Strontium stratigraphy of the upper Miocene Lithothamnion Limestone in the Majella Mountain,central Italy,and its palaeoenvironmental implications

The ⁸⁷Sr/⁸⁶Sr isotope ratio has been widely used as a physical tool to date and correlate carbonate successions due to the long Sr residence time in comparison with the ocean mixing time. If this method works on oceanic successions, marginal basins may show different Sr isotope records in comparison with the coeval ocean one due to sea‐level variations, continental run‐off and restricted water exchanges. In this work, we present the ⁸⁷Sr/⁸⁶Sr isotope record of the upper Miocene carbonate ramp of the Lithothamnion Limestone (Majella Mountain, central Apennines), as an example of the onset of restricted water exchanges between a marginal basin and the ocean water masses. The overall latemost Tortonian–early Messinian Sr isotope record of the Lithothamnion Limestone fits below the global reference line. This deviation has been interpreted as due to the strong control that freshwater input and enhanced continental run‐off, linked to the migration of the Apennine accretionary wedge and foredeep system, have had on the central Adriatic water chemistry. These results imply that an accurate oceanographic and geodynamic framework along with diagenetic overprint investigation has to be taken into consideration prior to apply SIS on carbonate successions on marginal basins, even when facies analyses indicate fully marine conditions. This seems to be the case for the upper Miocene Central Mediterranean carbonate successions, but may have more general validity and be extended to other recent or past marginal basins.     

A new coral‐associated decapod assemblage from the Upper Miocene (Messinian) Upper Coralline Limestone of Malta (Central Mediterranean)

Abstract: A rich coral‐associated decapod assemblage is recorded from the ‘Depiru Beds’ of the upper part of the Upper Coralline Limestone (Messinian, Upper Miocene), from the island of Malta. Nineteen species within 17 genera have been discovered, where 14 genera are new for Malta. Four new species are described, namely Micippa annamariae sp. nov., Pilumnus scaber sp. nov., Panopeus muelleri sp. nov. and Herbstia melitense sp. nov. Herbstia melitense sp. nov. constitutes the first record of the genus from the fossil record in the Mediterranean region. This discovery more than doubles the number of known fossil decapod species from Malta. The fossil bivalve Jouannetia (J.) semicaudata Des Moulins, 1830 and the extant decapod Maja goltziana D’Oliveira, 1888, are also recorded for the first time from Malta. Other Neogene coral‐associated decapod assemblages are investigated and correlated with the new assemblage from Malta. The migration of taxa between the Mediterranean region and the Paratethys, particularly during the Lower Badenian (Langhian), is evidenced by the strong affinity of the Maltese decapod assemblage with that of the Middle Miocene Badenian assemblages from Hungary, Poland and Ukraine. Upper Miocene, Messinian assemblages from Spain, Algeria and Morocco are also similar to that from Malta.     

Strontium isotope record of the Hygophum hygomii otoliths from the European middle Miocene

⁸⁷Sr/⁸⁶Sr values from otoliths of the worldwide-distributed fish Hygophum hygomii are used for the purpose of isotope chemostratigraphy. In order to evaluate the potential of H. hygomii otoliths for strontium (Sr) isotopic studies, we first compare the ⁸⁷Sr/⁸⁶Sr ratio of current representatives of the species with that of modern sea water. Then, three fossil otoliths of H. hygomii collected in middle Miocene sediments of the Aquitaine Basin (Lafaurie locality, SW France) and the Carpathian Foredeep of the Central Paratethys (Brno-Kralovo Pole locality, SE Czech Republic) are analysed. The age inferred from the ⁸⁷Sr/⁸⁶Sr ratio at Lafaurie places the two analysed otoliths within the time interval of 15.5–15.1 Ma. This time interval matches the published early Langhian age obtained from the ⁸⁷Sr/⁸⁶Sr ratio of bivalves measured at the same locality. At the Brno-Kralovo Pole, the ⁸⁷Sr/⁸⁶Sr ratio of the analysed otolith returns a wider timespan of 14.78–13.10 Ma, falling into an interval of poor time resolution of the ⁸⁷Sr/⁸⁶Sr chemostratigraphy. Comparisons with published biostratigraphic and paleoclimatic data suggest that the analysed fossil otoliths of H. hygomii were mineralized during the late part of the Langhian, at ∼14.2 Ma. This work represents a first attempt to use otoliths for ⁸⁷Sr/⁸⁶Sr chemostratigraphy, and indicates that such a use may represent a powerful tool for testing stratigraphic correlations in the future.     

