Ancient DNA from coral-hosted Symbiodinium reveal a static mutualism over the last 172 years.

Ancient DNA (aDNA) provides powerful evidence for detecting the genetic basis for adaptation to environmental change in many taxa. Among the greatest of changes in our biosphere within the last century is rapid anthropogenic ocean warming. This phenomenon threatens corals with extinction, evidenced by the increasing observation of widespread mortality following mass bleaching events. There is some evidence and conjecture that coral-dinoflagellate symbioses change partnerships in response to changing external conditions over ecological and evolutionary timescales. Until now, we have been unable to ascertain the genetic identity of Symbiodinium hosted by corals prior to the rapid global change of the last century. Here, we show that Symbiodinium cells recovered from dry, century old specimens of 6 host species of octocorals contain sufficient DNA for amplification of the ITS2 subregion of the nuclear ribosomal DNA, commonly used for genotyping within this genus. Through comparisons with modern specimens sampled from similar locales we show that symbiotic associations among several species have been static over the last century, thereby suggesting that adaptive shifts to novel symbiont types is not common among these gorgonians, and perhaps, symbiotic corals in general

Direct Wigner tomography of a superconducting anharmonic oscillator

The analysis of wave-packet dynamics may be greatly simplified when viewed in phase-space. While harmonic oscillators are often used as a convenient platform to study wave-packets, arbitrary state preparation in these systems is more challenging. Here, we demonstrate a direct measurement of the Wigner distribution of complex photon states in an anharmonic oscillator - a superconducting phase circuit, biased in the small anharmonicity regime. We test our method on both non-classical states composed of two energy eigenstates and on the dynamics of a phase-locked wavepacket. This method requires a simple calibration, and is easily applicable in our system out to the fifth level.Comment: 5 figures, 1 table and supplementary materia

Computational models for inferring biochemical networks

Biochemical networks are of great practical importance. The interaction of biological compounds in cells has been enforced to a proper understanding by the numerous bioinformatics projects, which contributed to a vast amount of biological information. The construction of biochemical systems (systems of chemical reactions), which include both topology and kinetic constants of the chemical reactions, is NP-hard and is a well-studied system biology problem. In this paper, we propose a hybrid architecture, which combines genetic programming and simulated annealing in order to generate and optimize both the topology (the network) and the reaction rates of a biochemical system. Simulations and analysis of an artificial model and three real models (two models and the noisy version of one of them) show promising results for the proposed method.The Romanian National Authority for Scientific Research, CNDI–UEFISCDI, Project No. PN-II-PT-PCCA-2011-3.2-0917

Expression of type I collagen mRNA in glomeruli of rats with passive Heymann nephritis

Expression of type I collagen mRNA in glomeruli of rats with passive Heymann nephritis. In passive Heymann nephritis (PHN) glomeruli exhibit marked basement membrane expansion around subepithelial immune deposits but they fail to show any change in mRNA levels of type IV collagen, laminin or fibronectin by Northern and slot-blot analysis, or in the amount or distribution of type IV collagen or laminin by immunohistology for up to 12 weeks after disease onset. On the other hand, in situ hybridization (ISH) revealed the appearance of positive cells exhibiting mRNA for the α1 chain of rat type I collagen two to three weeks after the onset of PHN in all glomeruli of all rats. Positive cells persisted for at least eight weeks. In many glomeruli, the location of the clusters of silver grains suggested that they were in visceral epithelial cells. In controls injected with normal sheep IgG, and in early PHN (<11 days after sheep anti-Fx1A), glomeruli were negative but cells in the renal capsule and adventitia of vessels showed strong ISH and served as positive controls. RNAse pre-treatment and the “sense” probe gave appropriately negative results. RNA from PHN glomeruli contained an α1 type I collagen transcript of the same size as that from rat fibroblasts. These results show that the evolution of glomerular basement membrane expansion in rat membranous nephropathy coincides with the induction of a matrix gene that is not normally expressed in glomerular cells. Further, they suggest that the intercalation of ectopically-expressed matrix molecules may contribute to the production of a disorganized basement membrane

Disk Imaging Survey of Chemistry with SMA (DISCS): I. Taurus Protoplanetary Disk Data

Chemistry plays an important role in the structure and evolution of protoplanetary disks, with implications for the composition of comets and planets. This is the first of a series of papers based on data from DISCS, a Submillimeter Array survey of the chemical composition of protoplanetary disks. The six Taurus sources in the program (DM Tau, AA Tau, LkCa 15, GM Aur, CQ Tau and MWC 480) range in stellar spectral type from M1 to A4 and offer an opportunity to test the effects of stellar luminosity on the disk chemistry. The disks were observed in 10 different lines at ~3" resolution and an rms of ~100 mJy beam-1 at ~0.5 km s-1. The four brightest lines are CO 2-1, HCO+ 3-2, CN 2_3-1_2 and HCN 3-2 and these are detected toward all sources (except for HCN toward CQ Tau). The weaker lines of CN 2_2-1_1, DCO+ 3-2, N2H+ 3-2, H2CO 3_03-2_02 and 4_14-3_13 are detected toward two to three disks each, and DCN 3-2 only toward LkCa 15. CH3OH 4_21-3_12 and c-C3H2 are not detected. There is no obvious difference between the T Tauri and Herbig Ae sources with regard to CN and HCN intensities. In contrast, DCO+, DCN, N2H+ and H2CO are detected only toward the T Tauri stars, suggesting that the disks around Herbig Ae stars lack cold regions for long enough timescales to allow for efficient deuterium chemistry, CO freeze-out, and grain chemistry.Comment: 29 pages, 4 figures, accepted for publication in Ap

