Showing papers by "Bielefeld University published in 2005"

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Abstract: The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Impact of bibliometrics upon the science system: Inadvertent consequences?

Abstract: Ranking of research institutions by bibliometric methods is an improper tool for research performance evaluation, even at the level of large institutions. The problem, however, is not the ranking as such. The indicators used for ranking are often not advanced enough, and this situation is part of the broader problem of the application of insufficiently developed bibliometric indicators used by persons who do not have clear competence and experience in the field of quantitative studies of science. After a brief overview of the basic elements of bibliometric analysis, I discuss the major technical and methodological problems in the application of publication and citation data in the context of evaluation. Then I contend that the core of the problem lies not necessarily at the side of the data producer. Quite often persons responsible for research performance evaluation, for instance scientists themselves in their role as head of institutions and departments, science administrators at the government level and other policy makers show an attitude that encourages 'quick and dirty' bibliometric analyses whereas better quality is available. Finally, the necessary conditions for a successful application of advanced bibliometric indicators as support tool for peer review are discussed.

Strong solutions of stochastic equations with singular time dependent drift

Abstract: We prove existence and uniqueness of strong solutions to stochastic equations in domains with unit diffusion and singular time dependent drift b up to an explosion time. We only assume local L q _L p -integrability of b in ℝ×G with d/p+2/q<1. We also prove strong Feller properties in this case. If b is the gradient in x of a nonnegative function ψ blowing up as G∋x→∂G, we prove that the conditions 2D t ψ≤Kψ,2D t ψ+Δψ≤Ke ɛψ ,ɛ ∈ [0,2), imply that the explosion time is infinite and the distributions of the solution have sub Gaussian tails.

Thermodynamics of two flavor QCD to sixth order in quark chemical potential

Abstract: We present results of a simulation of two flavor QCD on a 16{sup 3}x4 lattice using p4-improved staggered fermions with bare quark mass m/T=0.4. Derivatives of the thermodynamic grand canonical partition function Z(V,T,{mu}{sub u},{mu}{sub d}) with respect to chemical potentials {mu}{sub u,d} for different quark flavors are calculated up to sixth order, enabling estimates of the pressure and the quark number density as well as the chiral condensate and various susceptibilities as functions of {mu}{sub q}=({mu}{sub u}+{mu}{sub d})/2 via Taylor series expansion. Furthermore, we analyze baryon as well as isospin fluctuations and discuss the relation between the radius of convergence of the Taylor series and the chiral critical point in the QCD phase diagram. We argue that bulk thermodynamic observables do not, at present, provide direct evidence for the existence of a chiral critical point in the QCD phase diagram. Results are compared to high temperature perturbation theory as well as a hadron resonance gas model.

Static quark-antiquark interactions in zero and finite temperature QCD: I. Heavy quark free energies, running coupling, and quarkonium binding

Abstract: We analyze heavy quark free energies in 2-flavor QCD at finite temperature and the corresponding heavy quark potential at zero temperature. Static quark anti-quark sources in color singlet, octet and color averaged channels are used to probe thermal modifications of the medium. The temperature dependence of the running coupling, $\alpha_{qq}(r,T)$, is analyzed at short and large distances and is compared to zero temperature as well as quenched calculations. In parts we also compare our results to recent findings in 3-flavor QCD. We find that the characteristic length scale below which the running coupling shows almost no temperature dependence is almost twice as large as the Debye screening radius. Our analysis supports recent findings which suggest that $\chi_c$ and $\psi\prime$ are suppressed already at the (pseudo-) critical temperature and thus give a probe for quark gluon plasma production in heavy ion collision experiments, while $J/\psi$ may survive the transition and will dissolve at higher temperatures.

