Stable isotope and trace element stratigraphy across the Permian-Triassic transition: A redefinition of the boundary in the Velebit Mountain, Croatia

Stable isotopes of carbonates (delta(13)C(carb), delta(18)O(carb)), organic matter (delta(13)C(org), delta(15)N(org)) and major, trace and rare earth element (REE) compositions of marine carbonate rocks of Late Permian to Early Triassic age were used to establish the position of the Permian-Triassic boundary (PTB) at two continuous sections in the Velebit Mountain, Croatia. The chosen sections - Rizvanusa and Brezimenjaca - are composed of two lithostratigraphic units, the Upper Permian Transitional Dolomite and the overlying Sandy Dolomite. The contact between these units, characterized by the erosional features and sudden occurrence of ooids and siliciclastic grains, was previously considered as the chronostratigraphic PTB. The Sandy Dolomite is characterized by high content of non-carbonate material (up to similar to 30 wt.% insoluble residue), originated from erosion of the uplifted hinterland. A relatively rich assemblage of Permian fossils (including Geinitzina, Globivalvulina, Hemigordius, bioclasts of gastropods, ostracods and brachiopods) was found for the first time in Sandy Dolomite, 5 m above the lithologic boundary in the Rizvanusa section. A rather abrupt negative delta(13)C(carb) excursion in both sections appears in rocks showing no recognizable facies change within the Sandy Dolomite, -2 parts per thousand at Rizvanusa and -1.2 parts per thousand at Brezimenjaca, 11 m and 0.2 m above the lithologic contact, respectively. This level within the lower part of the Sandy Dolomite is proposed as the chemostratigraphic PTB. In the Rizvanusa section, the delta(13)C(org) values decline gradually from similar to-25 parts per thousand in the Upper Permian to similar to-29 parts per thousand in the Lower Triassic. The first negative delta(13)C(org) excursion occurs above the lithologic contact, within the uppermost Permian deposits, and appears to be related to the input of terrigenous material. The release of isotopically light microbial soil-biomass into the shallow-marine water may explain this sudden decrease of delta(13)C(org) values below the PTB. This would support the hypothesis that in the western Tethyan realm the land extinction, triggering a sudden drop of woody vegetation and related land erosion, preceded the marine extinction. The relatively low delta(15)N(org) values at the Permian-Triassic (P-Tr) transition level, close to approximate to 0 parts per thousand, and a secondary negative delta(13)C(org) excursion of -0.5 parts per thousand point to significant terrestrial input and primary contribution of cyanobacteria. The profiles of the concentrations of redox-sensitive elements (Ce, Mn, Fe, V), biogenic or biogenic-scavenged elements (P, Ba, Zn, V), Ce/Ce* values, and normalized trace elements, including Ba/Al, Ba/Fe, Ti/Al, Al/(Al + Fe + Mn) and Mn/Ti show clear excursions at the Transitional Dolomite-Sandy Dolomite lithologic boundary and the chemostratigraphic P-Tr boundary. The stratigraphic variations indicate a major regression phase marking the lithologic boundary, transgressive phases in the latest Permian and a gradual change into shallow/stagnant anoxic marine environment towards the P-Tr boundary level and during the earliest Triassic. (C) 2010 Elsevier B.V. All rights reserved.

Low-replicating viruses and strong anti-viral immune response associated with prolonged disease control in a superinfected HIV-1 LTNP elite controller.

OBJECTIVE: To study the causes for the lack of clinical progression in a superinfected HIV-1 LTNP elite controller patient.¦METHODOLOGY AND PRINCIPAL FINDINGS: We studied host genetic, virological and immunological factors associated with viral control in a SI long term non progressor elite controller (LTNP-EC). The individual contained both viruses and maintained undetectable viral loads for >20 years and he did not express any of the described host genetic polymorphisms associated with viral control. None of four full-length gp160 recombinants derived from the LTNP-EC replicated in heterologous peripheral blood mononuclear cells. CTL responses after SI were maintained in two samples separated by 9 years and they were higher in breadth and magnitude than responses seen in most of 250 treatment naïve patients and also 25 controller subjects. The LTNP-EC showed a neutralization response, against 4 of the 6 viruses analyzed, superior to other ECs.¦CONCLUSIONS: The study demonstrated that a strong and sustained cellular and humoral immune response and low replicating viruses are associated with viral control in the superinfected LTNP-EC.

