Dormancy within Staphylococcus epidermidis biofilms : a transcriptomic analysis by RNA-seq

The proportion of dormant bacteria within Staphylococcus epidermidis biofilms may determine its inflammatory profile. Previously, we have shown that S. epidermidis biofilms with higher proportions of dormant bacteria have reduced activation of murine macrophages. RNA-sequencing was used to identify the major transcriptomic differences between S. epidermidis biofilms with different proportions of dormant bacteria. To accomplish this goal, we used an in vitro model where magnesium allowed modulation of the proportion of dormant bacteria within S. epidermidis biofilms. Significant differences were found in the expression of 147 genes. A detailed analysis of the results was performed based on direct and functional gene interactions. Biological processes among the differentially expressed genes were mainly related to oxidation-reduction processes and acetyl-CoA metabolic processes. Gene set enrichment revealed that the translation process is related to the proportion of dormant bacteria. Transcription of mRNAs involved in oxidation-reduction processes was associated with higher proportions of dormant bacteria within S. epidermidis biofilm. Moreover, the pH of the culture medium did not change after the addition of magnesium, and genes related to magnesium transport did not seem to impact entrance of bacterial cells into dormancy.The authors thank Stephen Lorry at Harvard Medical School for providing CLC Genomics software. This work was funded by Fundacao para a Ciencia e a Tecnologia (FCT) and COMPETE grants PTDC/BIA-MIC/113450/2009, FCOMP-01-0124-FEDER-014309, FCOMP-01-0124-FEDER-022718 (FCT PEst-C/SAU/LA0002/2011), QOPNA research unit (project PEst-C/QUI/UI0062/2011), and CENTRO-07-ST24-FEDER-002034. The following authors had an individual FCT fellowship: VC (SFRH/BD/78235/2011) and AF (2SFRH/BD/62359/2009)

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P < 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P < 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk

Hf-W thermochronometry: Closure temperature and constraints on the accretion and cooling history of the H chondrite parent body

We obtained Hf-W metal-silicate isochrons for several H chondrites of petrologic types 4, 5, and 6 to constrain the accretion and high-temperature thermal history of the H chondrite parent body. The silicate fractions have 180Hf/184W ratios up to ∼ 51 and 182W/184W ratios up to ∼ 33 ε units higher than the whole-rock. These high 180Hf/184W and radiogenic W isotope ratios result in highly precise Hf-W ages. The Hf-W ages of the H chondrites become younger with increasing metamorphic grade and range from ΔtCAI = 1.7 ± 0.7 Ma for the H4 chondrite Ste. Marguerite to ΔtCAI = 9.6 ± 1.0 Ma for the H6 chondrites Kernouvé and Estacado. Closure temperatures for the Hf-W system in H chondrites were estimated from numerical simulations of W diffusion in high-Ca pyroxene, the major host of radiogenic 182W in H chondrites, and range from 800 ± 50 °C for H4 chondrites to 875 ± 75 °C for H6 chondrites. Owing to these high closure temperatures, the Hf-W system closed early and dates processes associated with the earliest evolution of the H chondrite parent body. Consequently, the high-temperature interval of ∼ 8 Ma as defined by the Hf-W ages is much shorter than intervals obtained from Rb-Sr and Pb-Pb dating. For H4 chondrites, heating on the parent body probably was insufficient to cause W diffusion in high-Ca pyroxene, such that the Hf-W age of ΔtCAI = 1.7 ± 0.7 Ma for Ste. Marguerite was not reset and most likely dates chondrule formation. This is consistent with Al-Mg ages of ∼ 2 Ma for L and LL chondrules and indicates that chondrules from all ordinary chondrites formed contemporaneously. The Hf-W ages for H5 and H6 chondrites of ΔtCAI = 5.9 ± 0.9 Ma and ΔtCAI = 9.6 ± 1.0 Ma correspond closely to the time of the thermal peak within the H chondrite parent body. Combined with previously published chronological data the Hf-W ages reveal an inverse correlation of cooling rate and metamorphic grade: shortly after their thermal peak H6 chondrites cooled at ∼ 10 °C/Ma, H5 chondrites at ∼ 30 °C/Ma and H4 chondrites at ∼ 55 °C/Ma. These Hf-W age constraints are most consistent with an onion-shell structure of the H chondrite parent body that was heated internally by energy released from 26Al decay. Parent body accretion started after chondrule formation at 1.7 ± 0.7 Ma and probably ended before 5.9 ± 0.9 Ma, when parts of the H chondrite parent body already had cooled from their thermal peak. The well-preserved cooling curves for the H chondrites studied here indicate that these samples derive from a part of the H chondrite parent body that remained largely unaffected by impact disruption and reassembly but such processes might have been important in other areas. The H chondrite parent body has a 180Hf/184W ratio of 0.63 ± 0.20, distinctly lower than the 180Hf/184W = 1.21 ± 0.06 of carbonaceous chondrite parent bodies. This difference reflects Hf-W fractionation within the first ∼ 2 Ma of the solar system, presumably related to processes in the solar nebula. © 2008 Elsevier B.V. All rights reserved

