RNA integrity in post-mortem samples: influencing parameters and implications on RT-qPCR assays

Abstract Messenger RNA (mRNA) profiling in postmortem human tissue might reveal information about gene expression at the time point of death or close to it. When working with post-mortem human tissue, one is confronted with a natural RNA degradation caused by several parameters which are not yet fully understood. The aims of the present study were to analyse the influence of impaired RNA integrity on the reliability of quantitative gene expression data and to identify ante-and post-mortem parameters that might lead to reduced RNA integrities in post-mortem human brain, cardiac muscle and skeletal muscle tissues. Furthermore, this study determined the impact of several parameters like type of tissue, age at death, gender and body mass index (BMI), as well as duration of agony, cause of death and post-mortem interval on the RNA integrity. The influence of RNA integrity on the reliability of quantitative gene expression data was analysed by generating degradation profiles for three gene transcripts. Based on the deduced cycle of quantification data, this study shows that reverse transcription quantitative polymerase chain reaction (RT-qPCR) performance is affected by impaired RNA integrity. Depending on the transcript and tissue type, a shift in cycle threshold values of up to two cycles was observed. Determining RNA integrity number of 136 post-mortem samples revealed significantly different RNA qualities among the three tissue types with brain revealing significantly lower integrities compared to skeletal and cardiac muscle. The body mass index was found to influence RNA integrity in skeletal muscle tissue (M. iliopsoas). Samples originating from deceased with a BMI>25 were of significantly lower integrity compared to samples from normal weight donors. Correct data normalisation was found to partly diminish the effects caused by impaired RNA quality. Nevertheless, it can be concluded that in post-mortem tissue with low RNA integrity numbers, the detection of large differences in gene expression activities might still be possible, whereas small expression differences are prone to misinterpretation due to degradation. Thus, when working with post-mortem Electronic supplementary material The online version of this articl

Formation of chlorite during thrust fault reactivation. Record of fluid origin and P-T conditions in the Monte Perdido thrust fault (southern Pyrenees)

The chemical and isotopic compositions of clay minerals such as illite and chlorite are commonly used to quantify diagenetic and low-grade metamorphic conditions, an approach that is also used in the present study of the Monte Perdido thrust fault from the South Pyrenean fold-and-thrust belt. The Monte Perdido thrust fault is a shallow thrust juxtaposing upper Cretaceous-Paleocene platform carbonates and Lower Eocene marls and turbidites from the Jaca basin. The core zone of the fault, about 6m thick, consists of intensely deformed clay-bearing rocks bounded by major shear surfaces. Illite and chlorite are the main hydrous minerals in the fault zone. Illite is oriented along cleavage planes while chlorite formed along shear veins (<50μm in thickness). Authigenic chlorite provides essential information about the origin of fluids and their temperature. δ18O and δD values of newly formed chlorite support equilibration with sedimentary interstitial water, directly derived from the local hanging wall and footwall during deformation. Given the absence of large-scale fluid flow, the mineralization observed in the thrust faults records the P-T conditions of thrust activity. Temperatures of chlorite formation of about 240°C are obtained via two independent methods: chlorite compositional thermometers and oxygen isotope fractionation between cogenetic chlorite and quartz. Burial depth conditions of 7km are determined for the Monte Perdido thrust reactivation, coupling calculated temperature and fluid inclusion isochores. The present study demonstrates that both isotopic and thermodynamic methods applied to clay minerals formed in thrust fault are useful to help constrain diagenetic and low-grade metamorphic condition

The Magmatic to Hydrothermal Evolution of the Intrusive Mont Saint-Hilaire Complex: Insights into the Late-stage Evolution of Peralkaline Rocks

