Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads

Abstract Background Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

A Metric to Evaluate and Synthesize Distributed Compliant Mechanisms

Compliant mechanisms with evenly distributed stresses have better load-bearing ability and larger range of motion than mechanisms with compliance and stresses lumped at flexural hinges. In this paper, we present a metric to quantify how uniformly the strain energy of deformation and thus the stresses are distributed throughout the mechanism topology. The resulting metric is used to optimize cross-sections of conceptual compliant topologies leading to designs with maximal stress distribution. This optimization framework is demonstrated for both single-port mechanisms and single-input single-output mechanisms. It is observed that the optimized designs have lower stresses than their nonoptimized counterparts, which implies an ability for single-port mechanisms to store larger strain energy, and single-input single-output mechanisms to perform larger output work before failure.

Quantitative 3D strain analysis in analogue experiments: Integration of X-ray computed tomography and digital volume correlation techniques

The combination of scaled analogue experiments, material mechanics, X-ray computed tomography (XRCT) and Digital Volume Correlation techniques (DVC) is a powerful new tool not only to examine the 3 dimensional structure and kinematic evolution of complex deformation structures in scaled analogue experiments, but also to fully quantify their spatial strain distribution and complete strain history. Digital image correlation (DIC) is an important advance in quantitative physical modelling and helps to understand non-linear deformation processes. Optical non-intrusive (DIC) techniques enable the quantification of localised and distributed deformation in analogue experiments based either on images taken through transparent sidewalls (2D DIC) or on surface views (3D DIC). X-ray computed tomography (XRCT) analysis permits the non-destructive visualisation of the internal structure and kinematic evolution of scaled analogue experiments simulating tectonic evolution of complex geological structures. The combination of XRCT sectional image data of analogue experiments with 2D DIC only allows quantification of 2D displacement and strain components in section direction. This completely omits the potential of CT experiments for full 3D strain analysis of complex, non-cylindrical deformation structures. In this study, we apply digital volume correlation (DVC) techniques on XRCT scan data of “solid” analogue experiments to fully quantify the internal displacement and strain in 3 dimensions over time. Our first results indicate that the application of DVC techniques on XRCT volume data can successfully be used to quantify the 3D spatial and temporal strain patterns inside analogue experiments. We demonstrate the potential of combining DVC techniques and XRCT volume imaging for 3D strain analysis of a contractional experiment simulating the development of a non-cylindrical pop-up structure. Furthermore, we discuss various options for optimisation of granular materials, pattern generation, and data acquisition for increased resolution and accuracy of the strain results. Three-dimensional strain analysis of analogue models is of particular interest for geological and seismic interpretations of complex, non-cylindrical geological structures. The volume strain data enable the analysis of the large-scale and small-scale strain history of geological structures.

International Clostridium difficile animal strain collection and large diversity of animal associated strains

BACKGROUND Clostridium difficile is an important cause of intestinal infections in some animal species and animals might be a reservoir for community associated human infections. Here we describe a collection of animal associated C. difficile strains from 12 countries based on inclusion criteria of one strain (PCR ribotype) per animal species per laboratory. RESULTS Altogether 112 isolates were collected and distributed into 38 PCR ribotypes with agarose based approach and 50 PCR ribotypes with sequencer based approach. Four PCR ribotypes were most prevalent in terms of number of isolates as well as in terms of number of different host species: 078 (14.3% of isolates; 4 hosts), 014/020 (11.6%; 8 hosts); 002 (5.4%; 4 hosts) and 012 (5.4%; 5 hosts). Two animal hosts were best represented; cattle with 31 isolates (20 PCR ribotypes; 7 countries) and pigs with 31 isolates (16 PCR ribotypes; 10 countries). CONCLUSIONS This results show that although PCR ribotype 078 is often reported as the major animal C. difficile type, especially in pigs, the variability of strains in pigs and other animal hosts is substantial. Most common human PCR ribotypes (014/020 and 002) are also among most prevalent animal associated C. difficile strains worldwide. The widespread dissemination of toxigenic C. difficile and the considerable overlap in strain distribution between species furthers concerns about interspecies, including zoonotic, transmission of this critically important pathogen.

