Returning genome sequences to research participants:Policy and practice

Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support. In addition, we identify a number of ethico-legal issues that require careful consideration, including returning data to family members, mitigating against unintended consequences, and ensuring appropriate governance. Finally, recognising that there is an opportunity cost to addressing these issues, we make some specific pragmatic suggestions for studies that are considering whether to share individual genomic datasets with individual study participants. If data are shared, research should be undertaken into the personal, familial and societal impact of receiving individual genome sequence data

Baghuk Mountain (Central Iran): high-resolution stratigraphy of a continuous Central Tethyan Permian–Triassic boundary section

Permian–Triassic boundary sections at Baghuk Mountain (Central Iran) are investigated with respect to their lithological succession, biostratigraphy (particularly conodonts, nautiloids and ammonoids) as well as chemostratigraphy (carbon isotopes). The rock successions consist of the Late Permian Hambast Formation, the youngest Permian Baghuk Member (new name for the “Boundary Clay”) and the Early Triassic Claraia beds. Correlation of the data allows the establishment of a high-resolution stratigraphy based on conodonts with seven Changhsingian zones. Abundant ammonoids enable the separation of ammonoid assemblages with the successive Wuchiapingian genera Prototoceras, Pseudotoceras and Vedioceras, as well as the Changhsingian genera Shevyrevites, Paratirolites, Alibashites, Abichites and Arasella. Griesbachian and Dienerian ammonoids are usually poorly preserved. Nautiloids occur predominantly in the Wuchiapingian part of the section with two successive assemblages dominated by the Liroceratidae and Tainoceratidae, respectively. Numerous Early Triassic strata contain microbialites of various outer morphology and microstructure. The carbon isotope curve (δ13Ccarb) shows a continuous late Changhsingian negative excursion continuing across the Baghuk Member with the lightest values at the base of the Triassic.</p

Ostracod diversity and environmental conditions of the Aras Valley section (NW-Iran) during the end-Permian mass extinction.

International audienc

Some Lithuanian ethnobotanical taxa: a linguistic view on Thorn Apple and related plants

<p>Abstract</p> <p>Background</p> <p>The perception and use of plants correspond with common plant names. The study of plant names may give insight into historical and recent use of plants.</p> <p>Methods</p> <p>Plant names in dictionaries and folklore have been evaluated. A etymological analysis of the names is provided. Onomasiological and semasiological aspects have been considered. Therefore, species named with names related to each other have been selected.</p> <p>Results</p> <p>Plant names containing the stem <it>dag</it>- or <it>deg</it>- may belong to either of two categories: incenses or thorny plants. Plants named in <it>durn</it>- have been in use as psychopharmaca. The name <it>rymo </it>points not to Rome but to the use of plants as anodyne or psychopharmaca.</p

Antioxidant activity of alkylresorcinols from rye bran and their protective effects on cell viability of PC-12 AC cells

Alkylresorcinols (ARs) are phenolic lipids that are present in high amounts in the bran layer of different cereals. Rye samples, cultivar Hazlet, and a white rye genotype, RT202, were analyzed for their antioxidant properties and AR content and composition, based on six fractions of the bran, where 1 was the outermost fraction and 6 was the bran fraction closest to the endosperm. Gas chromatography-mass spectrometry (GC-MS) analysis demonstrated that the most commonly found AR homologue in Hazlet rye is C19:0 and that the total amount of ARs decreases from the outermost to innermost fractions. The antioxidant activity using oxygen radical absorbance capacity (ORAC) for both white rye genotype RT202 and Hazlet brans was determined to decrease from the outermost fraction (136.05 μmol TE/g for Hazlet fraction 1 and 186.57 μmol TE/g for white rye genotype RT202 fraction 1) to the innermost fraction (9.84 μmol TE/g for Hazlet fraction 6 and 78.75 μmol TE/g for white rye genotype RT202 fraction 2). A positive relationship was seen with GC-MS results. Treatment of PC-12 AC cells with Hazlet fraction 1 increased mitochondrial biogenesis as determined using mitochondrial fluorescent dyes. In the presence of a prooxidant (AAPH), PC-12 AC cells were better protected from free radical attack when treated with Hazlet fraction 1 than with all other bran fractions. The results suggest that higher AR content in bran fractions confers antioxidant protection against free radical damage