Transcription factor CTF1 acts as a chromatin domain boundary that shields human telomeric genes from silencing.

Telomeres are associated with chromatin-mediated silencing of genes in their vicinity. However, how epigenetic markers mediate mammalian telomeric silencing and whether specific proteins may counteract this effect are not known. We evaluated the ability of CTF1, a DNA- and histone-binding transcription factor, to prevent transgene silencing at human telomeres. CTF1 was found to protect a gene from silencing when its DNA-binding sites were interposed between the gene and the telomeric extremity, while it did not affect a gene adjacent to the telomere. Protein fusions containing the CTF1 histone-binding domain displayed similar activities, while mutants impaired in their ability to interact with the histone did not. Chromatin immunoprecipitation indicated the propagation of a hypoacetylated histone structure to various extents depending on the telomere. The CTF1 fusion protein was found to recruit the H2A.Z histone variant at the telomeric locus and to restore high histone acetylation levels to the insulated telomeric transgene. Histone lysine trimethylations were also increased on the insulated transgene, indicating that these modifications may mediate expression rather than silencing at human telomeres. Overall, these results indicate that transcription factors can act to delimit chromatin domain boundaries at mammalian telomeres, thereby blocking the propagation of a silent chromatin structure.

The carbon-isotope shift at the Permian/ Triassic boundary in the southern Alps is gradual

Carbon isotope ratios in marine carbonate rocks have been shown to shift at some of the time boundaries associated with extinction events; for example, Cretaceous/Tertiary and Ordovician/ Silurian. The Permian/Triassic boundary, the greatest extinction event of the Phanerozoic, is also marked by a large d13C depletion. New carbon isotope results from sections in the southern Alps show that this depletion did not actually represent a single event, but was a complex change that spanned perhaps a million years during the late Permian and early Triassic. These results suggest that the Permian/Triassic (P/Tr) extinction may have been in part gradual and in part 'stepwise', but was not in any case a single catastrophic event.

Paleoenvironmental evolution of the Helvetic shallow-water carbonate platform near the Barremian-Aptian boundary, and its relationship with paleoceanographic and paleoclimatic change in the Tethys