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

Abstract: The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses This pathosystem has become a well-established model for studying bacterial infection strategies Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv vesicatoria strain 85-10, which comprises a 517-Mb circular chromosome and four plasmids The genome has a high G+C content (6475%) and signatures of extensive genome plasticity Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv citri and Xanthomonas campestris pv campestris and a structure completely different from Xanthomonas oryzae pv oryzae A total of 548 coding sequences (122%) are unique to X campestris pv vesicatoria In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gram-negative bacteria Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides

Overlaps in the Transcriptional Profiles of Medicago truncatula Roots Inoculated with Two Different Glomus Fungi Provide Insights into the Genetic Program Activated during Arbuscular Mycorrhiza

Abstract: Arbuscular mycorrhiza (AM) is a widespread symbiotic association between plants and fungal microsymbionts that supports plant development under nutrient-limiting and various stress conditions. In this study, we focused on the overlapping genetic program activated by two commonly studied microsymbionts in addition to identifying AM-related genes. We thus applied 16,086 probe microarrays to profile the transcriptome of the model legume Medicago truncatula during interactions with Glomus mosseae and Glomus intraradices and specified a total of 201 plant genes as significantly coinduced at least 2-fold, with more than 160 being reported as AM induced for the first time. Several hundred genes were additionally up-regulated during a sole interaction, indicating that the plant genetic program activated in AM to some extent depends on the colonizing microsymbiont. Genes induced during both interactions specified AM-related nitrate, ion, and sugar transporters, enzymes involved in secondary metabolism, proteases, and Kunitz-type protease inhibitors. Furthermore, coinduced genes encoded receptor kinases and other components of signal transduction pathways as well as AM-induced transcriptional regulators, thus reflecting changes in signaling. By the use of reporter gene expression, we demonstrated that one member of the AM-induced gene family encoding blue copper binding proteins (MtBcp1) was both specifically and strongly up-regulated in arbuscule-containing regions of mycorrhizal roots. A comparison of the AM expression profiles to those of nitrogen-fixing root nodules suggested only a limited overlap between the genetic programs orchestrating root endosymbioses.

The First wimpy halos

Abstract: Dark matter direct and indirect detection signals depend crucially on the dark matter distribution. While the formation of large scale structure is independent of the nature of the cold dark matter (CDM), the fate of inhomogeneities on subgalactic scales, and hence the present day CDM distribution on these scales, depends on the microphysics of the CDM particles. We study the density contrast of weakly interacting massive particles (WIMPs) on subgalactic scales. We calculate the damping of the primordial power spectrum due to collisional damping and free streaming of WIMPy CDM and show that free streaming leads to a CDM power spectrum with a sharp cut-off at about 10(-6) M-circle dot. We also calculate the transfer function for the growth of the inhomogeneities in the linear regime, taking into account the suppression in the growth of the CDM density contrast after matter-radiation equality due to baryons and show that our analytic results are in good agreement with numerical calculations. Combining the transfer function with the damping of the primordial fluctuations we produce a WMAP normalized primordial CDM power spectrum, which can serve as an input for high resolution CDM simulations. We find that the smallest inhomogeneities typically have comoving radius of about 1 pc and enter the nonlinear regime at a red-shift of 60 +/- 20. We study the effect of scale dependence of the primordial power spectrum on these numbers and also use the spherical collapse model to make simple estimates of the properties of the first generation of WIMP halos to form. We find that the very first WIMPy halos may have a significant impact on indirect dark matter searches.

Enols are common intermediates in hydrocarbon oxidation.

Abstract: Models for chemical mechanisms of hydrocarbon oxidation rely on spectrometric identification of molecular structures in flames. Carbonyl (keto) compounds are well-established combustion intermediates. However, their less-stable enol tautomers, bearing OH groups adjacent to carbon-carbon double bonds, are not included in standard models. We observed substantial quantities of two-, three-, and four-carbon enols by photoionization mass spectrometry of flames burning representative compounds from modern fuel blends. Concentration profiles demonstrate that enol flame chemistry cannot be accounted for purely by keto-enol tautomerization. Currently accepted hydrocarbon oxidation mechanisms will likely require revision to explain the formation and reactivity of these unexpected compounds.

