Geodynamic implications for zonal and meridional isotopic patterns across the northern Lau and North Fiji Basins

We present new Sr-Nd-Pb-Hf-He isotopic data for sixty-five volcanic samples from the northern Lau and North Fiji Basin. This includes forty-seven lavas obtained from forty dredge sites spanning an east-west transect across the Lau and North Fiji basins, ten ocean island basalt (OIB)-type lavas collected from seven Fijian islands, and eight OIB lavas sampled on Rotuma. For the first time we are able to map clear north-south and east-west geochemical gradients in 87Sr/86Sr across the northern Lau and North Fiji Basins: lavas with the most geochemically enriched radiogenic isotopic signatures are located in the northeast Lau Basin, while signatures of geochemical enrichment are diminished to the south and west away from the Samoan hotspot. Based on these geochemical patterns and plate reconstructions of the region, these observations are best explained by the addition of Samoa, Rurutu, and Rarotonga hotspot material over the past 4 Ma. We suggest that underplated Samoan material has been advected into the Lau Basin over the past ∼4 Ma. As the slab migrated west (and toward the Samoan plume) via rollback over time, younger and hotter (and therefore less viscous) underplated Samoan plume material was entrained. Thus, entrainment efficiency of underplated plume material was enhanced, and Samoan plume signatures in the Lau Basin became stronger as the trench approached the Samoan hotspot. The addition of subducted volcanoes to the Cook-Austral Volcanic Lineament material, first from the Rarotonga hotspot, then followed by the Rurutu hotspot, contributes to the extreme geochemical signatures observed in the northeast Lau Basin

High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation

Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a highresolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

Polycomb proteins maintain cell identity by repressing the expression of developmental regulators specific for other cell types. Polycomb repressive complex-2 (PRC2) catalyzes trimethylation of histone H3 lysine-27 (H3K27me3). Although repressed, PRC2 targets are generally associated with the transcriptional initiation marker H3K4me3, but the significance of this remains unclear. Here, we identify a class of short RNAs, ~50–200 nucleotides in length, transcribed from the 5′ end of polycomb target genes in primary T cells and embryonic stem cells. Short RNA transcription is associated with RNA polymerase II and H3K4me3, occurs in the absence of mRNA transcription, and is independent of polycomb activity. Short RNAs form stem-loop structures resembling PRC2 binding sites in Xist, interact with PRC2 through SUZ12, cause gene repression in cis, and are depleted from polycomb target genes activated during cell differentiation. We propose that short RNAs play a role in the association of PRC2 with its target genes.National Institutes of Health (U.S.) (Grant HG002668)National Institutes of Health (U.S.) (Grant NS055923

Geodynamic implications for zonal and meridional isotopic patterns across the northern Lau and North Fiji Basins

We present new Sr-Nd-Pb-Hf-He isotopic data for 65 volcanic samples from the northern Lau and North Fiji Basins. This includes 47 lavas obtained from 40 dredge sites spanning an east-west transect across the Lau and North Fiji basins, 10 ocean island basalt (OIB)-type lavas collected from seven Fijian islands, and eight OIB lavas sampled on Rotuma. For the first time, we are able to map clear north-south and east-west geochemical gradients in 87Sr/86Sr across the northern Lau and North Fiji Basins: lavas with the most geochemically enriched radiogenic isotopic signatures are located in the northeast Lau Basin, while signatures of geochemical enrichment are diminished to the south and west away from the Samoan hot spot. Based on these geochemical patterns and plate reconstructions of the region, these observations are best explained by the addition of Samoa, Rurutu, and Rarotonga hot spot material over the past 4 Ma. We suggest that underplated Samoan material has been advected into the Lau Basin over the past ∼4 Ma. As the slab migrated west (and toward the Samoan plume) via rollback over time, younger and hotter (and therefore less viscous) underplated Samoan plume material was entrained. Thus, entrainment efficiency of underplated plume material was enhanced, and Samoan plume signatures in the Lau Basin became stronger as the trench approached the Samoan hot spot. The addition of subducted volcanoes from the Cook-Austral Volcanic Lineament first from the Rarotonga hot spot, then followed by the Rurutu hot spot, contributes to the extreme geochemical signatures observed in the northeast Lau BasinMGJ acknowledges NSF grants EAR-1624840, EAR-1348082, and EAR-1347377. JBT acknowledges financial support from the French Agence Nationale de la Recherche through grant ANR-10-BLAN-0603 (M&Ms—Mantle Melting—Measurements, Models, Mechanisms). MDK acknowledges NSF support for the noble gas laboratory at WHOI (via OCE-1232985 and OCE −1259218) and the noble gas analytical efforts of Joshua Curtice. FEJ acknowledges funding from the Deep Carbon Observatory (DCO). We also thank Paul Hall for insightful discussions and two unnamed reviewers for their helpful comments

