Evaporites and the salinity of the ocean during the Phanerozoic: Implications for climate, ocean circulation and life

A compilation of data on volumes and masses of evaporite deposits is used as the basis for reconstruction of the salinity of the ocean in the past. Chloride is tracked as the only ion essentially restricted to the ocean, and past salinities are calculated from reconstructed chlorine content of the ocean. Models for ocean salinity through the Phanerozoic are developed using maximal and minimal estimates of the volumes of existing evaporite deposits, and using constant and declining volumes of ocean water through the Phanerozoic. We conclude that there have been significant changes in the mean salinity of the ocean accompanying a general decline throughout the Phanerozoic. The greatest changes are related to major extractions of salt into the young ocean basins which developed during the Mesozoic as Pangaea broke apart. Unfortunately, the sizes of these salt deposits are also the least well known. The last major extractions of salt from the ocean occurred during the Miocene, shortly after the large scale extraction of water from the ocean to form the ice cap of Antarctica. However, these two modifications of the masses of H2O and salt in the ocean followed in sequence and did not cancel each other out. Accordingly, salinities during the Early Miocene were between 37‰ and 39‰. The Mesozoic was a time of generally declining salinity associated with the deep sea salt extractions of the North Atlantic and Gulf of Mexico (Middle to Late Jurassic) and South Atlantic (Early Cretaceous). The earliest of the major extractions of the Phanerozoic occurred during the Permian. There were few large extractions of salt during the earlier Palaeozoic. The models suggest that this was a time of relatively stable but slowly increasing salinities ranging through the upper 40‰'s into the lower 50‰'s. Higher salinities for the world ocean have profound consequences for the thermohaline circulation of the ocean in the past. In the modern ocean, with an average salinity of about 34.7‰, the density of water is only very slightly affected by cooling as it approaches the freezing point. Consequently, salinization through sea-ice formation or evaporation is usually required to make water dense enough to sink into the ocean interior. At salinities above about 40‰ water continues to become more dense as it approaches the freezing point, and salinization is not required. The energy-consuming phase changes involved in sea-ice formation and evaporation would not be required for vertical circulation in the ocean. The hypothesized major declines in salinity correspond closely to the evolution of both planktonic foraminifera and calcareous nannoplankton. Both groups were restricted to shelf regions in the Jurassic and early Cretaceous, but spread into the open ocean in the mid-Cretaceous. Their availability to inhabit the open ocean may be directly related to the decline in salinity. The Permian extraction may have created stress for marine organisms and may have been a factor contributing to the end-Permian extinction. The modeling also suggests that there was a major salinity decline from the Late Precambrian to the Cambrian, and it is tempting to speculate that this may have been a factor in the Cambrian explosion of life

Evolution of the beta-propeller fold.

β-Propellers are toroidal folds, in which repeated, four-stranded β-meanders are arranged in a circular and slightly tilted fashion, like the blades of a propeller. They are found in all domains of life, with a strong preponderance among eukaryotes. Propellers show considerable sequence diversity and are classified into six separate structural groups by the SCOP and CATH databases. Despite this diversity, they often show similarities across groups, not only in structure but also in sequence, raising the possibility of a common origin. In agreement with this hypothesis, most propellers group together in a cluster map of all-β folds generated by sequence similarity, because of numerous pairwise matches, many of which are individually nonsignificant. In total, 45 of 60 propellers in the SCOP25 database, covering four SCOP folds, are clustered in this group and analysis with sensitive sequence comparison methods shows that they are similar at a level indicative of homology. Two mechanisms appear to contribute to the evolution of β-propellers: amplification from single blades and subsequent functional differentiation. The observation of propellers with nearly identical blades in genomic sequences show that these mechanisms are still operating today

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.

The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAST+, HMMER3, MUSCLE) and internally (e.g. HHpred, HHblits, PCOILS). While a beta version of the Toolkit was released 10 years ago, the current production-level release has been available since 2008 and has serviced more than 1.6 million external user queries. The usage of the Toolkit has continued to increase linearly over the years, reaching more than 400 000 queries in 2015. In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic inquiry to students in the life sciences. In this article, we report on the evolution of the Toolkit over the last ten years, focusing on the expansion of the tool repertoire (e.g. CS-BLAST, HHblits) and on infrastructural work needed to remain operative in a changing web environment

Pick-up ions and associated wave energy transport at Comet P/Halley: A case study

During the flyby of the spacecraft Giotto at comet p/Halley Poynting vectors and Elsässer variables have been determined to study wave propagation directions. The observed wave properties are compared with the theoretically predicted RH −, LH + and LH − wave modes. Between 10:36 and 19:11 SCET on March 13, 1986 the predicted dominating energy propagation direction mostly corresponds with the observed one. Only between 12:11 and 13:44 SCET there is no agreement. In this region the excitation of waves is dominated by pick‐up ions which are not locally implanted ions in the solar wind but have been picked‐up outside the plasma regime studied, and whose free energy is not already used up

What do experimental data "say" about growth of hadronic total cross-section?