Abstract:During my doctoral research, I focused on deciphering the interactions between sea-level and climate change during the Late Barremian-Early Aptian, their expression in the Tethys basin and in the Helvetic carbonate platform. The research highlights are summarized here in three points: In the Helvetic Alps, the transition between the Lower Schrattenkalk (Upper Barremian) and the Rawil Member (Lowermost Aptian) is characterized by a change from a predominantly photozoan to a heterozoan carbonate-producing system, which coincides in time with a general increase in detrital and nutrient input. The clay mineral record shows the appearance of kaolinite within the Rawil Member, whereas this mineral is absent from the uppermost Lower and lowermost Upper Schrattenkalk Members. This indicates the installation of a warmer and more humid climate during this time period. A negative peak in 513C is recorded at the top of the Lower Schrattenkalk Member, and correlates with the well-known negative excursion of -l%o occurring in other basins and dated as latest Barremian, thus confirming a latest Barremian and earliest Aptian age for the Lower Schrattenkalk and Rawil Members, respectively. Furthermore, a sequence stratigraphie framework has been defined for the Rawil Member, based on both the ecology of faunal and floral assemblages, and their palaeoenvironmental interpretation, as well as on the stacking pattern of limestone beds observed during field prospection. The presence of a sequence boundary is postulated near the top of the Lower Schrattenkalk Member, which is correlated with the earliest Aptian SbAl defined in Vercors (France). The SbAl is characterized by a maximum of proximal assemblages and by the disappearance of several benthic foraminiferal species. Within the Rawil Member itself, the stacking pattern and microfacies trends are interpreted to represent the TST of the first Aptian sequence. With regards to the pelagic setting in the Tethyan realm, I investigated the Gorgo a Cerbara section (central Italy). There, thin organic-rich layers occur episodically in pelagic carbonates of the upper Barremian portion of the Maiolica Formation. They are associated with high Corg:Ptot ratios, which indicate the presence of intermittent dysoxic to anoxic conditions. Coarse correlations are also observed between TOC, Ρ and biogenic silica contents, indicating links between Ρ availability, productivity, and organic matter preservation. The corresponding 813Ccarb and δ180 records remain, however, quite stable, indicating that these brief periods of enhanced TOC preservation did not have sufficient impact on the marine carbon household to deviate 6,3C records, and are probably not the consequence of major climate change. On the other hand, organic-rich layers become more frequent around the Barremian-Aptian boundary in both pelagic and hemi-pelagic environments (Gorgo a Cerbara and La Bédoule, France), which are correlated with negative excursions in 6l3Ccarb and 613Corg records. During the earliest Aptian, at Gorgo a Cerbara, the frequency of organic-rich intervals progressively increases and redox-sensitive trace-element enrichments become more frequent, until the highest TOC-enriched level just below the "Livello Selli", indicator of Oceanic Anoxic Event la (OAEla). The latter is associated with the well-known negative spike in 613Ccarb and S,3Corg records, a diminution in the δ,80 record interpreted as the consequence of a wanning interval, an important peak in Ρ accumulation and high Cor::Ptot ratios indicating the prevalence of anoxic conditions. The Selli Level (OAEla) documents a general cooling phase and coincides with maximum RSTE enrichments as well as high Corg:Ptot ratios, which confirm the importance of anoxic conditions during OAE1 a at this site.During the Early Aptian, environmental change on the platform is expressed by orbitolinids proliferation that may be induced by both climate change and sea-level rise. In the basin, the successive black shales horizons from the Late Barremian until the OAE la are interpreted as the progressive impact of palaeoenvironmental change probably linked to the formation of the Ontong- Java plate-basalt plateau.RésuméCe travail de thèse a permis d'investiguer les interactions entre les variations du niveau marin et les changements climatiques sur la plate-forme helvétique ainsi qu'en domaine pélagique à la limite Barrémien-Aptien (Crétacé).Dans les Alpes helvétiques, la limite Barrémien-Aptien est marquée par la transition du Schrattenkalk inférieur, caractérisé par des carbonates photozaires, au Membre de Rawil caractérisé par des carbonates héterozoaires. Cette transition est marquée par une arrivée massive d'éléments détritiques et un apport de nutriments ayant entraîné la prolifération de foraminifères agglutinés tels que les orbitolines. L'analyse des minéraux argileux indique l'apparition de la kaolinite durant le Membre de Rawil, interprétée comme l'installation d'un climat plus chaud et humide. Un pic négatif en 513C est enregistré au sommet du Schrattenkalk inférieur correspond à l'excursion négative de -1%0 bien connue en domaine pélagique et datée comme Barrémien terminal. Cette corrélation apporte un contrôle chronostratigraphique supplémentaire permettant de dater le Schrattenkalk inférieur du Barrémien sup. et le Membre de Rawil de l'Aptien inf. D'autre part, une étude stratigraphique, basée sur des observations de terrain et sur l'interprétation d'assemblages floristiques et faunistiques en terme de paléoenvironnement a permis de mettre en évidence une limite de séquence au sommet du Schrattenkalk inf., corrélable avec la SbAl définie dans le Vercors. Durant la mise en place du Membre de Rawil, l'évolution des microfaciès est interprétée comme le « Transgressive System Tract » de la première séquence aptienne.En domaine pélagique, de minces couches riches en matière organique (MO) apparaissent dès le Barrémien sup. dans la coupe de Gorgo a Cerbara (Italie). Elles sont associées à un ratio C:P élevé indiquant des conditions épisodiquement dysoxiques à anoxiques. De plus, une corrélation nette entre Carbone Organique Total (TOC), phosphore (P) et silice biogénique est observée correspondant à un lien entre Ρ disponible, productivité et préservation de la MO. Pourtant, dans le même temps, le ÔI3C et le δ1βΟ restent constants indiquant des conditions environnementales stables et un cycle du carbone non perturbé par la préservation de MO qui ne serait pas la conséquence d'un changement climatique global mais juste d'un effet local.Ala limite Barrémien-Aptien, en domaine hémi-pélagique (La Bédoule, France) et pélagique (Gorgo a Cerbara), les couches riches en MO sont plus fréquentes et plus épaisses, elles se sont déposées en même temps qu'un pic négatif en 513CCARB et ô13Coib probablement dû à un épisode volcanique. A l'Aptien inf. le TOC des niveaux riches en MO augmente progressivement en même temps que la teneur en éléments traces jusqu'au dernier enrichissement avant l'événement anoxique océanique la (OAE la) correspondant au « niveau critique inf. », indiquant des conditions anoxiques moins restreintes. Celui-ci est également caractérisé par le fameux pic négatif en Ô13C (C3), une diminution du δ180 interprétée comme un réchauffement, par un pic en Ρ et un ratio C:P élevé. L'OAE 1 a, quant à lui, enregistre un refroidissement et coïncide avec le maximum en éléments traces ainsi qu'un fort ratio C:P mettant en valeur l'importance des conditions anoxiques pendant 1ΌΑΕ la dans cette coupe alors qu'aucune perturbation n'est enregistrés à La Bédoule probablement à cause de conditions paléogéographiques locales.Durant l'Aptien inf., les changements environnementaux sur la plate-forme se marquent par la prolifération d'orbitolines due à un changement climatique et une hausse du niveau marin. En domaine profond, la succession de niveaux riches en MO du Barrémien sup. jusqu'à l'OAE la documente l'impact progressif de changements paléoenvironnementaux, probablement liés à la formation du plateau d'Ontong Java à l'ouest de l'océan Pacifique.

