Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage.

Shigatoxigenic Escherichia coli emerged as new food borne pathogens in the early 1980s, primarily driven by the dispersal of Shiga toxin-encoding lambdoid bacteriophages. At least some of these Stx phages display superinfection phenotypes, which differ significantly from lambda phage itself, driving through in situ recombination further phage evolution, increasing host range and potentially increasing the host's pathogenic profile. Here, increasing levels of Stx phage Φ24(B) integrase expression in multiple lysogen cultures are demonstrated along with apparently negligible repression of integrase expression by the cognate CI repressor. The Φ24(B) int transcription start site and promoter region were identified and found to differ from in silico predictions. The unidirectional activity of this integrase was determined in an in situ, inducible tri-partite reaction. This indicated that Φ24(B) must encode a novel directionality factor that is controlling excision events during prophage induction. This excisionase was subsequently identified and characterized through complementation experiments. In addition, the previous proposal that a putative antirepressor was responsible for the lack of immunity to superinfection through inactivation of CI has been revisited and a new hypothesis involving the role of this protein in promoting efficient induction of the Φ24(B) prophage is proposed.

Experimental methods of actuation, characterization and prototyping of hydrogels for bioMEMS/NEMS applications.

As a member of the smart polymer material group, stimuli responsive hydrogels have achieved a wide range of applications in microfluidic devices, micro/nano bio and environmental sensors, biomechanics and drug delivery systems. To optimize the utilization of a hydrogel in various micro and nano applications it is essential to have a better understanding of its mechanical and electrical properties. This paper presents a review of the different techniques used to determine a hydrogel's mechanical properties, including tensile strength, compressive strength and shear modulus and the electrical properties including electrical conductivity and dielectric permittivity. Also explored the effect of various prototyping factors and the mechanisms by which these factors are used to alter the mechanical and electrical properties of a hydrogel. Finally, this review discusses a wide range of hydrogel fabrication techniques and methods used, to date, to actuate this family of smart polymer material.

Rule-based modelling of conjugative plasmid transfer and incompatibility.

COSMIC-rules, an individual-based model for bacterial adaptation and evolution, has been used to study virtual transmission of plasmids within bacterial populations, in an environment varying between supportive and inhibitory. The simulations demonstrate spread of antibiotic resistance (R) plasmids, both compatible and incompatible, by the bacterial gene transfer process of conjugation. This paper describes the behaviour of virtual plasmids, their modes of exchange within bacterial populations and the impact of antibiotics, together with the rules governing plasmid transfer. Three case studies are examined: transfer of an R plasmid within an antibiotic-susceptible population, transfer of two incompatible R plasmids and transfer of two compatible R plasmids. R plasmid transfer confers antibiotic resistance on recipients. For incompatible plasmids, one or other plasmid could be maintained in bacterial cells and only that portion of the population acquiring the appropriate plasmid-encoded resistance survives exposure to the antibiotics. By contrast, the compatible plasmids transfer and mix freely within the bacterial population that survives in its entirety in the presence of the antibiotics. These studies are intended to inform models for examining adaptive evolution in bacteria. They provide proof of principle in simple systems as a platform for predicting the behaviour of bacterial populations in more complex situations, for example in response to changing environments or in multi-species bacterial assemblages.

Rule-based computing system for microbial interactions and communications: evolution in virtual bacterial populations.

