Identification of a novel retroviral gene unique to human immunodeficiency virus type 2 and simian immunodeficiency virus SIVMAC

Human and simian immunodeficiency-associated retroviruses are extraordinarily complex, containing at least five genes, tat, art, sor, R, and 3' orf, in addition to the structural genes gag, pol, and env. Recently, nucleotide sequence analysis of human immunodeficiency virus type 2 (HIV-2) and simian immunodeficiency virus SIVMAC revealed the existence of still another open reading frame, termed X, which is highly conserved between these two viruses but absent from HIV-1. In this report, we demonstrate for the first time that the X open reading frame represents a functional retroviral gene in both HIV-2 and SIVMAC and that it encodes a virion-associated protein of 14 and 12 kilodaltons, respectively. We also describe the production of recombinant TrpE/X fusion proteins in Escherichia coli and show that sera from some HIV-2-infected individuals specifically recognize these proteins

Putting into Question the Imaginary of Recovery: A Dialectical Reading of the Global Financial Crisis and its Aftermath

In this article we put into question the discourses that emerged during the Global Financial Crisis (GFC) and that coalesced around a particular socio-economic imaginary of ?recovery? over the period 2009-2012. Our reading of these discourses is very much guided by the notion of the dialectic as developed by Fredric Jameson, and as such this paper can be read as attempt to put his theoretical ideas to work. Through our dialectical reading we aim to create a certain estrangement effect that makes the imaginary of recovery seem very odd and unnatural. In order to achieve such an effect we postulate four theses which are deliberately antagonistic: first, that there has been no ?crisis of capitalism?; second, that we must change the valence of the GFC from negative to positive; third, that the relationship between finance capitalism and ?free markets? is deeply contradictory; and fourth, that we must resist the regulation discourse

Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition and inter-subunit electron transfer

Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail a3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located > 40 Å apart in the same monomer but adjacent in two neighbouring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in inter-subunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut

CO(2-1) Survey at 9 parsec resolution in the SMC

The Small Magellanic Cloud (SMC) is the closest low-metallicity galaxy to the Milky Way where the dynamical state of molecular clouds can be analyzed. We present a CO(2-1) survey at 9 pc resolution obtained with the APEX telescope in an extensive region of the SMC and characterize the properties of the molecular clouds. We study the dynamical state and stability of these clouds uniformly. We identify 177 molecular clouds within the SMC by using CPROPS, of which 124 clouds are fully resolved with signal-to-noise ratio $>$ 5. The scaling relationships show that the SMC clouds are (on average) less turbulent and less luminous than their inner Milky Way counterparts of similar size by a factor of 2 and 3, respectively, while for a fixed linewidth, the SMC clouds are over-luminous by a factor of 3.5. Using the virial masses, we derive a CO-to-H2 conversion factor for the SMC CO clouds of 10.5 M$_{\odot}(K km s^{-1} pc^{2})^{-1}$, measured at 9 pc resolution. We also determine a dust-based conversion factor of 28 M$_{\odot}(K km s^{-1} pc^{2})^{-1}$, obtained at 12 pc resolution. We find that the SMC clouds appear to be in approximate gravitational virial equilibrium. We find that the cumulative mass functions based on both the luminous mass and the virial mass are steeper than $\frac{dN}{dM} \propto M^{-2}$, suggesting that most of the molecular mass of the SMC is contained in low-mass clouds.Comment: 22 pages, 18 figures. Submitted to the Astronomy & Astrophysics (A&A) journa

Inter-species variation in colour perception

Inter-species variation in colour perception poses a serious problem for the view that colours are mind-independent properties. Given that colour perception varies so drastically across species, which species perceives colours as they really are? In this paper, I argue that all do. Specifically, I argue that members of different species perceive properties that are determinates of different, mutually compatible, determinables. This is an instance of a general selectionist strategy for dealing with cases of perceptual variation. According to selectionist views, objects simultaneously instantiate a plurality of colours, all of them genuinely mind-independent, and subjects select from amongst this plurality which colours they perceive. I contrast selectionist views with relationalist views that deny the mind-independence of colour, and consider some general objections to this strategy

Stem Cell Transplantation As A Dynamical System: Are Clinical Outcomes Deterministic?

Outcomes in stem cell transplantation (SCT) are modeled using probability theory. However the clinical course following SCT appears to demonstrate many characteristics of dynamical systems, especially when outcomes are considered in the context of immune reconstitution. Dynamical systems tend to evolve over time according to mathematically determined rules. Characteristically, the future states of the system are predicated on the states preceding them, and there is sensitivity to initial conditions. In SCT, the interaction between donor T cells and the recipient may be considered as such a system in which, graft source, conditioning and early immunosuppression profoundly influence immune reconstitution over time. This eventually determines clinical outcomes, either the emergence of tolerance or the development of graft versus host disease. In this paper parallels between SCT and dynamical systems are explored and a conceptual framework for developing mathematical models to understand disparate transplant outcomes is proposed.Comment: 23 pages, 4 figures. Updated version with additional data, 2 new figures and editorial revisions. New authors adde

Cities in fiction: Perambulations with John Berger

This paper explores selected novels by John Berger in which cities play a central role. These cities are places, partially real and partially imagined, where memory, hope, and despair intersect. My reading of the novels enables me to trace important themes in recent discourses on the nature of contemporary capitalism, including notions of resistance and universality. I also show how Berger?s work points to a writing that can break free from the curious capacity of capitalism to absorb and feed of its critique

Molecular dynamics simulations of oxide memristors: thermal effects

We have extended our recent molecular-dynamic simulations of memristors to include the effect of thermal inhomogeneities on mobile ionic species appearing during operation of the device. Simulations show a competition between an attractive short-ranged interaction between oxygen vacancies and an enhanced local temperature in creating/destroying the conducting oxygen channels. Such a competition would strongly affect the performance of the memristive devices.Comment: submit/0169777; 6 pages, 4 figure

Cold gas outflows from the Small Magellanic Cloud traced with ASKAP

Feedback from massive stars plays a critical role in the evolution of the Universe by driving powerful outflows from galaxies that enrich the intergalactic medium and regulate star formation. An important source of outflows may be the most numerous galaxies in the Universe: dwarf galaxies. With small gravitational potential wells, these galaxies easily lose their star-forming material in the presence of intense stellar feedback. Here, we show that the nearby dwarf galaxy, the Small Magellanic Cloud (SMC), has atomic hydrogen outflows extending at least 2 kiloparsecs (kpc) from the star-forming bar of the galaxy. The outflows are cold, $T<400~{\rm K}$, and may have formed during a period of active star formation $25 - 60$ million years (Myr) ago. The total mass of atomic gas in the outflow is $\sim 10^7$ solar masses, ${\rm M_{\odot}}$, or $\sim 3$% of the total atomic gas of the galaxy. The inferred mass flux in atomic gas alone, $\dot{M}_{HI}\sim 0.2 - 1.0~{\rm M_{\odot}~yr^{-1}}$, is up to an order of magnitude greater than the star formation rate. We suggest that most of the observed outflow will be stripped from the SMC through its interaction with its companion, the Large Magellanic Cloud (LMC), and the Milky Way, feeding the Magellanic Stream of hydrogen encircling the Milky Way.Comment: Published in Nature Astronomy, 29 October 2018, http://dx.doi.org/10.1038/s41550-018-0608-