EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter

Cell-cell communication is mediated by membrane receptors and their ligands, such as the Eph/ephrin system, orchestrating cell migration during development and in diverse cancer types. Epigenetic mechanisms are key for integrating external "signals", e.g., from neighboring cells, into the transcriptome in health and disease. Previously, we reported ephrinA5 to trigger transcriptional changes of lncRNAs and protein-coding genes in cerebellar granule cells, a cell model for medulloblastoma. LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression. Here, we investigate a lncRNA-mediated targeting of DNMT1 to specific gene loci by the combined power of in silico modeling of RNA/DNA interactions and wet lab approaches, in the context of the clinically relevant use case of ephrinA5-dependent regulation of cellular motility of cerebellar granule cells. We provide evidence that Snhg15, a cancer-related lncRNA, recruits DNMT1 to the Ncam1 promoter through RNA/DNA triplex structure formation and the interaction with DNMT1. This mediates DNA methylation-dependent silencing of Ncam1, being abolished by ephrinA5 stimulation-triggered reduction of Snhg15 expression. Hence, we here propose a triple helix recognition mechanism, underlying cell motility regulation via lncRNA-targeted DNA methylation in a clinically relevant context.

SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A

Improving an enzyme's (thermo-)stability or tolerance against solvents and detergents is highly relevant in protein engineering and biotechnology. Recent developments have tended toward data-driven approaches, where available knowledge about the protein is used to identify substitution sites with high potential to yield protein variants with improved stability, and subsequently, substitutions are engineered by site-directed or site-saturation (SSM) mutagenesis. However, the development and validation of algorithms for data-driven approaches have been hampered by the lack of availability of large-scale data measured in a uniform way and being unbiased with respect to substitution types and locations. Here, we extend our knowledge on guidelines for protein engineering following a data-driven approach by scrutinizing the impact of substitution sites on thermostability or/and detergent tolerance for Bacillus subtilis lipase A (BsLipA) at very large scale. We systematically analyze a complete experimental SSM library of BsLipA containing all 3439 possible single variants, which was evaluated as to thermostability and tolerances against four detergents under respectively uniform conditions. Our results provide systematic and unbiased reference data at unprecedented scale for a biotechnologically important protein, identify consistently defined hot spot types for evaluating the performance of data-driven protein-engineering approaches, and show that the rigidity theory and ensemble-based approach Constraint Network Analysis yields hot spot predictions with an up to ninefold gain in precision over random classification.

Genomic and phenotypic diversity of Clostridium difficile during long-term sequential recurrences of infection

Infection with the emerging pathogen Clostridioides (Clostridium) difficile might lead to colonization of the gastrointestinal tract of humans and mammals eventually resulting in antibiotic-associated diarrhea, which can be mild to possibly life-threatening. Recurrences after antibiotic treatment have been described in 15-30% of the cases and are either caused by the original (relapse) or by new strains (reinfection). In this study, we describe a patient with ongoing recurrent C. difficile infections over 13 months. During this time, ten C. difficile strains of six different ribotypes could be isolated that were further characterized by phenotypic and genomic analyses including motility and sporulation assays, growth fitness and antibiotic susceptibility as well as whole-genome sequencing. PCR ribotyping of the isolates confirmed that the recurrences were a mixture of relapses and reinfections. One recurrence was due to a mixed infection with three different strains of two different ribotypes. Furthermore, genomes were sequenced and multi-locus sequence typing (MLST) was carried out, which identified the strains as members of sequence types (STs) 10, 11, 14 and 76. Comparison of the genomes of isolates of the same ST originating from recurrent CDI (relapses) indicated little within-patient microevolution and some concurrent within-patient diversity of closely related strains. Isolates of ribotype 126 that are binary toxin positive differed from other ribotypes in various phenotypic aspects including motility, sporulation behavior and cell morphology. Ribotype 126 is genetically related to ribotype 078 that has been associated with increased virulence. Isolates of the ribotype 126 exhibited elongated cells and a chaining phenotype, which was confirmed by membrane staining and scanning electron microscopy. Furthermore, this strain exhibits a sinking behavior in liquid medium in stationary growth phase. Taken together, our observation has proven multiple CDI recurrences that were based on a mixture of relapses and reinfections.

