44 research outputs found

    Improved HIV and Substance Abuse Treatment Outcomes for Released HIV-Infected Prisoners: The Impact of Buprenorphine Treatment

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    HIV-infected prisoners fare poorly after release. Though rarely available, opioid agonist therapy (OAT) may be one way to improve HIV and substance abuse treatment outcomes after release. Of the 69 HIV-infected prisoners enrolled in a randomized controlled trial of directly administered antiretroviral therapy, 48 (70%) met DSM-IV criteria for opioid dependence. Of these, 30 (62.5%) selected OAT, either as methadone (N = 7, 14.5%) or buprenorphine/naloxone (BPN/NLX; N = 23, 48.0%). Twelve-week HIV and substance abuse treatment outcomes are reported as a sub-study for those selecting BPN/NLX. Retention was high: 21 (91%) completed BPN/NLX induction and 17 (74%) remained on BPN/NLX after 12 weeks. Compared with baseline, the proportion with a non-detectable viral load (61% vs 63% log10 copies/mL) and mean CD4 count (367 vs 344 cells/mL) was unchanged at 12 weeks. Opiate-negative urine testing remained 83% for the 21 who completed induction. Using means from 10-point Likert scales, opioid craving was reduced from 6.0 to 1.8 within 3 days of BPN/NLX induction and satisfaction remained high at 9.5 throughout the 12 weeks. Adverse events were few and mild. BPN/NLX therapy was acceptable, safe and effective for both HIV and opioid treatment outcomes among released HIV-infected prisoners. Future randomized controlled trials are needed to affirm its benefit in this highly vulnerable population

    Hypusine biosynthesis in ÎČ cells links polyamine metabolism to facultative cellular proliferation to maintain glucose homeostasis

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    Deoxyhypusine synthase (DHPS) utilizes the polyamine spermidine to catalyze the hypusine modification of the mRNA translation factor eIF5A and promotes oncogenesis through poorly-defined mechanisms. Because germline deletion of Dhps is embryonically lethal, its role in normal postnatal cellular function in vivo remains unknown. We generated a mouse model that enabled the inducible, postnatal deletion of Dhps specifically in postnatal islet ÎČ cells, which function to maintain glucose homeostasis. Removal of Dhps did not have an effect under normal physiologic conditions. However, upon development of insulin resistance, which induces ÎČ-cell proliferation, Dhps deletion caused alterations in proteins required for mRNA translation and protein secretion, reduced production of the cell cycle molecule cyclin D2, impaired ÎČ-cell proliferation, and induced overt diabetes. We found that hypusine biosynthesis was downstream of protein kinase C-ζ and was required for c-Myc-induced proliferation. Our studies reveal a requirement for DHPS in ÎČ cells to link polyamines to mRNA translation to effect facultative cellular proliferation and glucose homeostasis

    Protein 4.1B Contributes to the Organization of Peripheral Myelinated Axons

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    Neurons are characterized by extremely long axons. This exceptional cell shape is likely to depend on multiple factors including interactions between the cytoskeleton and membrane proteins. In many cell types, members of the protein 4.1 family play an important role in tethering the cortical actin-spectrin cytoskeleton to the plasma membrane. Protein 4.1B is localized in myelinated axons, enriched in paranodal and juxtaparanodal regions, and also all along the internodes, but not at nodes of Ranvier where are localized the voltage-dependent sodium channels responsible for action potential propagation. To shed light on the role of protein 4.1B in the general organization of myelinated peripheral axons, we studied 4.1B knockout mice. These mice displayed a mildly impaired gait and motility. Whereas nodes were unaffected, the distribution of Caspr/paranodin, which anchors 4.1B to the membrane, was disorganized in paranodal regions and its levels were decreased. In juxtaparanodes, the enrichment of Caspr2, which also interacts with 