Contrasting sensitivity of lake sediment n-alkanoic acids and n-alkanes to basin-scale vegetation and regional-scale precipitation δ2H in the Adirondack Mountains, NY (USA)

The hydrogen isotope values of plant waxes (δ2Hwax) primarily reflect plant source water. δ2Hwax preserved in lake sediments has therefore been widely used to investigate past hydroclimate. The processes by which plant waxes are integrated at regional and catchment scales are poorly understood and may affect the δ2Hwax values recorded in sediments. Here, we assess the variability of sedimentary δ2Hwax for two plant wax compound classes (n-alkanes and n-alkanoic acids) across 12 lakes in the Adirondack Mountains that receive similar regional precipitation δ2H but vary at the catchment-scale in terms of vegetation structure and basin morphology. Total long-chain (n-C27 to n-C35) alkane concentrations were similar across all sites (191 ± 53 µg/g TOC) while total long-chain (n-C28 and n-C30) alkanoic acid concentrations were more variable (117 ± 116 µg/g TOC) and may reflect shoreline vegetation composition. Lakes with shorelines dominated by evergreen gymnosperm plants had significantly higher concentrations of long-chain n-alkanoic acids relative to n-alkanes, consistent with our observations that deciduous angiosperms produced more long-chain n-alkanes than evergreen gymnosperms (471 and 33 µg/g TOC, respectively). In sediments, the most abundant chain lengths in each compound class were n-C29 alkane and n-C28 alkanoic acid, which had mean δ2H values of −188 ± 6‰ and −164 ± 9‰, respectively. Across sites, the range in sedimentary n-C29 alkane (22‰) and n-C28 alkanoic acid δ2H (35‰) was larger than expected based on the total range in modeled mean annual precipitation δ2H (4‰). We observed larger mean εapp (based on absolute values) for n-alkanes (−123‰) than for n-alkanoic acids (−97‰). Across sites, the δ2H offset between n-C29 alkane and the biosynthetic precursor n-C30 alkanoic acid (εC29-C30) ranged from −8 to −58‰, which was more variable than expected based on observations in temperate trees (−20 to −30‰). Sediments with greater aquatic organic matter contributions (lower C/N ratios) had significantly larger (absolute) εC29-C30 values, which may reflect long-chain n-alkanoic acids from aquatic sources. Concentration and δ2Hwax data in Adirondack lakes suggest that long-chain n-alkanes are more sensitive to regional-scale precipitation signals, while n-alkanoic acids are more sensitive to basin-scale differences in catchment vegetation and wax sourcing

Caledonian hot zone magmatism in the “Newer Granites”: insight from the Cluanie and Clunes plutons, Northern Scottish Highlands

Scottish “Newer” Granites record the evolution of the Caledonides resulting from Iapetus subduction and slab breakoff during the Silurian-Devonian Scandian Orogeny, but relationships between geodynamics, petrogenesis and emplacement are incomplete. Laser ablation U-Pb results from magmatic zircons at the Cluanie Pluton (Northern Highlands) identify clusters of concordant Silurian data points. A cluster with a weighted mean 206Pb/238U age of 431.6 ± 1.3 Ma (2 confidence interval, n = 6) records emplacement whilst older points (clustered at 441.8 ± 2.3 Ma, n = 9) record deep crustal hot zone magmatism prior to ascent. The Cluanie Pluton, and its neighbour the ∼428 Ma Clunes tonalite, have adakite-like high Na, Sr/Y, La/Yb and low Mg, Ni and Cr characteristics, and lack mafic facies common in other “Newer Granites”. These geochemical signatures indicate the tapping of batches of homogenised, evolved magma from the deeper crust. The emplacement age of the Cluanie Pluton confirms volumetrically modest subduction-related magmatism occurred beneath the Northern Highlands before slab breakoff, probably as a result of crustal thickening during the ∼450 Ma Grampian 2 event. Extensive new in-situ geochemical-geochronological studies for this terrane may further substantiate the deep crustal hot zone model and the association between Caledonian magmatism and potentially metallogenesis. The term “Newer Granites” is outdated as it ignores the demonstrated relationships between magmatism, Scandian orogenesis and slab breakoff. Hence, “Caledonian intrusions” would be a more appropriate generic term to cover those bodies related to either Iapetus subduction or to slab breakoff