Steep rise in norovirus cases and emergence of a new recombinant strain GII.P16-GII.2, Germany, winter 2016

Since early November 2016, the number of laboratory-confirmed norovirus infections reported in Germany has been increasing steeply. Here, we report the detection and genetic characterisation of an emerging norovirus recombinant, GII.P16-GII.2. This strain was frequently identified as the cause of sporadic cases as well as outbreaks in nine federal states of Germany. Our findings suggest that the emergence of GII.P16-GII.2 contributed to rising case numbers of norovirus gastroenteritis in Germany.

Backbone Dihedral Angle Prediction

More than two decades of research have enabled dihedral angle predictions at an accuracy that makes them an interesting alternative or supplement to secondary structure prediction that provides detailed local structure information for every residue of a protein. The evolution of dihedral angle prediction methods is closely linked to advancements in machine learning and other relevant technologies. Consequently recent improvements in large-scale training of deep neural networks have led to the best method currently available, which achieves a mean absolute error of 19° for phi, and 30° for psi. This performance opens interesting perspectives for the application of dihedral angle prediction in the comparison, prediction, and design of protein structures.

Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks

In many applications in soft and biological physics, there are multiple time and length scales involved but often with a distinct separation between them. For instance, in enzyme kinetics, enzymes are relatively large, move slowly and their copy numbers are typically small, while the metabolites (being transformed by these enzymes) are often present in abundance, are small in size and diffuse fast. It seems thus natural to apply different techniques to different time and length levels and couple them. Here we explore this possibility by constructing a stochastic-deterministic discrete-continuous reaction-diffusion model with mobile sources and sinks. Such an approach allows in particular to separate different sources of stochasticity. We demonstrate its application by modelling enzyme-catalysed reactions with freely diffusing enzymes and a heterogeneous source of metabolites. Our calculations suggest that using a higher amount of less active enzymes, as compared to fewer more active enzymes, reduces the metabolite pool size and correspondingly the lag time, giving rise to a faster response to external stimuli. The methodology presented can be extended to more complex systems and offers exciting possibilities for studying problems where spatial heterogeneities, stochasticity or discreteness play a role.

Clostridium difficile infections among adults and children in Mwanza/Tanzania: is it an underappreciated pathogen among immunocompromised patients in sub-Saharan Africa?

Little is known regarding the epidemiology Clostridium difficile in developing countries. Fresh stool samples from patients with diarrhoea were cultured anaerobically. C. difficile was detected in nine (6.4%) of 141 (95% confidence interval 4.2–13.1), of which seven (77.8%) were from children. HIV infection, prolonged hospitalization and antibiotic use were independent factors associated with the occurrence of C. difficile in the gastrointestinal tract. Two of the toxigenic isolates were typed as ribotype 045, and the other two had unknown ribotype. All C. difficile isolates were susceptible to metronidazole, moxifloxacin and clarithromycin, while three isolates were resistant to clarithromycin. C. difficile may be an important pathogen causing diarrhoea in sub-Saharan Africa among immunocompromised patients.

Scientific workflow optimization for improved peptide and protein identification

Background

Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task. However, these algorithms typically require the user to select instrument- and sample-dependent parameters, such as mass measurement error tolerances and number of missed enzymatic cleavages. In order to select the best algorithm and parameter set for a particular dataset, in-depth knowledge about the data as well as the algorithms themselves is needed. Most researchers therefore tend to use default parameters, which are not necessarily optimal.