4.1B, and of the associated TAG-1 and Kv1.1, was absent in mutant mice, whereas their levels were unaltered. Ultrastructural abnormalities were observed both at paranodes and juxtaparanodes. Axon calibers were slightly diminished in phrenic nerves and preterminal motor axons were dysmorphic in skeletal muscle. ÎČII spectrin enrichment was decreased along the axolemma. Electrophysiological recordings at 3 post-natal weeks showed the occurrence of spontaneous and evoked repetitive activity indicating neuronal hyperexcitability, without change in conduction velocity. Thus, our results show that in myelinated axons 4.1B contributes to the stabilization of membrane proteins at paranodes, to the clustering of juxtaparanodal proteins, and to the regulation of the internodal axon caliber

    Assessing parallel gene histories in viral genomes

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    Background: The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes. Results: The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. Conclusions: The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.IGB was funded by the disappeared Spanish Ministry for Science and Innovation (CGL2010-16713). Work in Valencia was supported by grant BFU2012-30805 from the Spanish Ministry of Economy and Competitiveness (MINECO) to SFE. BMC is the recipient of an IDIBELL PhD fellowship.Mengual-ChuliĂĄ, B.; Bedhomme, S.; Lafforgue, G.; Elena Fito, SF.; Bravo, IG. (2016). Assessing parallel gene histories in viral genomes. BMC Evolutionary Biology. 16:1-15. https://doi.org/10.1186/s12862-016-0605-4S11516Hess J, Goldman N. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited. PLoS ONE. 2011;6:e22783.Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013;497:327–31.Zhong B, Liu L, Yan Z, Penny D. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 2013;18:492–5.Song S, Liu L, Edwards SV, Wu S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci U S A. 2012;109:14942–7.Nichols R. Gene trees and species trees are not the same. Trends Ecol Evol. 2001;16:358–64.Maddison WP. Gene trees in species trees. Syst Biol. 1997;46:523–36.Suh A, Smeds L, Ellegren H. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol. 2015;13:e1002224.McBreen K, Lockhart PJ. Reconstructing reticulate evolutionary histories of plants. Trends Plant Sci. 2006;11:398–404.Dagan T, Martin W. The tree of one percent. Genome Biol. 2006;7:118.Beiko RG, Harlow TJ, Ragan MA. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A. 2005;102:14332–7.Cotton JA, Page RD. Going nuclear: Gene family evolution and vertebrate phylogeny reconciled. Proc Biol Sci. 2002;269:1555–61.Kuhner MK, Yamato J. Practical performance of tree comparison metrics. Syst Biol. 2015;64:205–14.Brochier C, Bapteste E, Moreira D, Philippe H. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 2002;18:1–5.Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF. Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol. 2005;5:33.Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing congruence in phylogenomic analysis. Syst Biol. 2008;57:104–15.Leigh JW, Schliep K, Lopez P, Bapteste E. Let them fall where they may: Congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol. 2011;28:2773–85.de Vienne DM, Ollier S, Aguileta G. Phylo-mcoa: A fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol Biol Evol. 2012;29:1587–98.Wang S, Luo X, Wei W, Zheng Y, Dou Y, Cai X. Calculation of evolutionary correlation between individual genes and full-length genome: A method useful for choosing phylogenetic markers for molecular epidemiology. PLoS ONE. 2013;8:e81106.Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 2014;31:1261–71.Weyenberg G, Huggins PM, Schardl CL, Howe DK, Yoshida R. Kdetrees: Non-parametric estimation of phylogenetic tree distributions. Bioinformatics. 2014;30:2280–7.de Queiroz A. For consensus (sometimes). Syst Biol. 1993;42:368–72.Miyamoto MM, Fitch WM. Testing the covarion hypothesis of molecular evolution. Mol Biol Evol. 1995;12:503–13.Sanderson MJ, Purvis A, Henze C. Phylogenetic supertrees: Assembling the trees of life. Trends Ecol Evol. 1998;13:105–9.Bininda-Emonds ORP. Phylogenetic supertrees: Combining information to reveal the tree of life. Comput Biol. Dordrecht (The Netherlands): Kluwer Academic Publishers; 2004.Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O’Connell MJ, Pentony MM, et al. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci. 2004;271:2551–8.Pisani D, Cotton JA, McInerney JO. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol. 2007;24:1752–60.Ane C, Larget B, Baum DA, Smith SD, Rokas A. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 2007;24:412–26.Gordon AD. A measure of the agreement between rankings. Biometrika. 1979;66:7–15.de Vienne DM, Giraud T, Martin OC. A congruence index for testing topological similarity between trees. Bioinformatics. 2007;23:3119–24.Suchard MA, Weiss RE, Sinsheimer JS, Dorman KS, Patel M, McCabe ERB. Evolutionary similarity among genes. J Am Stat Assoc. 2003;98:653–62.Edwards SV, Liu L, Pearl DK. High-resolution species trees without concatenation. Proc Natl Acad Sci U S A. 2007;104:5936–41.Liu L, Pearl DK. Species trees from gene trees: Reconstructing bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol. 2007;56:504–14.Liu L, Pearl DK, Brumfield RT, Edwards SV. Estimating species trees using multiple-allele DNA sequence data. Evolution. 2008;62:2080–91.Levasseur C, Lapointe FJ. War and peace in phylogenetics: A rejoinder on total evidence and consensus. Syst Biol. 2001;50:881–91.de Queiroz A, Gatesy J. The supermatrix approach to systematics. Trends Ecol Evol. 2007;22:34–41.Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006;23:254–67.Layeghifard M, Peres-Neto PR, Makarenkov V. Inferring explicit weighted consensus networks to represent alternative evolutionary histories. BMC Evol Biol. 2013;13:274.Stockham C, Wang LS, Warnow T. Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics. 2002;18 Suppl 1:S285–93.Bonnard C, Berry V, Lartillot N. Multipolar consensus for phylogenetic trees. Syst Biol. 2006;55:837–43.Guenoche A. Multiple consensus trees: A method to separate divergent genes. BMC Bioinformatics. 2013;14:46.Duggal R, Cuconati A, Gromeier M, Wimmer E. Genetic recombination of poliovirus in a cell-free system. Proc Natl Acad Sci U S A. 1997;94:13786–91.Reiter J, Perez-Vilaro G, Scheller N, Mina LB, Diez J, Meyerhans A. Hepatitis c virus rna recombination in cell culture. J Hepatol. 2011;55:777–83.Desbiez C, Lecoq H. Evidence for multiple intraspecific recombinants in natural populations of watermelon mosaic virus (wmv, potyvirus). Arch Virol. 2008;153:1749–54.Larsen RC, Miklas PN, Druffel KL, Wyatt SD. Nl-3 k strain is a stable and naturally occurring interspecific recombinant derived from bean common mosaic necrosis virus and bean common mosaic virus. Phytopathology. 2005;95:1037–42.Valli A, Lopez-Moya JJ, Garcia JA. Recombination and gene duplication in the evolutionary diversification of p1 proteins in the family potyviridae. J Gen Virol. 2007;88:1016–28.Gottschling M, Bravo IG, Schulz E, Bracho MA, Deaville R, Jepson PD, et al. Modular organizations of novel cetacean papillomaviruses. Mol Phylogenet Evol. 2011;59:34–42.Woolford L, Rector A, Van Ranst M, Ducki A, Bennett MD, Nicholls PK, et al. A novel virus detected in papillomas and carcinomas of the endangered western barred bandicoot (perameles bougainville) exhibits genomic features of both the papillomaviridae and polyomaviridae. J Virol. 2007;81:13280–90.Chen X, Zhang Q, He C, Zhang L, Li J, Zhang W, et al. Recombination and natural selection in hepatitis e virus genotypes. J Med Virol. 2012;84:1396–407.Cadar D, Csagola A, Kiss T, Tuboly T. Capsid protein evolution and comparative phylogeny of novel porcine parvoviruses. Mol Phylogenet Evol. 2013;66:243–53.Smith LM, McWhorter AR, Shellam GR, Redwood AJ. The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination. Virology. 2013;435:258–68.MĂŒnk C, Willemsen A, Bravo IG. An ancient history of gene duplications, fusions and losses in the evolution of apobec3 mutators in mammals. BMC Evol Biol. 2012;12:71.Daugherty MD, Malik HS. Rules of engagement: Molecular insights from host-virus arms races. Annu Rev Genet. 2012;46:677–700.Edgar RC. Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52.Stamatakis A, Ludwig T, Meier H. Raxml-iii: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21:456–63.Soria-Carrasco V, Talavera G, Igea J, Castresana J. The k tree score: Quantification of differences in the relative branch length and topology of phylogenetic trees. Bioinformatics. 2007;23:2954–6.Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. Selecton 2007: Advanced models for detecting positive and purifying selection using a bayesian inference approach. Nucleic Acids Res. 2007;35:W506–11.Doron-Faigenboim A, Pupko T. A combined empirical and mechanistic codon model. Mol Biol Evol. 2007;24:388–97.Swanson WJ, Nielsen R, Yang Q. Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol. 2003;20:18–20.Shukla DD, Ward CW, Brunt AA. The potyviridae. Wallingford (UK): CABI; 1994.Chung BY, Miller WA, Atkins JF, Firth AE. An overlapping essential gene in the potyviridae. Proc Natl Acad Sci U S A. 2008;105:5897–902.Tan Z, Wada Y, Chen J, Ohshima K. Inter- and intralineage recombinants are common in natural populations of turnip mosaic virus. J Gen Virol. 2004;85:2683–96.Bravo IG, de Sanjose S, Gottschling M. The clinical importance of understanding the evolution of papillomaviruses. Trends Microbiol. 2010;18:432–8.Klingelhutz AJ, Roman A. Cellular transformation by human papillomaviruses: Lessons learned by comparing high- and low-risk viruses. Virology. 2012;424:77–98.Bravo IG, Alonso A. Mucosal human papillomaviruses encode four different e5 proteins whose chemistry and phylogeny correlate with malignant or benign growth. J Virol. 2004;78:13613–26.Garcia-Vallve S, Alonso A, Bravo IG. Papillomaviruses: Different genes have different histories. Trends Microbiol. 2005;13:514–21.Bravo IG, Felez-Sanchez M. Papillomaviruses: Viral evolution, cancer and evolutionary medicine. Evol Med Public Health. 2015;2015:32–51.Aleman-Verdaguer ME, Goudou-Urbino C, Dubern J, Beachy RN, Fauquet C. Analysis of the sequence diversity of the p1, hc, p3, nib and cp genomic regions of several yam mosaic potyvirus isolates: Implications for the intraspecies molecular diversity of potyviruses. J Gen Virol. 1997;78(Pt 6):1253–64.Sakai J, Mori M, Morishita T, Tanaka M, Hanada K, Usugi T, et al. Complete nucleotide sequence and genome organization of sweet potato feathery mottle virus (s strain) genomic rna: The large coding region of the p1 gene. Arch Virol. 1997;142:1553–62.Tordo VM, Chachulska AM, Fakhfakh H, Le Romancer M, Robaglia C, Astier-Manifacier S. Sequence polymorphism in the 5’ntr and in the p1 coding region of potato virus y genomic rna. J Gen Virol. 1995;76(Pt 4):939–49.Verchot J, Carrington JC. Evidence that the potyvirus p1 proteinase functions in trans as an accessory factor for genome amplification. J Virol. 1995;69:3668–74.Salvador B, Saenz P, Yanguez E, Quiot JB, Quiot L, Delgadillo MO, et al. Host-specific effect of p1 exchange between two potyviruses. Mol Plant Pathol. 2008;9:147–55.Desbiez C, Lecoq H. The nucleotide sequence of watermelon mosaic virus (wmv, potyvirus) reveals interspecific recombination between two related potyviruses in the 5’ part of the genome. Arch Virol. 2004;149:1619–32.Majer E, Salvador Z, Zwart MP, Willemsen A, Elena SF, Daros JA. Relocation of the nib gene in the tobacco etch potyvirus genome. J Virol. 2014;88:4586–90.Pasin F, Simon-Mateo C, Garcia JA. The hypervariable amino-terminus of p1 protease modulates potyviral replication and host defense responses. PLoS Pathog. 2014;10:e1003985.Lopez-Lastra M, Rivas A, Barria MI. Protein synthesis in eukaryotes: The growing biological relevance of cap-independent translation initiation. Biol Res. 2005;38:121–46.Kang ST, Wang HC, Yang YT, Kou GH, Lo CF. The DNA virus white spot syndrome virus uses an internal ribosome entry site for translation of the highly expressed nonstructural protein icp35. J Virol. 2013;87:13263–78.Dolja VV, Haldeman-Cahill R, Montgomery AE, Vandenbosch KA, Carrington JC. Capsid protein determinants involved in cell-to-cell and long distance movement of tobacco etch potyvirus. Virology. 