Combustion at the focus: laser diagnostics and control

Abstract: Fifty years after the foundation of the Combustion Institute and almost 150 years after Michael Faraday's famous lectures on the combustion of a candle, combustion diagnostics have come a long way from visual inspection of a flame to detailed analysis of a combustion process with a multitude of sophisticated techniques, often using lasers. The extended knowledge on combustion phenomena gained by application of these diagnostic techniques, combined with equally advanced numerical simulation of the process, has been instrumental in designing modern combustion devices with efficient performance and reduced pollutant emission. Also, similar diagnostic techniques are now employed to develop sensors for process control in combustion. This article intends to give a perspective on the potential of combustion diagnostics by highlighting selected application examples and by guiding the reader to recent literature. In particular, techniques are emphasized, which permit measurement of important features of the chemical composition, sometimes in conjunction with flow field parameters. Although a complete image of present research and applications in combustion diagnostics and control is beyond the scope of this article, this overview may be a starting place where ideas may be found to solve specific combustion problems with the aid of diagnostics. (Less)

Intense-field many-body S-matrix theory

Abstract: Intense-field many-body S-matrix theory (IMST) provides a systematic ab initio approach to investigate the dynamics of atoms and molecules interacting with intense laser radiation. We review the derivation of IMST as well as its diagrammatic representation and point out its advantage over the conventional 'prior' and 'post' expansions which are shown to be special cases of IMST. The practicality and usefulness of the theory is illustrated by its application to a number of current problems of atomic and molecular ionization in intense fields. We also present a consistent S-matrix formulation of the quantum amplitude for high harmonic generation (HHG) and point out some of the most general properties of HHG radiation emitted by a single atom as well as its relation to coherent emission from many atoms. Experimental results for single and double (multiple) ionization of atoms and the observed distributions of coincidence measurements are analysed and the dominant mechanisms behind them are discussed. Ionization of more complex systems such as diatomic and polyatomic molecules in intense laser fields is analysed as well using IMST and the results are discussed with special attention to the role of molecular orbital symmetry and molecular orientation in space. The review ends with a summary and a brief outlook.

Oxidative stress and ozone: perception, signalling and response

Abstract: The primary site of ozone interaction with plant cells is the extracellular matrix where ozone challenges the antioxidant protection of the cells. Accordingly, ozone sensitivity generally correlates with the ascorbate status of the apoplast, which is an important signal initiation point. In addition, ozone sensing takes place by covalent modification of redox-sensitive components of the plasma membrane, for example ion channels like the plasma membrane Ca2+-channels. Subsequent intracellular signal transduction is an intriguing network of hormone, Ca2+ and MAPK signalling pathways, significantly overlapping with oxidative burst-induced pathogen signalling. Comparison of recent transcriptome analysis revealed that in addition to genes generally induced by all kinds of oxidative stress, for example, transcripts for PR-proteins and most antioxidant enzymes, approximately one-third of the responsive transcripts are ozone specific, indicating jasmonic acid, salicylic acid and ethylene-independent redox signalling triggered by extracellular redox sensing.

Mutation of Vps54 causes motor neuron disease and defective spermiogenesis in the wobbler mouse

Abstract: Vacuolar-vesicular protein sorting (Vps) factors are involved in vesicular trafficking in eukaryotic cells. We identified the missense mutation L967Q in Vps54 in the wobbler mouse, an animal model of amyotrophic lateral sclerosis, and also characterized a lethal allele, Vps54(beta-geo). Motoneuron survival and spermiogenesis are severely compromised in the wobbler mouse, indicating that Vps54 has an essential role in these processes.

Implicit and self-attributed motives to achieve: two separate but interacting needs.

Abstract: This research examined how implicit and self-attributed needs to achieve (labeled as n Ach and san Ach, respectively) combine with self-referenced and norm-referenced feedback to predict effort-related (task performance) and choice-related (task continuation) indexes of students' engagement in a mental concentration task. In Experiment 1 the authors found that in a task-focused setting, task performance was predicted by the joint effect of self-referenced feedback and n Ach, whereas task continuation was predicted by the joint effect of norm-referenced feedback and san Ach. In Experiment 2 the authors found that in an ego-focused setting, n Ach and san Ach interacted in the prediction of task performance but not of task continuation. In Experiment 3 the authors found that the effects of n Ach and san Ach on students' performance were mediated by the anticipated affective value of achievement outcomes. These findings are discussed in relation to a 2-system approach to achievement motivation.

