Controls on planktonic foraminifera apparent calcification depths for the northern equatorial Indian Ocean

Within the world’s oceans, regionally distinct ecological niches develop due to differences in water temperature, nutrients, food availability, predation and light intensity. This results in differences in the vertical dispersion of planktonic foraminifera on the global scale. Understanding the controls on these modern-day distributions is important when using these organisms for paleoceanographic reconstructions. As such, this study constrains modern depth habitats for the northern equatorial Indian Ocean, for 14 planktonic foraminiferal species (G. ruber, G. elongatus, G. pyramidalis, G. rubescens, T. sacculifer, G. siphonifera, G. glutinata, N. dutertrei, G. bulloides, G. ungulata, P. obliquiloculata, G. menardii, G. hexagonus, G. scitula) using stable isotopic signatures (δ18O and δ13C) and Mg/Ca ratios. We evaluate two aspects of inferred depth habitats: (1) the significance of the apparent calcification depth (ACD) calculation method/equations and (2) regional species-specific ACD controls. Through a comparison with five global, (sub)tropical studies we found the choice of applied equation and δ18Osw significant and an important consideration when comparing with the published literature. The ACDs of the surface mixed layer and thermocline species show a tight clustering between 73–109 m water depth coinciding with the deep chlorophyll maximum (DCM). Furthermore, the ACDs for the sub-thermocline species are positioned relative to secondary peaks in the local primary production. We surmise that food source plays a key role in the relative living depths for the majority of the investigated planktonic foraminifera within this oligotrophic environment of the Maldives and elsewhere in the tropical oceans

Convergent evolution of water conducting cells in Marchantia recruited the ZHOUPI gene promoting cell wall reinforcement and programmed cell death

A key adaptation of plants to life on land is the formation of water conducting cells (WCC) for efficient long-distance water transport. Based on morphological analyses it is thought that WCC have evolved independently on multiple occasions. For example, WCC have been lost in all but a few lineages of bryophytes but strikingly, within the liverworts a derived group, the complex thalloids, has evolved a novel externalised water conducting tissue composed of reinforced, hollow cells termed pegged rhizoids. Here we show that pegged rhizoid differentiation in Marchantia polymorpha is controlled by orthologues of the ZHOUPI and ICE bHLH transcription factors required for endosperm cell death in Arabidopsis seeds. By contrast, pegged rhizoid development was not affected by disruption of MpNAC5, the Marchantia orthologue of the VND genes that control WCC formation in flowering plants. We characterize the rapid, genetically controlled programmed cell death process that pegged rhizoids undergo to terminate cellular differentiation, and identify a corresponding upregulation of conserved putative plant cell death effector genes. Lastly, we show that ectopic expression of MpZOU1 increases production of pegged rhizoids and enhances drought tolerance. Our results support that pegged rhizoids having evolved independently of other WCC. We suggest that elements of the genetic control of developmental cell death are conserved throughout land plants and that the ZHOUPI/ICE regulatory module has been independently recruited to promote cell wall modification and programmed cell death in liverwort rhizoids and in the endosperm of flowering plant seed

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)

A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes

Assessing the impact of diagenesis on foraminiferal geochemistry from a low latitude, shallow-water drift deposit

Due to their large heat and moisture storage capabilities, the tropics are fundamental in modulating both regional and global climate. Furthermore, their thermal response during past extreme warming periods, such as super interglacials, is not fully resolved. In this regard, we present high-resolution (analytical) foraminiferal geochemical (δ18O and Mg/Ca) records for the last 1800 kyr from the shallow (487 m) Inner Sea drift deposits of the Maldives archipelago in the equatorial Indian Ocean. Considering the diagenetic susceptibility of these proxies, in carbonate-rich environments, we assess the integrity of a suite of commonly used planktonic and benthic foraminifera geochemical datasets (Globigerinoides ruber (white), Globigerinita glutinata (with bulla), Pulleniatina obliquiloculata (with cortex) and Cibicides mabahethi) and their use for future paleoceanographic reconstructions. Using a combination of spot Secondary Ion Mass Spectrometer, Electron Probe Micro-Analyzer and Scanning Electron Microscope image data, it is evident that authigenic overgrowths are present on both the external and internal test (shell) surfaces, yet the degree down-core as well as the associated bias is shown to be variable across the investigated species and proxies. Given the elevated authigenic overgrowth Mg/Ca (∼12–22 mmol/mol) and δ18O values (closer to the benthic isotopic compositions) the whole-test planktonic G. ruber (w) geochemical records are notably impacted beyond ∼627.4 ka (24.7 mcd). Yet, considering the setting (i.e. bottom water location) for overgrowth formation, the benthic foraminifera δ18O record is markedly less impacted with only minor diagenetic bias beyond ∼790.0 ka (28.7 mcd). Even though only the top of the G. ruber (w) and C. mabahethi records (whole-test data) would be suitable for paleo-reconstructions of absolute values (i.e. sea surface temperature, salinity, seawater δ18O), the long-term cycles, while dampened, appear to be preserved. Furthermore, planktonic species with thicker-tests (i.e. P. obliquiloculata (w/c)) might be better suited, in comparison to thinner-test counter-parts (i.e. G. glutinata (w/b), G. ruber (w)), for traditional whole- test geochemical studies in shallow, carbonate-rich environments. A thicker test equates to a smaller overall bias from the authigenic overgrowth. Overall, if the diagenetic impact is constrained, as done in this study, these types of diagenetically altered geochemical records can still significantly contribute to studies relating to past tropical seawater temperatures, latitudinal scale ocean current shifts and South Asian Monsoon dynamics

