Earliest Triassic microbialites in the South China Block and other areas; controls on their growth and distribution

Earliest Triassic microbialites (ETMs) and inorganic carbonate crystal fans formed after the end-Permian mass extinction (ca. 251.4 Ma) within the basal Triassic Hindeodus parvus conodont zone. ETMs are distinguished from rarer, and more regional, subsequent Triassic microbialites. Large differences in ETMs between northern and southern areas of the South China block suggest geographic provinces, and ETMs are most abundant throughout the equatorial Tethys Ocean with further geographic variation. ETMs occur in shallow-marine shelves in a superanoxic stratified ocean and form the only widespread Phanerozoic microbialites with structures similar to those of the Cambro-Ordovician, and briefly after the latest Ordovician, Late Silurian and Late Devonian extinctions. ETMs disappeared long before the mid-Triassic biotic recovery, but it is not clear why, if they are interpreted as disaster taxa. In general, ETM occurrence suggests that microbially mediated calcification occurred where upwelled carbonate-rich anoxic waters mixed with warm aerated surface waters, forming regional dysoxia, so that extreme carbonate supersaturation and dysoxic conditions were both required for their growth. Long-term oceanic and atmospheric changes may have contributed to a trigger for ETM formation. In equatorial western Pangea, the earliest microbialites are late Early Triassic, but it is possible that ETMs could exist in western Pangea, if well-preserved earliest Triassic facies are discovered in future work

The spread of marine anoxia on the northern Tethys margin during the Paleocene-Eocene Thermal Maximum

Records of the paleoenvironmental changes that occurred during the Paleocene-Eocene Thermal Maximum (PETM) are preserved in sedimentary rocks along the margins of the former Tethys Ocean and Peri-Tethys. This paper presents new geochemical data that constrain paleoproductivity, sediment delivery, and seawater redox conditions, from three sites that were located in the Peri-Tethys region. Trace and major element, iron speciation, and biomarker data indicate that water column anoxia was established during episodes when inputs of land-derived higher plant organic carbon and highly weathered detrital clays and silts became relatively higher. Anoxic conditions are likely to have been initially caused by two primary processes: (i) oxygen consumption by high rates of marine productivity, initially stimulated by the rapid delivery of terrestrially derived organic matter and nutrients, and (ii) phosphorus regeneration from seafloor sediments. The role of the latter process requires further investigation before its influence on the spread of deoxygenated seawater during the PETM can be properly discerned. Other oxygen-forcing processes, such as temperature/salinity-driven water column stratification and/or methane oxidation, are considered to have been relatively less important in the study region. Organic carbon enrichments occur only during the initial stages of the PETM as defined by the negative carbon isotope excursions at each site. The lack of observed terminal stage organic carbon enrichment does not support a link between PETM climate recovery and the sequestration of excess atmospheric CO2 as organic carbon in this region; such a feedback may, however, have been important in the early stages of the PETM

Depositional setting, provenance and tectonic-volcanic setting of Eocene-Recent deep-sea sediments of the oceanic Izu-Bonin forearc, NW Pacific (IODP Expedition 352)

New biostratigraphical, geochemical, and magnetic evidence is synthesized with IODP Expedition 352 shipboard results to understand the sedimentary and tectono-magmatic development of the Izu–Bonin outer forearc region. The oceanic basement of the Izu–Bonin forearc was created by supra-subduction zone seafloor spreading during early Eocene (c. 50–51 Ma). Seafloor spreading created an irregular seafloor topography on which talus locally accumulated. Oxide-rich sediments accumulated above the igneous basement by mixing of hydrothermal and pelagic sediment. Basaltic volcanism was followed by a hiatus of up to 15 million years as a result of topographic isolation or sediment bypassing. Variably tuffaceous deep-sea sediments were deposited during Oligocene to early Miocene and from mid-Miocene to Pleistocene. The sediments ponded into extensional fault-controlled basins, whereas condensed sediments accumulated on a local basement high. Oligocene nannofossil ooze accumulated together with felsic tuff that was mainly derived from the nearby Izu–Bonin arc. Accumulation of radiolarian-bearing mud, silty clay, and hydrogenous metal oxides beneath the carbonate compensation depth (CCD) characterized the early Miocene, followed by middle Miocene–Pleistocene increased carbonate preservation, deepened CCD and tephra input from both the oceanic Izu–Bonin arc and the continental margin Honshu arc. The Izu–Bonin forearc basement formed in a near-equatorial setting, with late Mesozoic arc remnants to the west. Subduction-initiation magmatism is likely to have taken place near a pre-existing continent–oceanic crust boundary. The Izu–Bonin arc migrated northward and clockwise to collide with Honshu by early Miocene, strongly influencing regional sedimentation

Multiple S-isotopic evidence for episodic shoaling of anoxic water during Late Permian mass extinction

Global fossil data show that profound biodiversity loss preceded the final catastrophe that killed nearly 90% marine species on a global scale at the end of the Permian. Many hypotheses have been proposed to explain this extinction and yet still remain greatly debated. Here, we report analyses of all four sulphur isotopes (32S, 33S, 34S and 36S) for pyrites in sedimentary rocks from the Meishan section in South China. We observe a sulphur isotope signal (negative δ34S with negative Δ33S) that may have resulted from limitation of sulphate supply, which may be linked to a near shutdown of bioturbation during shoaling of anoxic water. These results indicate that episodic shoaling of anoxic water may have contributed to the profound biodiversity crisis before the final catastrophe. Our data suggest a prolonged deterioration of oceanic environments during the Late Permian mass extinction

Size-Frequency Distributions along a Latitudinal Gradient in Middle Permian Fusulinoideans