The abrupt climate change at the Eocene-Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages.

Background and Aims Paleoclimatic data indicate that an abrupt climate change occurred at the Eocene-Oligocene (E-O) boundary affecting the distribution of tropical forests on Earth. The same period has seen the emergence of South-East (SE) Asia, caused by the collision of the Eurasian and Australian plates. How the combination of these climatic and geomorphological factors affected the spatio-temporal history of angiosperms is little known. This topic is investigated by using the worldwide sapindaceous clade as a case study. Methods Analyses of divergence time inference, diversification and biogeography (constrained by paleogeography) are applied to a combined plastid and nuclear DNA sequence data set. Biogeographical and diversification analyses are performed over a set of trees to take phylogenetic and dating uncertainty into account. Results are analysed in the context of past climatic fluctuations. Key Results An increase in the number of dispersal events at the E-O boundary is recorded, which intensified during the Miocene. This pattern is associated with a higher rate in the emergence of new genera. These results are discussed in light of the geomorphological importance of SE Asia, which acted as a tropical bridge allowing multiple contacts between areas and additional speciation across landmasses derived from Laurasia and Gondwana. Conclusions This study demonstrates the importance of the combined effect of geomorphological (the emergence of most islands in SE Asia approx. 30 million years ago) and climatic (the dramatic E-O climate change that shifted the tropical belt and reduced sea levels) factors in shaping species distribution within the sapindaceous clade.

A unique Permian-Triassic boundary section from the Neotethyan Hawasina Basin, Central Oman Mountains

In the Wadi Wasit area (Central Oman Mountains), Dienerian breccias are widespread. These breccias consist mostly of Guadalupian reefal blocks, often dolomitised, and some rare small-sized blocks of lowermost Triassic bivalve-bearing limestones. A unique block, with a size of about 200 m(3), including Permian and earliest Triassic faunas has been studied in detail. The so-called Wadi Wasit block consists of three major lithological units. A basal unstratified grey limestone is rich in various reef-building organisms (rugose corals, calcareous sponges, stromatoporoids) and has been dated as Middle Permian. It is disconformably overlain by well- and thin-bedded light grey to yellowish coloured limestones rich in molluscs. Two major lithologies (Coquina Limestone respectively Bioclastic Limestone unit) characterise the shelly limestones, their contact seems gradual. These two units are well-dated; they are of Griesbachian age and contain three conodont zones, the Parvus Zone, the Staeschei Zone and the Sosioensis Zone, and two ammonoid zones, the Ophiceras tibeticum Zone and an 'unnamed interval'. The third unit consists of a grey marly limestone containing Neospathodus kummeli (basal Dienerian). It is the first record of well-dated basal Triassic sediments in the Arabian Peninsula. The Coquina Limestone is dominated by the bivalve Promyalina with some Claraia and Eumorphotis. This bivalve association is interpreted as a pioneering opportunistic assemblage. Towards the top of the Bioclastic Limestone unit, the faunal diversity increases and contains probably more than 20 taxa of bivalves, microgastropods, crinoids, brachiopods, ammonoids, echinoid spines, ostracods and conodonts. The generic diversity of this biofacies exceeds by far any other Griesbachian assemblage known. Our data give new evidence for the geodynamical history for the distal carbonate shelf bordering the Hawasina Basin. A break in the sedimentation characterises the Late Permian. The basal Triassic shows a steady transgression and the breccias may record a distinct gravitational collapse of platform margins linked with sea-level low stand at the end of Induan time (late Dienerian-basal Smithian). delta(13)C(carb) isotopic analyses were performed and yield typical Permian values of around 4parts per thousand for the Reefal Limestone, with a strong negative shift across the Permian-Triassic boundary. During the Griesbachian values shift positively from 0.5 to 3.1parts per thousand parallel to an increase in faunal diversity and probably primary productivity. The detailed faunal analysis and the discovery of an unexpected diversity give,us a new understanding of the recovery of the Early Triassic marine ecosystem.

