Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains

There are many reports of ancient DNA from bacteria of the Mycobacterium tuberculosis complex (MTBC) being present in skeletons with and without osteological indications of tuberculosis. A possible complication in these studies is that extracts might also contain DNA from the microbiome of the individual whose remains are being analysed and/or from environmental bacteria that have colonised the skeleton after death. These contaminants might include ‘mycobacteria other than tuberculosis’ (MOTT), which are common in the environment, but which are not normally associated with clinical cases of tuberculosis. In this paper we show that MOTT of various types, as well as bacteria of related genera, are present in most if not all archaeological remains. Our results emphasise the complications inherent in the biomolecular study of archaeological human tuberculosis. The specificity of any polymerase chain reaction directed at the MTBC cannot be assumed and, to confirm that an amplification is authentic, a sequencing strategy must be applied that allows characterisation of the PCR product. Any variations from the reference MTBC sequence must then be checked against sequence data for MOTT and other species to ensure that the product does actually derive from MTBC. Our results also illustrate the challenges faced when assembling MTBC genome sequences from ancient DNA samples, as misidentification of MOTT sequence reads as MTBC would lead to errors in the assembly. Identifying such errors would be particularly difficult, if not impossible, if the MOTT DNA content is greater than that of the authentic MTBC. The difficulty in identifying and excluding MOTT sequences is exacerbated by the fact that many MOTT are still uncharacterized and hence their sequence features are unknown

Berg adder (Bitis atropos): An unusual case of acute poisoning

A 5-year-old boy presented to hospital with mild local cytotoxic and severe neurotoxic symptoms. The neurotoxic symptoms included ptosis, fixed dilated pupils and flaccid paralysis with respiratory failure. Mild hyponatraemia was also a clinical feature. After various unsuccessful treatment options were followed, the Tygerberg Poison Information Centre was contacted and a diagnosis of berg adder bite was made. Berg adder bites are uncommon and therefore not usually considered in the differential diagnosis of a patient presenting with an unexplained clinical picture. A timeous poison information helpline consultation is recommended in this situation

Light transport in cold atoms: the fate of coherent backscattering in the weak localization regime

The recent observation of coherent backscattering (CBS) of light by atoms has emphasized the key role of the velocity spread and of the quantum internal structure of the atoms. Firstly, using highly resonant scatterers imposes very low temperatures of the disordered medium in order to keep the full contrast of the CBS interference. This criterion is usually achieved with standard laser cooling techniques. Secondly, a non trivial internal atomic structure leads to a dramatic decrease of the CBS contrast. Experiments with Rubidium atoms (with a non trivial internal structure) and with Strontium (with the simplest possible internal structure) show this behaviour and confirm theoretical calculations

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

5-Formylcytosine (5fC) is a chemically edited, naturally occurring nucleobase which appears in the context of modified DNA strands. The understanding of the impact of 5fC on dsDNA physical properties is to date limited. In this work, we applied temperature-dependent 1H Chemical Exchange Saturation Transfer (CEST) NMR experiments to non-invasively and site-specifically measure the thermodynamic and kinetic influence of formylated cytosine nucleobase on the melting process involving dsDNA. Incorporation of 5fC within symmetrically positioned CpG sites destabilizes the whole dsDNA structure—as witnessed from the ∼2°C decrease in the melting temperature and 5–10 kJ mol−1 decrease in ΔG°—and affects the kinetic rates of association and dissociation. We observed an up to ∼5-fold enhancement of the dsDNA dissociation and an up to ∼3-fold reduction in ssDNA association rate constants, over multiple temperatures and for several proton reporters. Eyring and van’t Hoff analysis proved that the destabilization is not localized, instead all base-pairs are affected and the transition states resembles the single-stranded conformation. These results advance our knowledge about the role of 5fC as a semi-permanent epigenetic modification and assist in the understanding of its interactions with reader proteins

