ALBERT

Description: Volcanoes represent an important natural source of several trace elements to the atmosphere. For some species (e.g., As, Cd, Pb and Se) they may be the main natural source and thereby strongly influencing geochemical cycles from the local to the global scale. Mount Etna is one of the most actively degassing volcanoes in the world, and it is considered to be, on the long-term average, the major atmospheric point source of many environmental harmful compounds. Their emission occurs either through continuous passive degassing from open-conduit activity or through sporadic paroxysmal eruptive activity, in the form of gases, aerosols or particulate. To estimate the environmental impact of magma-derived trace metals and their depositions processes, rainwater and snow samples were collected at Mount Etna area. Five bulk collectors have been deployed at various altitudes on the upper flanks around the summit craters of the volcano; samples were collected every two week for a period of one year and analyzed for the main chemical-physical parameters (electric conductivity and pH) and for major and trace elements concentrations. Chemical analysis of rainwater clearly shows that the volcanic contribution is always prevailing in the sampling site closest to the summit crater (about 1.5 km). In the distal sites (5.5-10 km from the summit) and downwind of the summit craters, the volcanic contribution is also detectable but often overwhelmed by anthropogenic or other natural (seawater spray, geogenic dust) contributions. Volcanic contribution may derive from both dry and wet deposition of gases and aerosols from the volcanic plume, but sometimes also from leaching of freshly emitted volcanic ashes. In fact, in our background site (7.5 km in the upwind direction) volcanic contribution has been detected only following an ash deposition event. About 30 samples of fresh snow were collected in the upper part of the volcano, during the winters 2006 and 2007 to estimate deposition processes at high altitude during cold periods. Some of the samples were collected immediately after a major explosive event from the summit craters to understand the interaction between snow and fresh erupted ash. Sulphur, Chlorine and Fluorine, are the major elements that prevailingly characterize the volcanic contribution in atmospheric precipitation on Mount Etna, but high concentrations of many trace elements are also detected in the studied samples. In particular, bulk deposition samples display high concentration of Al, Fe, Ti, Cu, As, Rb, Pb, Tl, Cd, Cr, U and Ag, in the site most exposed to the volcanic emissions: median concentration values are about two orders of magnitude higher than those measured in our background site. Also in the snow samples the volcanic signature is clearly detectable and decreases with distance from the summit craters. Some of the analysed elements display very high enrichment values with respect to the average crust and, in the closest site to the summit craters, also deposition values higher than those measured in polluted urban or industrial sites.

Description: Published

Description: Vienna, Austria

Description: 4.5. Degassamento naturale

Description: open

Description: Improving the constraints on the atmospheric fate and depletion rates of acidic compounds persistently emitted by non-erupting (quiescent) volcanoes is important for quantitatively predicting the environmental impact of volcanic gas plumes. Here, we present new experimental data coupled with modelling studies to investigate the chemical processing of acidic volcanogenic species during tropospheric dispersion. Diffusive tube samplers were deployed at Mount Etna, a very active open-conduit basaltic volcano in eastern Sicily, and Vulcano Island, a closed-conduit quiescent volcano in the Aeolian Islands (northern Sicily). Sulphur dioxide (SO2), hydrogen sulphide (H2S), hydrogen chloride (HCl) and hydrogen fluoride (HF) concentrations in the volcanic plumes (typically several minutes to a few hours old) were repeatedly determined at distances from the summit vents ranging from 0.1 to ~10 km, and under different environmental conditions. At both volcanoes, acidic gas concentrations were found to decrease exponentially with distance from the summit vents (e.g., SO2 decreases from ~10,000 μg/m3 at 0.1 km from Etna’s vents down to ~7 _μg/m3 at ~10km distance), reflecting the atmospheric dilution of the plume within the acid gas-free background troposphere. Conversely, SO2/HCl, SO2/HF, and SO2/H2S ratios in the plume showed no systematic changes with plume aging, and fit source compositions within analytical error. Assuming that SO2 losses by reaction are small during short-range atmospheric transport within quiescent (ash-free) volcanic plumes, our observations suggest that, for these short transport distances, atmospheric reactions for H2S and halogens are also negligible. The one-dimensional model MISTRA was used to simulate quantitatively the evolution of halogen and sulphur compounds in the plume of Mt. Etna. Model predictions support the hypothesis of minor HCl chemical processing during plume transport, at least in cloud-free conditions. Larger variations in the modelled SO2/HCl ratios were predicted under cloudy conditions, due to heterogeneous chlorine cycling in the aerosol phase. The modelled evolution of the SO2/H2S ratios is found to be substantially dependent on whether or not the interactions of H2S with halogens are included in the model. In the former case, H2S is assumed to be oxidized in the atmosphere mainly by OH, which results in minor chemical loss for H2S during plume aging and produces a fair match between modelled and measured SO2/H2S ratios. In the latter case, fast oxidation of H2S by Cl leads to H2S chemical lifetimes in the early plume of a few seconds, and thus SO2 to H2S ratios that increase sharply during plume transport. This disagreement between modelled and observed plume compositions suggests that more in-detail kinetic investigations are required for a proper evaluation of H2S chemical processing in volcanic plumes.

Description: Published

Description: 1441-1450

Description: 1.2. TTC - Sorveglianza geochimica delle aree vulcaniche attive

Description: 4.5. Degassamento naturale

Description: JCR Journal

Description: open

Description: After some short test surveys, during the 2004–2005 summer expedition in Antarctica, a geomagnetic French-Italian observatory was installed on the plateau (geographic coordinates: 75.1 S, 123.4 E; corrected geomagnetic coordinates: 88.9 S, 54.3 E; UT=LT−8) very close to the geomagnetic pole. In this paper we present some peculiarities of the daily variation as observed at this polar cap observatory during the years 2005 and 2006, taking into account the different Loyd seasons and different interplanetary magnetic field conditions. Some interesting results emerge from the analysis, confirming the dependence of the daily variation (and of the associated polar current systems) on the IMF Bz and By components. In particular the analysis showed that different Bz conditions correspond to different contribution to daily variation of ionospheric and field aligned currents, while particular By conditions lead to a time shift of the diurnal variation, indicating an asymmetry with respect to the noon meridian.

Description: Published

Description: 2045–2051

Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale

Description: 1.6. Osservazioni di geomagnetismo

Description: JCR Journal

Description: reserved

Description: © 2008 Hutt et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Developmental Biology 8 (2008): 1, doi:10.1186/1471-213X-8-1.

Description: Environmental toxicants, whose actions are often mediated through the aryl hydrocarbon receptor (AhR) pathway, pose risks to the health and well-being of exposed species, including humans. Of particular concern are exposures during the earliest stages of development that while failing to abrogate embryogenesis, may have long term effects on newborns or adults. The purpose of this study was to evaluate the effect of maternal exposure to the AhR-specific ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the development of rat pre-implantation embryos with respect to nuclear and cytoskeletal architecture and cell lineage allocation. We performed a systematic 3 dimensional (3D) confocal microscopy analysis of rat pre-implantation embryos following maternal exposure to environmentally relevant doses of TCDD. Both chronic (50 ng/kg/wk for 3 months) and acute (50 ng/kg and 1 μg/kg at proestrus) maternal TCDD exposure disrupted morphogenesis at the compaction stage (8–16 cell), with defects including monopolar spindle formation, f-actin capping and fragmentation due to aberrant cytokinesis. Additionally, the size, shape and position of nuclei were modified in compaction stage pre-implantation embryos collected from treated animals. Notably, maternal TCDD exposure did not compromise survival to blastocyst, which with the exception of nuclear shape, were morphologically similar to control blastocysts. We have identified the compaction stage of pre-implantation embryogenesis as critically sensitive to the effects of TCDD, while survival to the blastocyst stage is not compromised. To the best of our knowledge this is the first in vivo study to demonstrate a critical window of pre-implantation mammalian development that is vulnerable to disruption by an AhR ligand at environmentally relevant doses.

Description: This research was supported by NIH/NIEHS-012916 (BKP), ESHE Fund (DFA), Hall Family Foundation (DFA and KJH) and Biomedical Research Training Grant KUMC (KJH).

Description: © 2007 Ioannidis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 8 (2007): 182, doi:10.1186/1471-2164-8-182.

Description: Background: The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria. Results: Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein). Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites. Conclusion: The sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.

Description: PI, PS, SS, GT and KB acknowledge support of their work from intramural funding from the University of Ioannina. SB, JDH, LB and JW acknowledge support of their work from the U.S. National Science Foundation grant EF-0328363. SB also acknowledges the support from the NASA Astrobiology Institute (NNA04CC04A)

Description: © 2007 Huse et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R143, doi:10.1186/gb-2007-8-7-r143.

Description: Additional data file 1 is a fasta file of the 43 known sequences used. Additional data file 2 is a gzip-compressed fasta file of the sequences output by the GS20. These sequences correspond to those included in Additional data files 3, 4, 5 but include only the final sequence information. Additional data files 3, 4, 5 are three compressed text files representing the text translations of the original GS20 binary output (sff) files for all of the sequencing used in the analysis, including sequence, flowgram and other run information. GS20 data are reported by region of the PicoTiterPlate™; we sequenced three plate regions.

Description: Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls. We performed an empirical study of the per-base error rate for the Roche GS20 system using sequences of the V6 hypervariable region from cloned microbial ribosomal DNA (tag sequencing). We calculated a 99.5% accuracy rate in unassembled sequences, and identified several factors that can be used to remove a small percentage of low-quality reads, improving the accuracy to 99.75% or better. By using objective criteria to eliminate low quality data, the quality of individual GS20 sequence reads in molecular ecological applications can surpass the accuracy of traditional capillary methods.

Description: This work was supported by National Aeronautics and Space Administration Astrobiology Institute Cooperative Agreement NNA04CC04A (to MLS), subcontracts from the Woods Hole Center for Oceans and Human Health from the National Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724-J Stegeman PI to HGM and MLS), grants from the WM Keck Foundation and the G Unger Vetlesen Foundation (to MLS), and a National Research Council Research Associateship Award (to JAH).

Description: © 2008 Salvador-Recatalà et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Physiology 8 (2008): 6, doi:10.1186/1472-6793-8-6.

Description: The function of voltage-gated calcium (Cav) channels greatly depends on coupling to cytoplasmic accessory β subunits, which not only promote surface expression, but also modulate gating and kinetic properties of the α1 subunit. Schistosomes, parasitic platyhelminths that cause schistosomiasis, express two β subunit subtypes: a structurally conventional β subunit and a variant β subunit with unusual functional properties. We have previously characterized the functional properties of the variant Cavβ subunit. Here, we focus on the modulatory phenotype of the conventional Cavβ subunit (SmCavβ) using the human Cav2.3 channel as the substrate for SmCavβ and the whole-cell patch-clamp technique. The conventional Schistosoma mansoni Cavβ subunit markedly increases Cav2.3 currents, slows macroscopic inactivation and shifts steady state inactivation in the hyperpolarizing direction. However, currents produced by Cav2.3 in the presence of SmCavβ run-down to approximately 75% of their initial amplitudes within two minutes of establishing the whole-cell configuration. This suppressive effect was independent of Ca2+, but dependent on intracellular Mg2+-ATP. Additional experiments revealed that SmCavβ lends the Cav2.3/SmCavβ complex sensitivity to Na+ ions. A mutant version of the Cavβ subunit lacking the first forty-six amino acids, including a string of twenty-two acidic residues, no longer conferred sensitivity to intracellular Mg2+-ATP and Na+ ions, while continuing to show wild type modulation of current amplitude and inactivation of Cav2.3. The data presented in this article provide insights into novel mechanisms employed by platyhelminth Cavβ subunits to modulate voltage-gated Ca2+ currents that indicate interactions between the Ca2+ channel complex and chelated forms of ATP as well as Na+ ions. These results have potentially important implications for understanding previously unknown mechanisms by which platyhelminths and perhaps other organisms modulate Ca2+ currents in excitable cells.

Description: This work was supported by NIH grant #s R01 AI-40522 and R01 AI-73660 to RMG and by NIH-NCRR grant # P41 RR001395 to the Biocurrents Research Center (BRC) at MBL.

Description: © 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 9 (2008): 210, doi:10.1186/1471-2164-9-210.

Description: The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.

Description: MR acknowledges support from DE-FG02-04ER63940. JTS acknowledges the support from the University of Washington NASA NAI program and the NSF Astrobiology IGERT program. TZW acknowledges support from a grant from the Fondation Fourmentin-Guilbert and AD acknowledges support from the European Union BioSapiens Network of Excellence, Grant LSHG CT-2003-503265

Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Genomics 10 (2009): 11, doi:10.1186/1471-2164-10-11.

Description: Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. Current results provide quantitative substitution preferences (or avoidance) of amino acids that lead to the adaptation of proteins to cold temperatures. These finding would help future efforts in selecting mutations for rational design of proteins with enhanced psychrophilic properties.

Description: This work was supported by a grant from Howard Hughes Medical Institute to Queens College, CUNY, and Queens College Research Enhancement Grant.

Description: © 2009 Sarkar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Research Notes 2 (2009): 101, doi:10.1186/1756-0500-2-101.

Description: GenBank(R) is a public repository of all publicly available molecular sequence data from a range of sources. In addition to relevant metadata (e.g., sequence description, source organism and taxonomy), publication information is recorded in the GenBank data file. The identification of literature associated with a given molecular sequence may be an essential first step in developing research hypotheses. Although many of the publications associated with GenBank records may not be linked into or part of complementary literature databases (e.g., PubMed), GenBank records associated with literature indexed in Medline are identifiable as they contain PubMed identifiers (PMIDs). Here we show that an analysis of 87,116,501 GenBank sequence files reveals that 42% are associated with a publication or patent. Of these, 71% are associated with PMIDs, and can therefore be linked to a citation record in the PubMed database. The remaining (29%) of publication-associated GenBank entries either do not have PMIDs or cite a publication that is not currently indexed by PubMed. We also identify the journal titles that are linked through citations in the GenBank files to the largest number of sequences. Our analysis suggests that GenBank contains molecular sequences from a range of disciplines beyond biomedicine, the initial scope of PubMed. The findings thus suggest opportunities to develop mechanisms for integrating biological knowledge beyond the biomedical field.

