells was confirmed by the reverse transcription-PCR analysis. A neighbor-joining tree constructed based on the nucleotide sequence information of urease genes showed that C. sputorum biovar paraureolyticus formed a cluster with Arcobacter butzleri, urease-positive thermophilic Campylobacter and some Helicobacter spp., separating those from the other urease-producing bacteria, suggesting a commonly shared ancestry among these organisms.

Structural analysis and expression of the full-length cytochrome P450 gene operon in Campylobacter lari

Two sets of PCR primers are constructed to clone the cytochrome P450 structural gene, including putative promoter and terminator structures, and its adjacent genetic loci in Campylobacter lari isolates. The putative open reading frames (ORFs) of the P450 genes from 11 C. lari isolates (n=5 for urease-negative (UN) C. lari; n=6 urease-positive thermophilic campylobacters [UPTC]) examined consisted of 1365 or 1371 bases (455 or 457 amino acid residues), differing from those of the other thermophilic campylobacters (1359 [453] for C. jejuni and C. upsaliensis; 1368 [456] for C. coli). Each of the putative ORFs from the 11 isolates examined was also shown to carry start and stop codons and ribosome binding sites. Two putative promoter structures, consisting of sequences at the -35- and -10-like regions were also identified upstream of the ORFs. A single copy of the P450 gene in the genome was identified with UN C. lari JCM2530(T) and UPTC CF89-12, based on Southern blot hybridisation analysis. In addition, when reverse transcription polymerase chain reaction (RT-PCR) analyses were carried out, the transcription of the P450 structural gene in C. lari organisms in vivo was confirmed. The transcription initiation site for the gene was also determined. High nucleotide sequence similarities (95.2-98.8%) of the full-length P450 structural gene were shown with each of the 12 C. lari isolates. The UN C. lari and UPTC organisms showed similar findings with the neighbour-joining method, based on the sequence information of the P450 structural gene.

In-plane transport and enhanced thermoelectric performance in thin films of the topological insulators Bi₂Te₃ and Bi₂Se₃

Several small-band-gap semiconductors are now known to protect metallic surface states as a consequence of the topology of the bulk electron wave functions. The known "topological insulators" with this behavior include the important thermoelectric materials Bi₂Te₃ and Bi₂Se₃, whose surfaces are observed in photoemission experiments to have an unusual electronic structure with a single Dirac cone. We study in-plane (i.e., horizontal) transport in thin films made of these materials. The surface states from top and bottom surfaces hybridize, and conventional diffusive transport predicts that the tunable hybridization-induced band gap leads to increased thermoelectric performance at low temperatures. Beyond simple diffusive transport, the conductivity shows a crossover from the spin-orbit-induced antilocalization at a single surface to ordinary localization.

Aharonov-Bohm oscillations in disordered topological insulator nanowires

A direct signature of electron transport at the metallic surface of a topological insulator is the Aharonov-Bohm oscillation observed in a recent study of Bi2Se3 nanowires [Peng, Nature Mater. 9, 225 (2010)] where conductance was found to oscillate as a function of magnetic flux ϕ through the wire, with a period of one flux quantum ϕ0=h/e and maximum conductance at zero flux. This seemingly agrees neither with diffusive theory, which would predict a period of half a flux quantum, nor with ballistic theory, which in the simplest form predicts a period of ϕ0 but a minimum at zero flux due to a nontrivial Berry phase in topological insulators. We show how h/e and h/2e flux oscillations of the conductance depend on doping and disorder strength, provide a possible explanation for the experiments, and discuss further experiments that could verify the theory.