Complete Genome Sequence and Analysis of the Multiresistant Nosocomial Pathogen Corynebacterium jeikeium K411, a Lipid-Requiring Bacterium of the Human Skin Flora

Abstract: Corynebacterium jeikeium is a “lipophilic” and multidrug-resistant bacterial species of the human skin flora that has been recognized with increasing frequency as a serious nosocomial pathogen. Here we report the genome sequence of the clinical isolate C. jeikeium K411, which was initially recovered from the axilla of a bone marrow transplant patient. The genome of C. jeikeium K411 consists of a circular chromosome of 2,462,499 bp and the 14,323-bp bacteriocin-producing plasmid pKW4. The chromosome of C. jeikeium K411 contains 2,104 predicted coding sequences, 52% of which were considered to be orthologous with genes in the Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium diphtheriae genomes. These genes apparently represent the chromosomal backbone that is conserved between the four corynebacteria. Among the genes that lack an ortholog in the known corynebacterial genomes, many are located close to transposable elements or revealed an atypical G+C content, indicating that horizontal gene transfer played an important role in the acquisition of genes involved in iron and manganese homeostasis, in multidrug resistance, in bacterium-host interaction, and in virulence. Metabolic analyses of the genome sequence indicated that the “lipophilic” phenotype of C. jeikeium most likely originates from the absence of fatty acid synthase and thus represents a fatty acid auxotrophy. Accordingly, both the complete gene repertoire and the deduced lifestyle of C. jeikeium K411 largely reflect the strict dependence of growth on the presence of exogenous fatty acids. The predicted virulence factors of C. jeikeium K411 are apparently involved in ensuring the availability of exogenous fatty acids by damaging the host tissue.

Vector opinion dynamics in a bounded confidence consensus model

Abstract: We study the continuum opinion dynamics of the compromise model of Krause and Hegselmann for a community of mutually interacting agents by solving numerically a rate equation. The opinions are here represented by two-dimensional vectors with real-valued components. We study the situation starting from a uniform probability distribution for the opinion configuration and for different shapes of the confidence range. In all cases, we find that the thresholds for consensus and cluster merging either coincide with their one-dimensional counterparts, or are very close to them. The symmetry of the final opinion configuration, when more clusters survive, is determined by the shape of the opinion space. If the latter is a square, which is the case we consider, the clusters in general occupy the sites of a square lattice, although we sometimes observe interesting deviations from this general pattern, especially near the center of the opinion space.

Four-Loop Decoupling Relations for the Strong Coupling

Abstract: We compute the matching relation for the strong coupling constant within the framework of QCD up to four-loop order. This allows a consistent five-loop running (once the $\beta$ function is available to this order) taking into account threshold effects. As a side product we obtain the effective coupling of a Higgs boson to gluons with five-loop accuracy.

Freestanding Nanosheets from Crosslinked Biphenyl Self‐Assembled Monolayers

Abstract: Freestanding nanosheets (see Figure) with the thickness of a single molecule and lateral dimensions in the micrometer range have been obtained by the release of self-assembled monolayers from the underlying surface by dissolution of the substrate or by scission of the anchor group-substrate bonds. The self-assembled monolayers are composed of biphenyl units that are crosslinked by electron irradiation.

Hard-loop dynamics of non-Abelian plasma instabilities.

Abstract: Non-Abelian plasma instabilities may be responsible for the fast apparent quark-gluon thermalization in relativistic heavy-ion collisions if their exponential growth is not hindered by nonlinearities. We study numerically the real-time evolution of instabilities in an anisotropic non-Abelian plasma with an SU(2) gauge group in the hard-loop approximation. We find exponential growth of non-Abelian plasma instabilities both in the linear and in the strongly nonlinear regimes, with only a brief phase of subexponential behavior in between.

Biologically plausible visual homing methods based on optical flow techniques

Abstract: Insects are able to return to important places in their environment by storing an image of the surroundings while at the goal, and later computing a home direction from a matching between this 'snapshot' image and the currently perceived image. Very similar ideas are pursued for the visual navigation of mobile robots. A wide range of different solutions for the matching between the two images have been suggested. This paper explores the application of optical flow techniques for visual homing. The performance of five different flow techniques and a reference method is analysed based on image collections from three different indoor environments. We show that block matching, two simple variants of block matching and two even simpler differential techniques produce robust homing behaviour, despite the simplicity of the matched features. Our analysis reveals that visual homing can succeed even in the presence of many incorrect feature correspondences, and that low-frequency features are sufficient for homing. In particular, the successful application of differential methods opens new vistas on the visual homing problem, both as plausible and parsimonious models of visual insect navigation, and as a starting point for novel robot navigation methods.