A New Fulmarine Petrel (Aves: Procellariiformes) from the Upper Miocene of the Western Mediterranean

A new sea bird, Pterodromoides minoricensis gen. et sp. nov., similar in size and proportions to species of the modern genus Pterodroma , is described from Late Miocene breccias situated on the north-west coast of Menorca. The cranial osteology is similar to that of fulmarine petrels, but the large orbitonasal opening and characters of the postcranial skeleton justify its classification as a separate genus. At least one other species of procellariid occurs in the accompanying fossil asemblage, suggesting that Late Tertiary ecological conditions favoured sea bird populations in this area of the Mediterranean.     

Structural insights into the stabilization of active,tetrameric DszC by its C‐terminus

Dibenzothiophene (DBT) is a typical sulfur‐containing compound found in fossil fuels. This compound and its derivatives are resistant to the hydrodesulfurization method often used in industry, but they are susceptible to enzymatic desulfurization via the 4S pathway, which is a well‐studied biochemical pathway consisting of four enzymes. DBT monooxygenase (DszC) from Rhodococcus erythropolis is involved in the first step of the 4S pathway. We determined the crystal structure of DszC, which reveals that, in contrast to several homologous proteins, the C‐terminus (410–417) of DszC participates in the stabilization of the substrate‐binding pocket. Analytical ultracentrifugation analysis and enzymatic assays confirmed that the C‐terminus is important for the stabilization of the active conformation of the substrate‐binding pocket and the tetrameric state. Therefore, the C‐terminus of DszC plays a significant role in the catalytic activity of this enzyme. Proteins 2014; 82:2733–2743. © 2014 Wiley Periodicals, Inc.     

An assessment of the diversity of early Miocene Scolopaci (Aves,Charadriiformes) from Saint‐Gérand‐le‐Puy (Allier,France)

Abstract: ‘Totanus’lartetianus, Elorius paludicola and ‘Tringa’gracilis are the three scolopacid birds from the early Miocene of Saint‐Gérand‐le‐Puy described by the French palaeontologist Milne‐Edwards in the 19th century. Since then, no revision of these taxa has been performed. Our re‐examination revealed that not much of the material originally assigned to ‘Totanus’lartetianus can be retained within the species. Presumably plesiomorphic features of the humerus – and potentially the coracoid we attributed to this taxon – indicate that it is misplaced in the extant scolopacid genus and may not even belong to the Scolopacidae (sandpipers and allies), and we therefore place it in the new genus Scolopacimilis. Comparisons of the material assigned to Elorius paludicola and ‘Tringa’gracilis show that they are morphologically similar, both exhibiting distinct scolopacid anatomical features. The latter, however, cannot be referred to the extant taxon Tringa and is classified into the new genus Parvelorius. We further introduce three new species, ?Elorius limosoides sp. nov., and ?Parvelorius calidris sp. nov., which we have tentatively assigned to the extinct scolopacid genera Elorius and Parvelorius, respectively, and Becassius charadriioides gen. et. sp. nov., which, together with Scolopacimilis, display a morphology uncharacteristic for extant Scolopaci. For the first time we have assigned skulls to some of the postcranial elements described in this study. The presence of at least six species of Scolopaci from the early Miocene considerably increases the number of members of the group known from this time.     

EGFR: Tale of the C‐terminal tail

The carboxy terminal tail of epidermal growth factor receptor (EGFR) plays a critical role in the regulation of the enzyme activity of the kinase. There is a good structural model for the mechanism by which the C‐terminal tail proximal to the kinase domain contributes to the negative regulation of the activity. Its conformation in the active state, conversely, has remained elusive due to its dynamic nature. A recently published structure of EGFR kinase domain shows the conformation of the proximal C‐terminal tail in the active kinase. Analysis of this conformational state of the C‐terminal tail is presented, and some of the mutagenesis data is revisited. © 2013 The Protein Society     

The Late Miocene coldspot of z-coral diversity in the Mediterranean: Patterns and causes

The Late Miocene distribution and diversity of zooxanthellate-like corals in the Mediterranean are analyzed in their paleobiogeographical framework, using our REEFCORAL database. The Late Miocene Mediterranean pool reached 20 z-coral genera. Although this fauna could build flourishing reef ecosystems during the Early Messinian, it was a relict fauna with severely limited speciation that lived on the edge of its ecological requirements in terms of solar energy and temperature range. Most z-coral genera, because they had long stratigraphic ranges and had survived previous extinctions, were able to adapt to the Messinian environments, which were unusual for such biotas. Hence, Porites, the most widespread genus in the region and also the most dominant in ecological assemblages, was the best equipped to cope with the drastic changes related to the Messinian Salinity Crisis.     