Optimisation of storage conditions for maintaining culturability of penicillin-susceptible and penicillin-resistant isolates of Streptococcus pneumoniae in transport medium

Methods employed by the World Health Organization (WHO) are used during this study to determine the optimum storage conditions for maintaining the culturability of Streptococcus pneumoniae in skimmed milk, tryptone, glucose and glycerin (STGG) transport medium. A comparison of S. pneumoniae strains sensitive and resistant to penicillin showed no significant difference in their survival ability in STGG medium. Furthermore, it is confirmed that storage at -70 degrees C remains most effective for maintaining viability by culture of S. pneumoniae. Storage at -20 degrees C would only be acceptable in the short-term, while storage at +4 degrees C is not recommended. Of note, this study has shown STGG medium at room temperature to be an efficient growth medium for pneumococci in the short-term. This work will help to establish robust sampling protocols when performing community studies to ensure culturability of comparison between community and laboratory pneumococci survival.

Confinement-induced berry phase and helicity-dependent photocurrents

The photocurrent in an optically active metal is known to contain a component that switches sign with the helicity of the incident radiation. At low frequencies, this current depends on the orbital Berry phase of the Bloch electrons via the "anomalous velocity" of Karplus and Luttinger. We consider quantum wells in which the parent material, such as GaAs, is not optically active and the relevant Berry phase only arises as a result of quantum confinement. Using an envelope approximation that is supported by numerical tight-binding results, it is shown that the Berry-phase contribution is determined for realistic wells by a cubic Berry phase intrinsic to the bulk material, the well width, and the well direction. These results for the Berry-phase effect suggest that it may already have been observed in quantum well experiments.

Molecular characterisation of the recA locus in clinical isolates of verocytotoxigenic E. coli O157:H7

Molecular epidemiology of verocytoxigenic Escherichia coli O157:H7 is important to help elucidate reservoirs and modes of transmission, particularly between animals and humans. As the recA gene locus is now beginning to gain application in bacterial genotyping schemes, and as it has not been examined previously in E. coli O157 isolates, this study aims to examine potential polymorphic variation as a possible epidemiological marker for the subspecies characterisation of clinically significant verocytotoxigenic E. coli O157:H7. A novel polymerase chain reaction (PCR) assay was designed to target a 638 bp region of the recA gene in E. coli O157 isolates. The PCR amplification of genomic DNA from extracted organisms was able to generate an amplicon of the expected size (approximately 638 bp) for all E. coli O157:H7 examined (n=80), as well as for other non-O157 E. coli and other members of the Enterobacteriaeceae including Citrobacter, Hafnia, Shigella, Enterobacter and Providencia. Subsequent restriction fragment length polymorphism (RFLP) and single-stranded conformational polymorphism (SSCP) analyses of these recA amplicons were able to differentiate E. coli O157 from the organisms examined, but were unable to distinguish between 79 isolates of wild-type E. coli O157, suggesting a highly conserved recA gene structure within the local population of organisms examined.

Photocatalytic inactivation of Cryptosporidium parvum on nanostructured titanium dioxide films

Control of waterborne gastrointestinal parasites represents a major concern to water industries worldwide. In developed countries, pathogens in drinking water supplies are normally removed by sand filtration followed by chemical disinfection. Cryptosporidium spp. are generally resistant to common disinfection techniques and alternative control strategies are being sought. In the current study, the photocatalytic inactivation of C. parvum oocysts was shown to occur in buffer solution (78.4% after 180 min) and surface water (73.7% after 180 min). Viability was assessed by dye exclusion, excystation, direct examination of oocysts and a novel gene expression assay based on lactate dehydrogenase 1 (LDH1) expression levels. Collectively, this confirmed the inactivation of oocysts and scanning electron microscopy (SEM) confirmed cleavage at the suture line of oocyst cell walls, revealing large numbers of empty (ghost) cells after exposure to photocatalytic treatment.

