Tracking a tuberculosis outbreak over 21 years: strain-specific single nucleotide polymorphism-typing combined with targeted whole genome sequencing.

BACKGROUND  Whole genome sequencing (WGS) is increasingly used in molecular-epidemiological investigations of bacterial pathogens, despite cost- and time-intensive analyses. We combined strain-specific single nucleotide polymorphism (SNP)-typing and targeted WGS to investigate a tuberculosis cluster spanning 21 years in Bern, Switzerland. METHODS  Based on genome sequences of three historical outbreak Mycobacterium tuberculosis isolates, we developed a strain-specific SNP-typing assay to identify further cases. We screened 1,642 patient isolates, and performed WGS on all identified cluster isolates. We extracted SNPs to construct genomic networks. Clinical and social data were retrospectively collected. RESULTS  We identified 68 patients associated with the outbreak strain. Most were diagnosed in 1991-1995, but cases were observed until 2011. Two thirds belonged to the homeless and substance abuser milieu. Targeted WGS revealed 133 variable SNP positions among outbreak isolates. Genomic network analyses suggested a single origin of the outbreak, with subsequent division into three sub-clusters. Isolates from patients with confirmed epidemiological links differed by 0-11 SNPs. CONCLUSIONS  Strain-specific SNP-genotyping allowed rapid and inexpensive identification of M. tuberculosis outbreak isolates in a population-based strain collection. Subsequent targeted WGS provided detailed insights into transmission dynamics. This combined approach could be applied to track bacterial pathogens in real-time and at high resolution.

Lake Van deep drilling project PALEOVAN

A complete succession of the lacustrine sediment sequence deposited during the last ∼600,000 years in Lake Van, Eastern Anatolia (Turkey) was drilled in 2010 supported by the International Continental Scientific Drilling Program (ICDP). Based on a detailed seismic site survey, two sites at a water depth of up to 360 m were drilled in summer 2010, and cores were retrieved from sub-lake-floor depths of 140 m (Northern Basin) and 220 m (Ahlat Ridge). To obtain a complete sedimentary section, the two sites were multiple cored in order to investigate the paleoclimate history of a sensitive semi-arid region between the Black, Caspian, and Mediterranean seas. This introductory paper provides background information of the deep drilling project and an overview of the studies presented in this special volume by the PALEOVAN science team dealing with chronology, paleomagnetism, paleoenvironmental proxies, geophysical and petrophysical investigations as well as pore-water and fluid transport.

Stability and relapse after orthodontic treatment of deep bite cases-a long-term follow-up study.

The purpose of this long-term follow-up study was twofold-firstly, to assess prevalence of relapse after treatment of deep bite malocclusion and secondly, to identify risk factors that predispose patients with deep bite malocclusion to relapse. Sixty-one former patients with overbite more than 50% incisor overlap before treatment were successfully recalled. Clinical data, morphometrical measurements on plaster casts before treatment, after treatment and at long-term follow-up, as well as cephalometric measurements before and after treatment were collected. The median follow-up period was 11.9 years. Patients were treated by various treatment modalities, and the majority of patients received at least a lower fixed retainer and an upper removable bite plate during retention. Relapse was defined as increase in incisor overlap from below 50% after treatment to equal or more than 50% incisor overlap at long-term follow-up. Ten per cent of the patients showed relapse to equal or larger than 50% incisor overlap, and their amount of overbite increase was low. Among all cases with deep bite at follow-up, gingival contact and palatal impingement were more prevalent in partially corrected noncompliant cases than in relapse cases. In this sample, prevalence and amount of relapse were too low to identify risk factors of relapse.

Classes of multichannel EEG microstates in light and deep hypnotic conditions

The study assessed the brain electric mechanisms of light and deep hypnotic conditions in the framework of EEG temporal microstates. Multichannel EEG of healthy volunteers during initial resting, light hypnosis, deep hypnosis, and eventual recovery was analyzed into temporal EEG microstates of four classes. Microstates are defined by the spatial configuration of their potential distribution maps ([Symbol: see text]potential landscapes') on the head surface. Because different potential landscapes must have been generated by different active neural assemblies, it is reasonable to assume that they also incorporate different brain functions. The observed four microstate classes were very similar to the four standard microstate classes A, B, C, D [Koenig, T. et al. Neuroimage, 2002;16: 41-8] and were labeled correspondingly. We expected a progression of microstate characteristics from initial resting to light to deep hypnosis. But, all three microstate parameters (duration, occurrence/second and %time coverage) yielded values for initial resting and final recovery that were between those of the two hypnotic conditions of light and deep hypnosis. Microstates of the classes B and D showed decreased duration, occurrence/second and %time coverage in deep hypnosis compared to light hypnosis; this was contrary to microstates of classes A and C which showed increased values of all three parameters. Reviewing the available information about microstates in other conditions, the changes from resting to light hypnosis in certain respects are reminiscent of changes to meditation states, and changes to deep hypnosis of those in schizophrenic states.