Ionic radii

Definition and Assumptions An ion is an atom with an electrical charge, achieved either by gaining or losing one or more electrons. The ionic radius of the ion (rion) of an atom (either a cation or anion) is a measure of the size of a spherical ion. The ionic radius is similar to but different from the atomic radius for the ionic size is dependent on the distribution of its outermost electrons and is inversely proportional to the effective nuclear charge experienced by ions. It is calculated from the internuclear distance between a cation and a neighboring anion in a lattice. Ionic radii are typically reported in picometers (pm, 1 × 10−12 m) or in the older literature as Angstroms (Å), where 1 Å = 100 pm. A typical range of ionic radii is 25–170 pm for four to eightfold coordination (see Table 1).N/

Tectonic implications of garnet-bearing mantle xenoliths exhumed by Quaternary magmatism in the Hangay dome, central Mongolia

Garnet-bearing mantle xenoliths have been recovered from Quaternary alkali basalts, both within and peripheral to the Hangay dome of central Mongolia. Microfabric analysis and thermobaromery, combining empirical thermobarometers and the self-consistent dataset of THERMOCALC, indicate that garnet websterites from the Shavaryn-Tsaram volcanic centre at the dome core were formed in the spinel-lherzolite upper mantle at pressures of 17–18 kbars and temperatures of 1,070–1,090°C, whereas garnet lherzolites were derived from greater depths (18–20 kbars). Garnet lherzolites from the Baga Togo Uul vents near the dome edge were formed at 18–22 kbars under significantly cooler conditions (960–1,000°C). These xenoliths reveal reaction coronas of (1) orthopyroxene, clinopyroxene, plagioclase and spinel mantling garnets; (2) spongy rims of olivine replacing orthopyroxene and (3) low-Na, low-Al clinopyroxene replacing primary clinopyroxene. Trace-element abundances indicate that clinopyroxene from these coronas is in chemical equilibrium with the host magma. The thermobarometric and textural data suggest that lherzolite xenoliths from both sites were derived from depths of 60–70 km and entrained in magma at 1,200–1,300°C. The average rate of ascent, as determined by olivine zoning, lies in the range 0.2–0.3 m s?1. The contrast in thermal profiles of the upper mantle between the two sites is consistent with a mantle plume beneath the Hangay dome with elevated thermal conditions beneath the core of the dome being comparable to estimates of the Pleistocene geotherm beneath the Baikal rift

Magmatic residence times of zoned phenocrysts: introduction and application of the binary element diffusion modelling (BEDM) technique

This paper describes a general technique, binary element diffusion modelling (BEDM), for determining single-crystal residence times in magmas that relies on modelling the diffusion of two or more elements in the crystal. BEDM has the advantage over other diffusion-based models in that it does not need a precisely defined initial compositional profile for the crystal at “zero time”, and instead requires that the concentrations of the two elements are correlated during crystallisation. Any differences subsequently observed between the two elements are caused by intracrystalline diffusion during residence in hot magma. These differences are removed by artificially ageing the slower-diffusing of the two elements, and the amount of time taken to “undo” the difference between the elements is simply related to the crystal residence time (=decoupling time) at high temperatures. The BEDM principle is demonstrated using artificial data and is then applied to literature data for Sr and Ba in a zoned sanidine crystal from the Bishop Tuff (Anderson et al., in J. Petrol 41(3):449–473, 2000). For this crystal, the method gives a residence time estimate of 114 ka at 800°C, which is then compared with estimates from other methods. In theory, the method can be further expanded for use as a geothermometer as well as geochronometer. However, this is not easily possible with the diffusivity data currently available