Paleoenvironmental model for Eocene foraminiferal limestones of the Adriatic carbonate platform (Istrian Peninsula)

The foraminiferal limestones from the Middle Eocene Central Istrian region illustrate progressive deepening of depositional gradients. Shifting of Lower Cuisian to Upper Lutetian microfacies can be described in terms of a ramp model. The Orthophragminae-bearing parts of the foraminiferal limestones are interpreted in terms of larger foraminiferal faunal associations, planktonic foraminiferal relative abundance, limitations of algal endosymbionts, foraminiferal lamellar thickness and flattening of test shapes. Microfacies I contains the most diverse larger foraminiferal association with a predominance of large, thick nummulitids, assilinids, and asterocyclinids. Microfacies II is characterized by a gradual increase of Orthophragminae diversity and abundance. Nummulitids, equally abundant, are dominated by lenticular and subspherical specimens. The reduction in number of nummulitid specimens with characteristic biconical radiate morphologies, and relative abundance of flattened orthophragminids, characterizes Microfacies III. Scattered biodestructed orthophragminid tests and planktonic foraminifera constitute Microfacies IV, indicating the end of a long-lasting, shallow-marine Adriatic Carbonate Platform regime.     

High-resolution biochronology and diversity dynamics of the Early Triassic ammonoid recovery: The Smithian faunas of the Northern Indian Margin

Based on new collections of abundant and well preserved material from the Salt Range (Pakistan), Spiti (Northern India) and Tulong (South Tibet), several recent studies focused on the taxonomic revision and detailed biostratigraphy of Smithian ammonoids. In this work, biochronological data for these three well-documented basins are analyzed by means of the Unitary Associations method, resulting in a biochronological scheme of unprecedented high-resolution for the Smithian of the Northern Indian Margin (NIM). Data for each basin are first processed separately, thus yielding three local biochronological zonations. Then, the three sequences are processed together as a regional three-section data set for the construction of an inter-basin sequence at the NIM level. The latter zonation comprises 16 Unitary Associations grouped into 13 zones for the entire Smithian. Analysis of ammonoid diversity dynamics based on this new highly resolved time frame highlights (i) a marked diversification during the early Smithian, (ii) a severe extinction during the late Smithian, and (iii) an overall very high turnover throughout the Smithian. At a global spatial scale and stage resolution, the diversity of Smithian ammonoid genera appears surprisingly high, as highlighted by a previous study. It is shown that at a smaller geographic scale and with the most highly resolved time frame, Smithian ammonoids of the NIM reached their explosive diversity peak essentially through extremely high turnover rates rather than through a classic diversification process of high origination rates coupled with low extinction rates. Based on recently published U/Pb ages, regional apparent total rates of origination and extinction of more than 100 species per My can be inferred for the Smithian ammonoids of the NIM.     

Human Risk Assessment for Nonylphenol

This article presents a risk assessment for human exposure to nonylphenol (NP). We critically reviewed and assessed all relevant full-text publications based on a variety of data quality attributes. Two categories of data, environmental monitoring and biomonitoring from exposed individuals, were used to estimate human exposure to NP. Environmental monitoring data included the measurement of NP in food, water, air, and dust. From these data and estimates of human intake rates for the sources, exposures were estimated from each source and source-specific Margins of Exposure (MOEs) calculated. However, the nature of the populations studied prevented the calculation of aggregate exposure calculations from these data. Rather, the most reliable estimates of aggregate exposure to NP were those derived from biomonitoring studies in exposed individuals. Using the daily absorbed dose estimates for NP, MOEs were calculated for these populations. The MOEs were based on the use of a No-Observed-Adverse-Effect-Level (NOAEL) for sensitive toxicological endpoints of interest, that is, systemic and reproductive toxicity from continuous-feeding more than 3.5 generations (13 mg/kg/day). The MOEs were all greater than 1000 (ranging from 2863 to 8.4 × 10⁷), clearly indicating reasonable certainty of no harm for source-specific and aggregate (based on biomonitoring) exposures to NP.     

Lower-Middle Cambrian boundary in open shelf facies of the Siberian Platform

In the Early and Middle Cambrian (of traditional usage), three broad facies belts were developed over the Siberian Platform. The lithofacies belts comprise evaporitic-carbonate, reef-shoal, and open-marine environments.Trilobites assemblages are most diverse in the open-marine lithofacies (Judoma-Olenek facies), represented especially by the Kuonamka Formation, in the eastern part of the platform. Species, genera and families of trilobites gradually increased through the Middle-Cambrian boundary interval in the Kuonamka Formation. Protolenidae dominated in the time represented by the Lermontovia Zone. In strata assigned to the Anabaraspis Zone, the protolenids disappear, the paradoxidids appear, and the diversity of dorypygids increases. The number of trilobite families increases in the Oryctocara and Kounamkites zones.Well represented in the Kuonamka formation of the eastern Siberian Platform are three levels of trilobites that have potential for global correlation. They are the Oryctocephalus reticulatus (=O. indicus latus), Oryctocephalus indicus, and Ovatoryctocara granulatus levels. The Lower-Middle Cambrian boundary in the South China correlates to the lower part of the Kounamkites Zone of the Siberian Platform.     