Description: INS and HM are funded in part by a research grant from the Ellison Medical Foundation and National Library of Medicine award R01LM009725 to INS.

Description: © 2009 Reitzel and Tarrant. This is an open-access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 9 (2009): 230, doi:10.1186/1471-2148-9-230.

Description: Nuclear receptors are a superfamily of metazoan transcription factors that regulate diverse developmental and physiological processes. Sequenced genomes from an increasing number of bilaterians have provided a more complete picture of duplication and loss of nuclear receptors in protostomes and deuterostomes but have left open the question of which nuclear receptors were present in the cnidarian-bilaterian ancestor. In addition, nuclear receptor expression and function are largely uncharacterized within cnidarians, preventing determination of conserved and novel nuclear receptor functions in the context of animal evolution. Here we report the first complete set of nuclear receptors from a cnidarian, the starlet sea anemone Nematostella vectensis. Genomic searches using conserved DNA- and ligand-binding domains revealed seventeen nuclear receptors in N. vectensis. Phylogenetic analyses support N. vectensis orthologs of bilaterian nuclear receptors in four nuclear receptor subfamilies within nuclear receptor family 2 (COUP-TF, TLL, HNF4, TR2/4) and one putative ortholog of GCNF (nuclear receptor family 6). Other N. vectensis genes grouped well with nuclear receptor family 2 but represented lineage-specific duplications somewhere within the cnidarian lineage and were not clear orthologs of bilaterian genes. Three nuclear receptors were not well-supported within any particular nuclear receptor family. The seventeen nuclear receptors exhibited distinct developmental expression patterns, with expression of several nuclear receptors limited to a subset of developmental stages. N. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation for mechanistic characterization of cnidarian nuclear receptor function.

Description: We are grateful for financial support from the Woods Hole Oceanographic Institution (WHOI) through the Tropical Research Initiative, the Ocean Life Institute (AMT), the Academic Programs Office, and to the Beacon Institute for Rivers and Estuaries (AMR).

Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.

Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.

Description: The National Center for Atmospheric Research is supported by the National Science Foundation.

Description: Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.

Description: Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.

Description: This work was supported by NIH grant RO1 RR07861, the NASA Astrobiology Institute grant NCC2-1054, grants from the Edward Mallinckrodt, Jr Foundation and the Sinsheimer Foundation, and NSF grants NSF DBI - 9984882 and NSF IIS - 9996304.

Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.

Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.

Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.

Description: From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006.

Description: © 2006 Nahum et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Description: EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs.

Description: This work was partly funded by the National Institutes of Health (R22/R33 Innovation and Development grant to David Pollock), the National Science Foundation (CBM2/EPSCOR), and the State of Louisiana (Biological Computation and Visualization Center, Governor's iotechnology Initiative, and startup funds to David Pollock).

Description: © 2006 Erdner and Anderson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 7 (2006): 88, doi:10.1186/1471-2164-7-88.

Description: Dinoflagellates are one of the most important classes of marine and freshwater algae, notable both for their functional diversity and ecological significance. They occur naturally as free-living cells, as endosymbionts of marine invertebrates and are well known for their involvement in "red tides". Dinoflagellates are also notable for their unusual genome content and structure, which suggests that the organization and regulation of dinoflagellate genes may be very different from that of most eukaryotes. To investigate the content and regulation of the dinoflagellate genome, we performed a global analysis of the transcriptome of the toxic dinoflagellate Alexandrium fundyense under nitrate- and phosphate-limited conditions using Massively Parallel Signature Sequencing (MPSS).

Description: This work was funded by National Science Foundation OCE-0136861 and OCE-0430724, National Institute of Environmental Health Sciences 1 P50 ES012742-01, and a grant from the Woods Hole Oceanographic Institution Ocean Life Institute.

Description: © 2003 BioMed Central. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 4 (2003): 235, doi:10.1186/gb-2003-4-11-235.

Description: One of the challenges for ‘post-genomic’ biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors.

Description: © 2006 Hutt and Albertini. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Journal of Experimental & Clinical Assisted Reproduction 3 (2006): 6, doi:10.1186/1743-1050-3-6.

Description: The publication of a report in Nature in 2004 by the Tilly group suggesting that mouse ovaries are capable of generating oocytes de novo post-natally, has sparked interest in a problem long thought to have been resolved from classical studies in a variety of mammalian species. Within a nearly two year time period, laboratories around the world have taken up the challenge to dogma raised by this initial report, either to test this concept in an experimental basic science setting or give direction to clinical applications that could result, were the original premises of this work in the mouse valid for extrapolation to humans. This review provides a status report for this promising area of research, (1) to summarize recent findings in the literature with respect to the validity of the original hypothesis proffered by the Tilly group, and, (2) to gauge the potential utility of ovarian stem cells as a treatment for certain forms of human infertility.

Description: Support and the funding provided from the Hall Family Foundation.

Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S3, doi:10.1186/1476-069X-7-S2-S3.

Description: Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.

Description: The Oceans and Human Health Initiative research described within this paper is supported by the National Science Foundation, The National Institute for Environmental Health Sciences and the National Oceanic and Atmospheric Administration. Grant numbers are: NIEHS P50 ES012742 and NSF OCE- 043072 (RJG, LAA-Z, MFP), NSF OCE04-32479 and NIEHS P50 ES012740 (RSF), NSF OCE-0432368 and NIEHS P50 ES12736 (HMS-G), NIEHS P50 ES012762 and NSF OCE-0434087 (JSM).

Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S6, doi:10.1186/1476-069X-7-S2-S6.

Description: We review the major linkages between the oceans and public health, focusing on exposures and potential health effects due to anthropogenic and natural factors including: harmful algal blooms, microbes, and chemical pollutants in the oceans; consumption of seafood; and flooding events. We summarize briefly the current state of knowledge about public health effects and their economic consequences; and we discuss priorities for future research. We find that: • There are numerous connections between the oceans, human activities, and human health that result in both positive and negative exposures and health effects (risks and benefits); and the study of these connections comprises a new interdisciplinary area, "oceans and human health." • The state of present knowledge about the linkages between oceans and public health varies. Some risks, such as the acute health effects caused by toxins associated with shellfish poisoning and red tide, are relatively well understood. Other risks, such as those posed by chronic exposure to many anthropogenic chemicals, pathogens, and naturally occurring toxins in coastal waters, are less well quantified. Even where there is a good understanding of the mechanism for health effects, good epidemiological data are often lacking. Solid data on economic and social consequences of these linkages are also lacking in most cases. • The design of management measures to address these risks must take into account the complexities of human response to warnings and other guidance, and the economic tradeoffs among different risks and benefits. Future research in oceans and human health to address public health risks associated with marine pathogens and toxins, and with marine dimensions of global change, should include epidemiological, behavioral, and economic components to ensure that resulting management measures incorporate effective economic and risk/benefit tradeoffs.

Description: Funding was provided in part by the NSF-NIEHS Oceans Centers at Woods Hole, University of Hawaii, University of Miami, and University of Washington, and the NOAA Oceans and Human Health Initiative Centers of Excellent in Charleston, Seattle and Milwaukee, the National Center for Environmental Health (NCEH) of the Centers for Disease Control and Prevention (CDC), and the WHOI Marine Policy Center. Grant numbers are: NIEHS P50 ES012742 and NSF OCE-043072 (HLKP, RJG, PH); NSF OCE 0432368 and NIEHS P50 ES12736 (LEF); NIEHS P50 ES012762 and NSF OCE-0434087 (EMF, AT, LRY); NSF OCE04-32479 and NIEHS P50 ES012740 (BAW)

Description: © 2007 Dietz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Ecology 7 (2007): 14, doi:10.1186/1472-6785-7-14.

Description: Free-ranging narwhals (Monodon monoceros) were instrumented in Admiralty Inlet, Canada with both satellite tags to study migration and stock separation and short-term, high-resolution digital archival tags to explore diving and feeding behaviour. Three narwhals were equipped with an underwater camera pod (Crittercam), another individual was equipped with a digital archival tag (DTAG), and a fifth with both units during August 2003 and 2004. Crittercam footage indicated that of the combined 286 minutes of recordings, 12% of the time was spent along the bottom. When the bottom was visible in the camera footage, the narwhals were oriented upside-down 80% of the time (range: 61 100%). The DTAG data (14.6 hours of recordings) revealed that during time spent below the surface, the two tagged narwhals were supine an average of 13% (range: 9–18%) of the time. Roughly 70% of this time spent in a supine posture occurred during the descent. Possible reasons for this upside-down swimming behaviour are discussed. No preference for a clockwise or counter-clockwise direction of roll was observed, discounting the possibility that rolling movements contribute to the asymmetric left-handed helical turns of the tusk.

Description: This study was funded by the National Environmental Research Institute, the Greenland Institute of Natural Resources (organized by Mads Peter Heide-Jørgensen), the Department of Fisheries and Oceans, the Nunavut Wildlife Research Trust Fund and the Danish Cooperation for the Environment in the Arctic (DANCEA). Ari D. Shapiro received financial support from the WHOI Academic Programs Office, the National Science Foundation Research Fellowship and the National Defense Science & Engineering Graduate Fellowship.

Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S1, doi:10.1186/1476-069X-7-S2-S1.

Description: The oceans are the dominant feature of the planet and are fundamentally linked to human history and to human health. Concerns about the impact of the oceans on human health can be traced to ancient times. Jewish law prohibited the consumption of shellfish, probably reflecting the fact that filter-feeding bivalves can accumulate pathogens and toxins. The Portuguese explorer Pedro Fernandes de Queirós described symptoms associated with ciguatera fish poisoning after eating Caribbean sea bream in 1606, and several of British explorer James Cook's crew experienced similar symptoms after eating fish off the coast of Vanuatu in 1774 [1]. Roughly 1,200 people died from the consumption of fish and shellfish contaminated with methyl mercury in Minamata (Japan) during the 20th century; an even larger number were affected by chronic long-term neurotoxicological impacts [2]. A tsunami caused by an undersea earthquake on December 26, 2004 killed more than 225,000 people in eleven countries bordering the Indian Ocean; and more than 1,400 people died within a single day when the storm surge generated by Hurricane Katrina overwhelmed the New Orleans levee system on August 29, 2005 [3]. Looking ahead, the International Panel on Climate Change has projected a sea level rise of as much as 88 cm during the 21st century as a result of global warming [4], with major implications for the welfare and sustainability of coastal communities.

Description: The support of the National Science Foundation (US) and the National Institute of Environmental Health Sciences (US) is gratefully acknowledged: Grant numbers NSF OCE04- 32479 and NIEHS P50 ES012740 (EAL), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), and NIEHS P50 ES012742 and NSF OCE-043072 (JJS).

Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License The definitive version was published in Environmental Health 7 (2008): S2, doi:10.1186/1476-069X-7-S2-S2.

Description: Harmful algal blooms (HABs) are one focus of the national research initiatives on Oceans and Human Health (OHH) at NIEHS, NOAA and NSF. All of the OHH Centers, from the east coast to Hawaii, include one or more research projects devoted to studying HAB problems and their relationship to human health. The research shares common goals for understanding, monitoring and predicting HAB events to protect and improve human health: understanding the basic biology of the organisms; identifying how chemistry, hydrography and genetic diversity influence blooms; developing analytical methods and sensors for cells and toxins; understanding health effects of toxin exposure; and developing conceptual, empirical and numerical models of bloom dynamics. In the past several years, there has been significant progress toward all of the common goals. Several studies have elucidated the effects of environmental conditions and genetic heterogeneity on bloom dynamics. New methods have been developed or implemented for the detection of HAB cells and toxins, including genetic assays for Pseudo-nitzschia and Microcystis, and a biosensor for domoic acid. There have been advances in predictive models of blooms, most notably for the toxic dinoflagellates Alexandrium and Karenia. Other work is focused on the future, studying the ways in which climate change may affect HAB incidence, and assessing the threat from emerging HABs and toxins, such as the cyanobacterial neurotoxin β-N-methylamino-L-alanine. Along the way, many challenges have been encountered that are common to the OHH Centers and also echo those of the wider HAB community. Long-term field data and basic biological information are needed to develop accurate models. Sensor development is hindered by the lack of simple and rapid assays for algal cells and especially toxins. It is also critical to adequately understand the human health effects of HAB toxins. Currently, we understand best the effects of acute toxicity, but almost nothing is known about the effects of chronic, subacute toxin exposure. The OHH initiatives have brought scientists together to work collectively on HAB issues, within and across regions. The successes that have been achieved highlight the value of collaboration and cooperation across disciplines, if we are to continue to advance our understanding of HABs and their relationship to human health.

Description: This work was funded through grants from the NSF/NIEHS Centers for Oceans and Human Health, NIEHS P50 ES012742 and NSF OCE-043072 (DLE and DMA), NSF OCE04-32479 and NIEHS P50 ES012740 (PB and RRB), NSF OCE-0432368 and NIEHS P50 ES12736 (LEB), NIEHS P50 ES012762 and NSF OCE-0434087 (RCS, KAL, MSP, MLW, and KAH). Additional support was provided by the ECOHAB Grant program NSF Grant OCE-9808173 and NOAA Grant NA96OP0099 (DMA), NOAA OHHI NA04OAR4600206 (RRB) and Washington State Sea Grant NA16RG1044 (RCS). KAL and VLT were supported in part by the West Coast Center for Oceans and Human Health (WCCOHH) as part of the NOAA Oceans and Human Health Initiative.

Description: © 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S5, doi:10.1186/1476-069X-7-S2-S5.

Description: Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.

Description: The authors acknowledge the financial support for the NSF/NIEHS and NOAA Centers for Oceans and Human Health

Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Direct 4 (2009): 46, doi:10.1186/1745-6150-4-46.

