A numerical study of two-photon ionization of helium using the Pyprop framework

Few-photon induced breakup of helium is studied using a newly developed ab initio numerical framework for solving the six-dimensional time-dependent Schroedinger equation. We present details of the method and calculate (generalized) cross sections for the process of two-photon nonsequential (direct) double ionization at photon energies ranging from 39.4 to 54.4 eV, a process that has been very much debated in recent years and is not yet fully understood. In particular, we have studied the convergence property of the total cross section in the vicinity of the upper threshold (54.4 eV), versus the pulse duration of the applied laser field. We find that the cross section exhibits an increasing trend near the threshold, as has also been observed by others, and show that this rise cannot solely be attributed to an unintended inclusion of the sequential two-photon double ionization process, caused by the bandwidth of the applied field.Comment: 7 pages, 3 figure

Dredging in the Spratly Islands: gaining land but losing reefs

Coral reefs on remote islands and atolls are less exposed to direct human stressors but are becoming increasingly vulnerable because of their development for geopolitical and military purposes. Here we document dredging and filling activities by countries in the South China Sea, where building new islands and channels on atolls is leading to considerable losses of, and perhaps irreversible damages to, unique coral reef ecosystems. Preventing similar damage across other reefs in the region necessitates the urgent development of cooperative management of disputed territories in the South China Sea. We suggest using the Antarctic Treaty as a positive precedent for such international cooperation

Quantum Chessboards in the Deuterium Molecular Ion

We present a new algorithm for vibrational control in deuterium molecules that is feasible with current experimental technology. A pump mechanism is used to create a coherent superposition of the D2+ vibrations. A short, intense infrared control pulse is applied after a chosen delay time to create selective interferences. A `chessboard' pattern of states can be realized in which a set of even- or odd-numbered vibrational states can be selectively annihilated or enhanced. A technique is proposed for experimental realization and observation of this effect using 5 fs pulses of 790 nm radiation, with intermediate intensity (5e13 W/cm2)Comment: 12 pages, 5 figure

Evolutionary relationships of Aurora kinases: Implications for model organism studies and the development of anti-cancer drugs

BACKGROUND: As key regulators of mitotic chromosome segregation, the Aurora family of serine/threonine kinases play an important role in cell division. Abnormalities in Aurora kinases have been strongly linked with cancer, which has lead to the recent development of new classes of anti-cancer drugs that specifically target the ATP-binding domain of these kinases. From an evolutionary perspective, the species distribution of the Aurora kinase family is complex. Mammals uniquely have three Aurora kinases, Aurora-A, Aurora-B, and Aurora-C, while for other metazoans, including the frog, fruitfly and nematode, only Aurora-A and Aurora-B kinases are known. The fungi have a single Aurora-like homolog. Based on the tacit assumption of orthology to human counterparts, model organism studies have been central to the functional characterization of Aurora kinases. However, the ortholog and paralog relationships of these kinases across various species have not been rigorously examined. Here, we present comprehensive evolutionary analyses of the Aurora kinase family. RESULTS: Phylogenetic trees suggest that all three vertebrate Auroras evolved from a single urochordate ancestor. Specifically, Aurora-A is an orthologous lineage in cold-blooded vertebrates and mammals, while structurally similar Aurora-B and Aurora-C evolved more recently in mammals from a duplication of an ancestral Aurora-B/C gene found in cold-blooded vertebrates. All so-called Aurora-A and Aurora-B kinases of non-chordates are ancestral to the clade of chordate Auroras and, therefore, are not strictly orthologous to vertebrate counterparts. Comparisons of human Aurora-B and Aurora-C sequences to the resolved 3D structure of human Aurora-A lends further support to the evolutionary scenario that vertebrate Aurora-B and Aurora-C are closely related paralogs. Of the 26 residues lining the ATP-binding active site, only three were variant and all were specific to Aurora-A. CONCLUSIONS: In this study, we found that invertebrate Aurora-A and Aurora-B kinases are highly divergent protein families from their chordate counterparts. Furthermore, while the Aurora-A family is ubiquitous among all vertebrates, the Aurora-B and Aurora-C families in humans arose from a gene duplication event in mammals. These findings show the importance of understanding evolutionary relationships in the interpretation and transference of knowledge from studies of model organism systems to human cellular biology. In addition, given the important role of Aurora kinases in cancer, evolutionary analysis and comparisons of ATP-binding domains suggest a rationale for designing dual action anti-tumor drugs that inhibit both Aurora-B and Aurora-C kinases

Copy number variants are produced in response to low‐dose ionizing radiation in cultured cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106089/1/em21840.pd