Correction to:A two million year record of low-latitude aridity linked to continental weathering from the Maldives (Progress in Earth and Planetary Science, (2018), 5, 1, (86), 10.1186/s40645-018-0238-x)

In the original version of this article (Kunkelova et al. 2018), published on 18 December 2018, there was 1 error in the author name of Dr. Yu

Antagonistic Roles of SEPALLATA3, FT and FLC Genes as Targets of the Polycomb Group Gene CURLY LEAF

In Arabidopsis, mutations in the Pc-G gene CURLY LEAF (CLF) give early flowering plants with curled leaves. This phenotype is caused by mis-expression of the floral homeotic gene AGAMOUS (AG) in leaves, so that ag mutations largely suppress the clf phenotype. Here, we identify three mutations that suppress clf despite maintaining high AG expression. We show that the suppressors correspond to mutations in FPA and FT, two genes promoting flowering, and in SEPALLATA3 (SEP3) which encodes a co-factor for AG protein. The suppression of the clf phenotype is correlated with low SEP3 expression in all case and reveals that SEP3 has a role in promoting flowering in addition to its role in controlling floral organ identity. Genetic analysis of clf ft mutants indicates that CLF promotes flowering by reducing expression of FLC, a repressor of flowering. We conclude that SEP3 is the key target mediating the clf phenotype, and that the antagonistic effects of CLF target genes masks a role for CLF in promoting flowering

A two million year record of low-latitude aridity linked to continental weathering from the Maldives

Tem uma correção em http://hdl.handle.net/10400.1/12390Indian-Asian monsoon has oscillated between warm/wet interglacial periods and cool/dry glacial periods with periodicities closely linked to variations in Earth’s orbital parameters. However, processes that control wet versus dry, i.e. aridity cyclical periods on the orbital time-scale in the low latitudes of the Indian-Asian continent remain poorly understood because records over millions of years are scarce. The sedimentary record from International Ocean Discovery Program (IODP) Expedition 359 provides a well-preserved, high-resolution, continuous archive of lithogenic input from the Maldives reflecting on low-latitude aridity cycles. Variability within the lithogenic component of sedimentary deposits of the Maldives results from changes in monsoon-controlled sedimentary sources. Here, we present X-ray fluorescence (XRF) core-scanning results from IODP Site U1467 for the past two million years, allowing full investigation of orbital periodicities. We specifically use the Fe/K as a terrestrial climate proxy reflecting on wet versus dry conditions in the source areas of the Indian-Asian landmass, or from further afield. The Fe/K record shows orbitally forced cycles reflecting on changes in the relative importance of aeolian (stronger winter monsoon) during glacial periods versus fluvial supply (stronger summer monsoon) during interglacial periods. For our chronology, we tuned the Fe/K cycles to precessional insolation changes, linking Fe/K maxima/minima to insolation minima/maxima with zero phase lag. Wavelet and spectral analyses of the Fe/K record show increased dominance of the 100 kyr cycles after the Mid Pleistocene Transition (MPT) at 1.25 Ma in tandem with the global ice volume benthic δ18O data (LR04 record). In contrast to the LR04 record, the Fe/K profile resolves 100-kyr-like cycles around the 130 kyr frequency band in the interval from 1.25 to 2 million years. These 100-kyr-like cycles likely form by bundling of two or three obliquity cycles, indicating that low-latitude Indian-Asian climate variability reflects on increased tilt sensitivity to regional eccentricity insolation changes (pacing tilt cycles) prior to the MPT. The implication of appearance of the 100 kyr cycles in the LR04 and the Fe/K records since the MPT suggests strengthening of a climate link between the low and high latitudes during this period of climate transition.SFRH/BPD/96960/2013; PTDC/MAR-PRO/3396/2014info:eu-repo/semantics/publishedVersio

Kicking against the PRCs - a domesticated transposase antagonises silencing mediated by polycomb group proteins and is an accessory component of polycomb repressive complex 2

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity.Fil: Liang, Shih Chieh. University of Edinburgh; Reino UnidoFil: Hartwig, Ben. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Perera, Pumi. University of Edinburgh; Reino UnidoFil: Mora Garcia, Santiago. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires; ArgentinaFil: de Leau, Erica. University of Edinburgh; Reino UnidoFil: Thornton, Harry. University of Edinburgh; Reino UnidoFil: Lima de Alves, Flavia. University of Edinburgh; Reino UnidoFil: Rapsilber, Juri. University of Edinburgh; Reino UnidoFil: Yang, Suxin. University of Edinburgh; Reino UnidoFil: James, Geo Velikkakam. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Schneeberger, Korbinian. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Finnegan, E. Jean. University of Edinburgh; Reino UnidoFil: Turck, Franziska. Max Planck Institute for Plant Breeding Research; AlemaniaFil: Goodrich, Justin. Mc Gill University; Canad