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.

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.

Rule-based simulation of temperate bacteriophage infection: restriction-modification as a limiter to infection in bacterial populations.

An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been employed to simulate interactions of virtual temperate bacteriophages (phages) and their bacterial hosts. Outcomes of infection mimic those of a phage such as lambda, which can enter either the lytic or lysogenic cycle, depending on the nutritional status of the host. Infection of different hosts possessing differing restriction and modification systems is also simulated. Phages restricted upon infection of one restricting host can be adapted (by host-controlled modification of the phage genome) and subsequently propagate with full efficiency on this host. However, such ability is lost if the progeny phages are passaged through a new host with a different restriction and modification system before attempted re-infection of the original restrictive host. The simulations show that adaptation and re-adaptation to a particular host-controlled restriction and modification system result in lower efficiency and delayed lysis of bacterial cells compared with infection of non-restricting host bacteria. Such biologically realistic simulations validate the use of the IbM approach to predicting behaviour of bacteriophages in bacterial populations. The applicability of the model for more complex scenarios aimed at predictive modelling of bacterial evolution in a changing environment and the implications for the spread of viruses in a wider context are discussed.

Bacterial foraging algorithm with varying population.

Most of evolutionary algorithms (EAs) are based on a fixed population. However, due to this feature, such algorithms do not fully explore the potential of searching ability and are time consuming. This paper presents a novel nature-inspired heuristic optimization algorithm: bacterial foraging algorithm with varying population (BFAVP), based on a more bacterially-realistic model of bacterial foraging patterns, which incorporates a varying population framework and the underlying mechanisms of bacterial chemotaxis, metabolism, proliferation, elimination and quorum sensing. In order to evaluate its merits, BFAVP has been tested on several benchmark functions and the results show that it performs better than other popularly used EAs, in terms of both accuracy and convergency.

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.

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.

The Colorectal Development Unit: impact on functional outcome for the electrically stimulated gracilis neoanal sphincter.

OBJECTIVE: A Colorectal Development Unit (CDU) was established to treat patients with end stage faecal incontinence with the electrically stimulated gracilis neoanal sphincter (ESGN). The aim of this study was to investigate the impact of the CDU on functional outcome and complications. METHODS: From March 1997 to March 2003, 53 patients underwent ESGN formation. Results were compared with 65 patients undergoing ESGN surgery prior to the establishment of the unit (pre-CDU) between 1988 and 1997, which were similar with regard to age, sex, aetiology and follow-up. RESULTS: Thirty-three (70%) CDU patients had a good functional outcome defined as continence to solid and liquid stool, a significant improvement when compared to the pre-CDU group, successful in 29 (45%) (P = 0.01). Episodes of technical complications leading to stimulator replacement were significantly reduced, from 25 to 3 over time (P < 0.001). Severe septic episodes were significantly reduced from 21 to four (P = 0.003) but there was no significant change in the incidence of postoperative evacuatory dysfunction. CONCLUSION: Since setting up a CDU, a successful outcome has been achieved in 33 (70%) of 47 patients undergoing ESGN surgery, which represents a significant improvement over time. This is probably related to improved patient assessment and selection, more reliable equipment and increased operative and peri-operative experience that come with a multidisciplinary team approach.

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.

A particle swarm optimizer with passive congregation.

This paper presents a particle swarm optimizer (PSO) with passive congregation to improve the performance of standard PSO (SPSO). Passive congregation is an important biological force preserving swarm integrity. By introducing passive congregation to PSO, information can be transferred among individuals of the swarm. A particle swarm optimizer with passive congregation (PSOPC) is tested with a set of 10 benchmark functions with 30 dimensions and compared to a global version of SPSO (GSPSO), a local version of SPSO (LSPSO), and PSO with a constriction factor (CPSO), respectively. Experimental results indicate that the PSO with passive congregation improves the search performance on the benchmark functions significantly.

An assessment of the risks associated with the use of antibiotic resistance genes in genetically modified plants: report of the Working Party of the British Society for Antimicrobial Chemotherapy.

Development of genetically modified (GM) plants is contentious, in part because bacterial antibiotic resistance (AR) genes are used in their construction and often become part of the plant genome. This arouses concern that cultivation of GM plants might provide a reservoir of AR genes that could power the evolution of new drug-resistant bacteria. We have considered bacterial DNA transfer systems (conjugation, transduction and transformation) and mechanisms of recombination (homologous recombination, transposition, site-specific recombination and DNA repair) that together might productively transfer AR genes from GM plants to bacterial cells, but are unable to identify a credible scenario whereby new drug-resistant bacteria would be created. However, we cannot entirely rule out the possibility of rare transfer events that involve novel mechanisms. Hence, we also considered if occasional transfers of AR genes (bla(TEM), aph(3'), aadA) from GM plants into bacteria would pose a threat to public health. These AR genes are common in many bacteria and each is found on mobile genetic elements that have moved extensively between DNA molecules and bacterial cells. This gene mobility has already severely compromised clinical use of antibiotics to which resistance is conferred. Accordingly, the argument that occasional transfer of these particular resistance genes from GM plants to bacteria would pose an unacceptable risk to human or animal health has little substance. We conclude that the risk of transfer of AR genes from GM plants to bacteria is remote, and that the hazard arising from any such gene transfer is, at worst, slight.

Individual-based modelling of bacterial ecologies and evolution.