Results

We have applied a new optimization framework for the Taverna scientific workflow management system (http://ms-utils.org/Taverna_Optimization.pdf) to find the best combination of parameters for a given scientific workflow to perform peptide-spectrum matching. The optimizations themselves are non-trivial, as demonstrated by several phenomena that can be observed when allowing for larger mass measurement errors in sequence database searches. On-the-fly parameter optimization embedded in scientific workflow management systems enables experts and non-experts alike to extract the maximum amount of information from the data. The same workflows could be used for exploring the parameter space and compare algorithms, not only for peptide-spectrum matching, but also for other tasks, such as retention time prediction.

Conclusion

Using the optimization framework, we were able to learn about how the data was acquired as well as the explored algorithms. We observed a phenomenon identifying many ammonia-loss b-ion spectra as peptides with N-terminal pyroglutamate and a large precursor mass measurement error. These insights could only be gained with the extension of the common range for the mass measurement error tolerance parameters explored by the optimization framework.

[Endophthalmitis, liver abscess, and cerebral and pulmonary emboli in a 48-year-old Vietnamese man]

We present the case of a 48-year-old Vietnamese man with endophthalmitis, liver abscess, and pulmonary and cerebral septic emboli. Klebsiella pneumoniae was isolated as the causative organism; there were no laboratory findings suggestive of invasive fungal infection. Klebsiella pneumoniae invasive syndrome is a rare disease in Germany. This case report exemplifies the necessity of a dedicated diagnostic approach that takes into consideration factors such as ethnic origin and accompanying diseases of the patient.

Comprehensive large-scale assessment of intrinsic protein disorder

MOTIVATION

Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started to collect disorder annotations from multiple experimental structures.

RESULTS

MobiDB annotates disorder for UniProt sequences, allowing us to conduct the first large-scale assessment of fast disorder predictors on 25 833 different sequences with X-ray crystallographic structures. In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations. (i) The predictors cluster according to their disorder definition, with a consensus giving more confidence. (ii) Previous assessments appear over-reliant on data annotated at the PDB chain level and performance is lower on entire UniProt sequences. (iii) Long disordered regions are harder to predict. (iv) Depending on the structural and functional types of the proteins, differences in prediction performance of up to 10% are observed.

AVAILABILITY

The datasets are available from Web site at URL: http://mobidb.bio.unipd.it/lsd.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

LOCUSTRA: accurate prediction of local protein structure using a two-layer support vector machine approach

Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al. (Proteins: Struct., Funct., Bioinf. 2000, 41, 271-287), we assess its prediction ability for an independent test set of 222 proteins and compare our method to three-class secondary structure prediction and direct prediction of dihedral angles. The prediction accuracy is Q16=61.0% for the 16 classes of the structural alphabet and Q3=79.2% for a simple mapping to the three secondary classes helix, sheet, and coil. We achieve a mean phi(psi) error of 24.74 degrees (38.35 degrees) and a median RMSDA (root-mean-square deviation of the (dihedral) angles) per protein chain of 52.1 degrees. These results compare favorably with related approaches. The LOCUSTRA web server is freely available to researchers at http://www.fz-juelich.de/nic/cbb/service/service.php.

Understanding protein folding: small proteins in silico

Recent improvements in methodology and increased computer power now allow atomistic computer simulations of protein folding. We briefly review several advanced Monte Carlo algorithms that have contributed to this development. Details of folding simulations of three designed mini proteins are shown. Adding global translations and rotations has allowed us to handle multiple chains and to simulate the aggregation of six beta-amyloid fragments. In a different line of research we have developed several algorithms to predict local features from sequence. In an outlook we sketch how such biasing could extend the application spectrum of Monte Carlo simulations to structure prediction of larger proteins.

Active control of type-I edge-localized modes with n=1 perturbation fields in the JET tokamak

Type-I edge-localized modes (ELMs) have been mitigated at the JET tokamak using a static external n=1 perturbation field generated by four error field correction coils located far from the plasma. During the application of the n=1 field the ELM frequency increased by a factor of 4 and the amplitude of the D(alpha) signal decreased. The energy loss per ELM normalized to the total stored energy, DeltaW/W, dropped to values below 2%. Transport analyses shows no or only a moderate (up to 20%) degradation of energy confinement time during the ELM mitigation phase.