Strain typing and antimicrobial susceptibility of methicillin-resistant coagulase-positive staphylococcal species in dogs and people associated with dogs in Thailand

AIMS This study was to investigate and to characterize methicillin-resistant coagulase-positive staphylococci (MRCoPS) harboring in dogs and people associated with dogs in Thailand. METHODS AND RESULTS Staphylococci were collected from 100 dogs, 100 dog owners, 200 small animal veterinarians and 100 people without pet association. Species of MRCoPS were identified phenotypically and genotypically. Molecular characteristics were determined by multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and SCCmec typing, and antimicrobial susceptibility was assayed by broth microdilution and by microarray analysis for resistance genes. Methicillin-resistant Staphylococcus pseudintermedius (MRSP), methicillin-resistant Staphylococcus schleiferi subsp. coagulans (MRSSc) and methicillin-resistant Staphylococcus aureus (MRSA) were isolated from dogs (45, 17 and 1%, respectively), veterinarians (8, 2 and 1·5%, respectively) and dog owners (3, 2 and 0%, respectively). Seventeen sequence types (STs) were identified among 83 MRSP isolates which specifically carried SCCmec V, II-III, ΨSCCmec57395 and three uncharacterized SCCmec types. MRSP ST 45, 68 and novel STs including 169, 178, 181 and 183 were shared among canine and human isolates. Most of MRSA ST398 and MRSSc carried SCCmec type V. The MRCoPS commonly displayed multiple resistances to tested antimicrobials and carried various resistance genes. CONCLUSION Variety of MRCoPS, especially new MRSP clones, distributed in dogs and people in Thailand. SIGNIFICANCE AND IMPACT OF THE STUDY The existence of MRCoPS circulating between dogs and humans in Thailand provides indirect evidence of interspecies transmission and represents a potential public health hazard.

Draft Genome Sequence of Aneurinibacillus migulanus Strain Nagano

ACKNOWLEDGMENTS This project was funded by the Kuwait Government (to F.N.A.), the European Union’s Seventh Framework Programme under grant agreement no. 245268 (ISEFOR; to L.B. and S.W.). Further support came from the SwissBOL project, financed by the Swiss Federal Office for the Environment (grant holder, L.B.) and the Sciex–Scientific Exchange Programme NMS.CH (to L.B. and L.L.).

Multifunctional cement composites strain and damage sensors applied on reinforced concrete (RC) structural elements

In this research, strain-sensing and damage-sensing functional properties of cement composites have been studied on a conventional reinforced concrete (RC) beam. Carbon nanofiber (CNFCC) and fiber (CFCC) cement composites were used as sensors on a 4 m long RC beam. Different casting conditions (in situ or attached), service location (under tension or compression) and electrical contacts (embedded or superficial) were compared. Both CNFCC and CFCC were suitable as strain sensors in reversible (elastic) sensing condition testing. CNFCC showed higher sensitivities (gage factor up to 191.8), while CFCC only reached gage factors values of 178.9 (tension) or 49.5 (compression). Furthermore, damage-sensing tests were run, increasing the applied load progressively up to the RC beam failure. In these conditions, CNFCC sensors were also strain sensitive, but no damage sensing mechanism was detected for the strain levels achieved during the tests. Hence, these cement composites could act as strain sensors, even for severe damaged structures near to their collapse.

Fault development and interaction in distributed strike-slip shear zones: an experimental approach

Analogue model experiments using both brittle and viscous materials were performed to investigate the development and interaction of strike-slip faults in zones of distributed shear deformation. At low strain, bulk dextral shear deformation of an initial rectangular model is dominantly accommodated by left-stepping, en echelon strike-slip faults (Riedel shears, R) that form in response to the regional (bulk) stress field. Push-up zones form in the area of interaction between adjacent left-stepping Riedel shears. In cross sections, faults bounding push-up zones have an arcuate shape or merge at depth. Adjacent left-stepping R shears merge by sideways propagation or link by short synthetic shears that strike subparallel to the bulk shear direction. Coalescence of en echelon R shears results in major, through-going faults zones (master faults). Several parallel master faults develop due to the distributed nature of deformation. Spacing between master faults is related to the thickness of the brittle layers overlying the basal viscous layer. Master faults control to a large extent the subsequent fault pattern. With increasing strain, relatively short antithetic and synthetic faults develop mostly between old, but still active master faults. The orientation and evolution of the new faults indicate local modifications of the stress field. In experiments lacking lateral borders, closely spaced parallel antithetic faults (cross faults) define blocks that undergo clockwise rotation about a vertical axis with continuing deformation. Fault development and fault interaction at different stages of shear strain in our models show similarities with natural examples that have undergone distributed shear.

Transient response in high-resolution Brillouin-based distributed sensing using probe pulses shorter than the acoustic relaxation time

We perform numerical simulations on a model describing a Brillouin-based temperature and strain sensor, testing its response when it is probed with relatively short pulses. Experimental results were recently published [e.g., Opt. Lett. 24, 510 (1999)] that showed a broadening of the Brillouin loss curve when the probe pulse duration is reduced, followed by a sudden and rather surprising reduction of the linewidth when the pulse duration gets shorter than the acoustic relaxation time. Our study reveals the processes responsible for this behavior. We give a clear physical insight into the problem, allowing us to define the best experimental conditions required for one to take the advantage of this effect.