Microdevices for extensional rheometry of low viscosity elastic liquids : a review

Extensional flows and the underlying stability/instability mechanisms are of extreme relevance to the efficient operation of inkjet printing, coating processes and drug delivery systems, as well as for the generation of micro droplets. The development of an extensional rheometer to characterize the extensional properties of low viscosity fluids has therefore stimulated great interest of researchers, particularly in the last decade. Microfluidics has proven to be an extraordinary working platform and different configurations of potential extensional microrheometers have been proposed. In this review, we present an overview of several successful designs, together with a critical assessment of their capabilities and limitations

MiRNA-Related SNPs and Risk of Esophageal Adenocarcinoma and Barrett's Esophagus: Post Genome-Wide Association Analysis in the BEACON Consortium.

Incidence of esophageal adenocarcinoma (EA) has increased substantially in recent decades. Multiple risk factors have been identified for EA and its precursor, Barrett's esophagus (BE), such as reflux, European ancestry, male sex, obesity, and tobacco smoking, and several germline genetic variants were recently associated with disease risk. Using data from the Barrett's and Esophageal Adenocarcinoma Consortium (BEACON) genome-wide association study (GWAS) of 2,515 EA cases, 3,295 BE cases, and 3,207 controls, we examined single nucleotide polymorphisms (SNPs) that potentially affect the biogenesis or biological activity of microRNAs (miRNAs), small non-coding RNAs implicated in post-transcriptional gene regulation, and deregulated in many cancers, including EA. Polymorphisms in three classes of genes were examined for association with risk of EA or BE: miRNA biogenesis genes (157 SNPs, 21 genes); miRNA gene loci (234 SNPs, 210 genes); and miRNA-targeted mRNAs (177 SNPs, 158 genes). Nominal associations (P0.50), and we did not find evidence for interactions between variants analyzed and two risk factors for EA/BE (smoking and obesity). This analysis provides the most extensive assessment to date of miRNA-related SNPs in relation to risk of EA and BE. While common genetic variants within components of the miRNA biogenesis core pathway appear unlikely to modulate susceptibility to EA or BE, further studies may be warranted to examine potential associations between unassessed variants in miRNA genes and targets with disease risk.This work was supported by the National Institutes of Health [R01CA136725 to T.L.V. and D.C.W, T32CA009168 to T.L.V, and K05CA124911 to T.L.V.]. Additional funding sources for individual studies included in the BEACON GWAS, and for BEACON investigators, have been acknowledged previously (16).This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pone.012861

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Interactions Between Genetic Variants and Environmental Factors Affect Risk of Esophageal Adenocarcinoma and Barrett's Esophagus.

BACKGROUND & AIMS: Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for esophageal adenocarcinoma (EA) and Barrett's esophagus (BE). However, variants in these loci account for a small fraction of cases of EA and BE. Genetic factors might interact with environmental factors to affect risk of EA and BE. We aimed to identify single nucleotide polymorphisms (SNPs) that may modify the associations of body mass index (BMI), smoking, and gastroesophageal reflux disease (GERD), with risks of EA and BE. METHODS: We collected data on single BMI measurements, smoking status, and symptoms of GERD from 2284 patients with EA, 3104 patients with BE, and 2182 healthy individuals (controls) participating in the Barrett's and Esophageal Adenocarcinoma Consortium GWAS, the UK Barrett's Esophagus Gene Study, and the UK Stomach and Oesophageal Cancer Study. We analyzed 993,501 SNPs in DNA samples of all study subjects. We used standard case-control logistic regression to test for gene-environment interactions. RESULTS: For EA, rs13429103 at chromosome 2p25.1, near the RNF144A-LOC339788 gene, showed a borderline significant interaction with smoking status (P = 2.18×10-7). Ever smoking was associated with an almost 12-fold increase in risk of EA among individuals with rs13429103-AA genotype (odds ratio=11.82; 95% CI, 4.03-34.67). Three SNPs (rs12465911, rs2341926, rs13396805) at chromosome 2q23.3, near the RND3-RBM43 gene, interacted with GERD symptoms (P = 1.70×10-7, P = 1.83×10-7, and P = 3.58×10-7, respectively) to affect risk of EA. For BE, rs491603 at chromosome 1p34.3, near the EIF2C3 gene, and rs11631094 at chromosome 15q14, at the SLC12A6 gene, interacted with BMI (P = 4.44×10-7) and pack-years of smoking history (P = 2.82×10-7), respectively. CONCLUSION: The associations of BMI, smoking, and GERD symptoms with risks of EA and BE appear to vary with SNPs at chromosomes 1, 2, and 15. Validation of these suggestive interactions is warranted.UK funding from MRC and Cancer Research U

