Depth-related distribution of a key gene of the tetraether lipid biosynthetic pathway in marine Thaumarchaeota

The distribution of isoprenoid glycerol dialkyl glycerol tetraethers (GDGT) lipids synthesized by Thaumarchaeota has been shown to be temperature-dependent in world oceans. Depth-related differences in the ammonia monooxygenase (amoA) of Thaumarchaeota have led to the classification of ‘shallow’ and ‘deep water’ clusters, potentially affecting GDGT distributions. Here, we investigate if this classification is also reflected in a key gene of the thaumarchaeotal lipid biosynthetic pathway coding for geranylgeranylglyceryl phosphate (GGGP) synthase. We investigated metagenomic databases, suspended particulate matter and surface sediment of the Arabian Sea oxygen minimum zone. These revealed significant differences in amoA and GGGP synthase between ‘shallow’ and ‘deep water’ Thaumarchaeota. Intriguingly, amoA and GGGP synthase sequences of benthic Thaumarchaeota clustered with the ‘shallow water’ rather than with ‘deep water’ Thaumarchaeota. This suggests that pressure and temperature are unlikely factors that drive the differentiation, and suggests an important role of ammonia concentration that is higher in benthic and ‘shallow water’ niches. Analysis of the relative abundance of GDGTs in the Arabian Sea and in globally distributed surface sediments showed differences in GDGT distributions from subsurface to deep waters that may be explained by differences in the GGGP synthase, suggesting a genetic control on GDGT distributions

Influence of baking conditions and formulation on furanic derivatives, 3-methylbutanal and hexanal and other quality characteristics of lab-made and commercial biscuits

Biscuit baking can cause the formation of heat-related toxic compounds, mainly through the Maillard reaction, including some volatile organic compounds (VOCs) that are potentially carcinogenic to humans. This study investigates the effects of different baking conditions and recipes on quality characteristics (moisture, water activity, colour, texture) and on the concentration of some VOCs (furfural, furfuryl acetate, 5-methylfurfural, furfuryl alcohol, 3-methylbutanal, hexanal) in biscuits. Specifically, lab-made biscuits baked under static and ventilated conditions and three commercial biscuit types categorised as shortbreads with eggs, with chocolate chips and dry petits were evaluated. Concerning the lab-made biscuits, the ventilated mode resulted in faster baking and a slightly lower concentration of investigated VOCs compared to the static mode. Besides the process conditions, the recipe also played a role in the final quality and target volatiles, whose concentrations were lower in dry petits than in shortbreads, which are characterised by higher sugar and fat contents

The principle of equivalence and projective structure in space-times

This paper discusses the extent to which one can determine the space-time metric from a knowledge of a certain subset of the (unparametrised) geodesics of its Levi-Civita connection, that is, from the experimental evidence of the equivalence principle. It is shown that, if the space-time concerned is known to be vacuum, then the Levi-Civita connection is uniquely determined and its associated metric is uniquely determined up to a choice of units of measurement, by the specification of these geodesics. It is further demonstrated that if two space-times share the same unparametrised geodesics and only one is assumed vacuum then their Levi-Civita connections are again equal (and so the other metric is also a vacuum metric) and the first result above is recovered.Comment: 23 pages, submitted to Classical and Quantum Gravit

Magnetic Monopoles in Ferromagnetic Spin-Triplet Superconductors

Using the $\phi$-mapping method, we argue that ferromagnetic spin-triplet superconductors allow formation of unstable magnetic monopoles. In particular, we show that the limit points and the bifurcation points of the $\phi$-mapping will serve as the interaction points of these magnetic monopoles.Comment: 4 pages, no figure

Analysis of a three-component model phase diagram by Catastrophe Theory

We analyze the thermodynamical potential of a lattice gas model with three components and five parameters using the methods of Catastrophe Theory. We find the highest singularity, which has codimension five, and establish its transversality. Hence the corresponding seven-degree Landau potential, the canonical form Wigwam or $A_6$, constitutes the adequate starting point to study the overall phase diagram of this model.Comment: 16 pages, Latex file, submitted to Phys. Rev.

Different seasonality of pelagic and benthic Thaumarchaeota in the North Sea

We have examined the spatial and seasonal distribution of Thaumarchaeota in the water column and sediment of the southern North Sea using the specific intact polar lipid (IPL) hexose-phosphohexose (HPH) crenarchaeol, as well as thaumarchaeotal 16S rRNA gene abundances and expression. In the water column, a higher abundance of Thaumarchaeota was observed in the winter season than in the summer, which is in agreement with previous studies, but this was not the case in the sediment where Thaumarchaeota were most abundant in spring and summer. This observation corresponds well with the idea that ammonia availability is a key factor in thaumarchaeotal niche determination. In the surface waters of the southern North Sea, we observed a spatial variability in HPH crenarchaeol, thaumarchaeotal 16S rRNA gene abundance and transcriptional activity that corresponded well with the different water masses present. In bottom waters, a clear differentiation based on water masses was not observed; instead, we suggest that observed differences in thaumarchaeotal abundance with depth may be related to resuspension from the sediment. This could be due to suspension of benthic Thaumarchaeota to the water column or due to delivery of e.g. resuspended sediment or ammonium to the water column, which could be utilized by pelagic Thaumarchaeota. This study has shown that the seasonality of Thaumarchaeota in water and sediment is different and highlights the importance of water masses, currents and sedimentary processes in determining the spatial abundance of Thaumarchaeota in the southern North Sea