The Cretaceous Mont Saint-Hilaire complex (Quebec, Canada) comprises three major rock units that were emplaced in the following sequence: (I) gabbros; (II) diorites; (III) diverse partly agpaitic foid syenites. The major element compositions of the rock-forming minerals, age-corrected Nd and oxygen isotope data for mineral separates and trace element data of Fe-Mg silicates from the various lithologies imply a common source for all units. The distribution of the rare earth elements in clinopyroxene from the gabbros indicates an ocean island basalt type composition for the parental magma. Gabbros record temperatures of 1200 to 800°C, variable silica activities between 0·7 and 0·3, and fO2 values between −0·5 and +0·7 (log ΔFMQ, where FMQ is fayalite-magnetite-quartz). The diorites crystallized under uniform aSiO2 (aSiO2 = 0·4-0·5) and more reduced fO2 conditions (log ΔFMQ ~ −1) between ~1100 and ~800°C. Phase equilibria in various foid syenites indicate that silica activities decrease from 0·6-0·3 at ~1000°C to <0·3 at ~550°C. Release of an aqueous fluid during the transition to the hydrothermal stage caused aSiO2 to drop to very low values, which results from reduced SiO2 solubilities in aqueous fluids compared with silicate melts. During the hydrothermal stage, high water activities stabilized zeolite-group minerals. Fluid inclusions record a complex post-magmatic history, which includes trapping of an aqueous fluid that unmixed from the restitic foid syenitic magma. Cogenetic aqueous and carbonic fluid inclusions reflect heterogeneous trapping of coexisting immiscible external fluids in the latest evolutionary stage. The O and C isotope characteristics of fluid-inclusion hosted CO2 and late-stage carbonates imply that the surrounding limestones were the source of the external fluids. The mineral-rich syenitic rocks at Mont Saint-Hilaire evolved as follows: first, alkalis, high field strength and large ion lithophile elements were pre-enriched in the (late) magmatic and subsequent hydrothermal stages; second, percolation of external fluids in equilibrium with the carbonate host-rocks and mixing processes with internal fluids as well as fluid-rock interaction governed dissolution of pre-existing minerals, element transport and precipitation of mineral assemblages determined by locally variable parameters. It is this hydrothermal interplay between internal and external fluids that is responsible for the mineral wealth found at Mont Saint-Hilair

Adolescents’ responses to the promotion and flavouring of e-cigarettes

Objectives The purpose of the study is to examine adolescents’ awareness of e-cigarette marketing and investigate the impact of e-cigarette flavour descriptors on perceptions of product harm and user image. Methods Data come from the 2014 Youth Tobacco Policy Survey, a cross-sectional in-home survey conducted with 11–16 year olds across the UK (n = 1205). Adolescents’ awareness of e-cigarette promotion, brands, and flavours was assessed. Perceptions of product harm, and likely user of four examples of e-cigarette flavours was also examined. Results Some participants had tried e-cigarettes (12 %) but regular use was low (2 %) and confined to adolescents who had also smoked tobacco. Most were aware of at least one promotional channel (82 %) and that e-cigarettes came in different flavours (69 %). Brand awareness was low. E-cigarettes were perceived as harmful (M = 3.54, SD = 1.19) but this was moderated by product flavours. Fruit and sweet flavours were perceived as more likely to be tried by young never smokers than adult smokers trying to quit (p < 0.001). Conclusions There is a need to monitor the impact of future market and regulatory change on youth uptake and perceptions of e-cigarettes

Interaction of rat alveolar macrophages with dental composite dust

Background: Dental composites have become the standard filling material to restore teeth, but during the placement of these restorations, high amounts of respirable composite dust (<5 mu m) including many nano-sized particles may be released in the breathing zone of the patient and dental operator. Here we tested the respirable fraction of several composite particles for their cytotoxic effect using an alveolar macrophage model system. Methods: Composite dust was generated following a clinical protocol, and the dust particles were collected under sterile circumstances. Dust was dispersed in fluid, and 5-mu m-filtered to enrich the respirable fractions. Quartz DQ12 and corundum were used as positive and negative control, respectively. Four concentrations (22.5 mu g/ml, 45 mu g/ml, 90 mu g/ml and 180 mu g/ml) were applied to NR8383 alveolar macrophages. Light and electron microscopy were used for subcellular localization of particles. Culture supernatants were tested for release of lactate dehydrogenase, glucuronidase, TNF-alpha, and H2O2. Results: Characterization of the suspended particles revealed numerous nano-sized particles but also many high volume particles, most of which could be removed by filtering. Even at the highest concentration (180 mu g/ml), cells completely cleared settled particles from the bottom of the culture vessel. Accordingly, a mixture of nano- and micron-scaled particles was observed inside cells where they were confined to phagolysosomes. The filtered particle fractions elicited largely uniform dose-dependent responses, which were elevated compared to the control only at the highest concentration, which equaled a mean cellular dose of 120 pg/cell. A low inflammatory potential was identified due to dose-dependent release of H2O2 and TNF-alpha. However, compared to the positive control, the released levels of H2O2 and TNF-alpha were still moderate, but their release profiles depended on the type of composite. Conclusions: Alveolar macrophages are able to phagocytize respirable composite dust particle inclusive nanoparticles. Since NR8383 cells tolerate a comparatively high cell burden (60 pg/cell) of each of the five materials with minimal signs of cytotoxicity or inflammation, the toxic potential of respirable composite dust seems to be low. These results are reassuring for dental personnel, but more research is needed to characterize the actual exposure and uptake especially of the pure nano fraction