Ring polymer simulations with global radius of curvature

We simulate three-dimensional flexible off-lattice ring polymers of length L up to L=4000 for various values of the global radius of curvature Rgrc=0.25 , 0.48, and 1.0 and Rgrc=2.0 . We utilize two different ensembles: one with a delta -function constraint on the radius, and the other with a theta -function. For both cases the global radius of curvature provides a valid regularization of polymers with thickness D=2Rgrc . The Flory-type critical exponent nu SAW of self-avoiding rings at D=2 is found to be nu SAW=0.5869(5) from the radii of gyration chain length scaling, while other D values produce consistent results. For our current implementation, the numerical effort of chain thickness calculations is bounded by a number O(LlnL) per single update. We also study low-temperature configurations of spatially dense Lennard-Jones homopolymers on a ring and identify some conformational building blocks.

Improved confinement due to open ergodic field lines imposed by the dynamic ergodic divertor in TEXTOR

The ergodization of the magnetic field lines imposed by the dynamic ergodic diverter (DED) in TEXTOR can lead both to confinement improvement and to confinement deterioration. The cases of substantial improvement are in resonant ways related to particular conditions in which magnetic flux tubes starting at the X points of induced islands are connected with the wall. This opening process is connected with a characteristic modification of the heat deposition pattern at the divertor target plate and leads to a substantial increase and steepening of the core plasma density and pressure. The improvement is tentatively attributed to a modification of the electric potential in the plasma carried by the open field lines. The confinement improvement bases on a spontaneous density built up due to the application of the DED and is primarily a particle confinement improvement.

BETTY: prediction of beta-strand type from sequence

Most secondary structure prediction programs do not distinguish between parallel and antiparallel beta-sheets. However, such knowledge would constrain the available topologies of a protein significantly, and therefore aid existing fold recognition algorithms. For this reason, we propose a technique which, in combination with existing secondary structure programs such as PSIPRED, allows one to distinguish between parallel and antiparallel beta-sheets. We propose the use of a support vector machine (SVM) procedure, BETTY, to predict parallel and antiparallel sheets from sequence. We found that there is a strong signal difference in the sequence profiles which SVMs can efficiently extract. With strand type assignment accuracies of 90.7% and 83.3% for antiparallel and parallel strands, respectively, our method adds considerably to existing information on current 3-class secondary structure predictions. BETTY has been implemented as an online service which academic researchers can access from our website http://www.fz-juelich.de/nic/cbb/service/service.php.

Support vector machines for prediction of dihedral angle regions

MOTIVATION

Most secondary structure prediction programs target only alpha helix and beta sheet structures and summarize all other structures in the random coil pseudo class. However, such an assignment often ignores existing local ordering in so-called random coil regions. Signatures for such ordering are distinct dihedral angle pattern. For this reason, we propose as an alternative approach to predict directly dihedral regions for each residue as this leads to a higher amount of structural information.

RESULTS

We propose a multi-step support vector machine (SVM) procedure, dihedral prediction (DHPRED), to predict the dihedral angle state of residues from sequence. Trained on 20,000 residues our approach leads to dihedral region predictions, that in regions without alpha helices or beta sheets is higher than those from secondary structure prediction programs.

