Genomic differences between type strain PG1 and field strains of Mycoplasma mycoides subsp. mycoides small-colony type

The recently accomplished complete genomic sequence analysis of the type strain PG1 of Mycoplasma mycoides subsp. mycoides small-colony type revealed four large repeated segments of 24, 13, 12, and 8 kb that are flanked by insertion sequence (IS) elements. Genetic analysis of type strain PG1 and African, European, and Australian field and vaccine strains revealed that the 24-kb genetic locus is repeated only in PG1 and not in other M. mycoides subsp. mycoides SC strains. In contrast, the 13-kb genetic locus was found duplicated in some strains originating from Africa and Australia but not in strains that were isolated from the European outbreaks. The 12- and 8-kb genetic loci were found in two and three copies, respectively, in all 28 strains analyzed. The flanking IS elements are assumed to lead to these tandem duplications, thus contributing to genomic plasticity. This aspect must be considered when designing novel diagnostic approaches and recombinant vaccines.

A naturally occurring prfA truncation in a Listeria monocytogenes field strain contributes to reduced replication and cell-to-cell spread

Listeria (L.) monocytogenes is an environmental bacterium that may become an intracellular pathogen upon ingestion to cause gastroenteritis, septicaemia, abortions, and/or fatal infections of the central nervous system. We here describe a L. monocytogenes field strain (JF5171) isolated from a bovine placenta in the context of abortion, which exhibited attenuation in bovine brain-slice cultures. The whole genome of strain JF5171 was sequenced, and the invasion, replication, and intercellular spread of JF5171 were further analyzed by quantification of colony forming units and immunofluorescence studies. Phospholipase and hemolysis activity of JF5171 were also quantified along with transcription levels of actA, hly and prfA. The data obtained were compared to those of the widely used L. monocytogenes reference strain, EGD-e. JF5171 exhibited reduced replication and lower levels of phospholipase and hemolysis activity. Invasion and cell-to-cell spread was strongly decreased compared to EGD-e, and actin polymerization was absent. A frame shift deletion was identified in the JF5171 coding region of the major regulator for virulence, prfA. This resulted in a truncated C-terminus sequence (WEN* vs. WGKLN*). In addition, a point mutation resulted in a lysine to arginine substitution at amino acid position 197. Complementation with prfA from EGD-e and with (EGD-e) prfA-K197N increased the replication and spread efficiency of JF5171. In contrast, complementation with the truncated version of prfA had no effect. Taken together, these results suggest that the truncated C-terminus of prfA considerably contributes to the strongly attenuated phenotype observed in vitro.

Temperature- and strain-rate-dependent microfabric evolution in monomineralic mylonite: evidence from in situ deformation of norcamphor

Norcamphor (C7H10O) was subjected to plane strain simple shear in a see-through deformation rig at four different strain rate and temperature conditions. Two transient stages in the microfabric evolution to steady state are distinguished. The grain scale mechanisms associated with the microstructural and textural evolution vary with the applied temperature, strain rate and strain. In high-temperature-low-strain-rate experiments, computer integrated polarization microscopy reveals that the texture evolution is closely related to the crystallographic rotation paths and rotation rates of individual grains. High c-axis rotation rates at low to intermediate shear strains are related to the development of a symmetrical c-axis cross girdle by the end of the first transient stage (γ = 1.5 to 2). During the second transient stage (γ = 1.5 to 6), the cross girdle yields to an oblique c-axis single girdle as c-axis rotation rates decrease and the relative activity of grain boundary migration recrystallization increases. Steady state (γ > 8) is characterized by a stable end orientation of the sample texture and the cyclic growth, rotation and consumption of individual grains within the aggregate.

"Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis

Background Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. tuberculosis genotype known as “Beijing” has repeatedly been associated with drug resistance and has been emerging in some parts of the world. “Beijing” strains are traditionally defined based on a characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit the phylogenetic classification of M. tuberculosis complex (MTBC) strains exhibiting the typical “Beijing” spoligotyping pattern. Methods and Findings MTBC strains were obtained from an ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We identified three MTBC strains from patients originating from Tibet, Portugal and Nepal which exhibited a spoligotyping patterns identical to the classical Beijing signature. However, based on three alternative molecular markers, these strains were assigned to Lineage 3 (also known as Delhi/CAS) rather than to Lineage 2 (also known as East-Asian lineage). Sequencing of the RD207 in one of these strains showed that the deletion responsible for this “Pseudo-Beijing” spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 in classical “Beijing” strains, which is consistent with an evolutionarily independent deletion event in the direct repeat (DR) region of MTBC. Conclusions We provide an example of convergent evolution in the DR locus of MTBC, and highlight the limitation of using spoligotypes for strain classification. Our results indicate that a proportion of “Beijing” strains may have been misclassified in the past. Markers that are more phylogenetically robust should be used when exploring strain-specific differences in experimental or clinical phenotypes.