Interaction of rat alveolar macrophages with dental composite dust

Background: Dental composites have become the standard filling material to restore teeth, but during the placement of these restorations, high amounts of respirable composite dust (<5 mu m) including many nano-sized particles may be released in the breathing zone of the patient and dental operator. Here we tested the respirable fraction of several composite particles for their cytotoxic effect using an alveolar macrophage model system. Methods: Composite dust was generated following a clinical protocol, and the dust particles were collected under sterile circumstances. Dust was dispersed in fluid, and 5-mu m-filtered to enrich the respirable fractions. Quartz DQ12 and corundum were used as positive and negative control, respectively. Four concentrations (22.5 mu g/ml, 45 mu g/ml, 90 mu g/ml and 180 mu g/ml) were applied to NR8383 alveolar macrophages. Light and electron microscopy were used for subcellular localization of particles. Culture supernatants were tested for release of lactate dehydrogenase, glucuronidase, TNF-alpha, and H2O2. Results: Characterization of the suspended particles revealed numerous nano-sized particles but also many high volume particles, most of which could be removed by filtering. Even at the highest concentration (180 mu g/ml), cells completely cleared settled particles from the bottom of the culture vessel. Accordingly, a mixture of nano- and micron-scaled particles was observed inside cells where they were confined to phagolysosomes. The filtered particle fractions elicited largely uniform dose-dependent responses, which were elevated compared to the control only at the highest concentration, which equaled a mean cellular dose of 120 pg/cell. A low inflammatory potential was identified due to dose-dependent release of H2O2 and TNF-alpha. However, compared to the positive control, the released levels of H2O2 and TNF-alpha were still moderate, but their release profiles depended on the type of composite. Conclusions: Alveolar macrophages are able to phagocytize respirable composite dust particle inclusive nanoparticles. Since NR8383 cells tolerate a comparatively high cell burden (60 pg/cell) of each of the five materials with minimal signs of cytotoxicity or inflammation, the toxic potential of respirable composite dust seems to be low. These results are reassuring for dental personnel, but more research is needed to characterize the actual exposure and uptake especially of the pure nano fraction

Palaeoenvironmental variability and carbon cycle perturbations during the Smithian-Spathian (Early Triassic) in Central Spitsbergen

The Early Triassic Smithian and Spathian time intervals are characterized by perturbations in the global carbon cycle, fluctuations in sea surface temperature, high turnover rates of marine nekton, and a change in terrestrial vegetation. Despite the importance of this time interval, comprehensive multiproxy investigations from Early Triassic high and middle latitude regions remain scarce due to the difficulty in accessing sections. The objective of this study is to increase our understanding of regional and local palaeoenvironmental and carbon cycle perturbations from a middle Smithian to late Spathian middle latitude section from Central Spitsbergen. Geochemical analyses show an increase in phosphorus and nitrogen just at and above the Smithian–Spathian boundary (SSB). High primary productivity led to increasingly anoxic conditions in bottom waters during the middle and late Spathian, enhancing the preservation of organic matter in the sediments. Anoxic conditions restrain phosphorus remineralization, allowing it to be recycled within the water column. This increase in anoxia is consistent with observations in other Arctic basins, demonstrating larger regional similarities in palaeoenvironmental conditions. The fluctuations in isostatic and eustatic sea levels affected organic carbon sequestration by regulating organic matter mineral interactions via the control of grain size within the sediment. This study demonstrates that local organic carbon sequestration in the Barents Sea shelf during the Spathian was influenced by a multitude of factors, including sedimentology, redox conditions, nutrient availability, and primary productivity. □ Vikinghøgda Formation, bulk rock geochemistry, particulate organic matter, extinction recovery, carbon isotopes, Stensiöfjellet Franziska R. Blattmann ✉ [[email protected]], Zoneibe A.S. Luz [[email protected]] and Torsten W. Vennemann [[email protected]], Institute of Earth Surface Dynamics, University of Lausanne, Quartier UNIL-Mouline, 1015 Lausanne, Switzerland; Elke Schneebeli-Hermann [[email protected]] and Hugo F.R. Bucher [[email protected]], Department of Palaeontology, University of Zürich, Karl-Schmid-Strasse 4, 8006 Zürich, Switzerland; Thierry Adatte [[email protected]], Institute of Earth Sciences, University of Lausanne, Quartier UNIL-Mouline, CH-1015 Lausanne, Switzerland; Christian Vérard [[email protected]], Section of Earth and Environmental Sciences, University of Geneva, Rue des Maraîchers 13, CH-1205 Geneva, Switzerland; Øyvind Hammer [[email protected]], Natural History Museum, University of Oslo, Pb. 1172 Blindern, 0318 Oslo, Norway; manuscript received on 08/08/2023; manuscript accepted on 02/02/2024; manuscript published on 20/06/2024 in Lethaia 57(2)

