Biomedical subjects
N R Thomson
Publications and source records attributed to N R Thomson.
Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.
The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.
Mass removal of chlorinated ethenes from rough-walled fractures using permanganate.
In situ chemical oxidation (ISCO) employing permanganate is an emerging technology that has been successful at enhancing mass removal from DNAPL source zones in unconsolidated media at the pilot-scale. The focus of this study was to evaluate the applicability of flushing a permanganate solution across two single vertical fractures in a laboratory environment to remove free phase DNAPL. The fracture experiments were designed to represent a portion of a larger fractured aquifer system impacted by a near-surface DNAPL spill over a shallow fractured rock aquifer. Each fracture was characterized by hydraulic and tracer tests, and the aperture field for one of the fractures was mapped using a co-ordinate measurement machine. Following DNAPL emplacement, a series of water and permanganate flushes were performed. To support observations from the fracture experiments, a set of batch experiments was conducted. The data from both fracture experiments showed that the post-oxidation effluent concentration was not impacted by the oxidant flush; however, changes in the aperture distribution, flow field, and flow rate were observed. These changes resulted in a significant decrease to the mass loading from the fractures, and were attributed to the build-up of oxidation by-products (manganese oxides and carbon dioxide) within the fracture which was corroborated by the batch experiment data and visual examination of the walls of one fracture. These results provide insight into the potential impact that a permanganate solution and oxidation by-products can have on the aperture distribution within a fracture and on DNAPL mass transfer rates. A permanganate flush or injection completed within a fractured rock aquifer may lead to the development of an insoluble product adjacent to the DNAPL which results in the reduction or complete elimination of advective regions near the DNAPL and reduces mass transfer rates. This outcome would have significant implications on the plume generating potential of the remaining DNAPL.
The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129.
Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.
Air distribution in the Borden aquifer during in situ air sparging.
A field experiment was conducted at Canadian Forces Base Borden (CFB Borden) to assess the air distribution from a single in situ air sparging injection point. This aquifer consists of fine to medium sand deposited in horizontal layers. The permeability at the study location varied from 10(-10) to 10(-14) m2 and distinct low permeability horizons were present at approximately 1.2, 2.0, and 2.9 m below the water table. Prior to air injection, a 15x15-m portion of the vadose zone was excavated to the water table (approximately 1 m below ground surface) in order to visually observe air release distribution at the water table. The water table was actively maintained 5 cm above the excavated surface. The sparging system operated for a period of 7 days with an injection flow rate of 200 m3/days (5 scfm). The resulting subsurface air distribution was assessed using a variety of techniques including neutron logging, borehole and surface ground penetrating radar, piezometric head measurements, surface visualization, and hydraulic testing. Through this combination of tests, it was demonstrated that variations in permeability and, hence, capillary pressure at the site were sufficient to cause the injected air to spread laterally, forming stratigraphically trapped air pockets beneath the low permeability horizons. The formation of these air pockets eventually resulted in a buildup of capillary pressure that exceeded the air entry pressure and allowed some air to migrate up through the lower permeability layers. Each of the assessment techniques employed generated information at different spatial scales that prevented a direct comparison of the results from the various techniques; however, the results from all techniques proved to be critical in the interpretation of the experimental data. As a consequence, the different assessment techniques should not be viewed as alternatives, but rather as complimentary techniques.
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).
Streptomyces coelicolor is a representative of the group of soil-dwelling, filamentous bacteria responsible for producing most natural antibiotics used in human and veterinary medicine. Here we report the 8,667,507 base pair linear chromosome of this organism, containing the largest number of genes so far discovered in a bacterium. The 7,825 predicted genes include more than 20 clusters coding for known or predicted secondary metabolites. The genome contains an unprecedented proportion of regulatory genes, predominantly those likely to be involved in responses to external stimuli and stresses, and many duplicated gene sets that may represent 'tissue-specific' isoforms operating in different phases of colonial development, a unique situation for a bacterium. An ancient synteny was revealed between the central 'core' of the chromosome and the whole chromosome of pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. The genome sequence will greatly increase our understanding of microbial life in the soil as well as aiding the generation of new drug candidates by genetic engineering.