Projected pH reductions by 2100 might put deep North Atlantic biodiversity at risk

This study aims to evaluate the potential for impacts of ocean acidification on North Atlantic deep-sea ecosystems in response to IPCC AR5 Representative Concentration Pathways (RCPs). Deep-sea biota is likely highly vulnerable to changes in seawater chemistry and sensitive to moderate excursions in pH. Here we show, from seven fully coupled Earth system models, that for three out of four RCPs over 17% of the seafloor area below 500 m depth in the North Atlantic sector will experience pH reductions exceeding −0.2 units by 2100. Increased stratification in response to climate change partially alleviates the impact of ocean acidification on deep benthic environments. We report on major pH reductions over the deep North Atlantic seafloor (depth >500 m) and at important deep-sea features, such as seamounts and canyons. By 2100, and under the high CO2 scenario RCP8.5, pH reductions exceeding −0.2 (−0.3) units are projected in close to 23% (~15%) of North Atlantic deep-sea canyons and ~8% (3%) of seamounts – including seamounts proposed as sites of marine protected areas. The spatial pattern of impacts reflects the depth of the pH perturbation and does not scale linearly with atmospheric CO2 concentration. Impacts may cause negative changes of the same magnitude or exceeding the current target of 10% of preservation of marine biomes set by the convention on biological diversity, implying that ocean acidification may offset benefits from conservation/management strategies relying on the regulation of resource exploitation.

Highlights in Analytical Chemistry in Switzerland: OMA & OPA - A Software Tool for Mass Spectrometric Sequencing of Nucleic Acids

Oligonucleotides comprising unnatural building blocks, which interfere with the translation machinery, have gained increased attention for the treatment of gene-related diseases (e.g. antisense, RNAi). Due to structural modifications, synthetic oligonucleotides exhibit increased biostability and bioavailability upon administration. Consequently, classical enzyme-based sequencing methods are not applicable to their sequence elucidation and verification. Tandem mass spectrometry is the method of choice for performing such tasks, since gas-phase dissociation is not restricted to natural nucleic acids. However, tandem mass spectrometric analysis can generate product ion spectra of tremendous complexity, as the number of possible fragments grows rapidly with increasing sequence length. The fact that structural modifications affect the dissociation pathways greatly increases the variety of analytically valuable fragment ions. The gas-phase dissociation of oligonucleotides is characterized by the cleavage of one of the four bonds along the phosphodiester chain, by the accompanying loss of nucleases, and by the generation of internal fragments due to secondary backbone cleavage. For example, an 18-mer oligonucleotide yields a total number of 272’920 theoretical fragment ions. In contrast to the processing of peptide product ion spectra, which nowadays is highly automated, there is a lack of tools assisting the interpretation of oligonucleotide data. The existing web-based and stand-alone software applications are primarily designed for the sequence analysis of natural nucleic acids, but do not account for chemical modifications and adducts. Consequently, we developed a software to support the interpretation of mass spectrometric data of natural and modified nucleic acids and their adducts with chemotherapeutic agents.

The VEINES-QOL/Sym questionnaire is a reliable and valid disease-specific quality of life measure for deep vein thrombosis in elderly patients.

PURPOSE To prospectively evaluate the psychometric properties of the Venous Insufficiency Epidemiological and Economic Study (VEINES-QOL/Sym) questionnaire, an instrument to measure disease-specific quality of life and symptoms in elderly patients with deep vein thrombosis (DVT), and to validate a German version of the questionnaire. METHODS In a prospective multicenter cohort study of patients aged ≥ 65 years with acute venous thromboembolism, we used standard psychometric tests and criteria to evaluate the reliability, validity, and responsiveness of the VEINES-QOL/Sym in patients with acute symptomatic DVT. We also performed an exploratory factor analysis. RESULTS Overall, 352 French- and German-speaking patients were enrolled (response rate of 87 %). Both language versions of the VEINES-QOL/Sym showed good acceptability (missing data, floor and ceiling effects), reliability (internal consistency, item-total and inter-item correlations), validity (convergent, discriminant, known-groups differences), and responsiveness to clinical change over time in elderly patients with DVT. The exploratory factor analysis of the VEINES-QOL/Sym suggested three underlying dimensions: limitations in daily activities, DVT-related symptoms, and psychological impact. CONCLUSIONS The VEINES-QOL/Sym questionnaire is a practical, reliable, valid, and responsive instrument to measure quality of life and symptoms in elderly patients with DVT and can be used with confidence in prospective studies to measure outcomes in such patients.