The Baryon asymmetry in the Standard Model with a low cut-off

Abstract: We study the generation of the baryon asymmetry in a variant of the standard model, where the Higgs field is stabilized by a dimension-six interaction. Analyzing the one-loop potential, we find a strong first order electroweak phase transition for Higgs masses up to at least 170 GeV. Dimension-six operators induce also new sources of CP violation. We compute the baryon asymmetry in the WKB approximation. Novel source terms in the transport equations enhance the generated baryon asymmetry. For a wide range of parameters the model predicts a baryon asymmetry close to the observed value.

The causal impact of rape myth acceptance on men's rape proclivity: comparing sexually coercive and noncoercive men

Abstract: Heightened temporary accessibility of men's rape myth acceptance (RMA) increases the correlation between RMA and rape proclivity (RP), suggesting a causal impact of RMA on RP (G. Bohner et al., 1998). We additionally examined previous sexual coercion as an indicator of chronic accessibility of RMA. In Study 1 (N = 107), the correlation between RMA and RP was higher: (a) if RMA was assessed before (versus after) RP; and (b) for men who had previously engaged in sexual coercion compared with men who had not. In Study 2 (N = 148), sexually coercive men were faster answering RMA items than were noncoercive men. Taken together, these findings indicate that the temporary and chronic accessibility of RMA independently affect the RMA-RP link. Copyright © 2005 John Wiley & Sons, Ltd.

Function of a fly motion-sensitive neuron matches eye movements during free flight.

Abstract: Sensing is often implicitly assumed to be the passive acquisition of information. However, part of the sensory information is generated actively when animals move. For instance, humans shift their gaze actively in a sequence of saccades towards interesting locations in a scene. Likewise, many insects shift their gaze by saccadic turns of body and head, keeping their gaze fixed between saccades. Here we employ a novel panoramic virtual reality stimulator and show that motion computation in a blowfly visual interneuron is tuned to make efficient use of the characteristic dynamics of retinal image flow. The neuron is able to extract information about the spatial layout of the environment by utilizing intervals of stable vision resulting from the saccadic viewing strategy. The extraction is possible because the retinal image flow evoked by translation, containing information about object distances, is confined to low frequencies. This flow component can be derived from the total optic flow between saccades because the residual intersaccadic head rotations are small and encoded at higher frequencies. Information about the spatial layout of the environment can thus be extracted by the neuron in a computationally parsimonious way. These results on neuronal function based on naturalistic, behaviourally generated optic flow are in stark contrast to conclusions based on conventional visual stimuli that the neuron primarily represents a detector for yaw rotations of the animal.

Exploring trial-by-trial modulations of the Simon effect.

Abstract: The present study investigates sequential modulations of the Simon effect The Simon effect involves faster responses to spatially corresponding than to noncorresponding stimuli, even when stimulus position is irrelevant Recently, the Simon effect has been shown to decrease or to disappear after noncorresponding predecessor trials Possible explanations for these sequential modulations include (a) the gating of position-based response activation (conflict monitoring), (b) repetition or alternation effects, and (c) the interaction between feature integration (binding) processes and stimulus-response (S-R) correspondence Three experiments tested different predictions of these models by comparing Simon effects after neutral trials with those after corresponding and noncorresponding trials, respectively, and by varying the stimulus-onset asynchrony (SOA) between and within experiments Experiments 1 and 2 revealed large Simon effects after corresponding trials, intermediate Simon effects after neutral trials, and small (or no) Simon effects after noncorresponding trials Moreover, some systematic effects of S-R repetitions and S-R alternations were observed Finally, the sequential modulations were maximal at short SOAs and decreased with increasing SOA, but still occurred at an SOA of 6 seconds The results seem to exclude repetition or alternation effects as the main cause of sequential modulations of the Simon effect, but both conflict monitoring and binding may contribute to these effects

Intentions Determine the Effect of Invisible Metacontrast-Masked Primes: Evidence for Top-Down Contingencies in a Peripheral Cuing Task

Abstract: In 5 experiments, the authors tested whether the processing of nonconscious spatial stimulus information depends on a prior intention. This test was conducted with the metacontrast dissociation paradigm. Experiment 1 demonstrated that masked primes that could not be discriminated above chance level affected responses to the visible stimuli that masked them. Experiments 2 and 3 showed that this effect was abolished when the task instruction was changed in such a way that the primes ceased to be task relevant. Experiments 4 and 5 demonstrated that a prime's effect depended on whether it was associated with the same response as the target or with an opposite response.

