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.

Referrals to ophthalmology: optometric and general practice comparison

PURPOSE

To assess referrals from primary care practitioners to an ophthalmological practice in order to determine whether any differences exist between the two primary care groups in the types of conditions referred, and in concurrence between reasons for referral and ophthalmological diagnosis.

METHODS

This study investigated patient referrals from general practitioners and optometrists to an ophthalmologist's practice in Belfast, over a period of 3 months from January 2007 to the end of March 2007. Anonymised data were divided into two groups depending on the referring practitioner. Within the two groups, patient numbers were sub-divided into 15 categories covering the range of diagnoses made. Preliminary diagnoses or reasons for referral were compared with the definitive diagnoses made by the ophthalmologist.

RESULTS

Optometrists contributed the greatest number of referrals (323) with 243 patients referred by general practitioners. Cataract was the most common condition referred by optometrists, and the second most common condition referred by general practitioners: agreement with ophthalmological diagnosis was high for both groups of primary care practitioners. Concurrence of referral reason with ophthalmological diagnosis for glaucoma was lower for general practitioners (56%) than for optometrists (76%), but optometrists referred more false positive patients for glaucoma than did general practitioners. The opposite was true for lid/tear duct/conjunctival conditions, the most common basis for referral by general practitioners.

CONCLUSIONS

The differences between the two primary care practitioner groups may reflect variations in training, skills and practice. Further investigation of the particular strengths of both groups, and how they can be optimised to promote effective shared care, is required.

Naproxen-PC: a GI safe and highly effective anti-inflammatory

We have been developing a family of phosphatidylcholine (PC)-associated NSAIDs, which appear to have improved GI safety and therapeutic efficacy in both rodent model systems and pilot clinical trials. As naproxen has been demonstrated to be associated with the lowest cardiovascular adverse events in comparison with both COX-2 selective inhibitors and conventional NSAIDs, we have been developing a Naproxen-PC formulation for evaluation in animal models and clinical trials. We have determined that an oil-based formulation of naproxen and triple strength soy lecithin provides excellent GI protection in both: 1) an acute NSAID-induced intestinal bleeding model in rats pretreated with L-NAME that are intragastrically administered a single dose of naproxen (at a dose of 50 mg/kg) vs the equivalent dose of Naproxen-PC; and 2) a more chronic model (at a naproxen dose of 25 mg/kg BID) in rats that have pre-existing hindpaw inflammation (induced with a intradermal injection of Complete Freund's Adjuvant/CFA). Both models demonstrate the superior GI safety of Naproxen-PC vs naproxen while this novel formulation had significant anti-inflammatory efficacy to reduce hindpaw edema and the generation of PGE(2) in the collected joint synovial fluid.

CONCLUSION

Naproxen-PC appears to induce significantly less GI injury and bleeding in two rodent model systems while maintaining anti-inflammatory and COX-inhibitory activity.

Concordance between common dry eye diagnostic tests

AIM

Large variations in results of diagnostic tests for mild to moderate dry eye are widely recognised. The purpose of this study was to assess if there was concordance between common dry eye diagnostic tests.

METHODS

A total of 91 subjects were recruited to the study. The tear film and ocular surface were evaluated using the phenol red thread test (PRT), tear film break-up time (TBUT), biomicroscopic examination and impression cytological assessment of conjunctival goblet cells. Dry eye symptoms were assessed using McMonnies' dry eye questionnaire (MQ) and statistical correlations between all tests were assessed.

RESULTS

This study cohort did not include severe aqueous deficient dry eye patients as determined by the PRT. A statistically significant difference was noted between PRT results and all other tests (p

CONCLUSION

A correlation was found only between tests assessing lipid/mucous deficiency (Meibomian gland evaluation, goblet cell density, TBUT and MQ).

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Key Words

• correlation dry eye diagnostic tests

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MESH Headings

• Adult
• Aged
• Aged, 80 and over
• Analysis of Variance
• Conjunctiva/pathology
• Diagnosis, Differential
• Diagnostic Techniques, Ophthalmological/standards
• Dry Eye Syndromes/diagnosis
• Female
• Humans
• Male
• Meibomian Glands/pathology
• Middle Aged
• Reproducibility of Results
• Tears/metabolism
• Young Adult

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Grants

• R01 EY019470 NEI NIH HHS

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