Continental degassing of 4He by surficial discharge of deep groundwater

Radiogenic He is produced by the decay of uranium and thorium in the Earth’s mantle and crust. From here, it is degassed to the atmosphere and eventually escapes to space. Assuming that all of the 4He produced is degassed, about 70% of the total He degassed from Earth comes from the continental crust. However, the outgoing flux of crustal He has not been directly measured at the Earth’s surface and the migration pathways are poorly understood. Here we present measurements of helium isotopes and the long-lived cosmogenic radio-isotope Kr in the deep, continental-scale Guarani aquifer in Brazil and show that crustal He reaches the atmosphere primarily by the surficial discharge of deep groundwater. We estimate that He in Guarani groundwater discharge accounts for about 20% of the assumed global flux from continental crust, and that other large aquifers may account for about 33%. Old groundwater ages suggest that He in the Guarani aquifer accumulates over half- to one-millionyear timescales. We conclude that He degassing from the continents is regulated by groundwater discharge, rather than episodic tectonic events, and suggest that the assumed steady state between crustal production and degassing of He, and its resulting atmospheric residence time, should be re-examined.

Cloning, sequencing and partial functional characterization of the 5' region of the human p75 tumor necrosis factor receptor-encoding gene (TNF-R)

A 1887-bp region at the 5' flank of the human p75 tumor necrosis factor receptor (p75 TNF-R)-encoding gene was found to be active in driving expression of the luc (luciferase-encoding) reporter gene, suggesting that it contains the promoter for the receptor. Rather unexpectedly, a 1827-bp region at the 3' end of the first intron of the p75 TNF-R gene also displayed promoter activity. This activity may be artefactual, reflecting only the presence of an enhancer in this region; yet it also raises the possibility that p75 TNF-R is controlled by more than one promoter and that it encodes various forms of the receptor, or even other proteins. We present here the nucleotide sequences of the 5' flanking and intron regions. Possible implications for the transcriptional regulation of the p75 TNF-R gene are discussed.

Ultrasound-assisted versus conventional catheter-directed thrombolysis for acute iliofemoral deep vein thrombosis

BACKGROUND For patients with acute iliofemoral deep vein thrombosis, it remains unclear whether the addition of intravascular high-frequency, low-power ultrasound energy facilitates the resolution of thrombosis during catheter-directed thrombolysis. METHODS AND RESULTS In a controlled clinical trial, 48 patients (mean age 50±21 years, 52% women) with acute iliofemoral deep vein thrombosis were randomized to receive ultrasound-assisted catheter-directed thrombolysis (N=24) or conventional catheter-directed thrombolysis (N=24). Thrombolysis regimen (20 mg r-tPA over 15 hours) was identical in all patients. The primary efficacy end point was the percentage of thrombus load reduction from baseline to 15 hours according to the length-adjusted thrombus score, obtained from standardized venograms and evaluated by a core laboratory blinded to group assignment. The percentage of thrombus load reduction was 55%±27% in the ultrasound-assisted catheter-directed thrombolysis group and 54%±27% in the conventional catheter-directed thrombolysis group (P=0.91). Adjunctive angioplasty and stenting was performed in 19 (80%) patients and in 20 (83%) patients, respectively (P>0.99). Treatment-related complications occurred in 3 (12%) and 2 (8%) patients, respectively (P>0.99). At 3-month follow-up, primary venous patency was 100% in the ultrasound-assisted catheter-directed thrombolysis group and 96% in the conventional catheter-directed thrombolysis group (P=0.33), and there was no difference in the severity of the post-thrombotic syndrome (mean Villalta score: 3.0±3.9 [range 0-15] versus 1.9±1.9 [range 0-7]; P=0.21), respectively. CONCLUSIONS In this randomized controlled clinical trial of patients with acute iliofemoral deep vein thrombosis treated with a fixed-dose catheter thrombolysis regimen, the addition of intravascular ultrasound did not facilitate thrombus resolution. CLINICAL TRIAL REGISTRATION URL http://www.clinicaltrials.gov. Unique identifier: NCT01482273.