Incorporating Fluctuations and Dynamics in Self-Consistent Field Theories for Polymer Blends

Abstract: We review various methods to investigate the statics and the dynamics of collective composition fluctuations in dense polymer mixtures within fluctuating-field approaches. The central idea of fluctuating-field theories is to rewrite the partition function of the interacting multi-chain systems in terms of integrals over auxiliary, often complex, fields, which are introduced by means of appropriate Hubbard--Stratonovich transformations. Thermodynamic averages such as the average composition and the structure factor can be expressed exactly as averages of these fields. We discuss different analytical and numerical approaches to studying such a theory: The self-consistent field approach solves the integrals over the fluctuating fields in saddle-point approximation. Generalized random phase approximations allow one to incorporate Gaussian fluctuations around the saddle point. Field theoretical polymer simulations are used to study the statistical mechanics of the full system with Complex Langevin or Monte Carlo methods. Unfortunately, they are hampered by the presence of a sign problem. In a dense system, the latter can be avoided without losing essential physics by invoking a saddle point approximation for the complex field that couples to the total density. This leads to the external potential theory. We investigate the conditions under which this approximation is accurate. Finally, we discuss recent approaches to formulate realistic time evolution equations for such models. The methods are illustrated by two examples: A study of the fluctuation-induced formation of a polymeric microemulsion in a polymer-copolymer mixture and a study of early-stage spinodal decomposition in a binary blend.

The 120 592 bp IncF plasmid pRSB107 isolated from a sewage-treatment plant encodes nine different antibiotic-resistance determinants, two iron-acquisition systems and other putative virulence-associated functions.

Abstract: The antibiotic-multiresistance IncF plasmid pRSB107 was isolated by a transformation-based approach from activated-sludge bacteria of a wastewater-treatment plant. It confers resistance to ampicillin, penicillin G, chloramphenicol, erythromycin, kanamycin, neomycin, streptomycin, sulfonamides, tetracycline and trimethoprim and against mercuric ions. Complete sequencing of this plasmid revealed that it is 120 592 bp in size and has a G+C content of 53·1 mol%. The plasmid backbone is composed of three replicons, RepFIA, RepFIB and RepFII, which are almost identical to corresponding regions located on the F-plasmid and on R100. The three replicons encode replication initiation (rep) and replication control, multimer resolution (mrs), post-segregational killing of plasmid-free cells (psk) and active plasmid partitioning (sopABC locus). Part of the F-leading region and remnants of the F-homologous DNA-transfer (tra) module complete the pRSB107 backbone. Plasmid pRSB107 contains a complex, highly mosaic 35 991 bp antibiotic-resistance region consisting of a Tn21- and a Tn10-derivative and a chloramphenicol-resistance module. The Tn21 derivative is composed of a mercury-resistance region (mer), a Tn4352B-like kanamycin/neomycin-resistance transposon, a streptomycin/sulfonamide-resistance module, remnants of the β-lactam-resistance transposon Tn1, a macrolide-resistance module flanked by copies of IS26 and IS6100, remnants of Tn402 integrating a class 1 integron and the Tn21-specific transposition module. A truncated version of the tetracycline-resistance transposon Tn10 and the chloramphenicol acetyltransferase gene catA complete the pRSB107 resistance region. In addition to antibiotic resistance, pRSB107 encodes the following putative virulence-associated functions: (i) an aerobactin iron-acquisition siderophore system (iuc/iut); (ii) a putative high-affinity Fe2+ uptake system which was previously identified on a pathogenicity island of Yersinia pestis and in the genome of the phytopathogen Erwinia carotovora subsp. atroseptica SCRI1043; (iii) an sn-glycerol-3-phosphate transport system (ugp); and (iv) the virulence-associated genes vagCD having a possible function in stable plasmid inheritance. All the accessory modules are framed by insertion sequences, indicating that pRSB107 was gradually assembled by integration of different horizontally acquired DNA segments via transposition or homologous recombination.