Approaches to measure the fitness of Burkholderia cepacia complex isolates

Members of the Burkholderia cepacia complex (Bcc) are highly resistant to many antibacterial agents and infection can be difficult to eradicate. A coordinated approach has been used to measure the fitness of Bcc bacteria isolated from cystic fibrosis (CF) patients with chronic Bcc infection using methods relevant to Bcc growth and survival conditions. Significant differences in growth rate were observed among isolates; slower growth rates were associated with isolates that exhibited higher MICs and were resistant to more antimicrobial classes. The nucleotide sequences of the quinolone resistance-determining region of gyrA in the isolates were determined and the ciprofloxacin MIC correlated with amino acid substitutions at codons 83 and 87. Biologically relevant methods for fitness measurement were developed and could be applied to investigate larger numbers of clinical isolates. These methods were determination of planktonic growth rate, biofilm formation, survival in water and survival during drying. We also describe a method to determine mutation rate in Bcc bacteria. Unlike in Pseudomonas aeruginosa where hypermutability has been detected in strains isolated from CF patients, we were unable to demonstrate hypermutability in this panel of Burkholderia cenocepacia and Burkholderia multivorans isolates.

Exciton condensation and charge fractionalization in a topological insulator film

An odd number of gapless Dirac fermions is guaranteed to exist at a surface of a strong topological insulator. We show that in a thin-film geometry and under external bias, electron-hole pairs that reside in these surface states can condense to form a novel exotic quantum state which we propose to call "topological exciton condensate" (TEC). This TEC is similar in general terms to the exciton condensate recently argued to exist in a biased graphene bilayer, but with different topological properties. It exhibits a host of unusual properties including a stable zero mode and a fractional charge +/-e/2 carried by a singly quantized vortex in the TEC order parameter.

Molecular characterisation of urease genes from urease-positive thermophilic campylobacters (UPTC)

This study aims to clarify the molecular characteristics of the urease gene operon from urease-positive thermophilic campylobacters (UPTC) obtained from different sources and in various countries. Sequence heterogeneity was observed for the promoter structures at the -35-like region among the 12 isolates examined. The most probable TTG start codon was suggested for the ureB and ureH genes, and for the ureA, E, F and G genes, ATG was suggested among all the isolates examined. Overlap was detected between ureA and ureB and between ureB and ureE among all the isolates examined. UPTC is the first example of an overlap between the two structural genes ureA and ureB. When the completely sequenced open reading frames (ORFs) for ureE, ureF, ureG and ureH were identified, non-coding regions between ureE and ureF, ureF and ureG, and ureG and ureH were also demonstrated. All six start codons of the six urease genes were demonstrated to be preceded by Shine-Dalgarno sequences among all the isolates examined. The Cys-His sequence corresponding to urease active sites were aligned perfectly and fully conserved among the three UPTC isolates examined. A putative and intrinsic p-independent transcriptional terminator was identified to be identical among all the isolates examined. A partial and putative ORF of about 200 bp in length showing high sequence similarity to GTP cyclohydrolase I was observed downstream of ureH.

Cloning and structural analysis of the full-length cytolethal distending toxin (cdt) gene operon from Campylobacter lari

Polymerase chain reaction (PCR) amplicons (approximately 2.5 kbp) encoding a cdt gene operon and two partial and putative open reading frames (ORFs) were identified in six urease-negative (UN) Campylobacter lari isolates using a new PCR primer pair constructed in silico. Three closely spaced and putative ORFs for cdtA, cdtB and cdtC, two putative promoters and a hypothetically intrinsic p-independent transcription terminator were found in the operon. Each ORF commenced with an ATG start codon and terminated with a TGA stop codon for cdtA and cdtB and a TAA for cdtC. Interestingly, an overlap of four nucleotides was detected between cdtA and cdtB and the non-coding region of six base pairs occurring between cdtB and cdtC. The start codons for the three cdt genes were preceded by Shine-Dalgarno sequences. Although nucleotide sequence differences were identified at seven loci in the cdtA gene, six in cdtB and two in cdtC among the seven isolates (including C. lari RM2100), no polymorphic sites occurred in the putative promoters, hypothetically intrinsic transcription terminator and the three ribosome binding sites among the seven isolates. All nine amino acid residues specific for both Escherichia coli cdtB and mammalian DNase I were completely conserved in the cdtB gene locus in the 26 C. lari isolates, as well as in C. jejuni and C. coli. No PCR amplicons were generated with urease-positive thermophilic campylobacters (UPTC; n=10) using the primer pair.