Geographic and species association of hepatitis B virus genotypes in non-human primates

AbstractInfection with hepatitis B virus (HBV) has been detected in human populations thoughout the world, as well as in a number of ape species (Pan troglodytes, Gorilla gorilla, gibbons [Nomascus and Hylobates species] and Pongo pygmaeus). To investigate the distribution of naturally occurring HBV infection in these species and other African Old World monkey species (Cercopithecidae), we screened 137 plasma samples from mainly wild caught animals by polymerase chain reaction (PCR) using several of highly conserved primers from the HB surface (HBs) gene, and for HBs antigen (HBsAg) by ELISA. None of the 93 Cercopithecidae screened (6 species) showed PCR or serology evidence for HBV infection; in contrast 2 from 8 chimpanzees and 5 from 22 gibbons were PCR-positive with each set of primers.Complete genome sequences from each of the positive apes were obtained and compared with all previously published complete and surface gene sequences. This extended phylogenetic analysis indicated that HBV variants from orangutans were interspersed by with HBV variants from southerly distributed gibbon species (H. agilis and H. moloch) occupying overlapping or adjacent habitat ranges with orangutans; in contrast, HBV variants from gibbon species in mainland Asia were phylogenetically distinct. A geographical rather than (sub)species association of HBV would account for the distribution of HBV variants in different subspecies of chimpanzees in Africa, and explain the inlier position of the previously described lowland gorilla sequence in the chimpanzee clade. These new findings have a number of implication for understanding the origins and epidemiology of HBV infection in non-human primates

Hartree-Fock Theory of Skyrmions in Quantum Hall Ferromagnets

We report on a study of the charged-skyrmion or spin-texture excitations which occur in quantum Hall ferromagnets near odd Landau level filling factors. Particle-hole symmetry is used to relate the spin-quantum numbers of charged particle and hole excitations and neutral particle-hole pair excitations. Hartree-Fock theory is used to provide quantitative estimates of the energies of these excitations and their dependence on Zeeman coupling strength, Landau level quantum numbers, and the thicknesses of the two-dimensional electron layers. For the case of $\nu$ near three we suggest the possibility of first order phase transitions with increasing Zeeman coupling strength from a many skyrmion state to one with many maximally spin-polarized quasiparticles.Comment: 26 pages, 10 figure

The effect of inter-edge Coulomb interactions on the transport between quantum Hall edge states

In a recent experiment, Milliken {\em et al.} demonstrated possible evidence for a Luttinger liquid through measurements of the tunneling conductance between edge states in the $\nu=1/3$ quantum Hall plateau. However, at low temperatures, a discrepancy exists between the theoretical predictions based on Luttinger liquid theory and experiment. We consider the possibility that this is due to long-range Coulomb interactions which become dominant at low temperatures. Using renormalization group methods, we calculate the cross-over behaviour from Luttinger liquid to the Coulomb interaction dominated regime. The cross-over behaviour thus obtained seems to resolve one of the discrepancies, yielding good agreement with experiment.Comment: 4 pages, RevTex, 2 postscript figures, tex file and figures have been uuencode

Lattice Pseudospin Model for ν=1\nu=1 Quantum Hall Bilayers

We present a new theoretical approach to the study of $\nu=1$ quantum Hall bilayer that is based on a systematic mapping of the microscopic Hamiltonian to an anisotropic SU(4) spin model on a lattice. To study the properties of this model we generalize the Heisenberg model Schwinger boson mean field theory (SBMFT) of Arovas and Auerbach to spin models with anisotropy. We calculate the temperature dependence of experimentally observable quantities, including the spin magnetization, and the differential interlayer capacitance. Our theory represents a substantial improvement over the conventional Hartree-Fock picture which neglects quantum and thermal fluctuations, and has advantages over long-wavelength effective models that fail to capture important microscopic physics at all realistic layer separations. The formalism we develop can be generalized to treat quantum Hall bilayers at filling factor $\nu=2$.Comment: 26 pages, 10 figures. The final version, to appear in PR

Spin instabilities and quantum phase transitions in integral and fractional quantum Hall states

The inter-Landau-level spin excitations of quantum Hall states at filling factors nu=2 and 4/3 are investigated by exact numerical diagonalization for the situation in which the cyclotron (hbar*omega_c) and Zeeman (E_Z) splittings are comparable. The relevant quasiparticles and their interactions are studied, including stable spin wave and skyrmion bound states. For nu=2, a spin instability at a finite value of epsilon=hbar*omega_c-E_Z leads to an abrupt paramagnetic to ferromagnetic transition, in agreement with the mean-field approximation. However, for nu=4/3 a new and unexpected quantum phase transition is found which involves a gradual change from paramagnetic to ferromagnetic occupancy of the partially filled Landau level as epsilon is decreased.Comment: 4 pages, 5 figures, submitted to Phys.Rev.Let

Morphometry and growth of sea pen species from dense habitats in the Gulf of St. Lawrence, eastern Canada

We examined four species of sea pen (Anthoptilum grandiflorum, Halipteris finmarchica, Pennatula aculeata and Pennatula grandis) collected from the Gulf of St. Lawrence and mouth of the Laurentian Channel, eastern Canada. An exponential length–weight relationship was found for all four species, where growth in weight was progressively greater than growth in length with increasing colony size. Halipteris finmarchica, P. grandis and P. aculeata presented the better allometric fits, explaining over 80% of the variance. In addition, a count of growth increments visible in transverse sections in 86 A. grandiflorum and 80 P. aculeata samples was made. Presumed ages ranged between 5 and 28 years for A. grandiflorum and 2 and 21 years for P. aculeata. Radiocarbon assays were inconclusive and could not be used to confirm these ages; further age validation is required. Radial growth of the rod is slow during the first years, increasing at intermediate sizes of the colony and slowing down again for large colonies. Similar results were obtained from the relationship between colony length and number of growth increments where a logistic model was the best fit to the data. On average Spearman’s rank correlations showed 11% of shared variance between sea pen length or weight and environmental variables. Bottom temperature and salinity, depth and summer primary production were significantly correlated to sea pen size for most species.En prensa1,48