Lentils enhance probiotic growth in yogurt and provide added benefit of antioxidant protection

We evaluated the antioxidant potential of lentil polysaccharides in stimulating the growth of probiotic bacteria in yogurt. Microbial counts, pH and total titratable acidity (TTA) were measured in yogurt samples containing starter cultures with or without probiotic bacteria, supplemented with whole ground green lentils. Additionally, the antioxidant potential of polysaccharides extracted from green, red, and dehulled red lentils were measured by oxygen radical absorbance capacity (ORAC) assay. Results demonstrate that green lentils selectively enhanced the number of probiotic bacteri

Suppressed competitive exclusion enabled the proliferation of Permian/Triassic boundary microbialites

During the earliest Triassic microbial mats flourished in the photic zones of marginal seas, generating widespread microbialites. It has been suggested that anoxic conditions in shallow marine environments, linked to the end‐Permian mass extinction, limited mat‐inhibiting metazoans allowing for this microbialite expansion. The presence of a diverse suite of proxies indicating oxygenated shallow sea‐water conditions (metazoan fossils, biomarkers and redox proxies) from microbialite successions have, however, challenged the inference of anoxic conditions. Here, the distribution and faunal composition of Griesbachian microbialites from China, Iran, Turkey, Armenia, Slovenia and Hungary are investigated to determine the factors that allowed microbialite‐forming microbial mats to flourish following the end‐Permian crisis. The results presented here show that Neotethyan microbial buildups record a unique faunal association due to the presence of keratose sponges, while the Palaeotethyan buildups have a higher proportion of molluscs and the foraminifera Earlandia. The distribution of the faunal components within the microbial fabrics suggests that, except for the keratose sponges and some microconchids, most of the metazoans were transported into the microbial framework via wave currents. The presence of both microbialites and metazoan associations were limited to oxygenated settings, suggesting that a factor other than anoxia resulted in a relaxation of ecological constraints following the mass extinction event. It is inferred that the end‐Permian mass extinction event decreased the diversity and abundance of metazoans to the point of significantly reducing competition, allowing photosynthesis‐based microbial mats to flourish in shallow water settings and resulting in the formation of widespread microbialites

Suppressed competitive exclusion enabled the proliferation of Permian/Triassic boundary microbialites

During the earliest Triassic microbial mats flourished in the photic zones of marginal seas, generating widespread microbialites. It has been suggested that anoxic conditions in shallow marine environments, linked to the end-Permian mass extinction, limited mat-inhibiting metazoans allowing for this microbialite expansion. The presence of a diverse suite of proxies indicating oxygenated shallow sea-water conditions (metazoan fossils, biomarkers and redox proxies) from microbialite successions have, however, challenged the inference of anoxic conditions. Here, the distribution and faunal composition of Griesbachian microbialites from China, Iran, Turkey, Armenia, Slovenia and Hungary are investigated to determine the factors that allowed microbialite-forming microbial mats to flourish following the end-Permian crisis. The results presented here show that Neotethyan microbial buildups record a unique faunal association due to the presence of keratose sponges, while the Palaeotethyan buildups have a higher proportion of molluscs and the foraminifera Earlandia. The distribution of the faunal components within the microbial fabrics suggests that, except for the keratose sponges and some microconchids, most of the metazoans were transported into the microbial framework via wave currents. The presence of both microbialites and metazoan associations were limited to oxygenated settings, suggesting that a factor other than anoxia resulted in a relaxation of ecological constraints following the mass extinction event. It is inferred that the end-Permian mass extinction event decreased the diversity and abundance of metazoans to the point of significantly reducing competition, allowing photosynthesis-based microbial mats to flourish in shallow water settings and resulting in the formation of widespread microbialites