Geographic gradients in body size within and among living species are commonly used to identify controls on the long-term evolution of organism size. However, the persistence of these gradients over evolutionary time remains largely unknown because ancient biogeographic variation in organism size is poorly documented. Middle Permian fusulinoidean foraminifera are ideal for investigating the temporal persistence of geographic gradients in organism size because they were diverse and abundant along a broad range of paleo-latitudes during this interval (∼275–260 million years ago). In this study, we determined the sizes of Middle Permian fusulinoidean fossils from three different paleo-latitudinal zones in order to examine the relationship between the size of foraminifers and regional environment. We recovered the following results: keriothecal fusulinoideans are substantially larger than nonkeriothecal fusulinoideans; fusulinoideans from the equatorial zone are typically larger than those from the north and south transitional zones; neoschwagerinid specimens within a single species are generally larger in the equatorial zone than those in both transitional zones; and the nonkeriothecal fusulinoideans Staffellidae and Schubertellidae have smaller size in the north transitional zone. Fusulinoidean foraminifers differ from most other marine taxa in exhibiting larger sizes closer to the equator, contrary to Bergmann's rule. Meridional variation in seasonality, water temperature, nutrient availability, and carbonate saturation level are all likely to have favored or enabled larger sizes in equatorial regions. Temporal variation in atmospheric oxygen concentrations have been shown to account for temporal variation in fusulinoidean size during Carboniferous and Permian time, but oxygen availability appears unlikely to explain biogeographic variation in fusulinoidean sizes, because dissolved oxygen concentrations in seawater typically increase away from the equator due to declining seawater temperatures. Consequently, our findings highlight the fact that spatial gradients in organism size are not always controlled by the same factors that govern temporal trends within the same clade

Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions

Folding of gene loci organized in tandem arrays reveals variation of chromatin structure as a function of cell differentiation

Resectable pancreatic small cell carcinoma

Primary pancreatic small cell carcinoma (SCC) is rare, with just over 30 cases reported in the literature. Only 7 of these patients underwent surgical resection with a median survival of 6 months. Prognosis of SCC is therefore considered to be poor, and the role of adjuvant therapy is uncertain. Here we report two institutions' experience with resectable pancreatic SCC. Six patients with pancreatic SCC treated at the Johns Hopkins Hospital (4 patients) and the Mayo Clinic (2 patients) were identified from prospectively collected pancreatic cancer databases and re-reviewed by pathology. All six patients underwent a pancreaticoduodenectomy. Clinicopathologic data were analyzed, and the literature on pancreatic SCC was reviewed. Median age at diagnosis was 50 years (range 27–60). All six tumors arose in the head of the pancreas. Median tumor size was 3 cm, and all cases had positive lymph nodes except for one patient who only had five nodes sampled. There were no perioperative deaths and three patients had at least one postoperative complication. All six patients received adjuvant therapy, five of whom were given combined modality treatment with radiation, cisplatin, and etoposide. Median survival was 20 months with a range of 9–173 months. The patient who lived for 9 months received chemotherapy only, while the patient who lived for 173 months was given chemoradiation with cisplatin and etoposide and represents the longest reported survival time from pancreatic SCC to date. Pancreatic SCC is an extremely rare form of cancer with a poor prognosis. Patients in this surgical series showed favorable survival rates when compared to prior reports of both resected and unresectable SCC. Cisplatin and etoposide appears to be the preferred chemotherapy regimen, although its efficacy remains uncertain, as does the role of combined modality treatment with radiation

Automated Workflow for Preparation of cDNA for Cap Analysis of Gene Expression on a Single Molecule Sequencer

Background: Cap analysis of gene expression (CAGE) is a 59 sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted to the HeliScope single molecule sequencer. Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol. Methodology: In this study we set out to adapt the protocol to a robotic workflow, which would increase throughput and reduce handling. The automated CAGE cDNA preparation system we present here can prepare 96 ‘HeliScope ready ’ CAGE cDNA libraries in 8 days, as opposed to 6 weeks by a manual operator.We compare the results obtained using the same RNA in manual libraries and across multiple automation batches to assess reproducibility. Conclusions: We show that the sequencing was highly reproducible and comparable to manual libraries with an 8 fold increase in productivity. The automated CAGE cDNA preparation system can prepare 96 CAGE sequencing samples simultaneously. Finally we discuss how the system could be used for CAGE on Illumina/SOLiD platforms, RNA-seq and fulllengt

Bottom-Water Conditions in a Marine Basin after the Cretaceous–Paleogene Impact Event: Timing the Recovery of Oxygen Levels and Productivity

An ultra-high-resolution analysis of major and trace element contents from the Cretaceous–Paleogene boundary interval in the Caravaca section, southeast Spain, reveals a quick recovery of depositional conditions after the impact event. Enrichment/depletion profiles of redox sensitive elements indicate significant geochemical anomalies just within the boundary ejecta layer, supporting an instantaneous recovery –some 102 years– of pre-impact conditions in terms of oxygenation. Geochemical redox proxies point to oxygen levels comparable to those at the end of the Cretaceous shortly after impact, which is further evidenced by the contemporary macrobenthic colonization of opportunistic tracemakers. Recovery of the oxygen conditions was therefore several orders shorter than traditional proposals (104–105 years), suggesting a probable rapid recovery of deep-sea ecosystems at bottom and in intermediate waters.This research was supported by Projects CGL2009-07603, CGL2008-03007, CGL2012-33281 and CGL2012-32659 (Secretaría de Estado de I+D+I, Spain), Projects RNM-3715 and RNM 05212, and Research Groups RNM-178 and 0179 (Junta de Andalucía)