Leftover prey remains: a new taphonomic mode from the Late Miocene Cerro Azul Formation of Central Argentina

The Cerro Azul Formation (La Pampa Province, Argentina) comprises a rich vertebrate fauna of small mammals dominated by notoungulates and rodents. The fauna pertains to the Late Miocene specifically to the Huayquerian Stage/Age. Taphonomic analysis of micro‐mammals from Estancia Ré locality evidenced that the faunal assemblage was accumulated by the activity of a predator. This assemblage was compared with others from the Cerro Azul Formation in Telén and Caleufú localities (La Pampa Province), previously interpreted as products of predator activities. These microfossil accumulations differ from assemblages attributed to pellets and faeces produced by modern predators (nocturnal and diurnal bird raptors and carnivore mammals). However, due to their anatomical representation, degree of bone breakage and presence of tooth marks, they are interpreted as accumulations of uneaten prey remains discarded by the predator. The predator involved could not be determined with certainty, although the presence of tooth marks in some skeletal remains and the presence of coprolites in Telén and Caleufú suggest that it could be a carnivore mammal. Similarities in the accumulation mechanism, patterns of preservation and sedimentary contexts in the three assemblages support the recognition of a new taphonomic mode, termed ‘leftover prey remains’.     

The first known fossil record of pygmy pipehorses (Teleostei: Syngnathidae: Hippocampinae) from the Miocene Coprolitic Horizon,Tunjice Hills,Slovenia

The first known fossil record of pygmy pipehorses is described. The fossils were collected in the Middle Miocene (Sarmatian) beds of the Coprolitic Horizon in the Tunjice Hills, Slovenia. They belong to a new genus and species Hippotropiscis frenki, which was similar to the extant representatives of Acentronura, Amphelikturus, Idiotropiscis, and Kyonemichthys genera. Hippotropiscis frenki lived among seagrasses and macroalgae and probably also on a mud and silt bottom in the temperate shallow coastal waters of the western part of the Central Paratethys Sea. The high coronet on the head, the ridge system and the high angle at which the head is angled ventrad indicate that Hippotropiscis is most related to Idiotropiscis and Hippocampus (seahorses) and probably separated from the main seahorse lineage later than Idiotropiscis.     

Structural transition from dimeric to tetrameric i‐motif,caused by the presence of TAA at the 3′‐end of human telomeric C‐rich sequence

Widely dispersed in genomic DNA, the tandem C‐rich repetitive stretches may fold below physiological pH, into i‐motif structures, stabilized by C·C⁺ pairing. Herein, structural status of a 9‐mer stretch d(CCCTAACCC), [the truncated double repeat of human telomeric sequence], and its extended version, comprising of additional ? TAA segment at the 3′‐end, representing the complete double repeat d(CCCTAACCCTAA), has been investigated. The pH dependent monophasic UV‐melting, Gel and CD data suggested that while the truncated version adopts a bimolecular i‐motif structure, its complete double repeat (12‐mer) sequence exists in two (bimolecular and tetramolecular) forms. A model is proposed for the tetramolecular i‐motif with conventional C · C⁺ base pairs, additionally stabilized by asymmetric A · A base pairs at the ?3′ TAA flanking ends and Watson–Crick A · T hydrogen bonding between intervening bases on antiparallel strands. Expanding the known topologies of DNA i‐motifs, such atypical geometries of i‐motifs may have implications in their recognition by proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 150–160, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Hydrophobic benzyl amines as supports for liquid‐phase C‐terminal amidated peptide synthesis: application to the preparation of ABT‐510

C‐terminal amidation is one of the most common modification of peptides and frequently found in bioactive peptides. However, the C‐terminal modification must be creative, because current chemical synthetic techniques of peptides are dominated by the use of C‐terminal protecting supports. Therefore, it must be carried out after the removal of such supports, complicating reaction work‐up and product isolation. In this context, hydrophobic benzyl amines were successfully added to the growing toolbox of soluble tag‐assisted liquid‐phase peptide synthesis as supports, leading to the total synthesis of ABT‐510 ( 2 ). Although an ethyl amide‐forming type was used in the present work, different types of hydrophobic benzyl amines could also be simply designed and prepared through versatile reductive aminations in one step. The standard acidic treatment used in the final deprotection step for peptide synthesis gave the desired C‐terminal secondary amidated peptide with no epimerization. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.     