The accuracy of parameter estimation from noisy data, with application to resonance peak estimation in distributed Brillouin sensing

Distributed Brillouin sensing of strain and temperature works by making spatially resolved measurements of the position of the measurand-dependent extremum of the resonance curve associated with the scattering process in the weakly nonlinear regime. Typically, measurements of backscattered Stokes intensity (the dependent variable) are made at a number of predetermined fixed frequencies covering the design measurand range of the apparatus and combined to yield an estimate of the position of the extremum. The measurand can then be found because its relationship to the position of the extremum is assumed known. We present analytical expressions relating the relative error in the extremum position to experimental errors in the dependent variable. This is done for two cases: (i) a simple non-parametric estimate of the mean based on moments and (ii) the case in which a least squares technique is used to fit a Lorentzian to the data. The question of statistical bias in the estimates is discussed and in the second case we go further and present for the first time a general method by which the probability density function (PDF) of errors in the fitted parameters can be obtained in closed form in terms of the PDFs of the errors in the noisy data.

The accuracy of parameter estimation from noisy data, with application to resonance peak estimation in distributed Brillouin sensing

Distributed Brillouin sensing of strain and temperature works by making spatially resolved measurements of the position of the measurand-dependent extremum of the resonance curve associated with the scattering process in the weakly nonlinear regime. Typically, measurements of backscattered Stokes intensity (the dependent variable) are made at a number of predetermined fixed frequencies covering the design measurand range of the apparatus and combined to yield an estimate of the position of the extremum. The measurand can then be found because its relationship to the position of the extremum is assumed known. We present analytical expressions relating the relative error in the extremum position to experimental errors in the dependent variable. This is done for two cases: (i) a simple non-parametric estimate of the mean based on moments and (ii) the case in which a least squares technique is used to fit a Lorentzian to the data. The question of statistical bias in the estimates is discussed and in the second case we go further and present for the first time a general method by which the probability density function (PDF) of errors in the fitted parameters can be obtained in closed form in terms of the PDFs of the errors in the noisy data.

Transient response in high-resolution Brillouin-based distributed sensing using probe pulses shorter than the acoustic relaxation time

We perform numerical simulations on a model describing a Brillouin-based temperature and strain sensor, testing its response when it is probed with relatively short pulses. Experimental results were recently published [e.g., Opt. Lett. 24, 510 (1999)] that showed a broadening of the Brillouin loss curve when the probe pulse duration is reduced, followed by a sudden and rather surprising reduction of the linewidth when the pulse duration gets shorter than the acoustic relaxation time. Our study reveals the processes responsible for this behavior. We give a clear physical insight into the problem, allowing us to define the best experimental conditions required for one to take the advantage of this effect.

A distributed and key-position fiber sensing system based on LPFG and WFBG assisted OTDR

An enhanced fiber sensing system used for distributed bending and key-position sensing is reported by integrating WFBGs, LPFG and OTDR, which also achieves strain and temperature sensitivities up to 0.047mv/με and 0.675mv/°C respectively. © 2014 OSA.

Fiber Bragg Gratings Strain Sensors for Railway Applications

Fiber optical sensors have played an important role in applications for monitoring the health of civil infrastructures, such as bridges, oil rigs, and railroads. Due to the reduction in cost of fiber-optic components and systems, fiber optical sensors have been studied extensively for their higher sensitivity, precision and immunity to electrical interference compared to their electrical counterparts. A fiber Bragg grating (FBG) strain sensor has been employed for this study to detect and distinguish normal and lateral loads on rail tracks. A theoretical analysis of the relationship between strain and displacement under vertical and horizontal strains on an aluminum beam has been performed, and the results are in excellent agreement with the measured strain data. Then a single FBG sensor system with erbium-doped fiber amplifier broadband source has been carried out. Force and temperature applied on the system have resulted in changes of 0.05 nm per 50 με and 0.094 nm per 10 oC at the center wavelength of the FBG. Furthermore, a low cost fiber-optic sensor system with a distributed feedback (DFB) laser as the light source has been implemented. We show that it has superior noise and sensitivity performances compared to strain gauge sensors. The design has been extended to accommodate multiple sensors with negligible cross talk. When two cascaded sensors on a rail track section are tested, strain readings of the sensor 20 inches away from the position of applied force decay to one seventh of the data of the sensor at the applied force location. The two FBG sensor systems can detect 1 ton of vertical load with a square wave pattern and 0.1 ton of lateral loads (3 tons and 0.5 ton, respectively, for strain gauges). Moreover, a single FBG sensor has been found capable of detecting and distinguishing lateral and normal strains applied at different frequencies. FBG sensors are promising alternatives to electrical sensors for their high sensitivity,ease of installation, and immunity to electromagnetic interferences.