The Upper Atmosphere of HD17156b

HD17156b is a newly-found transiting extrasolar giant planet (EGP) that orbits its G-type host star in a highly eccentric orbit (e~0.67) with an orbital semi-major axis of 0.16 AU. Its period, 21.2 Earth days, is the longest among the known transiting planets. The atmosphere of the planet undergoes a 27-fold variation in stellar irradiation during each orbit, making it an interesting subject for atmospheric modelling. We have used a three-dimensional model of the upper atmosphere and ionosphere for extrasolar gas giants in order to simulate the progress of HD17156b along its eccentric orbit. Here we present the results of these simulations and discuss the stability, circulation, and composition in its upper atmosphere. Contrary to the well-known transiting planet HD209458b, we find that the atmosphere of HD17156b is unlikely to escape hydrodynamically at any point along the orbit, even if the upper atmosphere is almost entirely composed of atomic hydrogen and H+, and infrared cooling by H3+ ions is negligible. The nature of the upper atmosphere is sensitive to to the composition of the thermosphere, and in particular to the mixing ratio of H2, as the availability of H2 regulates radiative cooling. In light of different simulations we make specific predictions about the thermosphere-ionosphere system of HD17156b that can potentially be verified by observations.Comment: 31 pages, 42 eps figure

Influence of subunit structure on the oligomerization state of light harvesting complexes: a free energy calculation study

Light harvesting complexes 2 (LH2) from Rhodospirillum (Rs.) molischianum and Rhodopseudomonas (Rps.) acidophila form ring complexes out of eight or nine identical subunits, respectively. Here, we investigate computationally what factors govern the different ring sizes. Starting from the crystal structure geometries, we embed two subunits of each species into their native lipid-bilayer/water environment. Using molecular dynamics simulations with umbrella sampling and steered molecular dynamics, we probe the free energy profiles along two reaction coordinates, the angle and the distance between two subunits. We find that two subunits prefer to arrange at distinctly different angles, depending on the species, at about 42.5 deg for Rs. molischianum and at about 38.5 deg for Rps. acidophila, which is likely to be an important factor contributing to the assembly into different ring sizes. Our calculations suggest a key role of surface contacts within the transmembrane domain in constraining these angles, whereas the strongest interactions stabilizing the subunit dimers are found in the C-, and to a lesser extent, N-terminal domains. The presented computational approach provides a promising starting point to investigate the factors contributing to the assembly of protein complexes, in particular if combined with modeling of genetic variants.Comment: 28 pages, 7 figures, LaTeX2e - requires elsart.cls (included), submitted to Chemical Physic

Fire on the Water: China, America, and the Future of the Pacific, by Robert Haddick

Robert Haddick proposes a revised U.S. strategy toward China. He argues agreeing with recent U.S. national security strategies—that continued U.S. forward presence is the only option that supports the American objectives of “an open international economic system; respect for universal values around the world; and a rules-based international order that promotes peace, security, and opportunity through stronger cooperation.” He articulates a two-front effort to ensure China rises within the existing international structure: positive reinforcement of good behavior combined with significant defense reforms to allow punishment of bad behavior

Gut microbiota-derived propionate reduces cancer cell proliferation in the liver

Peer reviewedPublisher PD

The Global Ant Genomics Alliance (GAGA)

Peer reviewe

Placental syncytiotrophoblast constitutes a major barrier to vertical transmission of Listeria monocytogenes.