Laboratory-scale in situ chemical oxidation of a perchloroethylene pool using permanganate.
In situ chemical oxidation (ISCO) is an emerging technology for the destruction of some chlorinated solvents present in subsurface environments. A laboratory investigation using a physical model was designed to assess the effectiveness of using permanganate as an oxidant to reduce the mass of a perchloroethylene (PCE) pool. The physical model was filled with silica sand overlying a silica flour base, simulating a two-dimensional saturated sand zone overlying a capillary barrier. PCE was introduced into the model so that it rested on top of the silica flour base, forming a dense nonaqueous phase liquid pool. The experimental methodology involved flushing the model with a permanganate solution for 146 days. During this period, measurements of chloride were used to assess the extent of pool oxidation. Before and after the oxidant flush, the quasi-steady state dissolution from the PCE pool was evaluated. Additionally, tracer studies were completed to assess changes in the flow field due to the oxidation process. At the termination of the experiment nine soil cores extracted from the model were used to detect the presence of MnO2 deposits and to quantify the mass of PCE remaining in the system. Excavation of the remaining material in the model revealed that the MnO2 distribution throughout the model was consistent with that observed in the cores. The oxidant flush was concluded before all of the pure phase PCE had been completely oxidized; however, approximately 45% of the PCE mass was removed, resulting in a fourfold decrease in the quasi-steady state aqueous phase mass loading of PCE from the pool. Measurements of chloride during the oxidant flush and of PCE in the soil cores suggested that the oxidation reaction occurred primarily at the upgradient edge of the PCE pool. MnO2 deposits within the model aquifer decreased the velocity of water directly above the pool, and the overall mass transfer from the remaining PCE pool. The results of this experimental study indicate that ISCO using permanganate is capable of removing substantial mass from a DNAPL pool; however, the performance of ISCO as a pool removal technology will be limited by the formation and precipitation of hydrous MnO2 that occurs during the oxidation process.
Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18.
Salmonella enterica serovar Typhi (S. typhi) is the aetiological agent of typhoid fever, a serious invasive bacterial disease of humans with an annual global burden of approximately 16 million cases, leading to 600,000 fatalities. Many S. enterica serovars actively invade the mucosal surface of the intestine but are normally contained in healthy individuals by the local immune defence mechanisms. However, S. typhi has evolved the ability to spread to the deeper tissues of humans, including liver, spleen and bone marrow. Here we have sequenced the 4,809,037-base pair (bp) genome of a S. typhi (CT18) that is resistant to multiple drugs, revealing the presence of hundreds of insertions and deletions compared with the Escherichia coli genome, ranging in size from single genes to large islands. Notably, the genome sequence identifies over two hundred pseudogenes, several corresponding to genes that are known to contribute to virulence in Salmonella typhimurium. This genetic degradation may contribute to the human-restricted host range for S. typhi. CT18 harbours a 218,150-bp multiple-drug-resistance incH1 plasmid (pHCM1), and a 106,516-bp cryptic plasmid (pHCM2), which shows recent common ancestry with a virulence plasmid of Yersinia pestis.
Genome sequence of Yersinia pestis, the causative agent of plague.
The Gram-negative bacterium Yersinia pestis is the causative agent of the systemic invasive infectious disease classically referred to as plague, and has been responsible for three human pandemics: the Justinian plague (sixth to eighth centuries), the Black Death (fourteenth to nineteenth centuries) and modern plague (nineteenth century to the present day). The recent identification of strains resistant to multiple drugs and the potential use of Y. pestis as an agent of biological warfare mean that plague still poses a threat to human health. Here we report the complete genome sequence of Y. pestis strain CO92, consisting of a 4.65-megabase (Mb) chromosome and three plasmids of 96.2 kilobases (kb), 70.3 kb and 9.6 kb. The genome is unusually rich in insertion sequences and displays anomalies in GC base-composition bias, indicating frequent intragenomic recombination. Many genes seem to have been acquired from other bacteria and viruses (including adhesins, secretion systems and insecticidal toxins). The genome contains around 150 pseudogenes, many of which are remnants of a redundant enteropathogenic lifestyle. The evidence of ongoing genome fluidity, expansion and decay suggests Y. pestis is a pathogen that has undergone large-scale genetic flux and provides a unique insight into the ways in which new and highly virulent pathogens evolve.