Description: Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes. Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.

Description: This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-08ER64511.

Description: © 2005 Serres and Riley. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 6 (2005): 33, doi:10.1186/1471-2164-6-33.

Description: Background: Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular) proteins consist of two or more components (modules) encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results: Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused) proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion: The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes it possible to generate protein groups related by both sequence and function, avoiding mixing of unrelated sequences. Organisms differ in sizes of groups of sequence-related proteins. A sample comparison of orthologs to selected E. coli paralogous groups correlates with known physiological and taxonomic relationships between the organisms.

Description: The research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-01ER63202 and by National Aeronautics and Space Administration Astrobiology grant NCC2-1054.

Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)

Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.

Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.

Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.

Description: © 2007 Huang and Gogarten. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Genome Biology 8 (2007): R99, doi:10.1186/gb-2007-8-6-r99.

Description: Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria. We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont. Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.

Description: This work was performed while JH held a National Research Council Associateship Award at the NASA Astrobiology Institute at the Marine Biological Laboratory in Woods Hole, Massachusetts (NCC2-1054). Additional support was provided through NSF (MCB-0237197) and NASA AISR (NNG04GP90G) grants to JPG.

Description: This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0 which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Evolutionary Biology 8 (2008): 14, doi:10.1186/1471-2148-8-14.

Description: Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches.

Description: This project was made possible by a collaborative grant from the National Science Foundation Assembling the Tree of Life program (EF 04-31117) that was awarded to L.A.K., D.B., J.L., D.J.P., and to the ATCC

Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Biology 7 (2009): 72, doi:10.1186/1741-7007-7-72.

Description: Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.The analyses of ca. 250,000 sequence reads revealed that the number of detected Operational Taxonomic Units (OTUs) far exceeded previous richness estimates from the same sites based on clone libraries and Sanger sequencing. More than 90% of this diversity was represented by OTUs with less than 10 sequence tags. We detected a substantial number of taxonomic groups like Apusozoa, Chrysomerophytes, Centroheliozoa, Eustigmatophytes, hyphochytriomycetes, Ichthyosporea, Oikomonads, Phaeothamniophytes, and rhodophytes which remained undetected by previous clone library-based diversity surveys of the sampling sites. The most important innovations in our newly developed bioinformatics pipeline employ (i) BLASTN with query parameters adjusted for highly variable domains and a complete database of public ribosomal RNA (rRNA) gene sequences for taxonomic assignments of tags; (ii) a clustering of tags at k differences (Levenshtein distance) with a newly developed algorithm enabling very fast OTU clustering for large tag sequence data sets; and (iii) a novel parsing procedure to combine the data from individual analyses. Our data highlight the magnitude of the under-sampled 'protistan gap' in the eukaryotic tree of life. This study illustrates that our current understanding of the ecological complexity of protist communities, and of the global species richness and genome diversity of protists, is severely limited. Even though 454 pyrosequencing is not a panacea, it allows for more comprehensive insights into the diversity of protistan communities, and combined with appropriate statistical tools, enables improved ecological interpretations of the data and projections of global diversity.

Description: The International Census of Marine Microbes and the W.M. Keck Foundation award to the Marine Biological Laboratory at Woods Hole (MA) supported the pyrosequencing part of this study. Further financial support came from a grant from the Deutsche Forschungsgemeinschaft to TS (STO414/3-1). Support for the unpublished work on Cariaco Basin protists came from NSF MCB-0348407 to VE (collaborative project with S Epstein at Northeastern University, Boston, MA, USA). Financial support to AC was provided by NSF MCB-0348045. Financial support to RC was provided by the ANR-Biodiversité project Aquaparadox.

Description: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Microbiology 9 (2009): 16, doi:10.1186/1471-2180-9-16.

Description: The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades – euglenids, kinetoplastids and diplonemids – that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond. We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 – 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world. Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".

Description: This work was supported by grants to BSL from the Tula Foundation (Centre for Microbial Diversity and Evolution), the National Science and Engineering Research Council of Canada (NSERC 283091-04) and the Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity. Funding for the collection of sediments and participation of VPE and JMB in this research was provided by the US National Science Foundation grant MCB-060484.

Description: © 2001 Samuel et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. The definitive version was published in BMC Microbiology 1 (2001): 4, doi:10.1186/1471-2180-1-4.

Description: Many bacteria swim by rotating helical flagellar filaments. Waterbury et al. discovered an exception, strains of the cyanobacterium Synechococcus that swim without flagella or visible changes in shape. Other species of cyanobacteria glide on surfaces. The hypothesis that Synechococcus might swim using traveling surface waves prompted this investigation. Results Using quick-freeze electron microscopy, we have identified a crystalline surface layer that encloses the outer membrane of the motile strain Synechococcus sp. WH8113, the components of which are arranged in a rhomboid lattice. Spicules emerge in profusion from the layer and extend up to 150 nm into the surrounding fluid. These spicules also send extensions inwards to the inner cell membrane where motility is powered by an ion-motive force. Conclusion The envelope structure of Synechococcus sp. WH8113 provides new constraints on its motile mechanism. The spicules are well positioned to transduce energy at the cell membrane into mechanical work at the cell surface. One model is that an unidentified motor embedded in the cell membrane utilizes the spicules as oars to generate a traveling wave external to the surface layer in the manner of ciliated eukaryotes.

Description: ADTS was supported by the Rowland Institute for Science and is an Amgen Fellow of the Life Sciences Research Foundation.

Description: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Evolutionary Biology 8 (2008): 144, doi:10.1186/1471-2148-8-144.

Description: Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. From the over 10.7 million taxonomic names that are part of the uBio system, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs) and societal importance (e.g., world wars). The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.

Description: The work presented here was funded in part by the MBLWHOI Library and the DAB Lindberg Research Fellowship from the Medical Library Association to INS.

Description: © 2008 Sarkar et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Bioinformatics 9 (2008): 103, doi:10.1186/1471-2105-9-103.

Description: The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices. To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis. Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.

Description: This work is funded in part by NSF DBI-0421604 to GC and RD. INS is supported in part by the Ellison Medical Foundation.

Description: 〈b〉Paleomagnetic determination of paleolatitude and rotation of Bering Island (Komandorsky Islands) Russia: comparison with rotations in the Aleutian Islands and Kamchatka〈/b〉〈br〉 P. S. Minyuk and D. B. Stone〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 329-348, https://doi.org/10.5194/smsps-4-329-2009, 2009〈br〉 A paleomagnetic study was carried out on Paleogene sedimentary rocks from Bering Island, Komandorsky islands, located at the far western end of the Aleutian Island Arc. The age of these sediments has been debated at length, but the combination of magnetostratigraphy with the fossil record indicates that the base of the section is of early Eocene (approximately 55 Ma) and the top latest Eocene age. Paleomagnetic data were obtained from 260 samples from 60 individual bedding units. The combined data show a clockwise rotation 〈i〉R〈/i〉=26.3°±8.5°, 〈i〉F〈/i〉=8.1°±2.5° with respect to the North American Plate and 〈i〉R〈/i〉=38°±8.8°, 〈i〉F〈/i〉=8.7°±2.7° with respect to the Eurasian Plate. They also show a shallowing of the inclination which yields a paleolatitude of 53°, 12° south of its expected latitude. The shallowing may have a component due to compaction, but the wide variation in sampled lithologies, combined with internal consistency of the data set, would argue against the shallowing being significant. To compare these data with other Aleutian Arc data we compiled a comprehensive survey of all available data sets. Out of these we selected four islands for which the data passed basic reliability criteria, namely Umnak, Amlia, Amchitka and Medny islands. All four showed significant clockwise rotation with respect to both North American and Eurasian polar wander paths. Several mechanisms can generate the observed rotation, ranging from block rotation driven by oblique relative motion of the Pacific plate, through lateral transport along the curve of the arc, to whole-arc rotation about its eastern end. The distribution and age spread of the rotation data are insufficient to discriminate between mechanisms, but it seems likely that different mechanism may have operated at different times and in different locations.

Description: 〈b〉Paleomagnetism of the Cretaceous rocks from Cape Kronotskiy, East Kamchatka and reconstruction of terrane trajectories in the NE Pacific area〈/b〉〈br〉 W. Harbert, N. V. Tsukanov, D. V. Alexeiev, C. Gaedicke, R. Freitag, B. V. Baranov, S. G. Skolotnev, W. Kramer, and W. Seifert〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 313-327, https://doi.org/10.5194/smsps-4-313-2009, 2009〈br〉 The Kamchatka Peninsula of northeastern Russia is located along the northwestern margin of the Bering Sea and consists of zones of complexly deformed accreted terranes. Paleomagnetic samples were collected for study from a Late Cretaceous aged locality at Cape Kronotskiy (λ=54°44.8´ N, φ=162°1.29´ E). Two components of magnetization were observed. During stepwise thermal demagnetization, the B-magnetic component was observed up to 600°C having a direction and associated uncertainty in stratigraphic coordinates of 〈i〉D〈sub〉s〈/sub〉〈/i〉=300.7°, 〈i〉I〈sub〉s〈/sub〉〈/i〉=48.7°, α〈sub〉95〈/sub〉=10.9°, k-value=11.8, n=17. The B component paleolatitude calculated from the Fisher mean in stratigraphic coordinates and associated statistics are λ〈sub〉obs〈/sub〉=30.4° N or S, λ〈sub〉95〈/sub〉=8.9°, n=17 (sites), k-value=11. Our overall study paleolatitude result is similar to a previously reported paleomagnetic study completed within this unit. Terrane trajectories calculated using the finite rotation poles of Engebretson et al. (1985), which are corrected for either Pacific-hotspot drift or True Polar Wander hotspot-spin axis relative motion, show that the sampled unit represents a far traveled tectonostratigraphic terrane and support a model in which accretion (docking) events of this composite or superterrane with the North America plate occur at approximately 40 Ma.

Description: 〈b〉Comparison of Cretaceous granitoids of the Chaun tectonic zone to those of the Taigonos Peninsula, NE Asia: rock chemistry, composition of rock forming minerals, and conditions of formation〈/b〉〈br〉 P. L. Tikhomirov, M. V. Luchitskaya, and I. R. Kravchenko-Berezhnoy〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 289-311, https://doi.org/10.5194/smsps-4-289-2009, 2009〈br〉 The Cretaceous granitoid complexes of the Eastern Taigonos and the Prybrezhny Taigonos belts (southern part of the Taigonos Peninsula), Tanyurer pluton of the Okhotsk-Chukotka volcanic belt, and the Peekiney, Moltykan, and Telekay plutons of the Chaun tectonic zone are discussed in relation to their structural position, petrography, rock and mineral chemistry and physicochemical conditions of melt crystallization. These granitoid plutons were generated through melting of a compositionally heterogeneous crustal source, with direct contribution from mafic melts produced in the mantle wedge above active or extinct Benioff zones. Variations of the trace-element composition of granitoids are controlled to a greater extent by local compositional peculiarities of the source regions than by the geodynamic regime as such. The final crystallization of these plutons occurred at comparatively shallow depths, between 1–2 and 6–7 km, in a temperature interval of 700–770°C. The depth of emplacement of the bodies decreases with increasing distance from the areas with oceanic and transitional type crust, as does the degree of incompatible element enrichment of the mantle and crustal sources of melts. Variations in fo〈sub〉2〈/sub〉 values at the late stages of crystallization of the plutons reach 3–4 orders of magnitude, exceeding the limits of the quartz-fayalite-magnetite (QFM) and nickel-nickel oxide (NNO) buffer equilibria, which likely results from local variations of the source composition.

Description: 〈b〉Thermogeodynamic manifestations in the Caucasus and their genesis〈/b〉〈br〉 G. E. Gugunava, J. K. Kiria, and T. B. Bochorishvili〈br〉 eEarth Discuss., 4, 77-89, doi:10.5194/eed-4-77-2009, 2009〈br〉 〈b〉Publication in eE not foreseen〈/b〉 (discussion: closed, 2 comments)〈br〉 In the work two aspects of thermal character are considered: first of all this is the connection of subduction phenomena with thermal life of the Caucasus on the basis of over interpreted data of magnetotelluric sounding, and secondly, origin of thermostressed condition of the Caucasus and its geological aspects which is manifested in the following: 〈br〉〈br〉 1. in the zones of anomalous thermodisplacements thermofaults should occur (Le Pishon et al., 1977). These thermofaults are in good correlation with deep faults which are distinguished by geological and seismic methods, these thermofaults may be earthquake sources (Spitak, Racha, etc. earthquakes), also may be channels through which magma derivates (giving mineral deposits) may penetrate on surface (Gugunava and Gijeishvili, 1989); 〈br〉〈br〉 2. in the body of sedimentary complex thermostressed seals and seal failures occur, which are apparently traps for oil-gas fluids. Good correlation of thermodense anomalies with oil deposits of the Caucasus is shown (Alexidze et al., 1985; Gugunava, 1980). 〈br〉〈br〉 Everything above mentioned was carried out within frames of stationary thermal model which did not allow us to reveal time characteristics of interconnection of geological medium and thermal field. 〈br〉〈br〉 Now investigations are being carried out within the frames of stationary thermal model and its interconnection with geological environment.