AVAILABILITY

DHPRED has been implemented as a web service, which academic researchers can access from our webpage http://www.fz-juelich.de/nic/cbb

Forced magnetic reconnection and field penetration of an externally applied rotating helical magnetic field in the TEXTOR tokamak

The magnetic field penetration process into a magnetized plasma is of basic interest both for plasma physics and astrophysics. In this context special measurements on the field penetration and field amplification are performed by a Hall probe on the dynamic ergodic divertor (DED) on the TEXTOR tokamak and the data are interpreted by a two-fluid plasma model. It is observed that the growth of the forced magnetic reconnection by the rotating DED field is accompanied by a change of the plasma fluid rotation. The differential rotation frequency between the DED field and the plasma plays an important role in the process of the excitation of tearing modes. The momentum input from the rotating DED field to the plasma is interpreted by both a ponderomotive force at the rational surface and a radial electric field modified by an edge ergodization.

Properties of geodesic acoustic modes and the relation to density fluctuations

The geodesic acoustic mode (GAM) is a high frequency branch of zonal flows, which is observed in toroidal plasmas. Because of toroidal curvature effects, density fluctuations are excited, which are investigated with the O-mode correlation reflectometer at TEXTOR. This Letter reports on the poloidal distribution of GAM induced density fluctuation and compares them with theoretical predictions. The influence of the GAM flows on the ambient turbulence is studied, too.

The ability of selected oral microorganisms to emit red fluorescence

Some novel caries detection and excavation devices rely on the ability of bacteria to produce red fluorescing compounds. The aim of this study was to examine the ability of selected oral microorganisms to emit red fluorescence. Streptococcus mutans, S. oralis, S. salivarius, S. sobrinus, Lactobacillus fermentans, L. casei, L. rhamnosus, Actinomyces naeslundi, A. israelii, Prevotella intermedia, and Fusobacterium nucleatum were inoculated onto Columbia agar with haemin and vitamin K and incubated anaerobically for up to 7 days in the dark. The resulting bacterial colonies were excited using filtered xenon light (405 +/- 20 nm) and digitally photographed through a 530-nm high-pass filter. The red and green portions of the colony fluorescence were analyzed using a computer program and the red/green ratio was calculated. All colonies emitted both red and green fluorescence. The green outweighed the red portion for the following species (in descending order) S. oralis, S. salivarius, S. mutans, F. nucleatum and S. sobrinus. The red portion was higher for the following species (in descending order) P. intermedia, A. naeslundi, A. israelii, L. fermentans, L. rhamnosus and L. casei. With all the bacteria examined, one color portion generally outweighed the other, giving the visual impression of either red or green fluorescence. We conclude that red fluorescence is well suited to detection of the bacteria which cause dentin caries but it is not suitable as an indicator of the presence and activity of the streptococci involved in initial caries.

Labeling of adult stem cells for in vivo-application in the human heart

Tissue regeneration with human hematopoietic or mesenchymal stem cells has become a fashionable research topic. In cardiology, intracoronary injection of adult stem cells has already been used for the treatment of human myocardial infarction and ischemic cardiomyopathy. The experimental background of such therapies, however, i.e. the potential of adult stem cells to regenerate myocardium through "transdifferentiation" of hematopoietic or mesenchymal stem cells into cardiomyocytes described in animal models, has recently been challenged by other experimental data. Nonetheless, clinical trials are continuing. This may be due to the fact that, in open-labeled pilot trials, a benefit of intracoronary injection of adult stem cells for the treatment of myocardial infarction has been described. As pilot trials may overemphasize the beneficial effects of intracoronary injection of bone marrow stem cells, controlled double-blinded randomised multicenter studies are warranted. Furthermore, a careful characterization of the cells involved in the proposed cardiac repair as well as in vivo-monitoring of such cells following intracoronary injection in humans might help to answer many essential questions linked to this important research topic. The latter requires biocompatible labeling. This review focuses on the technologies available for stem cell labeling and summarizes the arguments and contra-arguments to use these labeling technologies for application in humans.

Influence of the dynamic ergodic divertor on the density limit in TEXTOR

A significant influence of the dynamic ergodic divertor (DED) on the density limit in TEXTOR has been found. In Ohmic discharges, where without DED detachment normally arises at the density limit, a MARFE (multifaceted asymmetric radiation from the edge) develops when the DED is operated in a static regime. The threshold of the MARFE onset in the neutral beam heated plasmas is increased by applying 1 kHz ac DED at the high-field side. The theoretical predictions based on the parallel energy balance taking poloidal asymmetries into account agree well with the experimental observation.