Asymptotic analysis of the Gunn effect with realistic boundary conditions

A general asymptotic analysis of the Gunn effect in n-type GaAs under general boundary conditions for metal-semiconductor contacts is presented. Depending on the parameter values in the boundary condition of the injecting contact, different types of waves mediate the Gunn effect. The periodic current oscillation typical of the Gunn effect may be caused by moving charge-monopole accumulation or depletion layers, or by low- or high-field charge-dipole solitary waves. A new instability caused by multiple shedding of (low-field) dipole waves is found. In all cases the shape of the current oscillation is described in detail: we show the direct relationship between its major features (maxima, minima, plateaus, etc.) and several critical currents (which depend on the values of the contact parameters). Our results open the possibility of measuring contact parameters from the analysis of the shape of the current oscillation.

Stationary states and phase diagram for a model of the Gunn effect under realistic boundary conditions

A general formulation of boundary conditions for semiconductor-metal contacts follows from a phenomenological procedure sketched here. The resulting boundary conditions, which incorporate only physically well-defined parameters, are used to study the classical unipolar drift-diffusion model for the Gunn effect. The analysis of its stationary solutions reveals the presence of bistability and hysteresis for a certain range of contact parameters. Several types of Gunn effect are predicted to occur in the model, when no stable stationary solution exists, depending on the value of the parameters of the injecting contact appearing in the boundary condition. In this way, the critical role played by contacts in the Gunn effect is clearly established.

Numerical modeling of the effect of variation of boundary conditions on vadose zone hydraulic properties

An accurate estimation of hydraulic fluxes in the vadose zone is essential for the prediction of water, nutrient and contaminant transport in natural systems. The objective of this study was to simulate the effect of variation of boundary conditions on the estimation of hydraulic properties (i.e. water content, effective unsaturated hydraulic conductivity and hydraulic flux) in a one-dimensional unsaturated flow model domain. Unsaturated one-dimensional vertical water flow was simulated in a pure phase clay loam profile and in clay loam interlayered with silt loam distributed according to the third iteration of the Cantor Bar fractal object Simulations were performed using the numerical model Hydrus 1D. The upper and lower pressure heads were varied around average values of -55 cm for the near-saturation range. This resulted in combinations for the upper and lower constant head boundary conditions, respectively, of -50 and -60 cm, -40 and -70 cm, -30 and -80 cm, -20 and -90 cm, and -10 and -100 cm. For the drier range the average head between the upper and lower boundary conditions was set to -550 cm, resulting in the combinations -500 and -600 cm, -400 and -700 cm, -300 and -800 cm, -200 and -900 cm, and -100 and -1,000 cm, for upper and lower boundary conditions, respectively. There was an increase in water contents, fluxes and hydraulic conductivities with the increase in head difference between boundary conditions. Variation in boundary conditions in the pure phase and interlayered one-dimensional profiles caused significant deviations in fluxes, water contents and hydraulic conductivities compared to the simplest case (a head difference between the upper and lower constant head boundaries of 10 cm in the wetter range and 100 cm in the drier range).