Hydrography and circulation in the Filchner Depression, Weddell Sea, Antarctica

Cold and dense ice shelf water (ISW) emerging from the Filchner-Ronne Ice Shelf cavity in the southwestern Weddell Sea flows northward through the Filchner Depression to eventually descend the con- tinental slope and contribute to the formation of bottom water. New ship-born observations of hydrogra- phy and currents from Filchner Depression in January 2013 suggest that the northward flow of ISW takes place in a middepth jet along the eastern flank of the depression, thus questioning the traditional view with outflow along the western flank. This interpretation of the data is supported by results from a regional numerical model, which shows that ISW flowing northward along the eastern coast of Berkner Island turns eastward and crosses the depression to its eastern side upon reaching the Filchner ice front. The ice front represents a sudden change in the thickness of the water column and thus a potential vorticity barrier. Transport estimates of northward ISW flux based on observations ranges from 0.2 to 1.0 Sv.publishedVersio

Long serial analysis of gene expression for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 252-260, doi:10.1128/AEM.72.1.252-260.2006.The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.This work was supported by the Woods Hole Oceanographic Institution Ocean Life Institute, the J. Lamar Worzel Assistant Scientist Fund, and the Frank and Lisina Hoch Endowed Fund. A.G.M., S.R.B., and M.J.C. were supported in part by the Marine Biological Laboratory's Program in Global Infectious Diseases, funded by the Ellison Medical Foundation. Computational resources were provided by the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (Marine Biological Laboratory) through funds provided by the W. M. Keck Foundation and the G. Unger Vetlesen Foundation

Differential gene expression between fall- and spring-run Chinook salmon assessed by long serial analysis of gene expression

Author Posting. © American Fisheries Society, 2008. This article is posted here by permission of American Fisheries Society for personal use, not for redistribution. The definitive version was published in Transactions of the American Fisheries Society 137 (2008): 1378–1388, doi:10.1577/T07-222.1.Of all Pacific salmonids, Chinook salmon Oncorhynchus tshawytscha display the greatest variability in return times to freshwater. The molecular mechanisms of these differential return times have not been well described. Current methods, such as long serial analysis of gene expression (LongSAGE) and microarrays, allow gene expression to be analyzed for thousands of genes simultaneously. To investigate whether differential gene expression is observed between fall- and spring-run Chinook salmon from California's Central Valley, LongSAGE libraries were constructed. Three libraries containing between 25,512 and 29,372 sequenced tags (21 base pairs/tag) were generated using messenger RNA from the brains of adult Chinook salmon returning in fall and spring and from one ocean-caught Chinook salmon. Tags were annotated to genes using complementary DNA libraries from Atlantic salmon Salmo salar and rainbow trout O. mykiss. Differentially expressed genes, as estimated by differences in the number of sequence tags, were found in all pairwise comparisons of libraries (freshwater versus saltwater = 40 genes; fall versus spring = 11 genes; and spawning versus nonspawning = 51 genes). The gene for ependymin, an extracellular glycoprotein involved in behavioral plasticity in fish, exhibited the most differential expression among the three groupings. Reverse transcription polymerase chain reaction analysis verified the differential expression of ependymin between the fall- and spring-run samples. These LongSAGE libraries, the first reported for Chinook salmon, provide a window of the transcriptional changes during Chinook salmon return migration to freshwater and spawning and increase the amount of expressed sequence data.This work was supported with a grant from the California Department of Water Resources awarded to M.A.B.; J.C.B. received additional funding from the North Umpqua Foundation, Roseburg, Oregon

Quantum effects on Lagrangian points and displaced periodic orbits in the Earth-Moon system

Recent work in the literature has shown that the one-loop long distance quantum corrections to the Newtonian potential imply tiny but observable effects in the restricted three-body problem of celestial mechanics, i.e., at the Lagrangian libration points of stable equilibrium the planetoid is not exactly at equal distance from the two bodies of large mass, but the Newtonian values of its coordinates are changed by a few millimeters in the Earth-Moon system. First, we assess such a theoretical calculation by exploiting the full theory of the quintic equation, i.e., its reduction to Bring-Jerrard form and the resulting expression of roots in terms of generalized hypergeometric functions. By performing the numerical analysis of the exact formulas for the roots, we confirm and slightly improve the theoretical evaluation of quantum corrected coordinates of Lagrangian libration points of stable equilibrium. Second, we prove in detail that also for collinear Lagrangian points the quantum corrections are of the same order of magnitude in the Earth-Moon system. Third, we discuss the prospects to measure, with the help of laser ranging, the above departure from the equilateral triangle picture, which is a challenging task. On the other hand, a modern version of the planetoid is the solar sail, and much progress has been made, in recent years, on the displaced periodic orbits of solar sails at all libration points, both stable and unstable. The present paper investigates therefore, eventually, a restricted three-body problem involving Earth, Moon and a solar sail. By taking into account the one-loop quantum corrections to the Newtonian potential, displaced periodic orbits of the solar sail at libration points are again found to exist