Toroidal plasma rotation induced by the dynamic ergodic divertor in the TEXTOR tokamak

The first results of the Dynamic Ergodic Divertor in TEXTOR, when operating in the m/n=3/1 mode configuration, are presented. The deeply penetrating external magnetic field perturbation of this configuration increases the toroidal plasma rotation. Staying below the excitation threshold for the m/n=2/1 tearing mode, this toroidal rotation is always in the direction of the plasma current, even if the toroidal projection of the rotating magnetic field perturbation is in the opposite direction. The observed toroidal rotation direction is consistent with a radial electric field, generated by an enhanced electron transport in the ergodic layers near the resonances of the perturbation. This is an effect different from theoretical predictions, which assume a direct coupling between rotating perturbation and plasma to be the dominant effect of momentum transfer.

Operative Sanierung florider venöser Ulzera

Ziel: Die vorliegende Qualitätssicherungsstudie soll die Häufigkeit von Wundinfekten nach operativen Eingriffen wegen floridem Ulcus cruris venosum an der Abteilung Dermatologie der Universität Göttingen erfassen. Außerdem wird die präoperative Besiedlung der stationär vorbehandelten Ulzera mit pathogenen Mikroorganismen dargestellt. Methoden: 59 Patienten mit Ulcus cruris venosum wurden 95 operativen Eingriffen unterzogen (46-mal einseitig, 13-mal beidseitig; insgesamt 75 Operationen am oberflächlichen Venensystem und 20 paratibiale Fasziotomien). Allen Patienten wurde eine am präoperativen Antibiogramm orientierte perioperative antibiotische Prophylaxe (PAP) als Einmalgabe verabreicht. Ergebnisse: Präoperativ wurde auf den Ulzera am häufigsten eine Besiedlung durch Staphylococcus aureus, gefolgt von Proteus mirabilis, nachgewiesen. In 3 Fällen (5,1%) wurden Methicillin-resistente Staphylokokken gefunden. Cefazolin und Ciprofloxacin waren die häufigsten zur PAP verabreichten Antibiotika. Insgesamt beobachteten wir bei 5 von 59 Patienten (8,5%) postoperative Wundinfekte, in 3 Fällen waren die präoperativ nachgewiesenen pathogenen Keime Ursache der Wundinfektion. Schlussfolgerung: Der Prozentsatz postoperativer Wundinfekte nach Sanierung venöser Ulzera unter dem Schutz einer am präoperativen Antibiogramm orientierten PAP ist mit 8,5% vertretbar.

Dimerisation mutants of Lac repressor. I. A monomeric mutant, L251A, that binds Lac operator DNA as a dimer

Dimer formation between monomers of the Escherichia coli Lac repressor is substantially specificed by the interactions between three alpha-helices in each monomer which form a hydrophobic interface. As a first step in analysing the specificity of this interaction, we examined the mutant L251A. LacR bearing this mutation in a background lacking the C-terminal heptad repeats is completely incapable of forming dimers in solution, with a dimer-monomer equilibrium dissociation constant, or Kd, higher than 10(-5)M. This correlates with a 200-fold decrease in its ability to repress the lac operon in vivo compared to dimeric LacR. Surprisingly, the mutant is still capable of forming dimers upon binding to short operator DNA in vitro. Analysis of the kinetic parameters of binding of the mutant to operator DNA reveals a 2000 to 3000-fold increase in the equilibrium dissociation constant (Kd) of the mutant-DNA complex in comparison to dimeric LacR-operator complexes, with the change almost entirely due to a greater than 1000-fold decrease in association rate. The dissociation rate varies only by a factor of about two, in comparison to dimeric LacR. This change reflects a kinetic pathway in which dimer formation, in solution or on DNA, is the rate-limiting step. These findings have implications for the specificity and stability of the protein-protein interface in question.