The Middle Miocene climatic transition in the Southern Ocean: Evidence of paleoclimatic and hydrographic changes at Kerguelen plateau from planktonic foraminifers and stable isotopes

Middle Miocene (14.8–11.9 Ma) deep-sea sediments from ODP Hole 747A (Kerguelen Plateau, southern Indian Ocean) contain abundant, well-preserved and diverse planktonic foraminiferal assemblages. A detailed study of the climatic and hydrographic changes that occurred in this region during the Middle Miocene Climatic Transition led to the identification of an intense cooling phase (the Middle Miocene Shift). Abundance fluctuations of planktonic foraminiferal species with different paleoclimatic affinities, and oxygen and carbon stable isotopes have been integrated in a multi-proxy approach. Reconstruction of changes in foraminiferal faunal composition and diversity through time were the basis for identification of three foraminiferal biofacies. The most prominent faunal change took place at 13.8 Ma, when a fauna with warm-water affinity (marked by high abundance of Globorotalia miozea group and Globoturborotalita woodi plexus) was replaced by an oligotypic, opportunistic fauna with typical polar characters and dominated by neogloboquadrinids. This faunal change is interpreted as the result of foraminiferal migration from adjacent bioprovinces, caused by modifications in climate and hydrography. A positive 2.0‰ shift in δ¹⁸O (interpreted as the Mi3 event) and a related positive 1.0‰ shift in δ¹³C (corresponding to the CM6 event) accompanied this faunal turnover. These are interpreted to reflect substantial reorganization of Southern Ocean waters, the northward migration of the Polar Front and a strong increase in primary productivity. The second faunal change took place at 12.9 Ma and was characterized by the gradual decrease in abundance of the neogloboquadrinids and the recovery of Globorotalia praescitula/scitula group and Globigerinita glutinata. A positive 1.5‰ shift in δ¹⁸O (interpreted as the Mi4 event) and a concurrent gradual negative shift in δ¹³C accompanied this faunal change, witnessing further modifications of the climate/ocean system. Variations in sea surface temperature, considered as the main factor causing changes of surface hydrography at the Kerguelen Plateau, seem to have been driven by obliquity and long-term eccentricity, thus suggesting a key role played by the astronomical forcing on the evolution of Southern Ocean dynamics during the Middle Miocene. Also an evident 1.2 Myr modulation of the δ¹³C record suggests a main control of the long-term obliquity cycles on the carbon cycle dynamics. Particularly, the Mi3/CM6 events exactly fit with a node of the 1.2 Myr modulation cycles. This confirms the key role played by orbital parameters on high-latitude temperatures and Antarctic ice volume, and indirectly on global carbon burial and/or productivity. This climatic transition was marked also by changes in surface hydrography. From 14.8 to 13.8 Ma an intermediate-strength thermocline controlled by seasonality developed just below the photic zone. Weaker seasonality characterized the interval from 13.8 to 12.9 Ma, when the thermocline became shallower and sharper and favored intermediate-water foraminifers. From 12.9 Ma, seasonality increased again and an intermediate-strength thermocline re-developed.     

Novel Ca2+‐independent carbohydrate recognition of the C‐type lectins,SPL‐1 and SPL‐2, from the bivalve Saxidomus purpuratus