Description: 〈b〉Thermogeodynamic manifestations in the Caucasus and their genesis〈/b〉〈br〉 G. E. Gugunava, J. K. Kiria, and T. B. Bochorishvili〈br〉 eEarth Discuss., 4, 77-89, doi:10.5194/eed-4-77-2009, 2009〈br〉 〈b〉Publication in eE not foreseen〈/b〉 (discussion: closed, 2 comments)〈br〉 In the work two aspects of thermal character are considered: first of all this is the connection of subduction phenomena with thermal life of the Caucasus on the basis of over interpreted data of magnetotelluric sounding, and secondly, origin of thermostressed condition of the Caucasus and its geological aspects which is manifested in the following: 〈br〉〈br〉 1. in the zones of anomalous thermodisplacements thermofaults should occur (Le Pishon et al., 1977). These thermofaults are in good correlation with deep faults which are distinguished by geological and seismic methods, these thermofaults may be earthquake sources (Spitak, Racha, etc. earthquakes), also may be channels through which magma derivates (giving mineral deposits) may penetrate on surface (Gugunava and Gijeishvili, 1989); 〈br〉〈br〉 2. in the body of sedimentary complex thermostressed seals and seal failures occur, which are apparently traps for oil-gas fluids. Good correlation of thermodense anomalies with oil deposits of the Caucasus is shown (Alexidze et al., 1985; Gugunava, 1980). 〈br〉〈br〉 Everything above mentioned was carried out within frames of stationary thermal model which did not allow us to reveal time characteristics of interconnection of geological medium and thermal field. 〈br〉〈br〉 Now investigations are being carried out within the frames of stationary thermal model and its interconnection with geological environment.

Description: 〈b〉Holocene evolution and sedimentation rate of Alikes Lagoon, Zakynthos island, Western Greece: preliminary results〈/b〉〈br〉 P. Avramidis and N. Kontopoulos〈br〉 eEarth, 4, 23-29, doi:10.5194/ee-4-23-2009, 2009〈br〉 In the present study we present preliminary results from Alikes lagoon in Zakynthos island, an area that is one of the most seismically active regions of Greece. In order to estimate – interpret the Holocene evolution of the area and to reconstruct the palaeoenvironmental changes, we based on data derived from a 21 m sediment core. Sediment types, structure, colour, as well as contact depths and bed characteristics were recorded in the field. Standarised sedimentological analysis was carried out, on 46 samples including grain size analysis, calculation of moment measures, and micro- and molluscan fossils of 17 selected samples. Moreover, radiocarbon age determinations have been made on individual 〈i〉Cardium〈/i〉 shells from two horizons and whole – core Magnetic Susceptibility (MS) measurements were taken. The interpretation of depositional environments suggests a coastal environment (restricted-shallow) with reduced salinity such as a lagoon margin and in a tidal flat and/or marsh particularly. The maximum age of the studied sediments is about 8500 BP. The rate of sedimentation between 8280 BP while 5590 BP was 5.3 mm/yr and between 5590 BP and modern times is on the order of 1.03 mm/yr. These sedimentation rates results are similar to other coastal areas of western Greece.

Description: 〈b〉Morphology of the pore space in claystones – evidence from BIB/FIB ion beam sectioning and cryo-SEM observations〈/b〉〈br〉 G. Desbois, J. L. Urai, and P. A. Kukla〈br〉 eEarth, 4, 15-22, doi:10.5194/ee-4-15-2009, 2009〈br〉 The morphology of pore space has a strong effect on mechanical and transport properties of mudrocks and clay-rich fault gouge, but its characterization has been mostly indirect. We report on a study of Boom clay from a proposed disposal site of radioactive waste (Mol site, Belgium) using high resolution SEM at cryogenic temperature, with ion beam cross-sectioning to prepare smooth, damage free surfaces. Pores commonly have crack-like tips, preferred orientation parallel to bedding and power law size distribution. We define a number of pore types depending on shape and location in the microstructure: large jagged pores in strain shadows of clastic grains, high aspect ratio pores between similarly oriented phyllosilicate grains and crescent-shaped pores in saddle reefs of folded phyllosilicates. 3-D reconstruction by serial cross-sectioning shows 3-D connectivity of the pore space. These findings offer a new insight into the morphology of pores down to nano-scale in comparison to traditional pore size distributions calculated from mercury Injection experiments, explain slaking of clays by successive wetting and drying and provide the basis for microstructure-based models of transport in clays.

Description: 〈b〉Foraminiferal response to environmental changes in Kiel Fjord, SW Baltic Sea〈/b〉〈br〉 A. Nikulina, I. Polovodova, and J. Schönfeld〈br〉 eEarth, 3, 37-49, doi:10.5194/ee-3-37-2008, 2008〈br〉 The living benthic foraminiferal assemblages in Kiel Fjord (SW Baltic Sea) were investigated in the years 2005 and 2006. The faunal studies were accomplished by geochemical analyses of surface sediments. In general, sediment pollution by copper, zinc, tin and lead is assessed as moderate in comparison with levels reported from other areas of the Baltic Sea. However, the inner Kiel Fjord is still exposed to a high load of metals and organic matter due to enhanced accumulation of fine-grained sediments in conjunction with potential pollution sources as shipyards, harbours and intensive traffic. The results of our survey show that the dominant environmental forcing of benthic foraminifera is nutrients availability coupled with human impact. A comparison with faunal data from the 1960s reveals apparent changes in species composition and population densities. The stress-tolerant species 〈i〉Ammonia beccarii〈/i〉 invaded Kiel Fjord. 〈i〉Ammotium cassis〈/i〉 had disappeared that reflects apparently the changes in salinity over the last 10 years. These changes in foraminiferal community and a significant increase of test abnormalities indicate an intensified environmental stress since the 1960s.

Description: 〈b〉Holocene evolution and sedimentation rate of Alikes Lagoon, Zakynthos island, Western Greece: preliminary results〈/b〉〈br〉 P. Avramidis and N. Kontopoulos〈br〉 eEarth, 4, 23-29, doi:10.5194/ee-4-23-2009, 2009〈br〉 In the present study we present preliminary results from Alikes lagoon in Zakynthos island, an area that is one of the most seismically active regions of Greece. In order to estimate – interpret the Holocene evolution of the area and to reconstruct the palaeoenvironmental changes, we based on data derived from a 21 m sediment core. Sediment types, structure, colour, as well as contact depths and bed characteristics were recorded in the field. Standarised sedimentological analysis was carried out, on 46 samples including grain size analysis, calculation of moment measures, and micro- and molluscan fossils of 17 selected samples. Moreover, radiocarbon age determinations have been made on individual 〈i〉Cardium〈/i〉 shells from two horizons and whole – core Magnetic Susceptibility (MS) measurements were taken. The interpretation of depositional environments suggests a coastal environment (restricted-shallow) with reduced salinity such as a lagoon margin and in a tidal flat and/or marsh particularly. The maximum age of the studied sediments is about 8500 BP. The rate of sedimentation between 8280 BP while 5590 BP was 5.3 mm/yr and between 5590 BP and modern times is on the order of 1.03 mm/yr. These sedimentation rates results are similar to other coastal areas of western Greece.

Description: 〈b〉Foraminiferal response to environmental changes in Kiel Fjord, SW Baltic Sea〈/b〉〈br〉 A. Nikulina, I. Polovodova, and J. Schönfeld〈br〉 eEarth, 3, 37-49, doi:10.5194/ee-3-37-2008, 2008〈br〉 The living benthic foraminiferal assemblages in Kiel Fjord (SW Baltic Sea) were investigated in the years 2005 and 2006. The faunal studies were accomplished by geochemical analyses of surface sediments. In general, sediment pollution by copper, zinc, tin and lead is assessed as moderate in comparison with levels reported from other areas of the Baltic Sea. However, the inner Kiel Fjord is still exposed to a high load of metals and organic matter due to enhanced accumulation of fine-grained sediments in conjunction with potential pollution sources as shipyards, harbours and intensive traffic. The results of our survey show that the dominant environmental forcing of benthic foraminifera is nutrients availability coupled with human impact. A comparison with faunal data from the 1960s reveals apparent changes in species composition and population densities. The stress-tolerant species 〈i〉Ammonia beccarii〈/i〉 invaded Kiel Fjord. 〈i〉Ammotium cassis〈/i〉 had disappeared that reflects apparently the changes in salinity over the last 10 years. These changes in foraminiferal community and a significant increase of test abnormalities indicate an intensified environmental stress since the 1960s.

Description: 〈b〉Decline of coral reefs during late Paleocene to early Eocene global warming〈/b〉〈br〉 C. Scheibner and R. P. Speijer〈br〉 eEarth, 3, 19-26, doi:10.5194/ee-3-19-2008, 2008〈br〉 Since the 1980s the frequency of warming events has intensified and simultaneously widespread coral bleaching, and enhanced coral mortality have been observed. Yet, it remains unpredictable how tropical coral reef communities will react to prolonged adverse conditions. Possibly, coral reef systems are sufficiently robust to withstand continued environmental pressures. But if coral mortality increases, what will platform communities of the future look like? The co-evolution of early Paleogene carbonate platforms and palaeoclimate may provide insight. Here we document the impact of early Paleogene global warming on shallow-water carbonate platforms in the Tethys. Between 59 and 55 Ma, three discrete stages in platform development can be identified Tethys-wide: during the first stage carbonate platforms mainly consisted of coralgal reefs; during the second – transitional – stage coralgal reefs thrived only at middle latitudes and gave way to larger foraminifera as dominant carbonate producer in low latitudes; finally, during the third stage, newly developing larger foraminifera lineages completely took over the role as main carbonate-producing organisms in low to middle latitudes. We postulate that rising temperatures led to a stepwise demise of Paleocene coral reefs, giving way to an unprecedented expansion of larger foraminifera, dominating Tethyan platforms during the early Eocene.

Description: 〈b〉Palaeomagnetic investigations of sediments cores from Axios zone (N. Greece): implications of low inclinations in the Aegean〈/b〉〈br〉 E. Aidona, D. Kondopoulou, R. Scholger, A. Georgakopoulos, and A. Vafeidis〈br〉 eEarth, 3, 7-18, doi:10.5194/ee-3-7-2008, 2008〈br〉 Sediment cores from 13 deep boreholes (1–4.1 km) distributed within Axios zone in Northern Greece have been studied by means of palaeomagnetism. Both low field magnetic susceptibility and intensity of the natural remanent magnetization (NRM) indicate rather weakly magnetised materials. A set of 390 samples have been subjected to thermal and alternative field demagnetization. Isothermal remanent magnetization (IRM) acquisition curves and thermomagnetic analysis suggest the dominance of magnetite. Thin sections from 30 selected samples were studied in order to more precisely characterise their magnetic mineralogy. This investigation also reveals the presence of magnetite and pyrite in framboidal form. An attempt to re-orient some of the samples was partially successful by using the viscous component and the anisotropy method. These techniques were applied in order to correct the palaeomagnetic directions due to the orientation ambiguity of the core samples. The corrected mean direction converges towards an eastward value, in agreement with the overall pattern of the onshore results from previous investigations in the study area. 〈br〉〈br〉 Finally, the observed inclinations of characteristic remanences in these rocks are much lower than the expected ones but converge with those obtained from formations on land.

Description: 〈b〉Zoogeography of the bottom Foraminifera of the West-African coast〈/b〉〈br〉 V. Mikhalevich〈br〉 eEarth Discuss., 3, 1-9, doi:10.5194/eed-3-1-2008, 2008〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 8 comments)〈br〉 The sediment samples from the continental shelf of West-Equatorial Africa (from the Strait of Gibraltar to the Niger estuary), depths ranging from 0 to 69 m were found to contain 176 bottom foraminiferal species. For the majority of them (126 species), their areas of occurrences were mapped and the peculiar features of the geographical range and distribution were studied. The species natural habitats were established based on the taxonomical revision of the species in study all over the World Ocean based on the collections of the Zoological Institute RAS and wide literary data. The method of perforated cards was used to mark the geographical locations of all of the species studied. In order to establish the species geographic zonal distribution (together with their depth habitat) the five characteristic groups of the species were separated: 1. pan-oceanic (cosmopolitan), 2. widely spread tropical-boreal, 3. tropical-law boreal, 4. tropical-subtropical, 5. tropical. The percent of the species of each group among the species composition was established for the fauna of each station and for the whole region.

Description: 〈b〉Zoogeography of the bottom Foraminifera of the West-African coast〈/b〉〈br〉 V. Mikhalevich〈br〉 eEarth Discuss., 3, 1-9, doi:10.5194/eed-3-1-2008, 2008〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 8 comments)〈br〉 The sediment samples from the continental shelf of West-Equatorial Africa (from the Strait of Gibraltar to the Niger estuary), depths ranging from 0 to 69 m were found to contain 176 bottom foraminiferal species. For the majority of them (126 species), their areas of occurrences were mapped and the peculiar features of the geographical range and distribution were studied. The species natural habitats were established based on the taxonomical revision of the species in study all over the World Ocean based on the collections of the Zoological Institute RAS and wide literary data. The method of perforated cards was used to mark the geographical locations of all of the species studied. In order to establish the species geographic zonal distribution (together with their depth habitat) the five characteristic groups of the species were separated: 1. pan-oceanic (cosmopolitan), 2. widely spread tropical-boreal, 3. tropical-law boreal, 4. tropical-subtropical, 5. tropical. The percent of the species of each group among the species composition was established for the fauna of each station and for the whole region.

Description: 〈b〉Map – geographic locations related to the manuscript sequence〈/b〉〈br〉 〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 3-3, https://doi.org/10.5194/smsps-4-3-2009, 2009〈br〉

Description: 〈b〉Age and paleomagnetism of the Okhotsk-Chukotka Volcanic Belt (OCVB) near Lake El'gygytgyn, Chukotka, Russia〈/b〉〈br〉 D. B. Stone, P. W. Layer, and M. I. Raikevich〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 243-260, https://doi.org/10.5194/smsps-4-243-2009, 2009〈br〉 Paleomagnetic results from the upper two thirds of the whole section of the Okhotsk-Chukotka Volcanic Belt (OCVB) volcanics exposed in the area around Lake El'gygytgyn, Chukotka yield stable, consistent magnetic vectors and well-preserved reversed directions. The magnetostratigraphy and 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar geochronologic data reported here indicate that the sampled OCVB volcanics were erupted between about 90 and 67 Ma, and show no significant change in the apparent pole position over that time. The OCVB extends from northeast China, across Northeast Russia to the Bering Straight. This belt is made up of both extrusive and intrusive rocks, with the extrusive rocks and their associated sediments being dominant. The whole belt important in interpreting the paleogeography of the region because it overlies many of the accreted terranes of Northeast Russia. Most importantly, it overlies parts of the Chukotka-Alaska block which is thought to have moved out of the Arctic Ocean region, as well as terranes accreted from the south. These latter terranes have been rafted northwards on the paleo-plates of the Pacific, implying that the present relative paleogeography of all of the terranes overlain by the OCVB were essentially in place by 67 Ma, and possibly as early as 90 Ma. However, comparing our paleomagnetic pole position for the OCVB with those for North America and Eurasia (a proxy for Siberia) shows a statistically significant displacement of the OCVB pole to the south west. This implies that not only the OCVB, but the underlying terranes of northeast Russia, experienced southerly displacement with respect to the Siberian and North American platforms since the Late Cretaceous.

