GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers

Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. An additional challenge is cross-referencing between species, to compare human profiles with those obtained in a mouse model, for example. We have developed the web-based search engine GeneHopper to link different expression resources based on UniGene clusters and HomoloGene orthologs databases of the National Center for Biotechnology Information (NCBI)

Bubble observations and analysis of the Renland ice core

Bubbles in ice cores store various information about climate conditions during densification and pore close-off in former times. Very recently it was shown that bubbles can additionally be used as marker for cumulated strain within the ice. Bubble studies on the Renland ice core are from particular interest: the Renland ice core includes the oldest bubbly ice retrieved so far in ice core drilling projects and it contains bubbly ice that has been exposed to tremendous deformation and thinning. The Renland ice core of 584 m length was drilled through the ice cap during May-June 2015 in the framework of RECAP (Renland ice cap drilling project). The ice shows no clathrate formation. Preliminary considerations suggest Holocene and Glacial ice with Eemian ice close to bedrock. Core sections of the Renland ice core from selected depth intervals are measured with the means of X-ray computer tomography using the core-scale AWI-ICE CT. The measurements are performed with a spatial resolution of 15µm and provide 3d- bubble arrangements. Different bubble shape factors, bubble volume (porosity), bubble centre distributions and bubble next neighbor functions are derived. We present first depth profiles of these parameters and discuss the results in context of deformation mechanism and paleo climate. It will contribute to reconstruct the complex deformation history of the Renland ice cap

Melt in the Greenland EastGRIP ice core reveals Holocene warm events

We present a record of melt events obtained from the East Greenland Ice Core Project (EastGRIP) ice core in central northeastern Greenland, covering the largest part of the Holocene. The data were acquired visually using an optical dark-field line scanner. We detect and describe melt layers and lenses, seen as bubble-free layers and lenses, throughout the ice above the bubble–clathrate transition. This transition is located at 1150 m depth in the EastGRIP ice core, corresponding to an age of 9720 years b2k. We define the brittle zone in the EastGRIP ice core as that from 650 to 950 m depth, where we count on average more than three core breaks per meter. We analyze melt layer thicknesses, correct for ice thinning, and account for missing layers due to core breaks. Our record of melt events shows a large, distinct peak around 1014 years b2k (986 CE) and a broad peak around 7000 years b2k, corresponding to the Holocene Climatic Optimum. In total, we can identify approximately 831 mm of melt (corrected for thinning) over the past 10 000 years. We find that the melt event from 986 CE is most likely a large rain event similar to that from 2012 CE, and that these two events are unprecedented throughout the Holocene. We also compare the most recent 2500 years to a tree ring composite and find an overlap between melt events and tree ring anomalies indicating warm summers. Considering the ice dynamics of the EastGRIP site resulting from the flow of the Northeast Greenland Ice Stream (NEGIS), we find that summer temperatures must have been at least 3 ± 0.6 ∘C warmer during the Early Holocene compared to today

The solar photospheric abundance of hafnium and thorium. Results from CO5BOLD 3D hydrodynamic model atmospheres

Context: The stable element hafnium (Hf) and the radioactive element thorium (Th) were recently suggested as a suitable pair for radioactive dating of stars. The applicability of this elemental pair needs to be established for stellar spectroscopy. Aims: We aim at a spectroscopic determination of the abundance of Hf and Th in the solar photosphere based on a \cobold 3D hydrodynamical model atmosphere. We put this into a wider context by investigating 3D abundance corrections for a set of G- and F-type dwarfs. Method: High-resolution, high signal-to-noise solar spectra were compared to line synthesis calculations performed on a solar CO5BOLD model. For the other atmospheres, we compared synthetic spectra of CO5BOLD 3D and associated 1D models. Results: For Hf we find a photospheric abundance A(Hf)=0.87+-0.04, in good agreement with a previous analysis, based on 1D model atmospheres. The weak Th ii 401.9 nm line constitutes the only Th abundance indicator available in the solar spectrum. It lies in the red wing of an Ni-Fe blend exhibiting a non-negligible convective asymmetry. Accounting for the asymmetry-related additional absorption, we obtain A(Th)=0.09+-0.03, consistent with the meteoritic abundance, and about 0.1 dex lower than obtained in previous photospheric abundance determinations. Conclusions: Only for the second time, to our knowledge, has am non-negligible effect of convective line asymmetries on an abundance derivation been highlighted. Three-dimensional hydrodynamical simulations should be employed to measure Th abundances in dwarfs if similar blending is present, as in the solar case. In contrast, 3D effects on Hf abundances are small in G- to mid F-type dwarfs and sub-giants, and 1D model atmospheres can be conveniently used.Comment: A&A, in pres

Bipolar ice-core records constrain possible dates and global radiative forcing following the ∼74 ka Toba eruption