Outcomes of tuberculosis patients who start antiretroviral therapy under routine programme conditions in Malawi

SETTING: Public sector facilities in Malawi providing antiretroviral therapy (ART) to human immunodeficiency virus (HIV) positive patients, including those with tuberculosis (TB). OBJECTIVES: To compare 6-month and 12-month cohort treatment outcomes of HIV-positive TB patients and HIV-positive non-TB patients treated with ART. DESIGN: Retrospective data collection using ART patient master cards and ART patient registers. RESULTS: Between July and September 2005, 7905 patients started ART, 6967 with a non-TB diagnosis and 938 with a diagnosis of active TB. 6-month cohort outcomes of non-TB and TB patients censored on 31 March 2006 showed significantly more TB patients alive and on ART (77%) compared with non-TB patients (71%) (P < 0.001). Between January and March 2005, 4580 patients started ART, 4179 with a non-TB diagnosis and 401 with a diagnosis of active TB. 12-month cohort outcomes of non-TB and TB patients censored on 31 March 2006 showed significantly more TB patients alive and on ART (74%) compared with non-TB patients (66%) (P < 0.001). Other outcomes of default and transfer out were also significantly less frequent in TB compared with non-TB patients. CONCLUSION: HIV-positive TB patients on ART in Malawi have generally good treatment outcomes, and more patients need to access this HIV treatment

Transmission properties of a single metallic slit: From the subwavelength regime to the geometrical-optics limit

In this work we explore the transmission properties of a single slit in a metallic screen. We analyze the dependence of these properties on both slit width and angle of incident radiation. We study in detail the crossover between the subwavelength regime and the geometrical-optics limit. In the subwavelength regime, resonant transmission linked to the excitation of waveguide resonances is analyzed. Linewidth of these resonances and their associated electric field intensities are controlled by just the width of the slit. More complex transmission spectra appear when the wavelength of light is comparable to the slit width. Rapid oscillations associated to the emergence of different propagating modes inside the slit are the main features appearing in this regime.Comment: Accepted for publication in Phys. Rev.

Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria

Are Marine Group II Euryarchaeota significant contributors to tetraether lipids in the ocean?

The first line of evidence is the presence of GDGTs, including crenarchaeol, in suspended particulate matter (SPM) at 83 m, the archaeal community of which is nearly exclusively composed of MG-II (>94% of archaeal reads) (table 1 in ref. 1) as determined by pyrosequencing. However, according to Lincoln et al.’s definition, all SPM samples <100 m do not contain sufficient archaeal reads (i.e., <1,000) (figure S6 and table S2 in ref. 1) to draw any conclusion. This low abundance of archaeal DNA is also evident from the absence of detectable MG-I 16S rRNA gene copies (figure 2 in ref. 1). It is, however, not surprising that GDGTs were detected in the 83-m SPM sample because the lipid tracers used are core lipids. Core lipids do not occur as such in living cells, where they contain polar sugar and phospho head groups (e.g., ref. 2). Thus, by definition core lipid GDGTs are derived from dead material. The second line of evidence is based upon relating the presence of monohexose GDGTs in two SPM samples (although not the crucial 83-m sample) with archaeal diversity data. Although this approach uses intact polar lipids, it has been shown that monohexose GDGTs are also poor tracers of living archaeal cells (3) because they have a turnover time in the order of thousands of years (4), de facto also representing dead material.This dominance of dead lipid material readily explains the absence of any correlation of total MG-I+MG-II DNA abundance with total GDGT abundance (r2 = 0.06 and 0.04 for 0.3- to 3-µm and 3- to 57-µm fractions, respectively). Furthermore, it explains the much higher abundance of GDGTs in the large particle fraction compared to the small fraction (16–490 vs. 1–20 pg/L), contrasting its lower total archaeal abundance (0.3–1.8 × 105 vs. 1–7 × 105 cells/L) (figure 2 in ref. 1). We conclude that both lines of evidence are based on a comparison of minute amounts of archaeal DNA (often below detection limit) with unsuitable lipid tracers.The dominance of dead material and low abundance of archaeal cells make it impossible to infer the lipid composition of uncultivated MG-II from these samples, let alone to extrapolate this to the global ocean. In contrast, other studies, using abundant archaeal DNA and more suitable phospholipid GDGTs, do show a good match between MG-I DNA abundance and crenarchaeol concentration and not with MG-II (3, 5). Nevertheless, members of the Marine Group III Euryarchaeota have been suggested to contribute to GDGTs 0–3 (3); thus, members of the MG-II may potentially contribute to this pool of GDGTs as well. However, based on the data and arguments of Lincoln et al. (1) this is impossible to infer. The jury is, therefore, still out