We have developed a novel rule-based computing system of microbial interactions and communications, referred to as COSMIC-Rules, for simulating evolutionary processes within populations of virtual bacteria. The model incorporates three levels: the bacterial genome, the bacterial cell and an environment inhabited by such cells. The virtual environment in COSMIC-Rules can contain multiple substances, whose relative toxicity or nutrient status is specified by the genome of the bacterium. Each substance may be distributed uniformly or in a user-defined manner. The organisms in COSMIC-Rules possess individually-defined physical locations, size, cell division status and genomes. Genes and/or gene systems are represented by abstractions that may summate sometimes complex phenotypes. Central to COSMIC-Rules is a simplified representation of bacterial species, each containing a functional genome including, where desired, extrachromosomal elements such as plasmids and/or bacteriophages. A widely applicable computer representation of biological recognition systems based on bit string matching is essential to the model. This representation permits, for example, the modelling of protein-protein interactions, receptor-ligand interactions and DNA-DNA transactions. COSMIC-Rules is intended to inform studies on bacterial adaptation and evolution, and to predict behaviour of populations of pathogenic bacteria and their viruses. The framework is constructed for parallel execution across a large number of machines and efficiently utilises a 64 processor development cluster. It will run on any Grid system and has successfully tested simulations with millions of bacteria, of multiple species and utilising multiple substrates. The model may be used for large-scale simulations where a genealogical record for individual organisms is required.

Human seminal clusterin (SP-40,40). Isolation and characterization.

Molecular cloning of the human complement inhibitor SP-40,40, has revealed strong homology to a major rat and ram Sertoli cell product, sulfated glycoprotein-2, known also as clusterin. This study reports the purification and characterization of human seminal clusterin. Two-dimensional gel electrophoresis revealed charge differences between clusterin purified from semen and the serum-derived material. Both preparations demonstrate comparable hemagglutination (clustering) activity and inhibition of C5b-6 initiated hemolysis. The average clusterin concentration in normal seminal plasma is considerably higher than that found in serum. Mean seminal plasma clusterin concentrations were significantly lower in azoospermia caused by obstruction or seminiferous tubule failure than with oligospermia or normospermia. Only men with vasal agenesis had undetectable seminal clusterin, suggesting that some of the seminal clusterin is produced by the seminal vesicles. Immunofluorescence of human spermatozoa revealed that clusterin was detected on 10% of spermatozoa, predominantly those that were immature or had abnormal morphology. A pilot study of 25 patients suggests that seminal clusterin concentration, together with sperm motility and morphology, is correlated with the fertilization rate in vitro. The function of seminal clusterin is unknown. Its extensive distribution in the male genital tract and its high concentration in seminal plasma suggests an important role in male fertility.

The Paton individual-based model legacy.

Ray Paton oversaw the creation of a long lineage of Individual-based Models (IbMs) and this paper discusses the five most successful. All of these concern the development of adaptation, covering both evolutionary time and organism lifetime (somatic time). Of the five models discussed here, the first is based on a plant-herbivore model, the other four are based on a substrate-bacteria model, with the option of antibiotics.

A rule-based approach to the modelling of bacterial ecosystems.

This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.

Detection of genetically engineered traits among bacteria in the environment.

The release of genetically engineered microorganisms (GEMs) into the environment has, as its main aims, the benefits of improved agricultural yield and control of environmental pollution. However, effective and safe release programmes necessitate the development of sensitive, selective detection methods to monitor the environmental impact of released organisms.

Molecular mechanisms of intramolecular recombination-dependent recircularization of linearized plasmid DNA in Escherichia coli: requirements for the ruvA, ruvB, recG, recF and recR gene products.

Intramolecular recombinogenic recircularization (IRR) of linearized plasmid DNA was used to study mechanistic relationships between recombination functions in Escherichia coli in vivo. Homology requirement for IRR ranges from 1 to 11 bp, and does not exhibit any notable strain to strain variability, with recombination occurring at a large number of possible sites within the plasmid molecule. We show that recF- and recR-deficient strains exhibit greatly reduced IRR efficiency, although neither gene product is totally essential. Mutation of recF and recR does not alter the distribution of recombination sites nor the range of molecules produced during IRR. A recO-deficient strain did not exhibit dramatic reduction in efficiency of IRR, implying that RecF and RecR proteins maintain function during this mechanism in the absence of functional RecO. The main IRR mechanism is ruvA-, ruvB- and recG-dependent and there is a lower efficiency second IRR mechanism operating in ruvA, ruvB and recG mutants. Some evidence suggests that this second mechanism involves functions associated with the replisome.

Structural analysis of the pilE region of Neisseria gonorrhoeae P9.