Description: 〈b〉Tectonic reconstruction of Uda-Murgal arc and the Late Jurassic and Early Cretaceous convergent margin of Northeast Asia–Northwest Pacific〈/b〉〈br〉 S. D. Sokolov, G. Ye. Bondarenko, A. K. Khudoley, O. L. Morozov, M. V. Luchitskaya, M. I. Tuchkova, and P. W. Layer〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 273-288, https://doi.org/10.5194/smsps-4-273-2009, 2009〈br〉 A long tectonic zone composed of Upper Jurassic to Lower Cretaceous volcanic and sedimentary rocks is recognized along the Asian continent margin from the Mongol-Okhotsk fold and thrust belt on the south to the Chukotka Peninsula on the north. This belt represents the Uda-Murgal arc, which was developed along the convergent margin between Northeast Asia and Northwest Meso-Pacific. Several segments are identified in this arc based upon the volcanic and sedimentary rock assemblages, their respective compositions and basement structures. The southern and central parts of the Uda-Murgal arc were a continental margin belt with heterogeneous basement represented by metamorphic rocks of the Siberian craton, the Verkhoyansk terrigenous complex of Siberian passive margin and the Koni-Taigonos Late Paleozoic to Early Mesozoic island arc with accreted oceanic terranes. At the present day latitude of the Pekulney and Chukotka segments there was an ensimatic island arc with relicts of the South Anyui oceanic basin in a backarc basin. Accretionary prisms of the Uda-Murgal arc and accreted terranes contain fragments of Permian, Triassic to Jurassic and Jurassic to Cretaceous (Tithonian–Valanginian) oceanic crust and Jurassic ensimatic island arcs. Paleomagnetic and faunal data show significant displacement of these oceanic complexes and the terranes of the Taigonos Peninsula were originally parts of the Izanagi oceanic plate.

Description: 〈b〉Provenance analysis and tectonic setting of the Triassic clastic deposits in Western Chukotka, Northeast Russia〈/b〉〈br〉 M. I. Tuchkova, S. Sokolov, and I. R. Kravchenko-Berezhnoy〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 177-200, https://doi.org/10.5194/smsps-4-177-2009, 2009〈br〉 The study area is part of the Anyui subterrane of the Chukotka microplate, a key element in the evolution of the Amerasia Basin, located in Western Chukotka, Northeast Russia. The subterrane contains variably deformed, folded and cleaved rhythmic Triassic terrigenous deposits which represent the youngest stage of widespread marine deposition which form three different complexes: Lower-Middle Triassic, Upper Triassic (Carnian) and Upper Triassic (Norian). All of the complexes are represented by rhythmic interbeds of sandstone, siltstone and mudstone. Macrofaunas are not numerous, and in some cases deposits are dated by analogy to, or by their relationship with, other units dated with macrofaunas. The deposits are composed of pelagic sediments, low-density flows, high-density flows, and shelf facies associations suggesting that sedimentation was controlled by deltaic progradation on a continental shelf and subsequent submarine fan sedimentation at the base of the continental slope. Petrographic study of the mineral composition indicates that the sandstones are lithic arenites. Although the Triassic sandstones appear similar in outcrop and by classification, the constituent rock fragments are of diverse lithologies, and change in composition from lower grade metamorphic rocks in the Lower-Middle Triassic to higher grade metamorphic rocks in the Upper Triassic. This change suggests that the Triassic deposits represent an unroofing sequence as the source of the clastic material came from more deeply buried rocks with time.

Description: 〈b〉Multi-phase tectonic structures in the collision zone of the Kolyma-Omolon microcontinent and the eastern margin of the North Asian craton, Northeastern Russia〈/b〉〈br〉 A. V. Prokopiev and V. S. Oxman〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 65-70, https://doi.org/10.5194/smsps-4-65-2009, 2009〈br〉 The sequence of formation of structures is established in the zone of junction of the eastern margin of the North Asian craton and the northeastern flank of the Kolyma-Omolon microcontinent, in the area of bend of the Kolyma structural loop. Detailed structural studies revealed two phases in the formation of Mesozoic structures – an early thrust phase and a late strike-slip phase. Structures formed during each of the phases are described. Thrust structures are represented by the Setakchan nappe on which the minimum amount of horizontal displacement is estimated at 13–15 km. Later superposed left-lateral strike-slip faults have a north strike. Formation of these latter structures occurred during the second phase of collision between the Kolyma-Omolon microcontinent and the eastern margin of the North Asian craton.

Description: 〈b〉Geology of the Shelves surrounding the New Siberian Islands, Russian Arctic〈/b〉〈br〉 D. Franke and K. Hinz〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 35-44, https://doi.org/10.5194/smsps-4-35-2009, 2009〈br〉 A total of 11 700 km of multichannel seismic reflection data were acquired during recent reconnaissance surveys of the wide, shallow shelves of the Laptev and western East Siberian Seas around the New Siberian Islands. To the north of the Laptev Sea, the Gakkel Ridge, an active mid-ocean ridge which separates the North American and Eurasian Plates, meets abruptly the steep slope of the continental shelf. Extension has affected the Laptev Shelf since at least the Early Tertiary and has resulted in the formation of three major, generally north-south trending rift basins: the Ust' Lena Rift, the Anisin Basin, and the New Siberian Basin. Our data indicate that the rift basins on the Laptev Shelf are not continuous with those on the East Siberian Shelf. The latter shelf can best be described as an epicontinental platform which has undergone continuous subsidence since the Late Cretaceous. The greatest subsidence occurred in the NE, manifested by a major depocentre filled with inferred (?)Late Cretaceous to Tertiary sediments up to 5 s (twt) thick. On the basis of deep reflection data we revise and adjust Mesozoic domain boundaries around the New Siberian Islands.

Description: 〈b〉Use of remote sensing and GIS in mapping the environmental sensitivity areas for desertification of Egyptian territory〈/b〉〈br〉 A. Gad and I. Lotfy〈br〉 eEarth Discuss., 3, 41-85, doi:10.5194/eed-3-41-2008, 2008〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 3 comments)〈br〉 Desertification is defined in the first art of the convention to combat desertification as 〈i〉"land degradation in arid, semiarid and dry sub-humid areas resulting from climatic variations and human activities".〈/i〉 Its consequence include a set of important processes which are active in arid and semi arid environment, where water is the main limiting factor of land use performance in such ecosystem . Desertification indicators or the groups of associated indicators should be focused on a single process. They should be based on available reliable information sources, including remotely sensed images, topographic data (maps or DEM'S), climate, soils and geological data. The current work aims to map the Environmental Sensitivity Areas (ESA's) to desertification in whole territory of Egypt at a scale of 1:1 000 000. 〈br〉〈br〉 ETM satellite images, geologic and soil maps were used as main sources for calculating the index of Environmental Sensitivity Areas (ESAI) for desertification. The algorism is adopted from MEDALLUS methodology as follows; 〈br〉〈br〉 ESAI = (SQI * CQI * VQI)〈sup〉1/3〈/sup〉 〈br〉〈br〉 Where SQI is the soil quality index, CQI is the climate quality index and VQI is the vegetation quality index. The SQI is based on rating the parent material, slope, soil texture, and soil depth. The VQI is computed on bases of rating three categories (i.e. erosion protection, drought resistance and plant cover). The CQI is based on the aridity index, derived from values of annual rainfall and potential evapotranspiration. Arc-GIS 9 software was used for the computation and sensitivity maps production. 〈br〉〈br〉 The results show that the soil of the Nile Valley are characterized by a moderate SQI, however the those in the interference zone are low soil quality indexed. The dense vegetation of the valley has raised its VQI to be good, however coastal areas are average and interference zones are low. The maps of ESA's for desertification show that 86.1% of Egyptian territory is classified as very sensitive areas, while 4.3% as Moderately sensitive, and 9.6% as sensitive. 〈br〉〈br〉 It can be concluded that implementing the maps of sensitivity to desertification is rather useful in the arid and semi arid areas as they give more likely quantitative trend for frequency of sensitive areas. The integration of different factors contributing to desertification sensitivity may lead to plan a successful combating. The usage of space data and GIS proved to be suitable tools to rely estimation and to fulfill the needed large computational requirements. They are also useful in visualizing the sensitivity situation of different desertification parameters.

Description: 〈b〉Palaeomagnetic investigations of sediments cores from Axios zone (N. Greece): implications of low inclinations in the Aegean〈/b〉〈br〉 E. Aidona, D. Kondopoulou, R. Scholger, A. Georgakopoulos, and A. Vafeidis〈br〉 eEarth, 3, 7-18, doi:10.5194/ee-3-7-2008, 2008〈br〉 Sediment cores from 13 deep boreholes (1–4.1 km) distributed within Axios zone in Northern Greece have been studied by means of palaeomagnetism. Both low field magnetic susceptibility and intensity of the natural remanent magnetization (NRM) indicate rather weakly magnetised materials. A set of 390 samples have been subjected to thermal and alternative field demagnetization. Isothermal remanent magnetization (IRM) acquisition curves and thermomagnetic analysis suggest the dominance of magnetite. Thin sections from 30 selected samples were studied in order to more precisely characterise their magnetic mineralogy. This investigation also reveals the presence of magnetite and pyrite in framboidal form. An attempt to re-orient some of the samples was partially successful by using the viscous component and the anisotropy method. These techniques were applied in order to correct the palaeomagnetic directions due to the orientation ambiguity of the core samples. The corrected mean direction converges towards an eastward value, in agreement with the overall pattern of the onshore results from previous investigations in the study area. 〈br〉〈br〉 Finally, the observed inclinations of characteristic remanences in these rocks are much lower than the expected ones but converge with those obtained from formations on land.

Description: 〈b〉A seismic swarm near Neshkan, Chukotka, northeastern Russia, and implications for the boundary of the Bering plate〈/b〉〈br〉 K. G. Mackey, K. Fujita, B. M. Sedov, L. V. Gounbina, and S. Kurtkin〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 261-271, https://doi.org/10.5194/smsps-4-261-2009, 2009〈br〉 A seismic swarm lasting over two years occurred near the village of Neshkan, Chukotka, far northeastern Russia, beginning with a 〈i〉M〈sub〉L〈/sub〉〈/i〉, 4.2 (4.1 〈i〉m〈sub〉b〈/sub〉〈/i〉) earthquake on 9 December 2002. The swarm generated considerable anxiety among the local populace and authorities. Two temporary seismic stations were deployed during the latter part of September 2003, and recorded over 150 events with magnitudes up to 3.0. Eighteen locatable events appear to form a northeast striking linear trend, parallel to other seismicity trends in Chukotka, extending 20 km to the southwest from the village. We interpret this trend as a previously unknown fault. A small pond located ~1 km west of the village drained and some apparent surface deformation was observed over the course of the earthquake sequence. Relocation of historic seismicity in the region shows that a magnitude 6.0 in 1996 may have ruptured an adjacent fault segment. Other, less well located but larger, teleseismic events earlier in the 20th century may also have occurred on or near this fault. The seismicity is consistent a proposed region of transtension along the northern boundary of a Bering plate.

Description: 〈b〉South Anyui suture: tectono-stratigraphy, deformations, and principal tectonic events〈/b〉〈br〉 S. D. Sokolov, G. Ye. Bondarenko, P. W. Layer, and I. R. Kravchenko-Berezhnoy〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 201-221, https://doi.org/10.5194/smsps-4-201-2009, 2009〈br〉 Geochronologic and structural data from the terranes of the South Anyui suture zone record a protracted deformational history before, during and after an Early Cretaceous collision of the passive margin of the Chukotka-Arctic Alaska continental block with the active continental margin of the North Asian continent. Preceding this collision, the island arc complexes of the Yarakvaam terrane on the northern margin of the North Asian craton record Early Carboniferous to Neocomian ages in ophiolite, sedimentary, and volcanic rocks. Triassic to Jurassic amphibolites constrain the timing of subduction and intraoceanic deformation along this margin. The protracted (Neocomian to Aptian) collision of the Chukotka passive margin with the North Asian continent is preserved in a range of structural styles including first north verging folding, then south verging folding, and finally late collisional dextral strike slip motions which likely record a change from orthogonal collision to oblique collision. Due to this collision, the southern passive margin of Chukotka was overthrust by tectonic nappes composed of tectono-stratigraphic complexes of the South Anyui terrane. Greenschists with ages of 115–119 Ma are related to the last stages of this collision. The postcollisional orogenic stage (Albian to Cenomanian) is characterized by sinistral strike slip faults and an extensional environment.

Description: 〈b〉Deformation of the Northwestern Okhotsk Plate: How is it happening?〈/b〉〈br〉 D. Hindle, K. Fujita, and K. Mackey〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 147-156, https://doi.org/10.5194/smsps-4-147-2009, 2009〈br〉 The Eurasia (EU) – North America (NA) plate boundary zone across Northeast Asia still presents many open questions within the plate tectonic paradigm. Constraining the geometry and number of plates or microplates present in the plate boundary zone is especially difficult because of the location of the EU-NA euler pole close to or even upon the EU-NA boundary. One of the major challenges remains the geometry of the Okhotsk plate (OK). whose northwestern portion terminates on the EU-OK-NA triple junction and is thus caught and compressed between converging EU and NA. We suggest that this leads to a coherent and understandable large scale deformation pattern of mostly northwest-southeast trending strike-slip faults which split Northwest OK into several extruding slivers. When the fault geometry is analysed together with space geodetic and focal mechanism data it suggests a central block which is extruding faster bordered east and west by progressively slower extruding blocks until the OK plate boundary faults are encountered. Taking into account elastic loading from both the intra-OK faults and the OK-Pacific (PA) boundary reconciles geodetic motions with geologic slip rates on at least the OK-NA boundary which corresponds to the Ulakhan fault.