New Biotite and Muscovite Isotopic Reference Materials, USGS57 and USGS58, for δ2H Measurements–A Replacement for NBS 30

The advent of continuous-flow isotope-ratio mass spectrometry (CF-IRMS) coupled with a high temperature conversion (HTC) system enabled faster, more cost effective, and more precise δ2H analysis of hydrogen-bearing solids. Accurate hydrogen isotopic analysis by on-line or off-line techniques requires appropriate isotopic reference materials (RMs). A strategy of two-point calibrations spanning δ2H range of the unknowns using two RMs is recommended. Unfortunately, the supply of the previously widely used isotopic RM, NBS 30 biotite, is exhausted. In addition, recent measurements have shown that the determination of δ2H values of NBS 30 biotite on the VSMOW-SLAP isotope-delta scale by on-line HTC systems with CF-IRMS may be unreliable because hydrogen in this biotite may not be converted quantitatively to molecular hydrogen. The δ2HVSMOW-SLAP values of NBS 30 biotite analyzed by on-line HTC systems can be as much as 21 mUr (or ‰) too positive compared to the accepted value of −65.7 mUr, determined by only a few conventional off-line measurements. To ensure accurate and traceable on-line hydrogen isotope-ratio determinations in mineral samples, we here propose two isotopically homogeneous, hydrous mineral RMs with well-characterized isotope-ratio values, which are urgently needed. The U.S. Geological Survey (USGS) has prepared two such RMs, USGS57 biotite and USGS58 muscovite. The δ2H values were determined by both glassy carbon-based on-line conversion and chromium-based on-line conversion, and results were confirmed by off-line conversion. The quantitative conversion of hydrogen from the two RMs using the on-line HTC method was carefully evaluated in this study. The isotopic compositions of these new RMs with 1-σ uncertainties and mass fractions of hydrogen are: USGS57 (biotite) δ2HVSMOW-SLAP = −91.5 ± 2.4 mUr (n =24) Mass fraction hydrogen = 0.416 ± 0.002% (n=4) Mass fraction water = 3.74 ± 0.02% (n=4) USGS58 (muscovite) δ2HVSMOW-SLAP = −28.4 ± 1.6 mUr (n =24) Mass fraction hydrogen = 0.448 ± 0.002% (n=4) Mass fraction water = 4.03 ± 0.02% (n =4). These δ2HVSMOW-SLAP values encompass typical ranges for solid unknowns of crustal and mantle origin and are available to users for recommended two-point calibration

Hydrodynamics of a high Alpine catchment characterized by four natural tracers

Hydrological processes in high-elevation catchments are strongly influenced by alternating snow accumulation and melt in addition to summer rainfall. Although diverse water sources and flow paths that generate streamflow in the world's water towers emerge from these two driving inputs, a detailed process understanding remains poor. We measured a combination of natural tracers of water at a high frequency, including stable isotope compositions, electrical conductivity (EC), and water and soil temperature to characterize hydrological processes in a snow-dominated Alpine catchment and to understand the diversity of streamflow sources and flow paths. Stable isotope composition of the sampled water revealed the prominence of snowmelt year-round (even during winter baseflow), and a strong flushing of the entire system with snowmelt at the start of the main melt period, sometimes referred to as the freshet, led to a reset, or return to baseline, of the isotopic values in most sampled water. Soil temperature measurements help identify snow-free periods and indicate sub-snowpack local flow, for example, in the case of rain-on-snow events. Water temperature measurements in springs can indicate flow path depth. EC measurements reflect the magnitude of subsurface exchange and allow for the separation of subsurface snowmelt contribution to streamflow from the contribution of stored groundwater. These insights into the details of streamflow generation in such a dynamic environment were only made possible due to intense, year-round water sampling. The sampled tracers are revealed to complement each other in important ways particularly because they were sampled during winter and spring, both snow-covered periods, the importance of which is a key implication of this work.</p