We have determined the nucleotide sequence of an expressed structural pilus gene (pilE) derived from Neisseria gonorrhoeae strain P9-2. Detailed analysis of nucleotide sequences upstream from pilE revealed a silent, truncated pilin gene segment that was linked to families of DNA elements (RS1 and RS3) that have previously been identified at the major silent pilin gene locus (pilS1) and at pilE of the independently isolated N. gonorrhoeae strain MS11ms. A nucleotide sequence downstream from pilE was reminiscent of the recognition sequences of several recombinases, including Tn3 tnpR product (resolvase), suggesting a possible role for site-specific events in the recombinational modulation of pilus expression.

Synthesis and cell culture studies on the antiviral activity of 5-mercaptomethyl-2'-deoxyuridine.

Treatment of 5-mercaptomethyluracil (I) with trimethylsilyl chloride in the presence of triethylamine gave 2,4,5-tris-(trimethylsilyl)-5-mercaptomethyluracil (II) which, upon coupling with 2-deoxy-3,5-di-O-(p-toluoyl)-D-erythro-pentofuranosyl chloride, furnished as anomeric mixture of fully substituted 2'-deoxy ribonucleosides. The nucleoside with beta configuration (III) was predominantly formed and was isolated as a crystalline solid. The free nucleoside IV was obtained by removal of blocking groups by sodium methoxide catalyzed deacylation, deionization under reducing atmosphere, and chromatography on neutral alumina. IV is oxidized to the corresponding disulfide V in solution in the absence of thiols. IV was found to be markedly inhibitory against the herpes virus of infectious bovine rhinotracheitis (IBR). Against this virus, IV was found to be as potent as 5-iododeoxyuridine and cytosine arabinoside when added 18 hr before virus infection.

Posttranslational modifications of meningococcal pili. Identification of a common trisaccharide substitution on variant pilins of strain C311.

Neisseria meningitidis pili are filamentous protein structures that are essential adhesins in capsulate bacteria. Pili of adhesion variants of meningococcal strain C311 contain glycosyl residues on pilin (PilE), their major structural subunit. Recent studies have shown that a novel O-linked trisaccharide substituent, not previously found as a constituent of glycoproteins, is present within a peptide spanning amino acid residues 50 to 73 of the PilE molecule. The structure was shown to be Gal beta 1-4 Gal alpha 1-3 diacetamidotrideoxyhexose which is directly attached to pilin. Pilins derived from galactose epimerase (galE) mutants lack the digalactosyl moiety, but retain the diacetamidotrideoxyhexose substitution. These studies confirm our previous observations that meningococcal pili are glycosylated and provide the first structural evidence for the presence of covalently linked carbohydrate on pili. We have identified a completely novel protein/carbohydrate linkage on a multimeric protein that is an essential virulence determinant in N. meningitidis.

Paraduodenal hernia: diagnosis and surgical management.

Paraduodenal hernia is an unusual cause of intestinal obstruction, but one with which all surgeons should be familiar. We reviewed the anatomy, pathophysiology, initial symptoms, radiographic criteria for diagnosis, and subsequent therapy of five patients treated for paraduodenal hernia at Walter Reed Army Medical Center. Contrast radiography of the small intestine remains the mainstay of preoperative diagnosis. Essential components of treatment include bowel reduction and obliteration of the hernia defect by simple closure or by wide opening of the sac. Further recommendations include sparing the inferior mesenteric vessels during the repair of left paraduodenal hernias and transpositioning the right colon to the left side of the abdomen for repair of right paraduodenal hernias.

Surgical management of small-bowel radiation enteritis.

We treated 17 patients with severe small-bowel radiation enteritis surgically. Fourteen patients were female. Gynecologic malignant lesions (cervical, ovarian, and endometrial) were the most frequent sites of the primary tumors for which radiation was given. Thirteen patients had bowel obstruction, and the remainder had enterovaginal fistulae. Intestinal bypass, rather than resection, was the preferred approach in the treatment of these patients, and was used in 11 cases. Successful palliation was provided in nine patients, with minimal morbidity and no operative deaths. Follow-up at eight to 60 months has shown no further sequelae of radiation injury or of blind loop syndrome. This supports the relative safety of intestinal bypass for the surgical management of small-bowel radiation enteritis.

