Molecular biological methods for studying the gut microbiota : the EU human gut flora project

Seven European laboratories co-operated in a joint project (FAIR CT97-3035) to develop, refine and apply molecular methods towards facilitating elucidation of the complex composition of the human intestinal microflora and to devise robust methodologies for monitoring the gut flora in response to diet. An extensive database of 16S rRNA sequences for tracking intestinal bacteria was generated by sequencing the 16S rRNA genes of new faecal isolates and of clones obtained by amplification with polymerase chain reaction (PCR) on faecal DNA from subjects belonging to different age groups. The analyses indicated that the number of different species (diversity) present in the human gut increased with age. The sequence information generated, provided the basis for design of 16S rRNA-directed oligonucleotide probes to specifically detect bacteria at various levels of phylogenetic hierarchy. The probes were tested for their specificity and used in whole-cell and dot-blot hybridisations. The applicability of the developed methods was demonstrated in several studies and the major outcomes are described

Equation of state measurements of D2 on Nova

In this paper we describe principle Hugoniot measurements of liquid D{sub 2} up to P = 2.1 Mbar. We compressed liquid D{sub 2} with a Nova-laser-driven shock wave launched from an aluminum pusher. The Al/D{sub 2} interface and the shock front in the D{sub 2} are observed with temporally resolved radiography, to determine particle speed U{sub p}, shock speed U{sub s}, and the ratio of final density to initial density {rho}/{rho}{sub 0}. The pressure is calculated. These absolute EOS data reveal a compressibility comparable to the dissociation model

Characterization of ovine strains of Mycobacterium paratuberculosis by restriction endonuclease analysis and DNA hybridization

Restriction endonuclease analysis and DNA hybridization revealed five ovine strains of Mycobacterium paratuberculosis from South Africa had identical DNA patterns to an ovine strain from Canada. Genetically this strain type has features in common with the two major groups of M. paratuberculosis.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat XI Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.mn201

Variable expression and silencing of CRISPR-Cas9 targeted transgenes identifies the AAVS1 locus as not an entirely safe harbour

Background: Diseases such as hypertrophic cardiomyopathy (HCM) can lead to severe outcomes including sudden death. The generation of human induced pluripotent stem cell (hiPSC) reporter lines can be useful for disease modelling and drug screening by providing physiologically relevant in vitro models of disease. The AAVS1 locus is cited as a safe harbour that is permissive for stable transgene expression, and hence is favoured for creating gene targeted reporter lines.Methods: We generated hiPSC reporters using a plasmid-based CRISPR/Cas9 nickase strategy. The first intron of PPP1R12C, the AAVS1 locus, was targeted with constructs expressing a genetically encoded calcium indicator (R-GECO1.0) or HOXA9-T2A-mScarlet reporter under the control of a pCAG or inducible pTRE promoter, respectively. Transgene expression was compared between clones before, during and/or after directed differentiation to mesodermal lineages.Results: Successful targeting to AAVS1 was confirmed by PCR and sequencing. Of 24 hiPSC clones targeted with pCAG-R-GECO1.0, only 20 expressed the transgene and in these, the percentage of positive cells ranged from 0% to 99.5%. Differentiation of a subset of clones produced cardiomyocytes, wherein the percentage of cells positive for R-GECO1.0 ranged from 2.1% to 93.1%. In the highest expressing R-GECO1.0 clones, transgene silencing occurred during cardiomyocyte differentiation causing a decrease in expression from 98.93% to 1.3%. In HOXA9-T2A-mScarlet hiPSC reporter lines directed towards mesoderm lineages, doxycycline induced a peak in transgene expression after two days but this reduced by up to ten-thousand-fold over the next 8-10 days. Nevertheless, for R-GECO1.0 lines differentiated into cardiomyocytes, transgene expression was rescued by continuous puromycin drug selection, which allowed the Ca2+ responses associated with HCM to be investigated in vitro using single cell analysis.Conclusions: Targeted knock-ins to AAVS1 can be used to create reporter lines but variability between clones and transgene silencing requires careful attention by researchers seeking robust reporter gene expression

(In)finite extent of stationary perfect fluids in Newtonian theory

For stationary, barotropic fluids in Newtonian gravity we give simple criteria on the equation of state and the "law of motion" which guarantee finite or infinite extent of the fluid region (providing a priori estimates for the corresponding stationary Newton-Euler system). Under more restrictive conditions, we can also exclude the presence of "hollow" configurations. Our main result, which does not assume axial symmetry, uses the virial theorem as the key ingredient and generalises a known result in the static case. In the axially symmetric case stronger results are obtained and examples are discussed.Comment: Corrections according to the version accepted by Ann. Henri Poincar

Critical Statistical Charge for Anyonic Superconductivity

We examine a criterion for the anyonic superconductivity at zero temperature in Abelian matter-coupled Chern-Simons gauge field theories in three dimensions. By solving the Dyson-Schwinger equations, we obtain a critical value of the statistical charge for the superconducting phase in a massless fermion-Chern-Simons model.Comment: 11 pages; to appear in Phys Rev

The size of the proton - closing in on the radius puzzle

We analyze the recent electron-proton scattering data from Mainz using a dispersive framework that respects the constraints from analyticity and unitarity on the nucleon structure. We also perform a continued fraction analysis of these data. We find a small electric proton charge radius, r_E^p = 0.84_{-0.01}^{+0.01} fm, consistent with the recent determination from muonic hydrogen measurements and earlier dispersive analyses. We also extract the proton magnetic radius, r_M^p = 0.86_{-0.03}^{+0.02} fm, consistent with earlier determinations based on dispersion relations.Comment: 4 pages, 2 figures, fit improved, small modifications, section on continued fractions modified, conclusions on the proton charge radius unchanged, version accepted for publication in European Physical Journal

On Thermalization in de Sitter Space

We discuss thermalization in de Sitter space and argue, from two different points of view, that the typical time needed for thermalization is of order $R^{3}/l_{pl}^{2}$, where $R$ is the radius of the de Sitter space in question. This time scale gives plenty of room for non-thermal deviations to survive during long periods of inflation. We also speculate in more general terms on the meaning of the time scale for finite quantum systems inside isolated boxes, and comment on the relation to the Poincar\'{e} recurrence time.Comment: 14 pages, 2 figures, latex, references added. Improved discussion in section 3 adde

Hydrogen-Helium Mixtures at High Pressure

The properties of hydrogen-helium mixtures at high pressure are crucial to address important questions about the interior of Giant planets e.g. whether Jupiter has a rocky core and did it emerge via core accretion? Using path integral Monte Carlo simulations, we study the properties of these mixtures as a function of temperature, density and composition. The equation of state is calculated and compared to chemical models. We probe the accuracy of the ideal mixing approximation commonly used in such models. Finally, we discuss the structure of the liquid in terms of pair correlation functions.Comment: Proceedings article of the 5th Conference on Cryocrystals and Quantum Crystals in Wroclaw, Poland, submitted to J. Low. Temp. Phys. (2004