83 research outputs found
The computer simulation and prediction of rock fall
No full textThis thesis deals with the study of rock falls using a mathematical model, codified for computer use, entitled GeoFall. GeoFall, which was developed by the author, allows predictions to be made of rock fall trajectories, run out distances and kinetic energies for a rock of any arbitrary shape. Its main purpose is to assist in the design of remedial works. The mathematical model is based on rigid body mechanics, and analyses a fall in 2D space using a new theory of impact dynamics developed by Brach (1991). The main features and algorithms of the program are presented in this thesis. The performance of GeoFall was evaluated by comparing actual rock fall events described in several published papers with the output created by GeoFall. Also the output from GeoFall has been compared with the output from other rock fall simulation programs used to simulate the documented rockfalls. A new rock slope inventory system entitled the Rock Fall Risk Assessment System (RFRAS) has been developed by the author to determine the rock fall risk at specific rock fall sites. It consists of three phases of inspection, the slope survey, and the preliminary and detailed rating phases. The detailed rating phase uses 13 parameters that when assessed, evaluated and totalled, numerically differentiates slopes from the least to the most hazardous producing an overall rating in the range 21-1926. It not only allows the relative risk of rockfall between slopes to be assessed but it also categorises the rock fall risk and the potential number of future rockfalls. It has been tested on 18 slopes at ten locations in County Durham. The final part of the thesis details a new laboratory based procedure that can be used to determine the coefficients of restitution for any type of rock material. The normal coefficient of restitution has been determined for seven different types of rock, and the tangential coefficient of restitution has been determined for a local sandstone. Some tentative correlations between the normal coefficient of restitution and the rocks physical properties, such as its Unconfined Compressive Strength (UCS) have been presented
Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex
No full textCampylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation
Salmonella bongori provides insights into the evolution of the Salmonellae
No full textThe genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC
Salmonella Typhi sense host neuroendocrine stress hormones and release the toxin haemolysin e
No full textSalmonella enterica serovar Typhi (S. typhi) causes typhoid fever. We show that exposure of S. typhi to neuroendocrine stress hormones results in haemolysis, which is associated with the release of haemolysin E in membrane vesicles. This effect is attributed to increased expression of the small RNA micA and RNA chaperone Hfq, with concomitant downregulation of outer membrane protein A. Deletion of micA or the two-component signal-transduction system, CpxAR, abolishes the phenotype. The hormone response is inhibited by the β 2-blocker propranolol. We provide mechanistic insights into the basis of neuroendocrine hormone-mediated haemolysis by S. typhi, increasing our understanding of inter-kingdom signalling. © 2011 European Molecular Biology Organization Embo
Emerg Infect Dis
No full textHaemophilus ducreyi, which causes chancroid, has emerged as a cause of pediatric skin disease. Isolation of H. ducreyi in low-income settings is challenging, limiting phylogenetic investigation. Next-generation sequencing demonstrates that cutaneous strains arise from class I and II H. ducreyi clades and that class II may represent a distinct subspecies
RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
No full textBACKGROUND: Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR. RESULTS: We found that 528 chromosomal genes were differentially expressed in response to anaerobic conditions; of these, 228 genes were also influenced by FNR. Genes that were up-regulated in anaerobic conditions are involved in carbon transport and metabolism (e.g. ptsG, manX, murQ, cysP, cra), DNA topology and regulation (e.g. ygiP, stpA, hns), host interactions (e.g. yciD, nmpC, slyB, gapA, shf, msbB) and survival within the gastrointestinal tract (e.g. shiA, ospI, adiY, cysP). Interestingly, there was a marked effect of available oxygen on genes involved in Type III secretion system (T3SS), which is required for host cell invasion and pathogenesis. These genes, located on the large Shigella virulence plasmid, were down regulated in anaerobiosis in an FNR-dependent manner. We also confirmed anaerobic induction of csrB and csrC small RNAs in an FNR-independent manner. CONCLUSIONS: Anaerobiosis promotes survival and adaption strategies of Shigella, while modulating virulence plasmid genes involved in T3SS-mediated host cell invasion. The influence of FNR on this process is more extensive than previously appreciated, although aside from the virulence plasmid, this transcriptional regulator does not govern expression of genes on other horizontally acquired sequences on the chromosome such as pathogenicity islands
Soft biometrics for surveillance: an overview
No full textBiometrics is the science of automatically recognizing people based on physical or behavioral characteristics such as face, fingerprint, iris, hand, voice, gait and signature. More recently, the use of soft biometric traits has been proposed to improve the performance of traditional biometric systems and allow identification based on human descriptions. Soft biometric traits include characteristics such as height, weight, body geometry, scars, marks and tattoos (SMT), gender, etc. These traits offer several advantages over traditional biometric techniques. Soft biometric traits can be typically described using human understandable labels and measurements, allowing for retrieval and recognition solely based on verbal descriptions. Unlike many primary biometric traits, soft biometrics can be obtained at a distance without subject cooperation and from low quality video footage, making them ideal for use in surveillance applications. This chapter will introduce the current state-of-the-art in the emerging field of soft biometric
Emerg Infect Dis
No full textShigellae are sensitive indicator species for studying trends in the international transmission of antimicrobial-resistant Enterobacteriaceae. Orthodox Jewish communities (OJCs) are a known risk group for shigellosis; Shigella sonnei is cyclically epidemic in OJCs in Israel, and sporadic outbreaks occur in OJCs elsewhere. We generated whole-genome sequences for 437 isolates of S. sonnei from OJCs and non-OJCs collected over 22 years in Europe (the United Kingdom, France, and Belgium), the United States, Canada, and Israel and analyzed these within a known global genomic context. Through phylogenetic and genomic analysis, we showed that strains from outbreaks in OJCs outside of Israel are distinct from strains in the general population and relate to a single multidrug-resistant sublineage of S. sonnei that prevails in Israel. Further Bayesian phylogenetic analysis showed that this strain emerged approximately 30 years ago, demonstrating the speed at which antimicrobial drug-resistant pathogens can spread widely through geographically dispersed, but internationally connected, communities
Genome Sequence of Klebsiella pneumoniae Ecl8, a Reference Strain for Targeted Genetic Manipulation
No full textWe report the genome sequence of Klebsiella pneumoniae subsp. pneumoniae Ecl8, a spontaneous streptomycin-resistant mutant of strain ECL4, derived from NCIB 418. K. pneumoniae Ecl8 has been shown to be genetically tractable for targeted gene deletion strategies and so provides a platform for in-depth analyses of this species
An H-NS-like stealth protein aids horizontal DNA transmission in bacteria
No full textThe Sfh protein is encoded by self-transmissible plasmids involved in human typhoid and is closely related to the global regulator H-NS. We have found that Sfh provides a stealth function that allows the plasmids to be transmitted to new bacterial hosts with minimal effects on their fitness. Introducing the plasmid without the sfh gene imposes a mild H-NS– phenotype and a severe loss of fitness due to titration of the cellular pool of H-NS by the A+T-rich plasmid. This stealth strategy seems to be used widely to aid horizontal DNA transmission and has important implications for bacterial evolution
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