Diffusive spin transport

Information to be stored and transported requires physical carriers. The quantum bit of information (qubit) can for instance be realised as the spin 1/2 degree of freedom of a massive particle like an electron or as the spin 1 polarisation of a massless photon. In this lecture, I first use irreducible representations of the rotation group to characterise the spin dynamics in a least redundant manner. Specifically, I describe the decoherence dynamics of an arbitrary spin S coupled to a randomly fluctuating magnetic field in the Liouville space formalism. Secondly, I discuss the diffusive dynamics of the particle's position in space due to the presence of randomly placed impurities. Combining these two dynamics yields a coherent, unified picture of diffusive spin transport, as applicable to mesoscopic electronic devices or photons propagating in cold atomic clouds.Comment: Lecture notes, published in A. Buchleitner, C. Viviescas, and M. Tiersch (Eds.), "Entanglement and Decoherence. Foundations and Modern Trends", Lecture Notes in Physics 768, Springer, Berlin (2009

Deciphering the properties of the medium produced in heavy ion collisions at RHIC by a pQCD analysis of quenched large p⊥p_{\perp} π0\pi^0 spectra

We discuss the question of the relevance of perturbative QCD calculations for analyzing the properties of the dense medium produced in heavy ion collisions. Up to now leading order perturbative estimates have been worked out and confronted with data for quenched large $p_{\perp}$ hadron spectra. Some of them are giving paradoxical results, contradicting the perturbative framework and leading to speculations such as the formation of a strongly interacting quark-gluon plasma. Trying to bypass some drawbacks of these leading order analysis and without performing detailed numerical investigations, we collect evidence in favour of a consistent description of quenching and of the characteristics of the produced medium within the pQCD framework.Comment: 10 pages, 3 figure

Two- and Three-photon Fusion in Relativistic Heavy ion Collisions

The production of mesons in ultra-peripheral collisions of relativistic heavy ions is re-analyzed using a projection technique to calculate the amplitudes for the appropriate Feynman diagrams. The virtuality of the exchanged photons is fully accounted for in this approach. In the case of two-photon fusion, it is explicitly shown that the inclusion of nuclear form factors validates the equivalent photon approximation. However, this does not apply to three-photon fusion cross sections. The cross section of J/\psi production in ultra-peripheral collisions at RHIC and LHC are shown to be much smaller than the cross sections for the production of C=even mesons of similar masses.Comment: Version to be published in Nuclear Physics

Thermodynamics of non-local materials: extra fluxes and internal powers

The most usual formulation of the Laws of Thermodynamics turns out to be suitable for local or simple materials, while for non-local systems there are two different ways: either modify this usual formulation by introducing suitable extra fluxes or express the Laws of Thermodynamics in terms of internal powers directly, as we propose in this paper. The first choice is subject to the criticism that the vector fluxes must be introduced a posteriori in order to obtain the compatibility with the Laws of Thermodynamics. On the contrary, the formulation in terms of internal powers is more general, because it is a priori defined on the basis of the constitutive equations. Besides it allows to highlight, without ambiguity, the contribution of the internal powers in the variation of the thermodynamic potentials. Finally, in this paper, we consider some examples of non-local materials and derive the proper expressions of their internal powers from the power balance laws.Comment: 16 pages, in press on Continuum Mechanics and Thermodynamic

Two-Hole and Four-Hole Bound States in a t-J Ladder at half-filling

The two-hole excitation spectrum of the t-J ladder at half-filling is studied using linked-cluster series expansion methods. A rich spectrum of bound states emerges, particularly at small $t/J$. Their dispersion relations and coherence lengths are computed, along with the threshold behaviour as the bound states merge into the continuum. A class of 4-hole bound states is also studied, leading to the conclusion that phase separation occurs for $t/J \lesssim 0.5$, in agreement with other studies.Comment: revtex

η\eta Production in Peripheral Heavy-Ion Collisions

We estimate the impact parameter dependence of the production cross section for $\eta_c$ and $\eta_b$ mesons in peripheral heavy-ion collisions collisions. Total and elastic $\gamma\gamma$ cross sections are calculated in an equivalent photon approximation.Comment: 9 pages, uuencoded postscrip