This paper presents two approaches to the individual-based modelling of bacterial ecologies and evolution using computational tools. The first approach is a fine-grained model that is based on networks of interactivity between computational objects representing genes and proteins. The second approach is a coarser-grained, agent-based model, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of these computational models is discussed, and some results from simulation experiments are presented. Finally, the potential applications of the proposed models to the solution of real-world computational problems, and their use in improving our understanding of the mechanisms of evolution, are briefly outlined.

Use of a continent colonic conduit for treatment of refractory evacuatory disorder following construction of an electrically stimulated gracilis neoanal sphincter.

BACKGROUND: This study reports the outcome from the addition of a continent colonic conduit (CCC) to an electrically stimulated gracilis neoanal sphincter in patients with severe evacuatory disorder following formation of a neosphincter for end-stage faecal incontinence. METHODS: One hundred and twenty patients had an electrically stimulated gracilis neoanal sphincter constructed for end-stage faecal incontinence. Seven patients developed severe evacuatory disorders; construction of a CCC was required in six patients and an antegrade continence enema procedure in one. RESULTS: Median follow-up of the seven patients was 77 (range 6-96) months. Six patients with evacuatory disorders had a successful outcome, defined as continence to solid and liquid stool as well as correction of the evacuatory disorder. A stoma was formed in one patient. Patients who had previously undergone anorectal reconstructive surgery were more likely to develop an evacuatory disorder following construction of an electrically stimulated gracilis neoanal sphincter than patients operated on for other reasons (chi2 = 28.13, 1 d.f., P < 0.001). CONCLUSION: Construction of a CCC is a useful technique for the majority of patients with severe evacuatory disorders following the formation of an electrically stimulated gracilis neoanal sphincter, for whom the only alternative would be an end stoma. A CCC may be incorporated with construction of an electrically stimulated gracilis neoanal sphincter in patients at significant risk of postoperative severe evacuatory disorders.

A promoter polymorphism in the gene encoding interleukin-12 p40 (IL12B) is associated with mortality from cerebral malaria and with reduced nitric oxide production.

Interleukin-12 (IL-12) is an important regulatory cytokine in infection and immunity. Administration of IL-12 may reduce complications of severe malaria in rodents. Polymorphisms in IL12B, the gene encoding the IL-12 p40 subunit, influence the secretion of IL-12 and susceptibility to Type 1 diabetes. We therefore investigated whether IL12B polymorphisms may affect the outcome of severe malaria. Homozygosity for a polymorphism in the IL12B promoter was associated with increased mortality in Tanzanian children having cerebral malaria but not in Kenyan children with severe malaria. Furthermore, homozygotes for the IL12B promotor polymorphism had decreased production of nitric oxide, which is in part regulated by IL-12 activity. These studies suggest that IL12B polymorphisms, via regulation of IL-12 production, may influence the outcome of malaria infection in at least one African population.

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.

Synchronous perforation of a Meckel's diverticulum and a duodenal ulcer.

Dual perforation of the gastrointestinal tract is rare. We present a case of a patient who presented with a simultaneous perforation of a Meckel's diverticulum and a duodenal ulcer.

Lytic and lysogenic infection of diverse Escherichia coli and Shigella strains with a verocytotoxigenic bacteriophage.

A verocytotoxigenic bacteriophage isolated from a strain of enterohemorrhagic Escherichia coli O157, into which a kanamycin resistance gene (aph3) had been inserted to inactivate the verocytotoxin gene (vt2), was used to infect Enterobacteriaceae strains. A number of Shigella and E. coli strains were susceptible to lysogenic infection, and a smooth E. coli isolate (O107) was also susceptible to lytic infection. The lysogenized strains included different smooth E. coli serotypes of both human and animal origin, indicating that this bacteriophage has a substantial capacity to disseminate verocytotoxin genes. A novel indirect plaque assay utilizing an E. coli recA441 mutant in which phage-infected cells can enter only the lytic cycle, enabling detection of all infective phage, was developed.

Flagellin gene sequence variation in the genus Pseudomonas.

Flagellin gene (fliC) sequences from 18 strains of Pseudomonas sensu stricto representing 8 different species, and 9 representative fliC sequences from other members of the gamma sub-division of proteobacteria, were compared. Analysis was performed on N-terminal, C-terminal and whole fliC sequences. The fliC analyses confirmed the inferred relationship between P. mendocina, P. oleovorans and P. aeruginosa based on 16S rRNA sequence comparisons. In addition, the analyses indicated that P. putida PRS2000 was closely related to P. fluorescens SBW25 and P. fluorescens NCIMB 9046T, but suggested that P. putida PaW8 and P. putida PRS2000 were more closely related to other Pseudomonas spp. than they were to each other. There were a number of inconsistencies in inferred evolutionary relationships between strains, depending on the analysis performed. In particular, whole flagellin gene comparisons often differed from those obtained using N- and C-terminal sequences. However, there were also inconsistencies between the terminal region analyses, suggesting that phylogenetic relationships inferred on the basis of fliC sequence should be treated with caution. Although the central domain of fliC is highly variable between Pseudomonas strains, there was evidence of sequence similarities between the central domains of different Pseudomonas fliC sequences. This indicates the possibility of recombination in the central domain of fliC genes within Pseudomonas species, and between these genes and those from other bacteria.