Dynamic disulfide scanning of the membrane-inserting Pf3 coat protein reveals multiple YidC substrate contacts

The membrane insertase YidC inserts newly synthesized proteins into the plasma membrane. While defects in YidC homologs in animals and plants cause diseases, YidC in bacteria is essential for life. Membrane insertion and assembly of ATP synthase and respiratory complexes is catalyzed by YidC. To investigate how YidC interacts with membrane-inserting proteins, we generated single cysteine mutants in YidC and in the model substrate Pf3 coat protein. The single cysteine mutants were expressed and analyzed for disulfide formation during 30 s of synthesis. The results show that the substrate contacts different YidC residues in four of the six transmembrane regions. The residues are located either in the region of the inner leaflet, in the center, as well as in the periplasmic leaflet, consistent with the hypothesis that YidC presents a hydrophobic platform for inserting membrane proteins. In a YidC mutant where most of the contacting residues were mutated to serines, YidC function was severely disturbed and no longer active in a complementation test, suggesting that the residues are important for function. In addition, a Pf3 mutant with a defect in membrane insertion was deficient to contact the periplasmic residues of YidC.     

Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies

A major challenge in structural biology is to determine the configuration of domains and proteins in multidomain proteins and assemblies, respectively. All available data should be considered to maximize the accuracy and precision of these models. Small-angle X-ray scattering (SAXS) efficiently provides low-resolution experimental data about the shapes of proteins and their assemblies. Thus, we integrated SAXS profiles into our software for modeling proteins and their assemblies by satisfaction of spatial restraints. Specifically, we modeled the quaternary structures of multidomain proteins with structurally defined rigid domains as well as quaternary structures of binary complexes of structurally defined rigid proteins. In addition to SAXS profiles and the component structures, we used stereochemical restraints and an atomic distance-dependent statistical potential. The scoring function is optimized by a biased Monte Carlo protocol, including quasi-Newton and simulated annealing schemes. The final prediction corresponds to the best scoring solution in the largest cluster of many independently calculated solutions. To quantify how well the quaternary structures are determined based on their SAXS profiles, we used a benchmark of 12 simulated examples as well as an experimental SAXS profile of the homotetramer d-xylose isomerase. Optimization of the SAXS-dependent scoring function generally results in accurate models if sufficiently precise approximations for the constituent rigid bodies are available; otherwise, the best scoring models can have significant errors. Thus, SAXS profiles can play a useful role in the structural characterization of proteins and assemblies if they are combined with additional data and used judiciously. Our integration of a SAXS profile into modeling by satisfaction of spatial restraints will facilitate further integration of different kinds of data for structure determination of proteins and their assemblies.     

Bioerosional structures and pseudoborings from Late Jurassic and Late Cretaceous-Paleocene shallow-water carbonates (Northern Calcareous Alps, Austria and SE France) with special reference to cryptobiotic foraminifera

Examples of bioerosional processes (boring patterns) are described from shallow-water limestones of the Late Jurassic Plassen Carbonate Platform (PCP) and the Late Cretaceous to Paleocene Gosau Group of the Northern Calcareous Alps, Austria. Some micro-/macro-borings can be related to distinct ichnotaxa, others are classified in open nomenclature. In the Alpine Late Jurassic, bioerosional structures recorded from clasts in mass-flows allow palaeogeographical conclusions concerning the source areas. In particular, these are borings of the Trypanites-ichnofacies detected from clasts (Barmstein limestones) of the PCP or special type of bored ooids of unknown source areas or restricted autochthonous occurrences. In the Lower Gosau Subgroup, Gastrochaenolites macroborings occur in mobile carbonate clast substrates of shore zone deposits (“Untersberg Marmor”). Different types of borings are recorded from rudist shells and coral skeleton, some of which are referable to the ichnotaxon Entobia produced by endolithic sponges. In the present study, special attention is paid to the occurrences of the cryptobiotic foraminifera Troglotella incrustans Wernli and Fookes in the Late Jurassic and Tauchella endolithica Cherchi and Schroeder in the Late Cretaceous. The latter is so far only known to be from the Early Cenomanian of France and is reported here for the first time from the Late Turonian-Early Coniacian stratigraphic interval where it was found in turbulent carbonate deposits within borings penetrating bivalve shells or coralline algae. The records of cryptobiotic foraminifera from the Northern Calcareous Alps are supplemented by a single finding from the Middle Cenomanian of SE France. A palaeoenvironmental interpretation of the occurrences of the cryptobiotic foraminifera is provided.     