Listeria monocytogenes is an important cause of maternal-fetal infections and serves as a model organism to study these important but poorly understood events. L. monocytogenes can infect non-phagocytic cells by two means: direct invasion and cell-to-cell spread. The relative contribution of each method to placental infection is controversial, as is the anatomical site of invasion. Here, we report for the first time the use of first trimester placental organ cultures to quantitatively analyze L. monocytogenes infection of the human placenta. Contrary to previous reports, we found that the syncytiotrophoblast, which constitutes most of the placental surface and is bathed in maternal blood, was highly resistant to L. monocytogenes infection by either internalin-mediated invasion or cell-to-cell spread. Instead, extravillous cytotrophoblasts-which anchor the placenta in the decidua (uterine lining) and abundantly express E-cadherin-served as the primary portal of entry for L. monocytogenes from both extracellular and intracellular compartments. Subsequent bacterial dissemination to the villous stroma, where fetal capillaries are found, was hampered by further cellular and histological barriers. Our study suggests the placenta has evolved multiple mechanisms to resist pathogen infection, especially from maternal blood. These findings provide a novel explanation why almost all placental pathogens have intracellular life cycles: they may need maternal cells to reach the decidua and infect the placenta

FindFoci: a focus detection algorithm with automated parameter training that closely matches human assignments, reduces human inconsistencies and increases speed of analysis

Accurate and reproducible quantification of the accumulation of proteins into foci in cells is essential for data interpretation and for biological inferences. To improve reproducibility, much emphasis has been placed on the preparation of samples, but less attention has been given to reporting and standardizing the quantification of foci. The current standard to quantitate foci in open-source software is to manually determine a range of parameters based on the outcome of one or a few representative images and then apply the parameter combination to the analysis of a larger dataset. Here, we demonstrate the power and utility of using machine learning to train a new algorithm (FindFoci) to determine optimal parameters. FindFoci closely matches human assignments and allows rapid automated exploration of parameter space. Thus, individuals can train the algorithm to mirror their own assignments and then automate focus counting using the same parameters across a large number of images. Using the training algorithm to match human assignments of foci, we demonstrate that applying an optimal parameter combination from a single image is not broadly applicable to analysis of other images scored by the same experimenter or by other experimenters. Our analysis thus reveals wide variation in human assignment of foci and their quantification. To overcome this, we developed training on multiple images, which reduces the inconsistency of using a single or a few images to set parameters for focus detection. FindFoci is provided as an open-source plugin for ImageJ

RNA editing signature during myeloid leukemia cell differentiation

Adenosine deaminases acting on RNA (ADARs) are key proteins for hematopoietic stem cell self-renewal and for survival of differentiating progenitor cells. However, their specific role in myeloid cell maturation has been poorly investigated. Here we show that ADAR1 is present at basal level in the primary myeloid leukemia cells obtained from patients at diagnosis as well as in myeloid U-937 and THP1 cell lines and its expression correlates with the editing levels. Upon phorbol-myristate acetate or Vitamin D3/granulocyte macrophage colony-stimulating factor (GM-CSF)-driven differentiation, both ADAR1 and ADAR2 enzymes are upregulated, with a concomitant global increase of A-to-I RNA editing. ADAR1 silencing caused an editing decrease at specific ADAR1 target genes, without, however, interfering with cell differentiation or with ADAR2 activity. Remarkably, ADAR2 is absent in the undifferentiated cell stage, due to its elimination through the ubiquitin–proteasome pathway, being strongly upregulated at the end of the differentiation process. Of note, peripheral blood monocytes display editing events at the selected targets similar to those found in differentiated cell lines. Taken together, the data indicate that ADAR enzymes play important and distinct roles in myeloid cells

Subjective evaluation of the environmental quality in China's industrial corridors.

Based on 270 questionnaire surveys in 8 cities of 5 industrial corridors in China, this study aims to examine the effects of industry construction on the evaluation of environmental pollution, natural environment, built environment, personal perception and development and policy. The results show that the evaluations on environmental pollution and landscape design are both below the medium level, but the evaluations of the living comfort and safety are both above the medium level. Further analysis, females usually give lower evaluation scores than males, and age and health situations are negatively related to the evaluation results; People indicate a great desire to reduce the environmental pollution and protect the natural environment. Moreover, the landscape was analysed using colour extraction techniques based on video recording, there are significant correlations between industrial pixel ratio and evaluation results of air quality, vegetation pixel ratio and evaluation results of river water quality, and public facilities pixel ratio and evaluation results of comfort levels