Description: 〈b〉The Tommot pluton: a Middle Paleozoic rift-related alkaline gabbro and syenite complex, Yakutia, northeast Russia〈/b〉〈br〉 V. A. Trunilina, P. W. Layer, L. M. Parfenov, A. I. Zaitsev, and Y. S. Orlov〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 97-109, https://doi.org/10.5194/smsps-4-97-2009, 2009〈br〉 The Tommot pluton is located within the continental Omulevka terrane of the inner zone of the Verkhoyansk-Kolyma Mesozoic orogen. It is a small complex (~12 km〈sup〉2〈/sup〉) composed of alkaline-ultramafic rocks, alkaline and subalkaline gabbroids, and alkaline and quartz syenites. The pluton is unique both in the composition and age of its constituent rocks. Mineralogical-petrographical and geochemical studies of the rocks indicate that the alkaline rocks resulted from the melting of depleted mantle horizons. K-Ar, Rb-Sr, and 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar age determinations confirm a Paleozoic age of the rocks. Formation of the alkaline rocks is related to Middle Paleozoic rifting which occurred as two discrete events: a Late Devonian event, which affected the marginal part of the Siberian continent, and a Late Carboniferous event that reflects internal deformation of the Omulevka terrane or late-stage extension. A spatially associated alkali granite, the Somnitel'nyy pluton, is Late Jurassic–Early Cretaceous in age and is synchronous with accretion of the Kolyma-Omolon Superterrane to Siberia in the Mesozoic.

Description: 〈b〉Biography – Leonid M. Parfenov (1937–2002)〈/b〉〈br〉 K. Fujita, A. V. Prokopiev, and D. B. Stone〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 5-9, https://doi.org/10.5194/smsps-4-5-2009, 2009〈br〉

Description: 〈b〉Geochronology and thermochronology of Cretaceous plutons and metamorphic country rocks, Anyui-Chukotka fold belt, North East Arctic Russia〈/b〉〈br〉 E. L. Miller, S. M. Katkov, A. Strickland, J. Toro, V. V. Akinin, and T. A. Dumitru〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 157-175, https://doi.org/10.5194/smsps-4-157-2009, 2009〈br〉 U-Pb isotopic dating of seven granitoid plutons and associated intrusions from the Bilibino region (Arctic Chukotka, Russia) was carried out using the SHRIMP-RG. The crystallization ages of these granitoids, which range from approximately 116.9±2.5 to 108.5±2.7 Ma, bracket two regionally significant deformational events. The plutons cut folds, steep foliations and thrust-related structures related to sub-horizontal shortening at lower greenschist facies conditions (〈i〉D〈/i〉〈sub〉1〈/sub〉), believed to be the result of the collision of the Arctic Alaska-Chukotka microplate with Eurasia along the South Anyui Zone (SAZ). Deformation began in the Late Jurassic, based on fossil ages of syn-orogenic clastic strata, and involves strata as young as early Cretaceous (Valanginian) north of Bilibino and as young as Hauterivian-Barremian, in the SAZ. The second phase of deformation (〈i〉D〈/i〉〈sub〉2〈/sub〉) is developed across a broad region around and to the east of the Lupveem batholith of the Alarmaut massif and is interpreted to be coeval with magmatism. 〈i〉D〈/i〉〈sub〉2〈/sub〉 formed gently-dipping, high-strain foliations (〈i〉S〈/i〉〈sub〉2〈/sub〉). Growth of biotite, muscovite and actinolite define 〈i〉S〈/i〉〈sub〉2〈/sub〉 adjacent to the batholith, while chlorite and white mica define 〈i〉S〈/i〉〈sub〉2〈/sub〉 away from the batholith. Sillimanite (± andalusite) at the southeastern edge the Lupveem batholith represent the highest grade metamorphic minerals associated with 〈i〉D〈/i〉〈sub〉2〈/sub〉. 〈i〉D〈/i〉〈sub〉2〈/sub〉 is interpreted to have developed during regional extension and crustal thinning. Extension directions as measured by stretching lineations, quartz veins, boudinaged quartz veins is NE-SW to NW-SE. Mapped dikes associated with the plutons trend mostly NW-SE and indicate NE-SW directed extension. 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar ages from 〈i〉S〈/i〉〈sub〉2〈/sub〉 micas range from 109.3±1.2 to 103.0±1.8 Ma and are interpreted as post-crystallization cooling ages following a protracted period of magmatism and high heat flow. Regional uplift and erosion of many kilometers of cover produced a subdued erosional surface prior to the eruption of volcanic rocks of the Okhotsk-Chukotka volcanic belt (OCVB) whose basal units (~87 Ma) overlie this profound regional unconformity. A single fission track age on apatite from granite in the Alarmaut massif yielded an age of 90±11 Ma, in good agreement with this inference.

Description: 〈b〉Summary of Northeast Asia geodynamics and tectonics*〈/b〉〈br〉 L. M. Parfenov, G. Badarch, N. A. Berzin, A. I. Khanchuk, M. I. Kuzmin, W. J. Nokleberg, A. V. Prokopiev, M. Ogasawara, and H. Yan〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 11-33, https://doi.org/10.5194/smsps-4-11-2009, 2009〈br〉 The compilation, synthesis, description, and interpretation of regional geology and tectonics of major regions, such as Northeast Asia (Eastern Russia, Mongolia, Northern China, South Korea, and Japan) and the Circum-North Pacific (the Russian Far East, Alaska, and Canadian Cordillera), requires a complex methodology that includes: (1) definitions of key terms; (2) compilation of a regional geodynamics map that can be constructed according to modern tectonic concepts and definitions; and (3) formulation of a comprehensive tectonic model. This article presents a summary of the regional dynamics and tectonics of Northeast Asia as developed for a new summary geodynamics map of the region. This article also describes how a high-quality summary geodynamics map and companion tectonic analysis substantially aids in the understanding of the origin of major rock units, major structures, and contained mineral and fuel resources, and provides important guidelines for new research. 〈br〉〈br〉 * Prepared in memory of Leonid M. Parfenov, the leader of the geodynamics map team for the International collaborative project on NE Asia tectonics and metallogenesis.

Description: 〈b〉Detrital zircon geochronologic tests of the SE Siberia-SW Laurentia paleocontinental connection〈/b〉〈br〉 J. S. MacLean, J. W. Sears, K. R. Chamberlain, A. K. Khudoley, A. V. Prokopiev, A. P. Kropachev, and G. G. Serkina〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 111-116, https://doi.org/10.5194/smsps-4-111-2009, 2009〈br〉 Strikingly similar Late Mesoproterozoic stratigraphic sequences and correlative U-Pb detrital-zircon ages may indicate that the Sette Daban region of southeastern Siberia and the Death Valley region of southwestern North America were formerly contiguous parts of a Grenville foreland basin. The Siberian section contains large numbers of detrital zircons that correlate with Grenville, Granite-Rhyolite, and Yavapai basement provinces of North America. The sections in both Siberia and Death Valley exhibit west-directed thrust faults that may represent remnants of a Grenville foreland thrust belt. North American detrital-zircon components do not occur in Siberian samples above a ~600 Ma breakup unconformity, suggesting that rifting and continental separation blocked transfer of clastic sediment between the cratons by 600 Ma. Faunal similarities suggest, however, that the two cratons remained within the breeding ranges of Early Cambrian trilobites and archeocyathans.

Description: 〈b〉Seismotectonics of the Chersky Seismic Belt, eastern Sakha Republic (Yakutia) and Magadan District, Russia〈/b〉〈br〉 K. Fujita, B. M. Koz'min, K. G. Mackey, S. A. Riegel, M. S. McLean, and V. S. Imaev〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 117-145, https://doi.org/10.5194/smsps-4-117-2009, 2009〈br〉 The Chersky seismic belt represents a zone of deformation between the North American and Eurasian plates in northeast Russia. The belt extends from the Laptev Sea into the Chersky Range where it splits into two branches. One branch extends to Kamchatka and the Aleutian-Kurile Junction, while the other branch extends south towards Sakhalin Island. Focal mechanisms indicate a change from extension to transpression in the northern Verkhoyansk Range and generally left-lateral transpression in the Chersky Range extending to northern Kamchatka. The few focal mechanisms on the second branch suggest right-lateral transpression. A large number of faults, sub-parallel to the seismicity and presumed to be strike-slip, are visible in satellite imagery and topographic maps and are also associated with seismically generated landslides. 〈br〉〈br〉 These data support a model in which the Sea of Okhotsk forms the core of a separate Okhotsk microplate surrounded by diffuse boundaries on the north and west. Microseismicity in continental northeast Russia is most heavily concentrated within and between the fault systems along the northern boundary of the proposed Okhotsk plate and indicates a high level of deformation. The sense of slip on the faults (both from focal mechanisms and geology) are also generally consistent with the extrusion of the Okhotsk plate to the southeast as it is compressed between its larger neighbors. The northernmost part of the Okhotsk plate may be decoupled to some degree from the more stable central Sea of Okhotsk.

Description: 〈b〉Review of geology of the New Siberian Islands between the Laptev and the East Siberian Seas, North East Russia〈/b〉〈br〉 M. Kos'ko and E. Korago〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 45-64, https://doi.org/10.5194/smsps-4-45-2009, 2009〈br〉 The New Siberian Islands comprise De Long Islands, Anjou Islands, and Lyakhov Islands. Early Paleozoic, Mesozoic and Cenozoic sediments and igneous rocks are known on the De Long Islands. Cambrian slate, siltstone, mudstone and silicified limestone occur on Bennett Island. Ordovician volcanogenic turbidites, lavas, and small intrusions of andesite-basalt, basalt, dolerite, and porphyritic diorite were mapped on Henrietta Island. The igneous rocks are of calc-alkaline island arc series. The Ordovician age of the sequence was defined radiometrically. Early Paleozoic strata were faulted and folded presumably in the Caledonian time. Early Cretaceous sandstone and mudstone are known on Bennett Island. They are overlain by a 106–124 Ma basalt unit. Cenozoic volcanics are widespread on the De Long Islands. Zhokhov Island is an eroded stratovolcano. The volcanics are mostly of picrite-olivine type and limburgite. Radiometric dating indicates Miocene to Recent ages for Cenozoic volcanism. 〈br〉〈br〉 On the Anjou islands Lower-Middle Paleozoic strata consist of carbonates, siliciclastics, and clay. A Northwest-southeast syn-sedimentary facies zonation has been reconstructed. Upper Paleozoic strata are marine carbonate, clay and siliciclastic facies. Mudstone and clay predominate in the Triassic to Upper Jurassic section. Aptian-Albian coal bearing deposits uconformably overlap lower strata indicating Early Cretaceous tectonism. Upper Cretaceous units are mostly clay and siltstone with brown coal strata resting on Early Cretaceous weathered rhyolite. Cenozoic marine and nonmarine silisiclastics and clay rest upon the older units with a transgressive unconformity including a weathering profile in the older rocks. 〈br〉〈br〉 Manifestations of Paleozoic and Triassic mafic and Cretaceous acidic magmatism are also found on these islands. The pre-Cretaceous structure of the Anjou islands is of a block and fold type Late Cimmerian in age followed by faulting in Cenozoic time. 〈br〉〈br〉 The Lyakhov islands are located at the western end of the Late Cimmerian South Anyui suture. Sequences of variable age, composition, and structural styles are known on the Lyakhov Islands. These include an ancient metamorphic sequence, Late Paleozoic ophiolitic sequence, Late Mesozoic turbidite sequence, Cretaceous granites, and Cenozoic sediments. Fold and thrust imbricate structures have been mapped on southern Bol'shoi Lyakhov Island. North-northwestern vergent thrusts transect the Island and project offshore. Open folds of Jurassic–Early Cretaceous strata are characteristic of Stolbovoi and Malyi Lyakhov islands. 〈br〉〈br〉 Geology of the New Siberian Islands supports the concept of a circum Arctic Phanerozoic fold belt. The belt is comprised of Caledonian, Ellesmerian, Early Cimmerian and Late Cimmerian fold systems, manifested in many places on the mainland and on islands around the Arctic Ocean. Knowledge of the geology of the New Siberian Islands has been used to interpret anomalous gravity and magnetic field maps and Multi Channel Seismic (MCS) lines. Two distinguishing structural stages are universally recognized within the offshore sedimentary cover which correlate with the onshore geology of the New Siberian Islands. Dating of the upper structural stage and constituent seismic units is based on structural and stratigraphic relationships between Late Mesozoic and Cenozoic units in the archipelago. The Laptev Sea–western East Siberian Sea seismostratigraphic model for the upper structural stage has much in common with the seismostratigraphic model in the American Chukchi Sea.

Description: 〈b〉Editors and Acknowledgement〈/b〉〈br〉 〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 1-1, https://doi.org/10.5194/smsps-4-1-2009, 2009〈br〉

Description: 〈b〉Morphology of the pore space in claystones – evidence from BIB/FIB ion beam sectioning and cryo-SEM observations〈/b〉〈br〉 G. Desbois, J. L. Urai, and P. A. Kukla〈br〉 eEarth, 4, 15-22, doi:10.5194/ee-4-15-2009, 2009〈br〉 The morphology of pore space has a strong effect on mechanical and transport properties of mudrocks and clay-rich fault gouge, but its characterization has been mostly indirect. We report on a study of Boom clay from a proposed disposal site of radioactive waste (Mol site, Belgium) using high resolution SEM at cryogenic temperature, with ion beam cross-sectioning to prepare smooth, damage free surfaces. Pores commonly have crack-like tips, preferred orientation parallel to bedding and power law size distribution. We define a number of pore types depending on shape and location in the microstructure: large jagged pores in strain shadows of clastic grains, high aspect ratio pores between similarly oriented phyllosilicate grains and crescent-shaped pores in saddle reefs of folded phyllosilicates. 3-D reconstruction by serial cross-sectioning shows 3-D connectivity of the pore space. These findings offer a new insight into the morphology of pores down to nano-scale in comparison to traditional pore size distributions calculated from mercury Injection experiments, explain slaking of clays by successive wetting and drying and provide the basis for microstructure-based models of transport in clays.