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors

The competing effects of sulfide saturation versus degassing on the behavior of the chalcophile elements during the differentiation of hydrous melts

There is a lack of consensus regarding the roles of sulfide saturation versus volatile degassing on the partitioning of Cu and Ag during differentiation and eruption of convergent margin magmas. Because of their oxidized character, volatile-rich magmas from the Eastern Manus Back-arc Basin (EMBB) only reach sulfide saturation following magnetite-driven reduction of the melt: the so-called “magnetite crisis.” If sulfide saturation typically precedes volatile saturation, the magnetite crisis will limit the proportion of Cu and Ag that can partition from the melt into an exsolving volatile-rich phase, which may contribute to the sporadic occurrence of magmatic-hydrothermal ore deposits at convergent margins. However, it is unclear whether the magnetite crisis is a common or rare event during differentiation of volatile-rich magmas. We report major and trace element data for submarine volcanic glasses from the Tonga arc-proximal Valu Fa Ridge (VFR; SW Pacific). Cu-Se-Ag systematics of samples erupting at the southern VFR suggest magnetite fractionation-triggered sulfide saturation. The similarity in chalcophile element systematics of the southern VFR and EMBB samples is unlikely to be coincidental, and may indicate that the magnetite crisis is a common event during differentiation of hydrous melts. However, unlike many convergent margin magmas, it is unlikely that the evolving VFR and EMBB were saturated in a S-bearing volatile phase prior to magnetite fractionation. Hence, the metal-depleting magnetite crisis may be restricted to back-arc basin magmas that do not degas volatiles prior to magnetite fractionation and potentially convergent margin magmas fractionating at high pressures in the continental crust

Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation

Two T helper (Th) cell subsets, namely Th1 and Th2 cells, play an important role in inflammatory diseases. The two subsets are thought to counter-regulate each other, and alterations in their balance result in different diseases. This paradigm has been challenged by recent clinical and experimental data. Because of the large number of genes involved in regulating Th1 and Th2 cells, assessment of this paradigm by modeling or experiments is difficult. Novel algorithms based on formal methods now permit the analysis of large gene regulatory networks. By combining these algorithms with in silico knockouts and gene expression microarray data from human T cells, we examined if the results were compatible with a counter-regulatory role of Th1 and Th2 cells. We constructed a directed network model of genes regulating Th1 and Th2 cells through text mining and manual curation. We identified four attractors in the network, three of which included genes that corresponded to Th0, Th1 and Th2 cells. The fourth attractor contained a mixture of Th1 and Th2 genes. We found that neither in silico knockouts of the Th1 and Th2 attractor genes nor gene expression microarray data from patients with immunological disorders and healthy subjects supported a counter-regulatory role of Th1 and Th2 cells. By combining network modeling with transcriptomic data analysis and in silico knockouts, we have devised a practical way to help unravel complex regulatory network topology and to increase our understanding of how network actions may differ in health and disease

Direct measurements of meltwater runoff on the Greenland ice sheet surface

Meltwater runoff from the Greenland ice sheet surface influences surface mass balance (SMB), ice dynamics, and global sea level rise, but is estimated with climate models and thus difficult to validate. We present a way to measure ice surface runoff directly, from hourly in situ supraglacial river discharge measurements and simultaneous high-resolution satellite/drone remote sensing of upstream fluvial catchment area. A first 72-h trial for a 63.1-km2 moulin-terminating internally drained catchment (IDC) on Greenland?s midelevation (1,207?1,381 m above sea level) ablation zone is compared with melt and runoff simulations from HIRHAM5, MAR3.6, RACMO2.3, MERRA-2, and SEB climate/SMB models. Current models cannot reproduce peak discharges or timing of runoff entering moulins but are improved using synthetic unit hydrograph (SUH) theory. Retroactive SUH applications to two older field studies reproduce their findings, signifying that remotely sensed IDC area, shape, and supraglacial river length are useful for predicting delays in peak runoff delivery to moulins. Applying SUH to HIRHAM5, MAR3.6, and RACMO2.3 gridded melt products for 799 surrounding IDCs suggests their terminal moulins receive lower peak discharges, less diurnal variability, and asynchronous runoff timing relative to climate/SMB model output alone. Conversely, large IDCs produce high moulin discharges, even at high elevations where melt rates are low. During this particular field experiment, models overestimated runoff by +21 to +58%, linked to overestimated surface ablation and possible meltwater retention in bare, porous, low-density ice. Direct measurements of ice surface runoff will improve climate/SMB models, and incorporating remotely sensed IDCs will aid coupling of SMB with ice dynamics and subglacial systemspublishersversionPeer reviewe