Skyrmion Excitations in Quantum Hall Systems

Using finite size calculations on the surface of a sphere we study the topological (skyrmion) excitation in quantum Hall system with spin degree of freedom at filling factors around $\nu=1$. In the absence of Zeeman energy, we find, in systems with one quasi-particle or one quasi-hole, the lowest energy band consists of states with $L=S$, where $L$ and $S$ are the total orbital and spin angular momentum. These different spin states are almost degenerate in the thermodynamic limit and their symmetry-breaking ground state is the state with one skyrmion of infinite size. In the presence of Zeeman energy, the skyrmion size is determined by the interplay of the Zeeman energy and electron-electron interaction and the skyrmion shrinks to a spin texture of finite size. We have calculated the energy gap of the system at infinite wave vector limit as a function of the Zeeman energy and find there are kinks in the energy gap associated with the shrinking of the size of the skyrmion. breaking ground state is the state with one skyrmion of infinite size. In the presence of Zeeman energy, the skyrmion size is determined by the interplay of the Zeeman energy and electron-electronComment: 4 pages, 5 postscript figures available upon reques

Pathway-Based High-Throughput Chemical Screen Identifies Compounds That Decouple Heterochromatin Transformations

Heterochromatin protein 1 (HP1) facilitates the formation of repressive heterochromatin domains by recruiting histone lysine methyltransferase enzymes to chromatin, resulting in increased levels of histone H3K9me3. To identify chemical inhibitors of the HP1-heterochromatin gene repression pathway, we combined a cell-based assay that utilized chemical-mediated recruitment of HP1 to an endogenous active gene with high-throughput flow cytometry. Here we characterized small molecule inhibitors that block HP1-mediated heterochromatin formation. Our lead compounds demonstrated dose-dependent inhibition of HP1-stimulated gene repression and were validated in an orthogonal cell-based system. One lead inhibitor was improved by a change in stereochemistry, resulting in compound 2, which was further used to decouple the inverse relationship between H3K9 and H3K4 methylation states. We identified molecular components that bound compound 2, either directly or indirectly, by chemical affinity purification with a biotin-tagged derivative, followed by quantitative proteomic techniques. In summary, our pathway-based chemical screening approach resulted in the discovery of new inhibitors of HP1-mediated heterochromatin formation while identifying exciting new molecular interactions in the pathway to explore in the future. This modular platform can be expanded to test a wide range of chromatin modification pathways yielding inhibitors that are cell permeable and function in a physiologically relevant setting

Hamiltonian Description of Composite Fermions: Magnetoexciton Dispersions

A microscopic Hamiltonian theory of the FQHE, developed by Shankar and myself based on the fermionic Chern-Simons approach, has recently been quite successful in calculating gaps in Fractional Quantum Hall states, and in predicting approximate scaling relations between the gaps of different fractions. I now apply this formalism towards computing magnetoexciton dispersions (including spin-flip dispersions) in the $\nu=1/3$, 2/5, and 3/7 gapped fractions, and find approximate agreement with numerical results. I also analyse the evolution of these dispersions with increasing sample thickness, modelled by a potential soft at high momenta. New results are obtained for instabilities as a function of thickness for 2/5 and 3/7, and it is shown that the spin-polarized 2/5 state, in contrast to the spin-polarized 1/3 state, cannot be described as a simple quantum ferromagnet.Comment: 18 pages, 18 encapsulated ps figure

The WOCE–era 3–D Pacific Ocean circulation and heat budget

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 82 (2009): 281-325, doi:10.1016/j.pocean.2009.08.002.To address questions concerning the intensity and spatial structure of the 3–dimensional circulation within the Pacific Ocean and the associated advective and diffusive property flux divergences, data from approximately 3000 high–quality hydrographic stations collected on 40 zonal and meridional cruises have been merged into a physically consistent model. The majority of the stations were occupied as part of the World Ocean Circulation Experiment (WOCE), which took place in the 1990s. These data are supplemented by a few pre–WOCE surveys of similar quality, and time–averaged direct–velocity and historical hydrographic measurements about the equator. An inverse box model formalism is employed to estimate the absolute along–isopycnal velocity field, the magnitude and spatial distribution of the associated diapycnal flow and the corresponding diapycnal advective and diffusive property flux divergences. The resulting large–scale WOCE Pacific circulation can be described as two shallow overturning cells at mid– to low latitudes, one in each hemisphere, and a single deep cell which brings abyssal waters from the Southern Ocean into the Pacific where they upwell across isopycnals and are returned south as deep waters. Upwelling is seen to occur throughout most of the basin with generally larger dianeutral transport and greater mixing occurring at depth. The derived pattern of ocean heat transport divergence is compared to published results based on air–sea flux estimates. The synthesis suggests a strongly east/west oriented pattern of air–sea heat flux with heat loss to the atmosphere throughout most of the western basins, and a gain of heat throughout the tropics extending poleward through the eastern basins. The calculated meridional heat transport agrees well with previous hydrographic estimates. Consistent with many of the climatologies at a variety of latitudes as well, our meridional heat transport estimates tend toward lower values in both hemispheres.This work was funded by National Science Foundation grants OCE–9710102, OCE– 9712209 and OCE–0079383, and also benefited from work on closely related projects funded by NSF grants OCE–0223421 and OCE–0623261, and NOAA grant NA17RJ1223 funded through CICOR. For G.C.J. NASA funding came under Order W–19,314