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.

Constraints on the effective fluid theory of stationary branes

We develop further the effective fluid theory of stationary branes. This formalism applies to stationary blackfolds as well as to other equilibrium brane systems at finite temperature. The effective theory is described by a Lagrangian containing the information about the elastic dynamics of the brane embedding as well as the hydrodynamics of the effective fluid living on the brane. The Lagrangian is corrected order-by-order in a derivative expansion, where we take into account the dipole moment of the brane which encompasses finite-thickness corrections, including transverse spin. We describe how to extract the thermodynamics from the Lagrangian and we obtain constraints on the higher-derivative terms with one and two derivatives. These constraints follow by comparing the brane thermodynamics with the conserved currents associated with background Killing vector fields. In particular, we fix uniquely the one- and two-derivative terms describing the coupling of the transverse spin to the background space-time. Finally, we apply our formalism to two blackfold examples, the black tori and charged black rings and compare the latter to a numerically generated solution.

Low-energy constraints to αs

We briefly review some of the lower-energy constraints to the perturbative behaviour of the strong coupling αs, with some emphasis on the determination coming from the energy between two static sources calculated on the lattice.

New Constraints on Dark Matter Effective Theories from Standard Model Loops

We consider an effective field theory for a gauge singlet Dirac dark matter particle interacting with the standard model fields via effective operators suppressed by the scale Λ≳1  TeV. We perform a systematic analysis of the leading loop contributions to spin-independent Dirac dark matter–nucleon scattering using renormalization group evolution between Λ and the low-energy scale probed by direct detection experiments. We find that electroweak interactions induce operator mixings such that operators that are naively velocity suppressed and spin dependent can actually contribute to spin-independent scattering. This allows us to put novel constraints on Wilson coefficients that were so far poorly bounded by direct detection. Constraints from current searches are already significantly stronger than LHC bounds, and will improve in the near future. Interestingly, the loop contribution we find is isospin violating even if the underlying theory is isospin conserving.

Isotopic constraints on marine and terrestrial N2O emissions during the last deglaciation

Nitrous oxide (N2O) is an important greenhouse gas and ozone-depleting substance that has anthropogenic as well as natural marine and terrestrial sources. The tropospheric N2O concentrations have varied substantially in the past in concert with changing climate on glacial–interglacial and millennial timescales. It is not well understood, however, how N2O emissions from marine and terrestrial sources change in response to varying environmental conditions. The distinct isotopic compositions of marine and terrestrial N2O sources can help disentangle the relative changes in marine and terrestrial N2O emissions during past climate variations. Here we present N2O concentration and isotopic data for the last deglaciation, from 16,000 to 10,000 years before present, retrieved from air bubbles trapped in polar ice at Taylor Glacier, Antarctica. With the help of our data and a box model of the N2O cycle, we find a 30 per cent increase in total N2O emissions from the late glacial to the interglacial, with terrestrial and marine emissions contributing equally to the overall increase and generally evolving in parallel over the last deglaciation, even though there is no a priori connection between the drivers of the two sources. However, we find that terrestrial emissions dominated on centennial timescales, consistent with a state-of-the-art dynamic global vegetation and land surface process model that suggests that during the last deglaciation emission changes were strongly influenced by temperature and precipitation patterns over land surfaces. The results improve our understanding of the drivers of natural N2O emissions and are consistent with the idea that natural N2O emissions will probably increase in response to anthropogenic warming.

A feasible theory of truth over combinatory algebra

We define an applicative theory of truth TPT which proves totality exactly for the polynomial time computable functions. TPT has natural and simple axioms since nearly all its truth axioms are standard for truth theories over an applicative framework. The only exception is the axiom dealing with the word predicate. The truth predicate can only reflect elementhood in the words for terms that have smaller length than a given word. This makes it possible to achieve the very low proof-theoretic strength. Truth induction can be allowed without any constraints. For these reasons the system TPT has the high expressive power one expects from truth theories. It allows embeddings of feasible systems of explicit mathematics and bounded arithmetic. The proof that the theory TPT is feasible is not easy. It is not possible to apply a standard realisation approach. For this reason we develop a new realisation approach whose realisation functions work on directed acyclic graphs. In this way, we can express and manipulate realisation information more efficiently.

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.

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.

The effect of superiors' exogenous constraints on budget negotiations

In a world characterized by increasing pressure from financial and product markets, the question of how exogenous constraints affect internal coordination and control processes has become increasingly important. This experiment investigates how two exogenous constraints that superiors can face in budget negotiation settings, increased opportunity costs and financial pressure to meet unit targets, affect budget negotiations and subordinate effort. The results show that both constraints induce more cooperation, but in different ways. Financial pressure on the superior leads to more cooperative negotiation behavior by superiors and subordinates than increased opportunity costs. Specifically, subordinates do not take advantage of the superior's increased financial pressure to enforce lower budgets. After negotiation, both constraints strongly mitigate the negative effects of superior budget imposition on subordinate effort because exogenous constraints eliminate the effect of procedural fairness considerations on subordinate effort.

Ice core-based isotopic constraints on past carbon cycle changes

High-precision ice core data on both atmospheric CO2 concentrations and their carbon isotopic composition (δ13Catm) provide improved constraints on the marine and terrestrial processes responsible for carbon cycle changes during the last two interglacials and the preceding glacial/interglacial transitions.

cDNA Library Generation for the Analysis of Small RNAs by High-Throughput Sequencing

The RNome of a cell is highly diverse and consists besides messenger RNAs (mRNAs), transfer RNAs (tRNAs), and ribosomal RNAs (rRNAs) also of other small and long transcript entities without apparent coding potential. This class of molecules, commonly referred to as non-protein-coding RNAs (ncRNAs), is involved in regulating numerous biological processes and thought to contribute to cellular complexity. Therefore, much effort is put into their identification and further functional characterization. Here we provide a cost-effective and reliable method for cDNA library construction of small RNAs in the size range of 20-500 residues. The effectiveness of the described method is demonstrated by the analysis of ribosome-associated small RNAs in the eukaryotic model organism Trypanosoma brucei.

Age of cleft monazites in the eastern Tauern Window: constraints on crystallization conditions of hydrothermal monazite

Monazite-bearing Alpine clefts located in the Sonnblick region of the eastern Tauern Window, Austria, are oriented perpendicular to the foliation and lineation. Ion probe (SIMS) Th–Pb and U–Pb dating of four cleft monazites yields crystallization ages of different growth domains and aggregate regions ranging from 18.99 ± 0.51 to 15.00 ± 0.51 Ma. The crystallization ages obtained are overlapping or slightly younger than zircon fission track ages but older than zircon (U–Th)/He cooling ages from the same area. This constrains cleft monazite crystallization in this area to *300–200 �C. LA-ICP-MS data of dated hydrothermal monazites indicate that in graphite-bearing, reduced host lithologies, cleft monazite is poor in As and has higher La/Yb values and U concentrations, whereas in oxidised host rocks opposite trends are observed. Monazites show negative Eu anomalies and variable La/Yb values ranging from 520 to 6050. The positive correlation between Ca and Sr concentration indicates dissolution of plagioclase or carbonates as the source of these elements. The data show that early exhumation and cleft formation in the Tauern is related to metamorphic dome formation caused by the collision of the Adriatic with the European plate and that monazite crystallization in the clefts occurred later. Our data also demonstrate that hydrothermal monazite ages offer great potential in helping to constrain the chronology of exhumation in collisional orogens.