Description: 〈b〉Geometry of the Turkey-Arabia and Africa-Arabia plate boundaries in the latest Miocene to Mid-Pliocene: the role of the Malatya-Ovacık Fault Zone in eastern Turkey〈/b〉〈br〉 R. Westaway, T. Demir, and A. Seyrek〈br〉 eEarth, 3, 27-35, doi:10.5194/ee-3-27-2008, 2008〈br〉 We suggest a working hypothesis for the geometry of the strike-slip faults that formed the boundaries between the Turkish, African and Arabian plates in the latest Miocene to Mid-Pliocene (LMMP), between ~7–6 Ma and ~3.5 Ma. This geometry differed significantly from the modern geometry; the northern Dead Sea Fault Zone (DSFZ) was located east of its present line and the TR-AR boundary was formed by the Malatya-Ovacık Fault Zone (MOFZ), located well north of the modern East Anatolian Fault Zone (EAFZ). The MOFZ is potentially the most problematic aspect of such a scheme, given the dramatically different interpretations of it that have been proposed. However, the presently-available evidence, albeit limited, is consistent with our proposed interpretation. Significant differences between the proposed LMMP fault geometry and the modern geometry include, first, the transtensional geometry of the MOFZ, the modern EAFZ being typically a left-lateral transform fault zone but with localized transpression. Second, the MOFZ slip rate was much lower than the ~9–10 mm a〈sup〉−1〈/sup〉 EAFZ slip rate; it is estimated as ~2–3 mm a〈sup〉−1〈/sup〉, having produced no more than ~8 km of slip during its approximately three million year long activity. The Euler vector is tentatively inferred to have involved relative rotation between the Turkish and Arabian Plates at ~0.85±0.15° Ma〈sup〉−1〈/sup〉 about a pole at ~37.75±0.15° N, ~38.8±0.3° E. Third, unlike at present, there was no throughgoing linkage of left-lateral faulting between the LMMP DSFZ and the MOFZ; instead, the DSFZ terminated northward, and the MOFZ terminated southward, in a zone of localised crustal shortening adjoining the suture of the former Neotethys Ocean in the Kahramanmaraş-Pazarcık region of SE Turkey. The different motion of the Turkish plate relative to Arabia, and, thus, relative to Eurasia, means that senses and rates of crustal deformation can be expected to have been different during the LMMP phase from at present, throughout the eastern Mediterranean region.

Description: 〈b〉Late Pleistocene palaeoproductivity patterns during the last climatic cycle in the Guyana Basin as revealed by calcareous nannoplankton〈/b〉〈br〉 G.-E. López-Otálvaro, J. A. Flores, F. J. Sierro, I. Cacho, J.-O. Grimalt, E. Michel, E. Cortijo, and L. Labeyrie〈br〉 eEarth, 4, 1-13, doi:10.5194/ee-4-1-2009, 2009〈br〉 Variations in the assemblage and abundance of coccoliths reveal changes in oceanic and atmospheric dynamics in the Guyana Basin over the last climatic cycle, mainly linked to latitudinal variations in the ITCZ (Intertropical Convergence Zone). Records of the N ratio (a palaeoproductivity index of coccolithophores) allowed us to monitor nutri-thermocline fluctuations. Nannofossil accumulation rates (NAR) vary closely with the N ratio, indicating a strong correlation between these two palaeoproductivity proxies. Decreases in the N ratio and NAR values suggest lower palaeoproductivity during glacial substages, indicating a deep nutri-thermocline (deep stratification of the mixed layer) as a consequence of the piling up of warm water dragged by the NEC. This setting was favoured by the southern shift of the ITCZ and Trade winds which blew perpendicular to the Guyana coast. By contrast, increases in the N ratio and NAR values revealed higher palaeoproductivity during interglacial substages, suggesting a shoaling of the nutri-thermocline. This scenario is favoured by a northward displacement of the ITCZ with the southeast Trade winds blowing alongshore. Additionally, palaeoproductivity changes during substages of Marine Isotope Stage (MIS) 6-5 are of much higher amplitude than those recorded in substages of MIS 4-2 and the early Holocene. Similarities between the palaeoproductivity and the 65° N summer insolation records, suggest a link between the depth of nutri-thermocline, the latitudinal migration of the ITCZ and ice-sheet changes in the Northern Hemisphere.

Description: 〈b〉Decline of coral reefs during late Paleocene to early Eocene global warming〈/b〉〈br〉 C. Scheibner and R. P. Speijer〈br〉 eEarth, 3, 19-26, doi:10.5194/ee-3-19-2008, 2008〈br〉 Since the 1980s the frequency of warming events has intensified and simultaneously widespread coral bleaching, and enhanced coral mortality have been observed. Yet, it remains unpredictable how tropical coral reef communities will react to prolonged adverse conditions. Possibly, coral reef systems are sufficiently robust to withstand continued environmental pressures. But if coral mortality increases, what will platform communities of the future look like? The co-evolution of early Paleogene carbonate platforms and palaeoclimate may provide insight. Here we document the impact of early Paleogene global warming on shallow-water carbonate platforms in the Tethys. Between 59 and 55 Ma, three discrete stages in platform development can be identified Tethys-wide: during the first stage carbonate platforms mainly consisted of coralgal reefs; during the second – transitional – stage coralgal reefs thrived only at middle latitudes and gave way to larger foraminifera as dominant carbonate producer in low latitudes; finally, during the third stage, newly developing larger foraminifera lineages completely took over the role as main carbonate-producing organisms in low to middle latitudes. We postulate that rising temperatures led to a stepwise demise of Paleocene coral reefs, giving way to an unprecedented expansion of larger foraminifera, dominating Tethyan platforms during the early Eocene.

Description: 〈b〉Characteristics of chlorites in seismogenic fault zones: the Taiwan Chelungpu Fault Drilling Project (TCDP) core sample〈/b〉〈br〉 Y. Hashimoto, O. Tadai, M. Tanimizu, W. Tanikawa, T. Hirono, W. Lin, T. Mishima, M. Sakaguchi, W. Soh, S. R. Song, K. Aoike, T. Ishikawa, M. Murayama, K. Fujimoto, T. Fukuchi, M. Ikehara, H. Ito, H. Kikuta, M. Kinoshita, K. Masuda, T. Matsubara, O. Matsubayashi, K. Mizoguchi, N. Nakamura, K. Otsuki, T. Shimamoto, H. Sone, and M. Takahashi〈br〉 eEarth, 3, 1-6, doi:10.5194/ee-3-1-2008, 2008〈br〉 The iron content and the asymmetry of iron and magnesium ions in chlorites are examined for the Chelungpu Fault in Taiwan, which is a seismogenic fault. The samples are collected from the cores drilled for the Taiwan Chelungpu Fault Drilling Project (TCDP, borehole B). Three fault zones are recognized as candidates for the source of seismogenic materials. The fault zones are composed of fractured-damaged rocks, breccia, gray gouge, black gouge, and black material. Chlorite from each type of rock was analyzed by using X-ray diffraction (XRD). The iron content and asymmetry of the iron and magnesium ions in the chlorites were estimated from the XRD peak ratios. The hydroxide and silicate layers of chlorite in the black gouge and black material have low iron contents. Many studies have suggested that a temperature rise occurred at the fault zones. In addition, the temperature rise can result in the production of iron oxides such as magnetite or maghemite, as reported by other studies. However, the temperature rise cannot explain the low value of iron content in the chlorites. Another reason for the low value of iron content is the variation in the pH of the fluid, which can be controlled by radical reactions. Therefore, on the basis of chlorite characteristics, the reactions at the seismogenic fault are due not only to the thermal decomposition resulting from the temperature rise and but also to rock-fluid interactions.

Description: 〈b〉Characteristics of chlorites in seismogenic fault zones: the Taiwan Chelungpu Fault Drilling Project (TCDP) core sample〈/b〉〈br〉 Y. Hashimoto, O. Tadai, M. Tanimizu, W. Tanikawa, T. Hirono, W. Lin, T. Mishima, M. Sakaguchi, W. Soh, S. R. Song, K. Aoike, T. Ishikawa, M. Murayama, K. Fujimoto, T. Fukuchi, M. Ikehara, H. Ito, H. Kikuta, M. Kinoshita, K. Masuda, T. Matsubara, O. Matsubayashi, K. Mizoguchi, N. Nakamura, K. Otsuki, T. Shimamoto, H. Sone, and M. Takahashi〈br〉 eEarth, 3, 1-6, doi:10.5194/ee-3-1-2008, 2008〈br〉 The iron content and the asymmetry of iron and magnesium ions in chlorites are examined for the Chelungpu Fault in Taiwan, which is a seismogenic fault. The samples are collected from the cores drilled for the Taiwan Chelungpu Fault Drilling Project (TCDP, borehole B). Three fault zones are recognized as candidates for the source of seismogenic materials. The fault zones are composed of fractured-damaged rocks, breccia, gray gouge, black gouge, and black material. Chlorite from each type of rock was analyzed by using X-ray diffraction (XRD). The iron content and asymmetry of the iron and magnesium ions in the chlorites were estimated from the XRD peak ratios. The hydroxide and silicate layers of chlorite in the black gouge and black material have low iron contents. Many studies have suggested that a temperature rise occurred at the fault zones. In addition, the temperature rise can result in the production of iron oxides such as magnetite or maghemite, as reported by other studies. However, the temperature rise cannot explain the low value of iron content in the chlorites. Another reason for the low value of iron content is the variation in the pH of the fluid, which can be controlled by radical reactions. Therefore, on the basis of chlorite characteristics, the reactions at the seismogenic fault are due not only to the thermal decomposition resulting from the temperature rise and but also to rock-fluid interactions.

Description: 〈b〉Syn- and post-orogenic exhumation of metamorphic rocks in North Aegean〈/b〉〈br〉 R. Lacassin, N. Arnaud, P. H. Leloup, R. Armijo, and B. Meyer〈br〉 eEarth, 2, 51-63, doi:10.5194/ee-2-51-2007, 2007〈br〉 The Olympos-Ossa-Pelion (OOP) ranges, in NW Aegean, encompass Greece highest summit and are located near the extremity of the North Anatolian Fault (NAF). Structural and thermochronological data gathered in the OOP ranges show that the main exhumation of metamorphic nappes occurred in the Eocene, at ca. 43–39 Ma. This early exhumation, associated with ductile, then brittle-ductile normal faulting with northeastward transport, is coeval with orogenic shortening in the close area. Cooling rates, and likely exhumation, have been low between ~40 Ma and ~20 Ma. 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar crystallization ages (between 20 and 15 Ma) appears related to brittle-ductile normal faulting and likely associated with Neogene Aegean back-arc extension. The dating of a diabase dyke, and the geometry of associated brittle jointing, of onshore and offshore active normal faults suggest a shift in extension direction after 4Ma, possibly in relation with the propagation of the NAF in northern Aegean.

Description: 〈b〉Syn- and post-orogenic exhumation of metamorphic rocks in North Aegean〈/b〉〈br〉 R. Lacassin, N. Arnaud, P. H. Leloup, R. Armijo, and B. Meyer〈br〉 eEarth, 2, 51-63, doi:10.5194/ee-2-51-2007, 2007〈br〉 The Olympos-Ossa-Pelion (OOP) ranges, in NW Aegean, encompass Greece highest summit and are located near the extremity of the North Anatolian Fault (NAF). Structural and thermochronological data gathered in the OOP ranges show that the main exhumation of metamorphic nappes occurred in the Eocene, at ca. 43–39 Ma. This early exhumation, associated with ductile, then brittle-ductile normal faulting with northeastward transport, is coeval with orogenic shortening in the close area. Cooling rates, and likely exhumation, have been low between ~40 Ma and ~20 Ma. 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar crystallization ages (between 20 and 15 Ma) appears related to brittle-ductile normal faulting and likely associated with Neogene Aegean back-arc extension. The dating of a diabase dyke, and the geometry of associated brittle jointing, of onshore and offshore active normal faults suggest a shift in extension direction after 4Ma, possibly in relation with the propagation of the NAF in northern Aegean.

Description: 〈b〉Impact vesiculation – a new trigger for volcanic bubble growth and degassing〈/b〉〈br〉 D. A. Rothery, J. M. Sumner, O. Spieler, and D. B. Dingwell〈br〉 eEarth Discuss., 2, 151-167, doi:10.5194/eed-2-151-2007, 2007〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 3 comments)〈br〉 We highlight a potentially important trigger for bubble growth and degassing in volcanic bombs. We have successfully triggered bubble growth in previously unvesiculated samples of silicate melt during experiments to simulate volcanic bomb impact, by firing pellets at, and dropping weights onto, melt samples. We call this phenomenon "impact vesiculation". Further work is required on real volcanic bombs to establish the extent to which impact vesiculation occurs in nature. However, our experiments are sufficient to demonstrate that impact vesiculation is a viable processes and should be borne in mind in analysis of bubble populations and degassing histories of bombs and spatter-fed lava flows. Degassing caused by impact vesiculation can occur only at ground-level, so any attempt to calculate the amount of erupted gas available for transport high into the atmosphere by convection above the source of a fountain-fed lava flow that is based on subtracting the volatile content of fluid inclusions from the volatile content of the resulting lava flow would be an overestimate if significant impact vesiculation has occurred.