Corynebacterium thomssenii sp. nov., a Corynebacterium with N-acetyl-beta-glucosaminidase activity from human clinical specimens

A strain of a previously undescribed non-lipophilic coryneform bacterium was isolated from pleural fluids of a patient with chronic renal failure, stroke and pneumonia. Slow fermentative acid production from glucose, maltose and sucrose, and strong N-acetyl-beta-glucosaminidase activity were the most characteristic features of the bacterium. Chemotaxonomic characterization unambiguously indicated that the organism belonged to the genus Corynebacterium. The results of comparative 16S rRNA gene sequence analysis revealed that the isolate represented a new species within the genus, for which the name Corynebacterium thomssenii sp. nov. is proposed. The type strain is DSM 44276.

Tsukamurella tyrosinosolvens sp. nov

Chemotaxonomic and 16S ribosomal DNA sequence analyses of four bacterial isolates from blood cultures from patients with cardiac pacemaker implants and sputa of patients with chronic lung infections clearly demonstrated that these bacteria belong to the genus Tsukamurella. DNA-DNA hybridization data, as well as the physiological characteristics of the isolates, indicate that they are closely related and belong to a single species that differs from previously described members of the genus Tsukamurella. The name Tsukamurella tyrosinosolvens sp. nov. is proposed for these isolates, and the new species is represented by strain IMMIB D-1397T (= DSM 44234T). Strain IMMIB D-1397T exhibits 53.4, 53.5, and 54.7% DNA-DNA relatedness to Tsukamurella paurometabola DSM 20162T, Tsukamurella inchonensis DSM 44067T, and Tsukamurella pulmonis DSM 44142T, respectively.

Chlamydial antibodies in semen: search for "silent" chlamydial infections in asymptomatic andrological patients

The importance of a serological diagnostic workup in male genitourinary infections with Chlamydia trachomatis and its relevance for male infertility is still under debate. In a prospective study, antichlamydial serum and seminal plasma antibodies of 131 consecutive patients (mean age 31: 20-57) without evidence of acute urethritis and with negative urethral chlamydial culture were investigated. The antibody determination was carried out with a genus specific rELISA. In patients with positive seminal plasma IgA, chlamydial genome was evaluated by polymerase chain reaction (PCR). The results were associated with standard semen parameters according to evaluated WHO guidelines. Specific serum IgG antibodies were found in 51 patients (38.9%), IgA in 39 (29.7%); both antibodies were present in 25 patients (19%). Seminal plasma IgG was demonstrable in seven patients (5.3%), IgA in 26 (19.9%), and five patients were positive for both antibody classes (3.8%). Of the 26 men positive for specific seminal plasma IgA antibodies 12 did not demonstrate a serum antibody reaction. Only two patients with positive IgA titers in their seminal plasma showed a positive chlamydial genome reaction in PCR (8%). Men with antichlamydial seminal plasma IgA and/or IgG did not differ significantly in any of the standard semen sperm parameters from men testing negative for antibodies, with the exception of peroxidase positive leukocytes (p < 0.01), nor was there an association between any of the ejaculate parameters and any of the antibody titers. The data of about 40% antichlamydial serum antibody findings without a significant association with seminal plasma antibodies and no clinical signs of infection seem to reflect a history of urogenital infection. The unique presence of seminal plasma IgA in 12 of 26 cases may be caused by a local antibody response due to a "silent" infection. Thus, seminal plasma IgA was associated with signs of inflammation, whereas, there was no association with genome or pathogen demonstration. Therefore, it appears to be necessary to reevaluate genus-specific seminal plasma IgA antibodies with a species-specific microimmunofluorescence test and to compare these results with a genome screening using PCR or in situ hybridization.