Pathogenesis and classification of eosinophil disorders: a review of recent developments in the field

Eosinophils and their products play an essential role in the pathogenesis of various reactive and neoplastic disorders. Depending on the underlying disease, molecular defect and involved cytokines, hypereosinophilia may develop and may lead to organ damage. In other patients, persistent eosinophilia is accompanied by typical clinical findings, but the causative role and impact of eosinophilia remain uncertain. For patients with eosinophil-mediated organ pathology, early therapeutic intervention with agents reducing eosinophil counts can be effective in limiting or preventing irreversible organ damage. Therefore, it is important to approach eosinophil disorders and related syndromes early by using established criteria, to perform all appropriate staging investigations, and to search for molecular targets of therapy. In this article, we review current concepts in the pathogenesis and evolution of eosinophilia and eosinophil-related organ damage in neoplastic and non-neoplastic conditions. In addition, we discuss classifications of eosinophil disorders and related syndromes as well as diagnostic algorithms and standard treatment for various eosinophil-related disorders.

Does work stress make you shorter? An ambulatory field study of daily work stressors, job control, and spinal shrinkage

Body height decreases throughout the day due to fluid loss from the intervertebral disk. This study investigated whether spinal shrinkage was greater during workdays compared with nonwork days, whether daily work stressors were positively related to spinal shrinkage, and whether job control was negatively related to spinal shrinkage. In a consecutive 2-week ambulatory field study, including 39 office employees and 512 days of observation, spinal shrinkage was measured by a stadiometer, and calculated as body height in the morning minus body height in the evening. Physical activity was monitored throughout the 14 days by accelerometry. Daily work stressors, daily job control, biomechanical workload, and recreational activities after work were measured with daily surveys. Multilevel regression analyses showed that spinal disks shrank more during workdays than during nonwork days. After adjustment for sex, age, body weight, smoking status, biomechanical work strain, and time spent on physical and low-effort activities during the day, lower levels of daily job control significantly predicted increased spinal shrinkage. Findings add to knowledge on how work redesign that increases job control may possibly contribute to preserving intervertebral disk function and preventing occupational back pain.

Small ruminant lentivirus genotype B and E interaction: evidences on the role of Roccaverano strain on reducing proviral load of the challenging CAEV strain

Live attenuated vaccines provide the most consistent protective immunity in experimental models of lentivirus infections. In this study we tested the hypothesis that animals infected with a naturally attenuated small ruminant lentivirus field strain of genotype E may control a challenge infection with a virulent strain of the caprine arthritis encephalitis virus (CAEV-CO). Within genotype E, Roccaverano strain has been described as attenuated since decreased arthritic pathological indexes were recorded in Roccaverano-infected animals compared to animals of the same breed infected with genotype B strains. Moreover, under natural conditions, animals double-infected with genotypes B and E appear less prone to develop SRLV-related disease, leading to a putative protective role of Roccaverano strain. Here we present evidence that goats experimentally infected with the avirulent genotype E SRLV-Roccaverano strain control the proviral load of a pathogenic challenge virus (CAEV-CO strain) more efficiently than naïve animals and appear to limit the spread of histological lesions to the contralateral joints.

From transient to steady state deformation and grain size: A thermodynamic approach using elasto-visco-plastic numerical modeling

Numerical simulation experiments give insight into the evolving energy partitioning during high-strain torsion experiments of calcite. Our numerical experiments are designed to derive a generic macroscopic grain size sensitive flow law capable of describing the full evolution from the transient regime to steady state. The transient regime is crucial for understanding the importance of micro structural processes that may lead to strain localization phenomena in deforming materials. This is particularly important in geological and geodynamic applications where the phenomenon of strain localization happens outside the time frame that can be observed under controlled laboratory conditions. Ourmethod is based on an extension of the paleowattmeter approach to the transient regime. We add an empirical hardening law using the Ramberg-Osgood approximation and assess the experiments by an evolution test function of stored over dissipated energy (lambda factor). Parameter studies of, strain hardening, dislocation creep parameter, strain rates, temperature, and lambda factor as well asmesh sensitivity are presented to explore the sensitivity of the newly derived transient/steady state flow law. Our analysis can be seen as one of the first steps in a hybrid computational-laboratory-field modeling workflow. The analysis could be improved through independent verifications by thermographic analysis in physical laboratory experiments to independently assess lambda factor evolution under laboratory conditions.