Description: 〈b〉Impact vesiculation – a new trigger for volcanic bubble growth and degassing〈/b〉〈br〉 D. A. Rothery, J. M. Sumner, O. Spieler, and D. B. Dingwell〈br〉 eEarth Discuss., 2, 151-167, doi:10.5194/eed-2-151-2007, 2007〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 3 comments)〈br〉 We highlight a potentially important trigger for bubble growth and degassing in volcanic bombs. We have successfully triggered bubble growth in previously unvesiculated samples of silicate melt during experiments to simulate volcanic bomb impact, by firing pellets at, and dropping weights onto, melt samples. We call this phenomenon "impact vesiculation". Further work is required on real volcanic bombs to establish the extent to which impact vesiculation occurs in nature. However, our experiments are sufficient to demonstrate that impact vesiculation is a viable processes and should be borne in mind in analysis of bubble populations and degassing histories of bombs and spatter-fed lava flows. Degassing caused by impact vesiculation can occur only at ground-level, so any attempt to calculate the amount of erupted gas available for transport high into the atmosphere by convection above the source of a fountain-fed lava flow that is based on subtracting the volatile content of fluid inclusions from the volatile content of the resulting lava flow would be an overestimate if significant impact vesiculation has occurred.

Description: 〈b〉Geometry of the Turkey-Arabia and Africa-Arabia plate boundaries in the latest Miocene to Mid-Pliocene: the role of the Malatya-Ovacık Fault Zone in eastern Turkey〈/b〉〈br〉 R. Westaway, T. Demir, and A. Seyrek〈br〉 eEarth, 3, 27-35, doi:10.5194/ee-3-27-2008, 2008〈br〉 We suggest a working hypothesis for the geometry of the strike-slip faults that formed the boundaries between the Turkish, African and Arabian plates in the latest Miocene to Mid-Pliocene (LMMP), between ~7–6 Ma and ~3.5 Ma. This geometry differed significantly from the modern geometry; the northern Dead Sea Fault Zone (DSFZ) was located east of its present line and the TR-AR boundary was formed by the Malatya-Ovacık Fault Zone (MOFZ), located well north of the modern East Anatolian Fault Zone (EAFZ). The MOFZ is potentially the most problematic aspect of such a scheme, given the dramatically different interpretations of it that have been proposed. However, the presently-available evidence, albeit limited, is consistent with our proposed interpretation. Significant differences between the proposed LMMP fault geometry and the modern geometry include, first, the transtensional geometry of the MOFZ, the modern EAFZ being typically a left-lateral transform fault zone but with localized transpression. Second, the MOFZ slip rate was much lower than the ~9–10 mm a〈sup〉−1〈/sup〉 EAFZ slip rate; it is estimated as ~2–3 mm a〈sup〉−1〈/sup〉, having produced no more than ~8 km of slip during its approximately three million year long activity. The Euler vector is tentatively inferred to have involved relative rotation between the Turkish and Arabian Plates at ~0.85±0.15° Ma〈sup〉−1〈/sup〉 about a pole at ~37.75±0.15° N, ~38.8±0.3° E. Third, unlike at present, there was no throughgoing linkage of left-lateral faulting between the LMMP DSFZ and the MOFZ; instead, the DSFZ terminated northward, and the MOFZ terminated southward, in a zone of localised crustal shortening adjoining the suture of the former Neotethys Ocean in the Kahramanmaraş-Pazarcık region of SE Turkey. The different motion of the Turkish plate relative to Arabia, and, thus, relative to Eurasia, means that senses and rates of crustal deformation can be expected to have been different during the LMMP phase from at present, throughout the eastern Mediterranean region.

Description: 〈b〉Late Pleistocene palaeoproductivity patterns during the last climatic cycle in the Guyana Basin as revealed by calcareous nannoplankton〈/b〉〈br〉 G.-E. López-Otálvaro, J. A. Flores, F. J. Sierro, I. Cacho, J.-O. Grimalt, E. Michel, E. Cortijo, and L. Labeyrie〈br〉 eEarth, 4, 1-13, doi:10.5194/ee-4-1-2009, 2009〈br〉 Variations in the assemblage and abundance of coccoliths reveal changes in oceanic and atmospheric dynamics in the Guyana Basin over the last climatic cycle, mainly linked to latitudinal variations in the ITCZ (Intertropical Convergence Zone). Records of the N ratio (a palaeoproductivity index of coccolithophores) allowed us to monitor nutri-thermocline fluctuations. Nannofossil accumulation rates (NAR) vary closely with the N ratio, indicating a strong correlation between these two palaeoproductivity proxies. Decreases in the N ratio and NAR values suggest lower palaeoproductivity during glacial substages, indicating a deep nutri-thermocline (deep stratification of the mixed layer) as a consequence of the piling up of warm water dragged by the NEC. This setting was favoured by the southern shift of the ITCZ and Trade winds which blew perpendicular to the Guyana coast. By contrast, increases in the N ratio and NAR values revealed higher palaeoproductivity during interglacial substages, suggesting a shoaling of the nutri-thermocline. This scenario is favoured by a northward displacement of the ITCZ with the southeast Trade winds blowing alongshore. Additionally, palaeoproductivity changes during substages of Marine Isotope Stage (MIS) 6-5 are of much higher amplitude than those recorded in substages of MIS 4-2 and the early Holocene. Similarities between the palaeoproductivity and the 65° N summer insolation records, suggest a link between the depth of nutri-thermocline, the latitudinal migration of the ITCZ and ice-sheet changes in the Northern Hemisphere.

Description: 〈b〉Use of remote sensing and GIS in mapping the environmental sensitivity areas for desertification of Egyptian territory〈/b〉〈br〉 A. Gad and I. Lotfy〈br〉 eEarth Discuss., 3, 41-85, doi:10.5194/eed-3-41-2008, 2008〈br〉 〈b〉Revised manuscript has not been submitted〈/b〉 (discussion: closed, 3 comments)〈br〉 Desertification is defined in the first art of the convention to combat desertification as 〈i〉"land degradation in arid, semiarid and dry sub-humid areas resulting from climatic variations and human activities".〈/i〉 Its consequence include a set of important processes which are active in arid and semi arid environment, where water is the main limiting factor of land use performance in such ecosystem . Desertification indicators or the groups of associated indicators should be focused on a single process. They should be based on available reliable information sources, including remotely sensed images, topographic data (maps or DEM'S), climate, soils and geological data. The current work aims to map the Environmental Sensitivity Areas (ESA's) to desertification in whole territory of Egypt at a scale of 1:1 000 000. 〈br〉〈br〉 ETM satellite images, geologic and soil maps were used as main sources for calculating the index of Environmental Sensitivity Areas (ESAI) for desertification. The algorism is adopted from MEDALLUS methodology as follows; 〈br〉〈br〉 ESAI = (SQI * CQI * VQI)〈sup〉1/3〈/sup〉 〈br〉〈br〉 Where SQI is the soil quality index, CQI is the climate quality index and VQI is the vegetation quality index. The SQI is based on rating the parent material, slope, soil texture, and soil depth. The VQI is computed on bases of rating three categories (i.e. erosion protection, drought resistance and plant cover). The CQI is based on the aridity index, derived from values of annual rainfall and potential evapotranspiration. Arc-GIS 9 software was used for the computation and sensitivity maps production. 〈br〉〈br〉 The results show that the soil of the Nile Valley are characterized by a moderate SQI, however the those in the interference zone are low soil quality indexed. The dense vegetation of the valley has raised its VQI to be good, however coastal areas are average and interference zones are low. The maps of ESA's for desertification show that 86.1% of Egyptian territory is classified as very sensitive areas, while 4.3% as Moderately sensitive, and 9.6% as sensitive. 〈br〉〈br〉 It can be concluded that implementing the maps of sensitivity to desertification is rather useful in the arid and semi arid areas as they give more likely quantitative trend for frequency of sensitive areas. The integration of different factors contributing to desertification sensitivity may lead to plan a successful combating. The usage of space data and GIS proved to be suitable tools to rely estimation and to fulfill the needed large computational requirements. They are also useful in visualizing the sensitivity situation of different desertification parameters.

Description: 〈b〉Geotectonic setting of the Tertiary Uyandina and Indigirka-Zyryanka basins, Republic Sakha (Yakutia), Northeast Russia, using coal rank data〈/b〉〈br〉 H.-J. Paech〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 85-96, https://doi.org/10.5194/smsps-4-85-2009, 2009〈br〉 Outcrops along the Inach River in the Uyandina basin and those along the Myatis' River in the Indigirka-Zyryanka basin were studied in detail and sampled for coal rank determinations. The Uyandina basin is an intramontane pull-apart basin characterized by extensional structures within the Moma rift system. The coal rank is below 0.3% vitrinite reflectance (〈i〉R〈sub〉r〈/sub〉〈/i〉), which indicates shallow, immature conditions of basin formation and very low subsidence. The Myatis' River coal-bearing outcrops in the Indigirka-Zyryanka basin reveal compression induced by continent collision. The compressive deformation includes also lowermost Pliocene strata. Due to the position in the Verkhoyansk-Chersky fold belt adjacent to the Kolyma-Omolon microcontinent the Indigirka-Zyryanka basin has much in common with a foredeep, i.e. the asymmetry in thickness and tectonic structure. The vitrinite reflectance data (〈i〉R〈sub〉r〈/sub〉〈/i〉) which range from 0.25% to more than 5% reinforce the accepted models that describe basin subsidence and geothermal history and the tectonic deformation.

Description: 〈b〉Structural studies near Pevek, Russia: implications for formation of the East Siberian Shelf and Makarov Basin of the Arctic Ocean〈/b〉〈br〉 E. L. Miller and V. E. Verzhbitsky〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 223-241, https://doi.org/10.5194/smsps-4-223-2009, 2009〈br〉 The Pevek region of Arctic Russia provides excellent beach cliff exposure of sedimentary and igneous rocks that yield detailed information on the nature, progression and timing of structural events in this region. Regional folding and thrust faulting, with the development of a south-dipping axial plane cleavage/foliation developed during N-S to NE-SW directed shortening and formation of the Chukotka-Anyui fold belt. This deformation involves strata as young as Valanginian (136–140 Ma, Gradstein et al., 2004). Fold-related structures are cut by intermediate to silicic batholiths, plutons and dikes of Cretaceous age. Reported K-Ar whole rock and mineral ages on the granitoids range from 144 to 85 Ma, but to the south, more reliable U-Pb zircon ages on compositionally similar plutons yield a much narrower age range of ~120–105 Ma (Miller et al., this volume) and a pluton in Pevek yields a U-Pb age on zircon of 108.1±1.1 Ma with evidence for inheritance of slightly older 115 Ma zircons. Magmas were intruded during an episode of E-W to ENE-WSW directed regional extension based on the consistent N-S to NNW-SSE orientation of over 800 mapped dikes and quartz veins. Analysis of small-offset faults and slickensides yield results compatible with those inferred from the dikes. Younger tectonic activity across this region is minor and the locus of magmatic activity moved southward towards the Pacific margin as represented by the 〈90 Ma Okhotsk-Chukotsk volcanic belt (OCVB). A lengthy period of uplift and erosion occurred after emplacement of Cretaceous plutons and produced the peneplain beneath the younger OCVB. 〈br〉〈br〉 Based on our studies, we speculate that ~120–105 Ma magmatism, which heralds a change in tectonic regime from compression to extension, could represent one of the consequences of the inception of rifting in the Amerasian Basin of the Arctic, forming the Makarov Basin north of the Siberian shelf at this longitude. A synthesis of available seismic reflection, gravity and magnetic data for the offshore Siberian Shelf reveals a widespread, seismically mappable basement-sedimentary cover contact that deepens northward towards the edge of the shelf with few other significant basins. Various ages have been assigned to the oldest strata above the unconformity, ranging from Cretaceous (Albian – 112–100 Ma) to Tertiary (Paleocene–Eocene – ~60–50 Ma). The period of uplift and erosion documented along the Arctic coast of Russia at this longitude could represent the landward equivalent of the (yet undrilled) offshore basement-sedimentary cover contact, thus overlying sedimentary sequences could be as old as early Late Cretaceous. Although quite speculative, these conclusions suggest that land-based geologic, structural, petrologic and geochronologic studies could provide useful constraints to help resolve the plate tectonic history of the Arctic Ocean.

Description: 〈b〉Middle Paleozoic-Mesozoic boundary of the North Asian craton and the Okhotsk terrane: new geochemical and geochronological data and their geodynamic interpretation〈/b〉〈br〉 A. V. Prokopiev, J. Toro, J. K. Hourigan, A. G. Bakharev, and E. L. Miller〈br〉 Stephan Mueller Spec. Publ. Ser., 4, 71-84, https://doi.org/10.5194/smsps-4-71-2009, 2009〈br〉 The Okhotsk terrane, located east of the South Verkhoyansk sector of the Verkhoyansk fold-and-thrust belt, has Archean crystalline basement and Riphean to Early Paleozoic sedimentary cover similar to that of the adjacent the North Asian craton. However, 2.6 Ga biotite orthogneisses of the Upper Maya uplift of the Okhotsk terrane yielded Early Devonian 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar cooling ages, evidence of a Mid-Paleozoic metamorphic event not previously known. These gneisses are also intruded by 375±2 Ma (Late Devonian) calc-alkaline granodiorite plutons that we interpret as part of a continental margin volcanic arc. Therefore, Late Devonian rifting, which affected the entire eastern margin of North Asia separating the Okhotsk terrane from the North Asian craton, was probably a back-arc event. 〈br〉〈br〉 Our limited 〈sup〉40〈/sup〉Ar/〈sup〉39〈/sup〉Ar data from the South Verkhoyansk metamorphic belt suggests that low grade metamorphism and deformation started in the Late Jurassic due to accretion of the Okhotsk terrane to the North Asia margin along the Bilyakchan fault. Shortening and ductile strain continued in the core of the South Verkhoyansk metamorphic belt until about 120 Ma due to paleo-Pacific subduction along the Uda-Murgal continental margin arc.