Therapy of uncomplicated falciparum malaria: a randomized trial comparing artesunate plus sulfadoxine-pyrimethamine versus sulfadoxine-pyrimethamine alone in Irian Jaya, Indonesia.

Combining artesunate with existing antimalarial drugs may improve cure rates, delay emergence of resistance, and reduce transmission. We performed a randomized comparative trial to quantify the effect of adding artesunate to sulfadoxine-pyrimethamine in the treatment of uncomplicated falciparum malaria in Indonesia. Using a modified 1997 World Health Organization protocol for assessment of therapeutic efficacy of antimalarial drugs, 105 patients (stratified by age/ethnic group) were randomized: 53 received artesunate orally, 4 mg/kg of body weight, a single daily dose for three days, plus sulfadoxine-pyrimethamine orally (1.25 mg of pyrimethamine/kg of body weight), a single dose on day 0, and 52 patients received sulfadoxine-pyrimethamine alone. Six from the combination group were withdrawn from analysis, as were six of the sulfadoxine-pyrimethamine group. Treatment failure rates on day 14 were 0% in the artesunate plus sulfadoxine-pyrimethamine group and 8.7% in the sulfadoxine-pyrimethamine group (P = 0.12). Treatment failure rates on day 28 were 4.4% and 15.2%, respectively (P = 0.16). Relative risk of treatment failure at 28 days was 0.3 (95% confidence interval [CI] = 0.1-1.3). Mean fever clearance time (1.3 versus 1.7 days) and mean parasite clearance time (1.4 versus 2.0 days) were both faster in the artesunate plus sulfadoxine-pyrimethamine group than in the sulfadoxine-pyrimethamine group (P = 0.08 and P < 0.0001, respectively). Only 20 (39.2%) of 51 patients treated with artesunate plus sulfadoxine-pyrimethamine were still parasitemic on day 1 compared with 45 (86.5%) of 52 patients treated with sulfadoxine-pyrimethamine alone (P = 0.000001, relative risk [RR] = 0.4, 95% CI = 0.3-0.6). Gametocyte carriage was lower following artesunate plus sulfadoxine-pyrimethamine than following sulfadoxine-pyrimethamine (RR = 0.5, 95% CI = 0.2-1.0 on day 7 and RR = 0.5, 95% CI = 0.2-1.1 on day 14). Mild diarrhea, rash, and itching resolved without treatment. Combined artesunate plus sulfadoxine-pyrimethamine resulted in more rapid fever and parasiteclearance, was well tolerated, reduced risk of treatment failure, and lowered gametocyte carriage.

Development and application of molecular tools in the study of IncN-related plasmids from lakewater sediments.

Homology to IncN, P, Q and W inc regions was investigated amongst 114 Hg(2+)-resistant or antibiotic-resistant bacteria isolated from lakewater sediments. No hybridisation signals were found with Inc P, Q and W probes, and only one plasmid, pLV1402, hybridised to the IncN probe. PCR primers designed to conserved regions in the replicon of the IncN plasmid pCU1 and the related beta replicon from pGSH500 were used to amplify a 978-bp fragment from pLV1402, with sequence analysis showing a close relationship (99.2% identity) between their replication genes. A 387-bp region from the pLV1402 rep gene was used to re-screen the isolates and identified another related plasmid, pLV1403. A 3.7-kb probe containing the alpha replicon from pGSH500 hybridised to both pLV1402 and pLV1403, suggesting that both are multi-replicon plasmids. The PCR primers and probes described will be useful in future studies of plasmid diversity.

Combined molecular ecological and confocal laser scanning microscopic analysis of peat bog methanogen populations.

Confocal laser scanning microscopy, using fluorescently labelled oligonucleotide probes targeting the 16S rRNA of different physiological groups of methanogens, was used to identify which methanogenic genera were present and to describe their in situ spatial locations in samples taken at different depths from blanket peat bog cores. Total bacterial DNA was also extracted and purified from the samples and used as template for amplification of 16S rRNA and regions of methyl CoM reductase-encoding genes using the polymerase chain reaction, as well as for oligonucleotide hybridisation experiments. These techniques, used in concert, demonstrated that methanogens of several physiological groups were present in highest numbers in the mid regions of 25 cm deep peat cores. Some discrepancies were apparent in the findings of the microscopic and molecular methods, though these may be partially accounted for by the different sensitivities of the techniques employed. The combined approaches used in this study gave an insight into the diversity and distribution of methanogens in peat environments not possible using molecular ecological methods alone.

The role of capsular polysaccharide K21b of Klebsiella and of the structurally related colanic-acid polysaccharide of Escherichia coli in resistance to phagocytosis and serum killing.

The behaviour of strains of Klebsiella aerogenes of capsular serotype K21 and strains of Escherichia coli producing a structurally related polysaccharide (colanic acid) was analysed by phagocytic and serum-killing assays. The cell-surface characteristics of these strains and of non-capsulate strains derived from them were also investigated by partitioning experiments in aqueous two-polymer phase systems. The possession of K21-type capsule by K. aerogenes or colanic-acid polysaccharide by E. coli conferred a strong negative charge on capsulate bacteria. Negatively charged bacteria of E. coli producing colanic-acid capsules, however, like non-capsulate K. aerogenes, were susceptible to uptake by polymorphonuclear leukocytes. In contrast, K21 polysaccharide conferred on klebsiellae considerable resistance to phagocytic uptake. The finding that ingested non-capsulate derivative strains of K. aerogenes were less rapidly degraded by phagocytes than E. coli strains suggested that other components of the cell surface of Klebsiella, notably lipopolysaccharide, may be involved in protection against phagocytic killing. The presence of colanic-acid capsules on E. coli conferred little resistance to the bactericidal activity of human serum or phagocytic uptake and did not protect against intracellular killing by polymorphonuclear leukocytes.

Surface properties of diarrhoeagenic Escherichia coli isolates.

The surface properties of various Escherichia coli isolates associated with diarrhoeal illness were compared by aqueous partitioning between polyethylene glycol (PEG) and Dextran phases. Two well characterised strains of enteropathogenic E. coli (EPEC) were found to be very hydrophobic, based on the critical polymer concentration. EPEC strain E2348 cured of the EPEC adherence factor (EAF) plasmid had much reduced surface hydrophobicity. Partitioning of a series of diarrhoeagenic E. coli strains demonstrated that the majority of EAF+ EPEC strains were significantly more hydrophobic than EAF- EPEC strains. E. coli strains defined as enteroaggregative on the basis of hybridisation with a specific DNA probe showed much greater heterogeneity in their partitioning behaviour, possibly indicating that the AAF/I pili were not expressed in all strains. The E. coli K-12 strain used as a transformation host for adhesion studies had very low surface hydrophobicity but had a detectable negative charge. No alteration in these properties was observed when transformed with EPEC and recombinant plasmids known to specify adherence to tissue culture cells.

The genetic basis of head and neck carcinoma.

Research over the past few years has pointed to a genetic basis for numerous cancers. Efforts in this regard are ongoing in squamous carcinoma of the head and neck. Today surgeons and residents in training need to stay up to date on molecular biology and the genetic sequences that are necessary to form a malignancy. In addition, these changes offer diagnosticians and therapists novel ways both to diagnose and treat malignancies. An evolution in molecular genetics, tumor virology, and tumor biology has led to our understanding of how malignancies arise. There are two pathways of cancer production: the activation of an oncogene or the mutation of a tumor suppressor gene. This review discusses the interaction of these genetic changes in the development of squamous carcinoma of the head and neck, their relationship to tobacco and alcohol use, as well as methods to detect the presence of malignancy and novel techniques that may be used to treat malignancies in the future.