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.

Microfabric memory of vein quartz for strain localization in detachment faults: A case study on the Simplon fault zone

This manuscript deals with the adaptation of quartz-microfabrics to changing physical deformation conditions, and discusses their preservation potential during subsequent retrograde deformation. Using microstructural analysis, a sequence of recrystallization processes in quartz, ranging from Grain-Boundary Migration Recrystallization (GBM) over Subgrain-Rotation Recrystallization (SGR) to Bulging Nucleation (BLG) is detected for the Simplon fault zone (SFZ) from the low strain rim towards the internal high strain part of the large-scale shear zone. Based on: (i) the retrograde cooling path; (ii) estimates of deformation temperatures; and (iii) spatial variation of dynamic recrystallization processes and different microstructural characteristics, continuous strain localization with decreasing temperature is inferred. In contrast to the recrystallization microstructures, crystallographic preferred orientations (CPO) have a longer memory. CPO patterns indicative of prism and rhomb glide systems in mylonitic quartz veins, overprinted at low temperatures (�400 �C), suggest inheritance of a high-temperature deformation. In this way, microstructural, textural and geochemical analyses provide information for several million years of the deformation history. The reasons for such incomplete resetting of the rock texture is that strain localization is caused by change in effective viscosity contrasts related to temporal large- and small-scale temperature changes during the evolution of such a long-lived shear zone. The spatially resolved, quantitative investigation of quartz microfabrics and associated recrystallization processes therefore provide great potential for an improved understanding of the geodynamics of large-scale shear zones.

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.

Moments of tension and strain in psychotherapy and how they promote a good alliance and outcome

It is well established that the therapeutic relationship contributes about as much to therapy outcome as ‘technical’ intervention. Furthermore, it follows clear prescriptive concepts in the same manner as technical interventions do. ‘Motive Oriented Therapeutic Relationship’ is such a concept for establishing a solid basis for whatever therapeutic work the patients’ problems require (Grawe, 1980, 1992; Caspar, 1996). Yet, the therapeutic relationship doesn’t explain everything because other factors play a significant role too. Previous studies showed that outcome is clearly better when therapists achieved a generally high quality of a therapeutic relationship when they did not shy away from possibly threatening interventions such as confrontations. This ratio of a fruitful alliance and marginally present confrontations in the same session also showed significant correlations with patient’s assessment of alliance and progress in therapy (Figlioli et al., 2009). The current state of research in the field, however, does not give any answers to questions like how good and bad confrontations can be characterized or what role does the intensity, respectively frequency of confrontations play in the process of psychotherapy. Therefore, we analyzed a sample of 80 therapies of 3 sessions each representing either good or bad outcome. Independent raters judged moment by moment how therapists used confrontative interventions. 20 cases, which showed an excellent or a very poor outcome, as well as an unexpected pattern were analyzed in further quantitative details. We found that confrontations are correlated to good outcome when they are uttered implicitly, related to an important topic of the patient (e.g. one of the defined therapy goals), long but weak, embedded in prior complementarity and not in the first three sessions of a therapy, as well as not an interactional discrepancy between the patient and the therapist.

Small quantity but large effect — How minor phases control strain localization in upper mantle shear zones

Low viscosity domains such as localized shear zones exert an important control on the geodynamics of the uppermost mantle. Grain size reduction and subsequent strain localization related to a switch from dislocation to diffusion creep is one mechanism to form low viscosity domains. To sustain strain localization, the grain size of mantle minerals needs to be kept small over geological timescales. One way to keep olivine grain sizes small is by pinning of mobile grain boundaries during grain growth by other minerals (second phases). Detailed microstructural studies based on natural samples from three shear zones formed at different geodynamic settings, allowed the derivation of the olivine grain-size dependence on the second-phase content. The polymineralic olivine grain-size evolution with increasing strain is similar in the three shear zones. If the second phases are to pin the mobile olivine grain boundary the phases need to be well mixed before grain growth. We suggest that melt-rock and metamorphic reactions are crucial for the initial phase mixing in mantle rocks. With ongoing deformation and increasing strain, grain boundary sliding combined with mass transfer processes and nucleation of grains promotes phase mixing resulting in fine-grained polymineralic mixtures that deform by diffusion creep. Strain localization due to the presence of volumetrically minor minerals in polymineralic mantle rocks is only important at high strain deformation (ultramylonites) at low temperatures (<~800°C). At smaller strain and stress conditions and/or higher temperatures other parameters like overall energy available to deform a given rock volume, the inheritance of mechanical anisotropies or the presence of water or melts needs to be considered to explain strain localization in the upper mantle.