Massive gene decay in the leprosy bacillus.
Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.
Action perception and outcome valence: effects on children's inferences of intentionality and moral and liking judgments.
The influences of different action-outcome scenarios on children's evaluative judgments and inferences of outcome intentionality were assessed. One hundred forty-five kindergartners, 2nd graders, and 4th graders heard 4 stories about child actors who engaged in 1 action or 3 equifinal actions and caused a positive or negative outcome. The stories made no mention of the actors' anticipated outcome so that we could assess the children's inferences of whether the actors wanted and had tried to cause the outcome. Children also rated their liking for the actors and the actors' morality. Children's moral and liking judgments were not significantly differentiated by action condition. However, actors who caused positive outcomes received favorable liking and moral judgments, and actors who caused negative outcomes received neutral liking and moral judgments. Children's intentionality inferences varied by the actors' actions and were moderated by outcome valence. The authors discuss children's apparent use of the valence rule when inferring intentionality and their reluctance to judge harshly actors who cause negative outcomes when not privy to the actors' intentions.
The decaying genome of Mycobacterium leprae.
Everything that we need to know about Mycobacterium leprae, a close relative of the tubercle bacillus, is encrypted in its genome. Inspection of the 3.27 Mb genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus identified 1,605 genes encoding proteins and 50 genes for stable RNA species. Comparison with the genome sequence of Mycobacterium tuberculosis revealed an extreme case of reductive evolution, since less than half of the genome contains functional genes while inactivated or pseudogenes are highly abundant. The level of gene duplication was approximately 34% and, on classification of the proteins into families, the largest functional groups were found to be involved in the metabolism and modification of fatty acids and polyketides, transport of metabolites, cell envelope synthesis and gene regulation. Reductive evolution, gene decay and genome downsizing have eliminated entire metabolic pathways, together with their regulatory circuits and accessory functions, particularly those involved in catabolism. This may explain the unusually long generation time and account for our inability to culture the leprosy bacillus.
Air distribution during in situ air sparging: an overview of mathematical modeling.
The performance of in situ air sparging is controlled by the distribution of air pathways in the subsurface, which is in turn controlled by the structure of the medium to be sparged. The specific pathways that the air follows are determined, at the grain scale, by the distribution of air entry pressures of the pores. At the field scale, pore size distributions are usually correlated with heterogeneous structures (e.g. layers) within the medium, which control the macroscopic distribution of the air. The processes that produce an observed air distribution at a particular site are complicated, and are potentially well suited to modeling with multiphase flow models. Recent numerical modeling of heterogeneous media appears to successfully represent expected distributions of air; however, current models do not provide a tool to predict sparging performance. For this to be the case, the models need to represent the detailed structure of the medium at the site to be studied, as well as to capture the relevant aspects of the discrete air/water distribution (i.e., represent air channels at the centimeter or smaller scale). This will, in general, require a level of site data that is not available and numerical models that require many millions of computational elements. As a consequence, at least for the foreseeable future, numerical modeling of the air sparging process will continue to play a vital role as a conceptual tool with limited predictive capability at sites.
Experimental determination of the kinetic rate law for the oxidation of perchloroethylene by potassium permanganate.
Flushing soils contaminated with trichloroethylene (TCE) and perchloroethylene (PCE) with a permanganate (MnO4-) solution has been shown to reduce the solvent content of the soil. Experiments were performed to quantify the rate at which KMnO4 oxidizes aqueous solutions of PCE over a range of concentrations. In a series of homogeneous reactors, aqueous phase PCE concentrations were monitored over time in nine experimental trials with excess oxidant concentrations ranging from 5 to 30 g/l. Analysis of the data was performed to quantify the oxidation reaction order with respect to PCE and KMnO4 and the reaction rate constant. The reaction between PCE and KMnO4 was determined to be first-order with respect to both PCE and KMnO4 with an overall specific reaction rate coefficient of 2.45+/-0.65 M(-1) min(-1).
Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control.
Serratia sp. ATCC 39006 produces the carbapenem antibiotic, carbapen-2-em-3-carboxylic acid and the red pigment, prodigiosin. We have previously reported the characterization of a gene, carR, controlling production of carbapenem in this strain. We now describe further characterization of the carR locus to locate the genes encoding carbapenem biosynthetic and resistance functions. A novel family of diverse proteins showing sequence similarity to the C-terminal domain of CarF (required for carbapenem resistance) is described. We also report the isolation of the locus involved in the biosynthesis of the red pigment, prodigiosin. A cosmid containing approximately 35 kb of the Serratia chromosome encodes synthesis of the pigment in the heterologous host, Erwinia carotovora, demonstrating, for the first time, that the complete prodigiosin biosynthetic gene cluster had been cloned and functionally expressed. We report the isolation of a third locus in Serratia, containing convergently transcribed genes, smaI and smaR, encoding LuxI and LuxR homologues respectively. SmaI directs the synthesis of N-acyl homoserine lactones involved in the quorum sensing process. We demonstrate that biosynthesis of the two secondary metabolites, carbapenem antibiotic and prodigiosin pigment, is under pheromone-mediated transcriptional regulation in this bacterium. Finally, we describe a new prodigiosin-based bioassay for detection of some N-acyl homoserine lactones.
A pheromone-independent CarR protein controls carbapenem antibiotic synthesis in the opportunistic human pathogen Serratia marcescens.
Strain ATCC 39006 of Serratia marcescens makes the same carbapenem, (5R)-carbapen-2-em-3-carboxylic acid (Car), as the Erwinia carotovora strain GS101. Unlike E. carotovora, where the onset of production occurs in the late-exponential phase of growth in response to the accumulation of the small diffusible pheromone N-(3-oxohexanoyl)-L-homoserine lactone (OHHL), in S. marcescens carbapenem is produced throughout the growth phase and does not appear to involve any diffusible pheromone molecule. Two cosmids capable of restoring antibiotic production in E. carotovora group I carbapenem mutants were isolated from an S. marcescens gene library. These cosmids were shown to contain a homologue of the E. carotovora carR gene, encoding a CarR protein with homology to the LuxR family of transcriptional regulators. The S. marcescens carR was subcloned and shown to be capable of complementing in trans, in the absence of OHHL, an E. carotovora carR carI double mutant, releasing the heterologous E. carotovora host from pheromone dependence for carbapenem production. The apparent OHHL-independence of the S. marcescens CarR explains the constitutive nature of carbapenem production in this strain of S. marcescens.
The rap and hor proteins of Erwinia, Serratia and Yersinia: a novel subgroup in a growing superfamily of proteins regulating diverse physiological processes in bacterial pathogens.
The enteric bacterium Serratia marcescens is an opportunistic human pathogen. The strain ATCC39006 makes the red pigment, prodigiosin (Pig), and the beta-lactam antibiotic carbapenem (Car). Mutants were isolated that were concomitantly defective for Pig and Car production. These mutants were found to have a mutation in the rap gene (Regulation of Antibiotic and Pigment). Sequence analysis of the rap gene revealed a predicted protein product showing strong homology to SlyA, originally thought to be a haemolytic virulence determinant in Salmonella typhimurium. Homologues of rap were detected in several bacterial genera, including Salmonella, Yersinia, Enterobacter, and species of the plant pathogen, Erwinia. The Erwinia hoeEr (homologue of rap) and the Yersinia horYe genes were also found to be very similar to rap and slyA. Marker exchange mutagenesis of horEr revealed that it encoded a regulatory protein controlling the production of antibiotic and exoenzyme virulence determinants in the phytopathogen, Erwinia carotovora subspecies carotovora. We have shown that these new homologues of SlyA form a highly conserved subgroup of a growing superfamily of bacterial regulatory proteins controlling diverse physiological processes in human, animal and plant pathogens.