Parp1 Localizes within the Dnmt1 Promoter and Protects Its Unmethylated State by Its Enzymatic Activity

Aberrant hypermethylation of CpG islands in housekeeping gene promoters and widespread genome hypomethylation are typical events occurring in cancer cells. The molecular mechanisms behind these cancer-related changes in DNA methylation patterns are not well understood. Two questions are particularly important: (i) how are CpG islands protected from methylation in normal cells, and how is this protection compromised in cancer cells, and (ii) how does the genome-wide demethylation in cancer cells occur. The latter question is especially intriguing since so far no DNA demethylase enzyme has been found.Our data show that the absence of ADP-ribose polymers (PARs), caused by ectopic over-expression of poly(ADP-ribose) glycohydrolase (PARG) in L929 mouse fibroblast cells leads to aberrant methylation of the CpG island in the promoter of the Dnmt1 gene, which in turn shuts down its transcription. The transcriptional silencing of Dnmt1 may be responsible for the widespread passive hypomethylation of genomic DNA which we detect on the example of pericentromeric repeat sequences. Chromatin immunoprecipitation results show that in normal cells the Dnmt1 promoter is occupied by poly(ADP-ribosyl)ated Parp1, suggesting that PARylated Parp1 plays a role in protecting the promoter from methylation.In conclusion, the genome methylation pattern following PARG over-expression mirrors the pattern characteristic of cancer cells, supporting our idea that the right balance between Parp/Parg activities maintains the DNA methylation patterns in normal cells. The finding that in normal cells Parp1 and ADP-ribose polymers localize on the Dnmt1 promoter raises the possibility that PARylated Parp1 marks those sequences in the genome that must remain unmethylated and protects them from methylation, thus playing a role in the epigenetic regulation of gene expression

First evidence of Renlandian (c. 950–940 Ma) orogeny in mainland Scotland:Implications for the status of the Moine Supergroup and circum-North Atlantic correlations

Central problems in the interpretation of the Neoproterozoic geology of the North Atlantic region arise from uncertainties in the ages of, and tectonic drivers for, Tonian orogenic events recorded in eastern Laurentia and northern Baltica. The identification and interpretation of these events is often problematic because most rock units that record Tonian orogenesis were strongly reworked at amphibolite facies during the Ordovician-Silurian Caledonian orogeny. Lu-Hf and Sm-Nd geochronology and metamorphic modelling carried out on large (>1 cm) garnets from the Meadie Pelite in the Moine Nappe of the northern Scottish Caledonides indicate prograde metamorphism between 950 and 940 Ma at pressures of 6–7 kbar and temperatures of 600 °C. This represents the first evidence for c. 950 Ma Tonian (Renlandian) metamorphism in mainland Scotland and significantly extends its geographic extent along the palaeo-Laurentian margin. The Meadie Pelite is believed to be part of the Morar Group within the Moine Supergroup. If this is correct: 1) the Morar Group was deposited between 980 ± 4 Ma (age of the youngest detrital zircon; Peters, 2001, youngest published zircon date is 947 ± 189 (Friend et al., 2003)) and c. 950 Ma (age of regional metamorphism reported here), 2) an orogenic unconformity must separate the Morar Group from the 883 ± 35 Ma (Cawood et al., 2004) Glenfinnan and Loch Eil groups, and 3) the term ‘Moine Supergroup’ may no longer be appropriate. The Morar Group is broadly correlative with similar aged metasedimentary successions in Shetland, East Greenland, Svalbard, Ellesmere Island and northern Baltica. All these successions were deposited after c. 1030 Ma, contain detritus from the Grenville orogen, and were later deformed and metamorphosed at 950–910 Ma during accretionary Renlandian orogenesis along an active plate margin developed around this part of Rodinia