Platform-basin transect of a middle to late Jurassic large-scale carbonate platform system (Shotori mountains,Tabas area,east-central Iran)

Summary Following a phase of predominantly siliciclastic sedimentation in the Early and Middle Jurassic, a large-scale, low-latitude carbonate depositional system was established in the northern part of the Tabas Block, part of the central-east Iranian microplate, during the Callovian and persisted until the latest Oxfordian/Early Kimmeridgian. Running parallel to the present eastern block margin, a NNW/SSE-trending carbonate platform developed in an area characterized by reduced subsidence rates (Shotori Swell). The growth of this rimmed, flat-topped barrier platform strongly influenced the Upper Jurassic facies pattern and sedimentary history of the Tabas Block. The platform sediments, represented by the predominantly fine-grained carbonates of the Esfandiar Limestone Formation, pass eastward into slope to basin sediments of the Qal'eh Dokhtar Limestone Formation (platform-derived allochthonites, microbialites, and peri-platform muds). Towards the west, they interfinger with bedded limestones and marlstones (Kamar-e-Mehdi Formation), which were deposited in an extensive shelf lagoon. In a N−S direction, the Esfandiar Platform can be traced for about 170 km, in an E-W direction, the platform extended for at least 35–40 km. The width of the eastern slope of the platform is estimated at 10–15 km, the width of the western shelf lagoon varied considerably (>20–80 km). During the Late Callovian to Middle Oxfordian, the Esfandiar Platform flourished under arid climatic conditions and supplied the slope and basinal areas with large amounts of carbonates (suspended peri-platform muds and gravitational sediments). Export pulses of platform material, e.g. ooids and aggregate grains, into the slope and basinal system are interpreted as highstand shedding related to relative sealevel variations. The high-productivity phase was terminated in the Late Oxfordian when the eastern platform areas drowned and homogeneous deep water marls of the Upper Oxfordian to Kimmeridgian Korond Formation onlapped both the Qal'eh Dokhtar Limestone Formation and the drowned Esfandiar Limestone Formation. Tectonic instability, probably caused by faulting at the margins of the Tabas Block in connection with rotational movements of the east-central Iranian block assemblage, was responsible for the partial drowning of the eastern platform areas. In some areas, relicts of the platform persisted to produce shallow-water sediments into the Kimmeridgian.     

Reef reconstruction after extinction events of the latest ordovician in the Yangtze platform,South China

Summary Early Silurian reef reconstruction on the Yangtze Platform, in the northern part of the South China Block, is preceded by a combination of regional and global processes. During most of Ashgill time (Late Ordovician), the area was dominated by Wufeng Formation deep water graptolitic black shales. Reefs largely disappeard in the middle of the Ashgill Stage, from the northwestern margin of Cathaysian Land (southeastern South China Block), in advance of the Late Ordovician glaciation and mass extinction, due to regional sea-level changes and regional uplift, unrelated to the mass extinction itselt. Late Ordovician microbial mudmound occurrence is also found in the western margin of the Yangtze Platform, its age corresponding to theDicellograptus complexus graptolite biozone of pre-extinction time. On the Yangtze Platform, a thin, non-reef-bearing carbonate, the Kuanyinchiao Formation (=Nancheng Formation in some sites), thickness generally no more than 1m, occurs near several landmasses as a result of Hirnantian regression. Reappearance of the earliest Silurian carbonates consisting of rare skeletal lenses in the upper part of Lungmachi Formation, are correlated to theacensus graptolite biozone, early Rhuddanian of Shiqian, northeastern Guizhou, near Qianzhong Land. Carbonate sediments gradually developed into beds rich in brachiopods and crinoids in the lower part of Xiangshuyuan Formation, middle Rhuddanian. In the middle part of Xiangshuyan Formation, biostromes, containing abundant and high diversity benthic faunas such as corals, crinoids and brachiopods, show beginnings of reconstruction of reef facies. Substantial reef recovery occurred in the upper part of Xiangshuyuan Formation, lower Aeronian, as small patch reefs and biostromes. During the late Aeronian, carbonate sediments, especially reefs and reef-related facies, expanded on the upper Yangtze Platform, and radiation of reefs occurred in Ningqiang Formation, upper Telychian. The long period of reef recovery, taking several million years, remains difficult to explain, because redistribution of any refugia faunas would be expected to take place soon after the extinction. Reefs and reef-related facies subsequently declined after Telychian time due to regional uplift of the major portion of the Yangtze Platform. Carbonate facies are therefore uncommon in South China during the rest of Silurian time.