Novel Ca²⁺‐independent C‐type lectins, SPL‐1 and SPL‐2, were purified from the bivalve Saxidomus purpuratus. They are composed of dimers with either identical (SPL‐2 composed of two B‐chains) or distinct (SPL‐1 composed of A‐ and B‐chains) polypeptide chains, and show affinity for N‐acetylglucosamine (GlcNAc)‐ and N‐acetylgalactosamine (GalNAc)‐containing carbohydrates, but not for glucose or galactose. A database search for sequence similarity suggested that they belong to the C‐type lectin family. X‐ray crystallographic analysis revealed definite structural similarities between their subunits and the carbohydrate‐recognition domain (CRD) of the C‐type lectin family. Nevertheless, these lectins (especially SPL‐2) showed Ca²⁺‐independent binding affinity for GlcNAc and GalNAc. The crystal structure of SPL‐2/GalNAc complex revealed that bound GalNAc was mainly recognized via its acetamido group through stacking interactions with Tyr and His residues and hydrogen bonds with Asp and Asn residues, while widely known carbohydrate‐recognition motifs among the C‐type CRD (the QPD [Gln‐Pro‐Asp] and EPN [Glu‐Pro‐Asn] sequences) are not involved in the binding of the carbohydrate. Carbohydrate‐binding specificities of individual A‐ and B‐chains were examined by glycan array analysis using recombinant lectins produced from Escherichia coli cells, where both subunits preferably bound oligosaccharides having terminal GlcNAc or GalNAc with α‐glycosidic linkages with slightly different specificities.     

C‐terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilumD‐aldohexose dehydrogenase

The D ‐aldohexose dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum (AldT) is a homotetrameric enzyme that catalyzes the oxidation of several D ‐aldohexoses, especially D ‐mannose. AldT comprises a unique C‐terminal tail motif (residues 247–255) that shuts the active‐site pocket of the neighboring subunit. The functional role of the C‐terminal tail of AldT has been investigated using mutational and crystallographic analyses. A total of four C‐terminal deletion mutants (Δ254, Δ253, Δ252, and Δ249) and two site‐specific mutants (Y86G and P254G) were expressed by Escherichia coli and purified. Enzymatic characterization of these mutants revealed that the C‐terminal tail is a requisite and that the interaction between Tyr86 and Pro254 is critical for enzyme activity. The crystal structure of the Δ249 mutant was also determined. The structure showed that the active‐site loops undergo a significant conformational change, which leads to the structural deformation of the substrate‐binding pocket. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Biogeography and evolution of Abies (Pinaceae) in the Mediterranean Basin: the roles of long‐term climatic change and glacial refugia

Aim The genus Abies exemplifies plant diversification related to long‐term climatic, geological and evolutionary changes. Today, the Mediterranean firs comprise nine species, one natural hybrid and several varieties. Here I summarize current knowledge concerning the origin and evolution of the genus Abies in the Mediterranean Basin and propose a comprehensive hypothesis to explain the isolation and speciation pattern of Mediterranean firs. Location The Mediterranean Basin. Methods The literature on Abies was reviewed, focusing on the morphology, fossil records, molecular ecology, phytosociology and biogeography of the genus in the Mediterranean Basin. Results Abies fossils from the western Mediterranean indicate a wide Tertiary circum‐Mediterranean distribution of the Abies ancestor. Palaeogeographical data also suggest a single eastern Mediterranean Tertiary ancestor. Following the Miocene to Pliocene climate crisis and marine transgressions, the ancestor of the northern Mediterranean firs is hypothesized to have separated into two eastern groups, one on the Balkan Peninsula and the other in Asia Minor. However, land bridges may have permitted gene flow at times. A southward migration of A. alba to refugia, where older fir species may have remained isolated since the Miocene, could explain recent findings indicating that morphologically distant species are more closely related than expected based on such morphological classification. Main conclusions The Abies genus appears to have undergone significant morphological differentiation that does not necessarily imply reproductive isolation. That is, long‐term Mediterranean Basin dryness along a south‐eastern to north‐western gradient may have caused an initial Miocene–Pliocene speciation sequence. Pleistocene glacial cycles probably forced migrations to occur, leading to repeated contact between fir species in glacial refugia.     

The first known fossil record of pipehorses (Teleostei: Syngnathidae: Haliichthyinae) from the Miocene Coprolitic Horizon from the Tunjice Hills,Slovenia

The first known fossil specimens of pipehorses (Haliichthyinae) were unearthed from the Middle Miocene (Sarmatian) beds of the Coprolitic Horizon in the Tunjice Hills, Slovenia. These fossil pipehorses belong to a new genus and species Hippohaliichthys edis, which was similar to the extant species Haliichthys taeniophorus. The body morphology indicates that the described fossil pipehorses were also closely related to the pygmy pipehorse Hippotropiscis frenki and the seahorse Hippocampus sarmaticus, two taxa which were also found in the Coprolitic Horizon. The described fossil material of pipehorses indicates that seahorses evolved from a group of pipehorses that were similar in size and shape to extant and fossil pipehorses of the Haliichthyinae subfamily.