Agonist-Specific Desensitization of PGE2-Stimulated cAMP Signaling due to upregulated Phosphodiesterase Expression in Human Lung Fibroblasts

Pulmonary fibrosis is characterized by fibroblasts persisting in an activated form, producing excessive fibrous material that destroys alveolar structure. The second messenger molecule cyclic 3′,5′-adenosine monophosphate (cAMP) has antifibrotic properties, and prostaglandin E2 (PGE2) can stimulate cAMP production through prostaglandin E (EP)2 and EP4 receptors. Although EP receptors are attractive therapeutic targets, the effects of long-term exposure to PGE2 have not been characterized. To determine the effects of long-term exposure of lung fibroblasts to PGE2, human fetal lung (HFL)-1 cells were treated for 24 h with 100 nM PGE2 or other cAMP-elevating agents. cAMP levels stimulated by acute exposure to PGE2 were measured using a fluorescent biosensor. Pretreatment for 24 h with PGE2 shifted the concentration-response curve to PGE2 rightward by approximately 22-fold but did not affect responses to the beta-adrenoceptor agonist isoproterenol. Neither isoproterenol nor forskolin pretreatment altered PGE2 responses, implying that other cAMP-elevating agents do not induce desensitization. Use of EP2- and EP4-selective agonists and antagonists suggested that PGE2-stimulated cAMP responses in HFL-1 cells are mediated by EP2 receptors. EP2 receptors are resistant to classical mechanisms of agonist-specific receptor desensitization, so we hypothesized that increased PDE activity mediates the loss of signaling after PGE2 pretreatment. PGE2 treatment upregulated messenger RNA for PDE3A, PDE3B, PDE4B, and PDE4D and increased overall PDE activity. The PDE4 inhibitor rolipram partially reversed PGE2- mediated desensitization and PDE4 activity was increased, but rolipram did not alter responses to isoproterenol. The PDE3 inhibitor cilostazol had minimal effect. These results show that long-term exposure to PGE2 causes agonist-specific desensitization of EP2 receptor-stimulated cAMP signaling through the increased expression of PDE isozymes, most likely of the PDE4 family

Disk Imaging Survey of Chemistry with SMA: II. Southern Sky Protoplanetary Disk Data and Full Sample Statistics

This is the second in a series of papers based on data from DISCS, a Submillimeter Array observing program aimed at spatially and spectrally resolving the chemical composition of 12 protoplanetary disks. We present data on six Southern sky sources - IM Lup, SAO 206462 (HD 135344b), HD 142527, AS 209, AS 205 and V4046 Sgr - which complement the six sources in the Taurus star forming region reported previously. CO 2-1 and HCO+ 3-2 emission are detected and resolved in all disks and show velocity patterns consistent with Keplerian rotation. Where detected, the emission from DCO+ 3-2, N2H+ 3-2, H2CO 3-2 and 4-3,HCN 3-2 and CN 2-1 are also generally spatially resolved. The detection rates are highest toward the M and K stars, while the F star SAO 206462 has only weak CN and HCN emission, and H2CO alone is detected toward HD 142527. These findings together with the statistics from the previous Taurus disks, support the hypothesis that high detection rates of many small molecules depend on the presence of a cold and protected disk midplane, which is less common around F and A stars compared to M and K stars. Disk-averaged variations in the proposed radiation tracer CN/HCN are found to be small, despite two orders of magnitude range of spectral types and accretion rates. In contrast, the resolved images suggest that the CN/HCN emission ratio varies with disk radius in at least two of the systems. There are no clear observational differences in the disk chemistry between the classical/full T Tauri disks and transitional disks. Furthermore, the observed line emission does not depend on measured accretion luminosities or the number of infrared lines detected, which suggests that the chemistry outside of 100 AU is not coupled to the physical processes that drive the chemistry in the innermost few AU.Comment: accepted for publication in ApJ, 41 pages including 7 figure

A Multidisciplinary Approach to Pancreas Cancer in 2016: A Review

In this article, we review our multidisciplinary approach for patients with pancreatic cancer. Specifically, we review the epidemiology, diagnosis and staging, biliary drainage techniques, selection of patients for surgery, chemotherapy, radiation therapy, and discuss other palliative interventions. The areas of active research investigation and where our knowledge is limited are emphasized

Climate change promotes parasitism in a coral symbiosis.

Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change