We reanalyse $\bar p p$ and $pp$ high energy data of the elastic scattering above $\sqrt{s}=5$ GeV on the total cross-section $\sigma_{tot}$ and on the forward $\rho$-ratio for various models of Pomeron, utilizing two methods. The first one is based on analytic amplitudes, the other one relies on assumptions for $\sigma_{tot}$ and on dispersion relation for $\rho$. We argue that it is not possible, from fitting only existing data for forward scattering, to select a definite asymptotic growth with the energy of $\sigma_{tot}$. We find equivalent fits to the data together with a logarithmic Pomeron giving a behavior $\sigma_{tot} \propto \ln ^\gamma s$, $\gamma\in [0.5,2.20]$ and with a supercritical Pomeron giving a behavior $\sigma_{tot} \propto s^\epsilon$, $\epsilon\in [0.01,0.10]$.Comment: LaTeX, 18 pages, 5 eps figures included, to be published in Il Nuovo Ciment

Vortex lattices in a stirred Bose-Einstein condensate

We stir with a focused laser beam a Bose-Einstein condensate of $^{87}$Rb atoms confined in a magnetic trap. We observe the formation of a single vortex for a stirring frequency exceeding a critical value. At larger rotation frequencies we produce states of the condensate for which up to eleven vortices are simultaneously present. We present measurements of the decay of a vortex array once the stirring laser beam is removed

Modulations of DNA contacts by linker histones and post-translational modifications determine the mobility and modifiability of nucleosomal H3 tails.

Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function

Radial and latitudinal dependencies of discontinuities in the solar wind between 0.3 and 19 AU and ?80° and +10°

International audienceDirectional discontinuities (DD) from 5 missions at 7 different locations between 0.3 and 19 AU and ?80° and +10° in the 3D heliosphere are investigated during minimum solar activity. The data are surveyed using the identification criteria of Burlaga (1969) (B) and Tsurutani and Smith (1979) (TS). The rate of occurrence depends linearly on the solar wind velocity caused by the geometric effect of investigating a larger plasma volume if the solar wind velocity ?sw increases. The radial dependence is proportional to r?0.78 (TS criterion) and r?1.28 (B criterion), respectively. This dependence is not only due to an increasing miss rate with increasing distance. The DDs must be unstable or some other physical effect must exist. After normalization of the daily rates to 400 km/s and 1 AU, no dependence on heliographic latitude or on solar wind structures is observable. This means that the DDs are uniformly distributed on a spherical shell. Normalized 64 DD per day are identified with both criteria. But large variations of the daily rate still occur, indicating that other influences must exist. The ratio of the rates of rotational (RDs) and tangential discontinuities (TDs) depends on the solar wind structures. In high speed streams, relatively more RDs exist than in low speed streams. In the inner heliosphere (r r ? over the transition evolves to an increase of smaller ? with increasing distance from the sun. The evolution is yielded by the anisotropic RDs with small ?. The spatial thickness dkm in kilometers increases with distance. The thickness drg normalized to the proton gyro radius decreases by a factor of 50 between 0.3 and 19 AU, from 201.3 rg down to 4.3 rg. In the middle heliosphere, the orientation of the normals relative to the local magnetic field is essentially uniform except for the parallel direction where no DDs occur. This indicates that RDs propagating parallel to B play a special role. In addition, in only a few cases is [?] parallel to [B / ?], which is required by the MHD theory for RDs. The DDs have strongly enhanced values of proton gyro radius rg for ? ~ 90°. In contrast, in the inner heliosphere, only a small increase in rg with ? is observed

Coherent η\eta-photoproduction on 4^4He and 12^{12}C in the near-threshold region

Coherent $\eta$ meson photoproduction on $^4$He and $^{12}$C is considered in the near-threshold region. The elementary $\eta$ photoproduction operator includes contributions from the $S_{11}(1535)$ and $D_{13}(1520)$ resonances as well as $t$-channel vector meson exchange and the nucleon pole terms. Due to the suppression of the dominant $S_{11}(1535)$ resonance for spin and isospin saturated nuclei, the reaction is mainly governed by $\omega$ exchange. Furthermore, the influence of Fermi motion and of different prescriptions for the choice of the invariant reaction energy $W_{\gamma N}$ in the elementary amplitude is studied.Comment: 27 pages revtex including 9 postscript figure

Protein sequence analysis using the MPI Bioinformatics Toolkit

The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best‐performing bioinformatics tools and databases, including the state‐of‐the‐art protein sequence comparison methods HHblits and HHpred. The Toolkit currently includes 35 external and in‐house tools, covering functionalities such as sequence similarity searching, prediction of sequence features, and sequence classification. Due to this breadth of functionality, the tight interconnection of its constituent tools, and its ease of use, the Toolkit has become an important resource for biomedical research and for teaching protein sequence analysis to students in the life sciences. In this article, we provide detailed information on utilizing the three most widely accessed tools within the Toolkit: HHpred for the detection of homologs, HHpred in conjunction with MODELLER for structure prediction and homology modeling, and CLANS for the visualization of relationships in large sequence datasets. Basic Protocol 1: Sequence similarity searching using HHpred Alternate Protocol: Pairwise sequence comparison using HHpred Support Protocol: Building a custom multiple sequence alignment using PSI‐BLAST and forwarding it as input to HHpred Basic Protocol 2: Calculation of homology models using HHpred and MODELLER Basic Protocol 3: Cluster analysis using CLAN