The Younger Toba Tuff eruption ∼74 ka ago in Indonesia, is among the largest known supereruptions in the Quaternary and its potential impact on the climate system and human evolution remains controversially debated. The eruption is dated radiometrically to 73.88 ± 0.32 ka (1σ, Storey et al., 2012) and it occurred at the abrupt cooling transition from Greenland Interstadial 20 to Greenland Stadial 20. The precise stratigraphic position of volcanic fallout detected in ice cores from both polar ice sheets has previously been narrowed down to four potential candidates. Here, we compile all available Greenland and Antarctic sulfate records, together with electrical conductivity records and recently obtained sulfur isotope records to identify, quantify and characterize these Toba candidates in terms of their likely latitudinal position of eruption, sulfur emission strength and radiative forcing. We identify that the youngest event of the four candidates is composed of two separate eruptions, both likely located in the extra-tropical Northern Hemisphere. We deem the two older events unlikely candidates for the Toba eruption because of their limited sulfur emission strengths. The second youngest event has the largest sulfur output of the Toba candidates, and it is also larger than any other volcanic event identified in ice core records over the last 60 kyr. Comparable amounts of sulfate deposits in Greenland and Antarctica strongly suggest a tropical source. We thus propose the second youngest event (74,156 years before 2000 CE) to be most likely associated with the Toba eruption. The estimated stratospheric sulfate loading of the proposed Toba eruption is 535 ± 96 Tg, which is 3 times that of Samalas 1258 CE, 6 times that of Tambora (1815) CE and 20 times that of Pinatubo (1991) CE. We derive the continuous time-series of volcanic sulfate deposition, sulfur emission strength and radiative forcing over the 74.8–73.8 ka time window, suitable for conducting experiments with climate models that either require prescribed forcing field or interactively reproduce aerosol processes. We estimate the cumulative volcanic sulfur emission strength and the radiative forcing of the two younger events and they are found to be much stronger than those at the onset of the Younger Dryas and those preceding the Little Ice Age. Stacked Greenland water isotope records show an accelerated transition trend and abrupt shift after the proposed Toba eruption and suggest that the Greenland moisture source moved southward shortly after the Toba eruption. The Toba eruption may thus have an amplifying effect on the cooling transition leading to Greenland Stadial 20

Volcanism and the Greenland ice cores: A new tephrochronological framework for the last glacial-interglacial transition (LGIT) based on cryptotephra deposits in three ice cores

Chemical profiles from Greenland ice cores show that the frequency of volcanism was higher during the last glacial-interglacial transition (LGIT) and early Holocene, (17–9 ka b2k) than in any other period during the last 110 kyr. This increased frequency has partly been linked to climate-driven melting of the Icelandic ice sheet during the last deglaciation, with regional isostatic changes thought to alter mantle viscosity and lead to more eruptions. Our study is the first to construct a comprehensive tephrochronological framework from Greenland ice cores over the LGIT to aid in the reconstruction of volcanic activity over this period. The framework is based on extensive high-resolution sampling of three Greenland ice cores between 17.4 and 11.6 ka b2k and comprises a total of 64 cryptotephra deposits from the NGRIP, GRIP and NEEM ice cores. We show that many of these tephras are preserved within the core without an associated chemical signature in the ice, which implies that reconstructions of volcanism based solely on glacio-chemical indicators might underestimate the number of events. Single glass shards from each deposit were geochemically characterised to trace the volcanic source and many of these deposits could be correlated between cores. We show that the 64 deposits represent tephra deposits from 42 separate volcanic events, and of these, 39 are from Iceland, two from the north Pacific region (Japan and USA) and one has an unknown source. Six deposits can be correlated to terrestrial and/or marine tephra deposits in the Northern Hemisphere and the remaining 36 are unreported in other archives. We did not locate tephra from the compositionally distinctive Laacher See eruption (∼13 ka b2k) in our records. Combining our new discoveries with the previously published tephra framework, raises the number of individual tephra horizons found in Greenland ice over this interval to 50. This significantly improves the regional tephrochronological framework, our knowledge of the eruptive history of Iceland during the LGIT and provides new tephra constraints over key LGIT climate events. Consequentially, this framework can guide sampling strategies of future tephra studies in the terrestrial and marine realms aiming to link these records to the Greenland ice cores to assess regional climate synchroneity

A North Atlantic tephrostratigraphical framework for 130-60 ka b2k:new tephra discoveries, marine-based correlations, and future challenges

Building chronological frameworks for proxy sequences spanning 130–60 ka b2k is plagued by difficulties and uncertainties. Recent developments in the North Atlantic region, however, affirm the potential offered by tephrochronology and specifically the search for cryptotephra. Here we review the potential offered by tephrostratigraphy for sequences spanning 130–60 ka b2k. We combine newly identified cryptotephra deposits from the NGRIP ice-core and a marine core from the Iceland Basin with previously published data from the ice and marine realms to construct the first tephrostratigraphical framework for this time-interval. Forty-three tephra or cryptotephra deposits are incorporated into this framework; twenty three tephra deposits are found in the Greenland ice-cores, including nine new NGRIP tephras, and twenty separate deposits are preserved in various North Atlantic marine sequences. Major, minor and trace element results are presented for the new NGRIP horizons together with age estimates based on their position within the ice-core record. Basaltic tephras of Icelandic origin dominate the framework with only eight tephras of rhyolitic composition found. New results from marine core MD99-2253 also illustrate some of the complexities and challenges of assessing the depositional integrity of marine cryptotephra deposits. Tephra-based correlations in the marine environment provide independent tie-points for this time-interval and highlight the potential of widening the application of tephrochronology. Further investigations, however, are required, that combine robust geochemical fingerprinting and a rigorous assessment of tephra depositional processes, in order to trace coeval events between the two depositional realms

An osteometrical method for sexing cattle bones: the metacarpals from 17th century Carnide, Lisbon, Portugal

Measurements taken on 47 complete and 44 distal fragments of cattle metacarpals from 17th century AD Carnide, Lisbon, separate into two groups. Comparison with 21 ancient DNA sexed specimens and modern specimens of known sex (seven Barrosã cows and a Barrosã bull), indicates that the Carnide metacarpals probably belonged to both cows and bulls/oxen. We use the 47 complete metacarpals as a “sexed reference sample” in order to find which measurements generally taken by zooarchaeologists on the distal metacarpal help separate males from females. Widths appear to be most useful. The modern Barrosã cattle in our collection, selected for their meat, have wider metacarpals than the ones from Carnide; the latter were perhaps more generalist animals.info:eu-repo/semantics/publishedVersio

The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders

Abstract: Objectives: In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. Methods: We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. Results: The genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style. Conclusion: We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange