Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

HOST GALAXY IDENTIFICATION FOR SUPERNOVA SURVEYS

Host galaxy identification is a crucial step for modern supernova (SN) surveys such as the Dark Energy Survey and the Large Synoptic Survey Telescope, which will discover SNe by the thousands. Spectroscopic resources are limited, and so in the absence of real-time SN spectra these surveys must rely on host galaxy spectra to obtain accurate redshifts for the Hubble diagram and to improve photometric classification of SNe. In addition, SN luminosities are known to correlate with host-galaxy properties. Therefore, reliable identification of host galaxies is essential for cosmology and SN science. We simulate SN events and their locations within their host galaxies to develop and test methods for matching SNe to their hosts. We use both real and simulated galaxy catalog data from the Advanced Camera for Surveys General Catalog and MICECATv2.0, respectively. We also incorporate "hostless" SNe residing in undetected faint hosts into our analysis, with an assumed hostless rate of 5%. Our fully automated algorithm is run on catalog data and matches SNe to their hosts with 91% accuracy. We find that including a machine learning component, run after the initial matching algorithm, improves the accuracy (purity) of the matching to 97% with a 2% cost in efficiency (true positive rate). Although the exact results are dependent on the details of the survey and the galaxy catalogs used, the method of identifying host galaxies we outline here can be applied to any transient survey

FIRST CASE OF AUTOCHTHONOUS HUMAN VISCERAL LEISHMANIASIS IN THE URBAN CENTER OF RIO DE JANEIRO: CASE REPORT

Visceral leishmaniasis is an anthropozoonosis that is caused by protozoa of the genus Leishmania, especially Leishmania (Leishmania) infantum, and is transmitted to humans by the bite of sandflies of the genus Lutzomyia, such as Lutzomyia longipalpis. There are many reservoirs, including Canis familiaris. It is a chronic infectious disease with systemic involvement that is characterized by three phases: the initial period, the state period and the final period. The main symptoms are fever, malnutrition, hepatosplenomegaly, and pancytopenia. This article reports a case of a patient diagnosed with visceral leishmaniasis in the final period following autochthonous transmission in the urban area of Rio de Janeiro. The case reported here is considered by the Municipal Civil Defense and Health Surveillance of Rio de Janeiro to be the first instance of autochthonous visceral leishmaniasis in humans in the urban area of this city. The patient was discharged and is undergoing a follow-up at the outpatient clinic, demonstrating clinical improvement

Molecular and physiological basis of Saccharomyces cerevisiae tolerance to adverse lignocellulose-based process conditions

Lignocellulose-based biorefineries have been gaining increasing attention to substitute current petroleum-based refineries. Biomass processing requires a pretreatment step to break lignocellulosic biomass recalcitrant structure, which results in the release of a broad range of microbial inhibitors, mainly weak acids, furans, and phenolic compounds. Saccharomyces cerevisiae is the most commonly used organism for ethanol production; however, it can be severely distressed by these lignocellulose-derived inhibitors, in addition to other challenging conditions, such as pentose sugar utilization and the high temperatures required for an efficient simultaneous saccharification and fermentation step. Therefore, a better understanding of the yeast response and adaptation towards the presence of these multiple stresses is of crucial importance to design strategies to improve yeast robustness and bioconversion capacity from lignocellulosic biomass. This review includes an overview of the main inhibitors derived from diverse raw material resultants from different biomass pretreatments, and describes the main mechanisms of yeast response to their presence, as well as to the presence of stresses imposed by xylose utilization and high-temperature conditions, with a special emphasis on the synergistic effect of multiple inhibitors/stressors. Furthermore, successful cases of tolerance improvement of S. cerevisiae are highlighted, in particular those associated with other process-related physiologically relevant conditions. Decoding the overall yeast response mechanisms will pave the way for the integrated development of sustainable yeast cell--based biorefineries.This study was supported by the Portuguese Foundation for Science and Technology (FCT) by the strategic funding of UID/BIO/04469/2013 unit, MIT Portugal Program (Ph.D. grant PD/BD/128247/ 2016 to Joana T. Cunha), Ph.D. grant SFRH/BD/130739/2017 to Carlos E. Costa, COMPETE 2020 (POCI-01-0145-FEDER-006684), BioTecNorte operation (NORTE-01-0145-FEDER-000004), YeasTempTation (ERA-IB-2-6/0001/2014), and MultiBiorefinery project (POCI-01-0145-FEDER-016403). Funding by the Institute for Bioengineering and Biosciences (IBB) from FCT (UID/BIO/04565/2013) and from Programa Operacional Regional de Lisboa 2020 (Project N. 007317) was also receiveinfo:eu-repo/semantics/publishedVersio

UV-luminous, star-forming hosts of z similar to 2 reddened quasars in the Dark Energy Survey

We present the first rest-frame UV population study of 17 heavily reddened, high-luminosity [E(B − V)QSO ≳ 0.5; Lbol > 1046 erg s−1] broad-line quasars at 1.5 < z < 2.7. We combine the first year of deep, optical, ground-based observations from the Dark Energy Survey (DES) with the near-infrared VISTA Hemisphere Survey and UKIDSS Large Area Survey data, from which the reddened quasars were initially identified. We demonstrate that the significant dust reddening towards the quasar in our sample allows host galaxy emission to be detected at the rest-frame UV wavelengths probed by the DES photometry. By exploiting this reddening effect, we disentangle the quasar emission from that of the host galaxy via spectral energy distribution fitting. We find evidence for a relatively unobscured, star-forming host galaxy in at least 10 quasars, with a further three quasars exhibiting emission consistent with either star formation or scattered light. From the rest-frame UV emission, we derive instantaneous, dust-corrected star formation rates (SFRs) in the range 25 < SFRUV < 365 M⊙ yr−1, with an average SFRUV = 130 ± 95 M⊙ yr−1. We find a broad correlation between SFRUV and the bolometric quasar luminosity. Overall, our results show evidence for coeval star formation and black hole accretion occurring in luminous, reddened quasars at the peak epoch of galaxy formation

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications

Imprint of DES super-structures on the Cosmic Microwave Background

Small temperature anisotropies in the Cosmic Microwave Background can be sourced by density perturbations via the late-time integrated Sachs-Wolfe effect. Large voids and superclusters are excellent environments to make a localized measurement of this tiny imprint. In some cases excess signals have been reported. We probed these claims with an independent data set, using the first year data of the Dark Energy Survey in a different footprint, and using a different super-structure finding strategy. We identified 52 large voids and 102 superclusters at redshifts $0.2 < z < 0.65$. We used the Jubilee simulation to a priori evaluate the optimal ISW measurement configuration for our compensated top-hat filtering technique, and then performed a stacking measurement of the CMB temperature field based on the DES data. For optimal configurations, we detected a cumulative cold imprint of voids with $\Delta T_{f} \approx -5.0\pm3.7~\mu K$ and a hot imprint of superclusters $\Delta T_{f} \approx 5.1\pm3.2~\mu K$ ; this is $\sim1.2\sigma$ higher than the expected $|\Delta T_{f}| \approx 0.6~\mu K$ imprint of such super-structures in $\Lambda$CDM. If we instead use an a posteriori selected filter size ($R/R_{v}=0.6$), we can find a temperature decrement as large as $\Delta T_{f} \approx -9.8\pm4.7~\mu K$ for voids, which is $\sim2\sigma$ above $\Lambda$CDM expectations and is comparable to previous measurements made using SDSS super-structure data

Combining dark energy survey science verification data with near-infrared data from the ESO VISTA hemisphere survey

We present the combination of optical data from the Science Verification phase of the Dark Energy Survey (DES) with near infrared data from the ESO VISTA Hemisphere Survey (VHS). The deep optical detections from DES are used to extract fluxes and associated errors from the shallower VHS data. Joint 7-band ($grizYJK$) photometric catalogues are produced in a single 3 sq-deg DECam field centred at 02h26m$-$04d36m where the availability of ancillary multi-wavelength photometry and spectroscopy allows us to test the data quality. Dual photometry increases the number of DES galaxies with measured VHS fluxes by a factor of $\sim$4.5 relative to a simple catalogue level matching and results in a $\sim$1.5 mag increase in the 80\% completeness limit of the NIR data. Almost 70\% of DES sources have useful NIR flux measurements in this initial catalogue. Photometric redshifts are estimated for a subset of galaxies with spectroscopic redshifts and initial results, although currently limited by small number statistics, indicate that the VHS data can help reduce the photometric redshift scatter at both $z1$. We present example DES+VHS colour selection criteria for high redshift Luminous Red Galaxies (LRGs) at $z\sim0.7$ as well as luminous quasars. Using spectroscopic observations in this field we show that the additional VHS fluxes enable a cleaner selection of both populations with $<$10\% contamination from galactic stars in the case of spectroscopically confirmed quasars and $<0.5\%$ contamination from galactic stars in the case of spectroscopically confirmed LRGs. The combined DES+VHS dataset, which will eventually cover almost 5000 sq-deg, will therefore enable a range of new science and be ideally suited for target selection for future wide-field spectroscopic surveys.We thank the referee, Nicholas Cross, for a very useful report on this manuscript. MB acknowledges a postdoctoral fellowship via OL’s Advanced European Research Council Grant (TESTDE). Funding for the DES Projects has been provided by the U.S. Department of Energy, the U.S. National Science Foundation, the Ministry of Science and Education of Spain, the Science and Technology Facilities Council of the United Kingdom, the Higher Education Funding Council for England, the National Center for Supercomputing Applications at the University of Illinois at Urbana- Champaign, the Kavli Institute of Cosmological Physics at the University of Chicago, Financiadora de Estudos e Projetos, Fundac¸ ˜ao Carlos Chagas Filho de Amparo `a Pesquisa do Estado do Rio de Janeiro, Conselho Nacional de Desenvolvimento Cient´ıfico e Tecnol ´ogico and the Minist´erio da Ciˆencia e Tecnologia, the Deutsche Forschungsgemeinschaft and the Collaborating Institutions in the Dark Energy Survey. The Collaborating Institutions are Argonne National Laboratories, the University of California at Santa Cruz, the University of Cambridge, Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas-Madrid, the University of Chicago, University College London, the DES-Brazil Consortium, the Eidgen¨ossische Technische Hochschule (ETH) Z¨urich, Fermi National Accelerator Laboratory, the University of Edinburgh, the University of Illinois at Urbana-Champaign, the Institut de Ciencies de l’Espai (IEEC/CSIC), the Institut de Fisica d’Altes Energies, the Lawrence Berkeley National Laboratory, the Ludwig-Maximilians Universit ¨at and the associated Excellence Cluster Universe, the University of Michigan, the National Optical Astronomy Observatory, the University of Nottingham, The Ohio State University, the University of Pennsylvania, the University of Portsmouth, SLAC National Laboratory, Stanford University, the University of Sussex, and Texas A&M University. The DES participants from Spanish institutions are partially supported by MINECO under grants AYA2009-13936, AYA2012- 39559, AYA2012-39620, and FPA2012-39684, which include FEDER funds from the European Union. We are grateful for the extraordinary contributions of our CTIO colleagues and the DES Camera, Commissioning and Science Verification teams in achieving the excellent instrument and telescope conditions that have made this work possible. The success of this project also relies critically on the expertise and dedication of the DES Data Management organisation. The analysis presented here is based on observations obtained as part of the VISTA Hemisphere Survey, ESO Progam, 179.A- 2010 (PI: McMahon) and data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 179.A-2006 (PI: Jarvis). Data for the OzDES spectroscopic survey were obtained with the Anglo-Australian Telescope (program numbers 12B/11 and 13B/12). Parts of this research were conducted by the Australian Research Council Centre of Excellence for All-sky Astrophysics (CAASTRO), through project number CE110001020. TMD acknowledges the support of the Australian Research Council through Future Fellowship, FT100100595.This is the final published version. It first appeared at http://mnras.oxfordjournals.org/content/446/3/2523.abstract

UV-luminous, star-forming hosts of z ~ 2 reddened quasars in the Dark Energy Survey

We present the first rest-frame UV population study of 17 heavily reddened, high-luminosity (E(B-V)$_{\rm{QSO}}\gtrsim$ 0.5; L$_{\rm{bol}}>$ 10$^{46}$ergs$^{-1}$) broad-line quasars at $1.5 < z < 2.7$. We combine the first year of deep, optical, ground-based observations from the Dark Energy Survey (DES) with the near infrared VISTA Hemisphere Survey (VHS) and UKIDSS Large Area Survey (ULAS) data, from which the reddened quasars were initially identified. We demonstrate that the significant dust reddening towards the quasar in our sample allows host galaxy emission to be detected at the rest-frame UV wavelengths probed by the DES photometry. By exploiting this reddening effect, we disentangle the quasar emission from that of the host galaxy via spectral energy distribution (SED) fitting. We find evidence for a relatively unobscured, star-forming host galaxy in at least ten quasars, with a further three quasars exhibiting emission consistent with either star formation or scattered light. From the rest-frame UV emission, we derive instantaneous, dust-corrected star formation rates (SFRs) in the range 25 < SFR$_{\rm{UV}}$ < 365 M$_{\odot}$yr$^{-1}$, with an average SFR$_{\rm{UV}}$ = 130 $\pm$ 95 M$_{\odot}$yr$^{-1}$. We find a broad correlation between SFR$_{\rm{UV}}$ and the bolometric quasar luminosity. Overall, our results show evidence for coeval star formation and black hole accretion occurring in luminous, reddened quasars at the peak epoch of galaxy formation