Stability of genomic DNA fragment patterns in methicillin resistant Staphylococcus aureus (MRSA) during the course of intra- and interhospital spread

The analysis of genomic DNA fragment patterns has revealed as a powerful tool for strain discrimination in Staphylococcus aureus; for use as an epidemiological marker, stability during the course of an outbreak is an essential prerequisite. Genomic DNA fragment patterns (SmaI restriction, pulsed-field electrophoresis) of four different epidemic MRSA strains were compared along with intra- and interhospital and country-wide spread over more than 12 months in Germany. Strain I was isolated from infections in 8 hospitals. In one hospital a subclone arised which differed from the original strain by 4 fragments. Strain II was spread among 4 hospitals, isolates from three of these hospitals exhibited a variability of one to three fragments in the 150-200 kb range. Two hospitals in the Hannover-area were affected by strain III; in 17 isolates of this strain a variability up to three fragments was found in the 170-200 kb range. Strain IV was isolated from 19 cases of infections in 3 hospitals in Berlin. The fragment patterns were completely stable. When S. aureus strains are typed by genomic DNA fragment patterns, a variability in a definite range of molecular masses during the course of an epidemic should be taken into consideration.

Transrectal prostatic sonography as a useful diagnostic means for patients with chronic prostatitis or prostatodynia

OBJECTIVE

To evaluate the sonographic changes that occur in patients with chronic prostatitis and compare them with those of non-inflammatory prostatodynia using transrectal prostatic sonography (TPS).

PATIENTS AND METHODS

In a prospective study, TPS findings were analysed in 88 men with chronic prostatitis and 53 patients with prostatodynia, all of whom had undergone a standardized diagnostic procedure to detect inflammation.

RESULTS

A statistically significant accumulation of prostatic calcifications and unilateral seminal gland alterations was demonstrated in patients with chronic inflammation. Nevertheless, both findings were also present in patients with prostatodynia (22% and 11%, respectively).

CONCLUSION

TPS is widely recommended for differential diagnosis in cases of chronic prostatitis and prostatodynia. Prostatic calcifications and seminal vesical abnormalities are regarded as typical signs of inflammation. The results of this study show that these sonographic abnormalities are indicative but do not prove the presence of chronic prostatitis.

[Diphtheria--isolation of an endemic Corynebacterium diphtheriae strain in Southern Lower Saxony]

After decades of only limited epidemiological and clinical importance diphtheria (especially of the upper respiratory tract) is regaining increasing interest of public health officials, as recent case reports in national and international publications clearly demonstrate. In March 1993 we observed a case of tracheobronchial Corynebacterium diphtheriae mitis infection in a 66-year old man from the South of Lower Saxony with clinical presentation of mucopurolent exacerbation of chronic bronchitis. The C. diphtheriae mitis strain was identified by microbiological and biochemical tests; however, its expression of toxin remains scientifically controversial. Investigations by the local public health officer suggest an endemic strain of C. diphtheriae. In this paper case report and results of investigations by the local public health officer are described in detail, stressing the need for widespread preventive inoculation not only in the younger but especially in the elderly population.

Candida tropicalis endophthalmitis following penetrating keratoplasty

A case of Candida tropicalis endophthalmitis following penetrating keratoplasty is presented. The donor was an alcoholic, who died of bronchopneumonia and pancreatitis. We presume the candida infection was transmitted by the donor because Candida tropicalis was cultured in life from the donor's throat swab and corresponding fungal elements were discovered post mortem in kidney sections of the donor.

[Bacterial flora of the eyelids following preoperative disinfection]

After careful preoperative disinfection of the periorbita, the eye, and the lids, cultures were taken from the upper and lower lash bases of 100 patients waiting for intraocular operations. Despite the careful disinfection 36% of the cultures from the upper and 48% of those from the lower lash bases were positive. A method of covering the lids adequately with adhesive material is recommended as a means of avoiding this potential source of infection.