1995;206:1007–16.Carrington JC, Jensen PE, Schaad MC. Genetic evidence for an essential role for potyvirus ci protein in cell-to-cell movement. Plant J. 1998;14:393–400.Wei T, Zhang C, Hong J, Xiong R, Kasschau KD, Zhou X, et al. Formation of complexes at plasmodesmata for potyvirus intercellular movement is mediated by the viral protein p3n-pipo. PLoS Pathog. 2010;6:e1000962.Felez-Sanchez M, Trosemeier JH, Bedhomme S, Gonzalez-Bravo MI, Kamp C, Bravo IG. Cancer, warts, or asymptomatic infections: Clinical presentation matches codon usage preferences in human papillomaviruses. Genome Biol Evol. 2015;7:2117–35.Doorbar J, Gallimore PH. Identification of proteins encoded by the l1 and l2 open reading frames of human papillomavirus 1a. J Virol. 1987;61:2793–9.Hughes FJ, Romanos MA. E1 protein of human papillomavirus is a DNA helicase/atpase. Nucleic Acids Res. 1993;21:5817–23.Sarafi TR, McBride AA. Domains of the bpv-1 e1 replication protein required for origin-specific DNA binding and interaction with the e2 transactivator. Virology. 1995;211:385–96.Chen G, Stenlund A. Characterization of the DNA-binding domain of the bovine papillomavirus replication initiator e1. J Virol. 1998;72:2567–76.McBride AA. Replication and partitioning of papillomavirus genomes. Adv Virus Res. 2008;72:155–205.McBride A, Myers G. The e2 proteins: An update. In: Laboratory HPLAN. Los Alamos: Myers, G., and coworkers; 1997. p. III54–99.Kirnbauer R, Booy F, Cheng N, Lowy DR, Schiller JT. Papillomavirus l1 major capsid protein self-assembles into virus-like particles that are highly immunogenic. Proc Natl Acad Sci U S A. 1992;89:12180–4.Penrose KJ, McBride AA. Proteasome-mediated degradation of the papillomavirus e2-ta protein is regulated by phosphorylation and can modulate viral genome copy number. J Virol. 2000;74:6031–8.Poddar A, Reed SC, McPhillips MG, Spindler JE, McBride AA. The human papillomavirus type 8 e2 tethering protein targets the ribosomal DNA loci of host mitotic chromosomes. J Virol. 2009;83:640–50.Lai MC, Teh BH, Tarn WY. A human papillomavirus e2 transcriptional activator. The interactions with cellular splicing factors and potential function in pre-mrna processing. J Biol Chem. 1999;274:11832–41.Zou N, Lin BY, Duan F, Lee KY, Jin G, Guan R, et al. The hinge of the human papillomavirus type 11 e2 protein contains major determinants for nuclear localization and nuclear matrix association. J Virol. 2000;74:3761–70.Steger G, Schnabel C, Schmidt HM. The hinge region of the human papillomavirus type 8 e2 protein activates the human p21(waf1/cip1) promoter via interaction with sp1. J Gen Virol. 2002;83:503–10.Hughes AL, Hughes MA. Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Res. 2005;113:81–8.Ahola H, Bergman P, Strom AC, Moreno-Lopez J, Pettersson U. Organization and expression of the transforming region from the european elk papillomavirus (eepv). Gene. 1986;50:195–205.Chen Z, Schiffman M, Herrero R, Desalle R, Burk RD. Human papillomavirus (hpv) types 101 and 103 isolated from cervicovaginal cells lack an e6 open reading frame (orf) and are related to gamma-papillomaviruses. Virology. 2007;360:447–53.Nobre RJ, Herraez-Hernandez E, Fei JW, Langbein L, Kaden S, Grone HJ, et al. E7 oncoprotein of novel human papillomavirus type 108 lacking the e6 gene induces dysplasia in organotypic keratinocyte cultures. J Virol. 2009;83:2907–16.Stevens H, Rector A, Bertelsen MF, Leifsson PS, Van Ranst M. Novel papillomavirus isolated from the oral mucosa of a polar bear does not cluster with other papillomaviruses of carnivores. Vet Microbiol. 2008;129:108–16.Stevens H, Rector A, Van Der Kroght K, Van Ranst M. Isolation and cloning of two variant papillomaviruses from domestic pigs: Sus scrofa papillomaviruses type 1 variants a and b. J Gen Virol. 2008;89:2475–81.Dyson N, Howley PM, Munger K, Harlow E. The human papilloma virus-16 e7 oncoprotein is able to bind to the retinoblastoma gene product. Science. 1989;243:934–7.Werness BA, Levine AJ, Howley PM. Association of human papillomavirus types 16 and 18 e6 proteins with p53. Science. 1990;248:76–9.Huibregtse JM, Scheffner M, Howley PM. A cellular protein mediates association of p53 with the e6 oncoprotein of human papillomavirus types 16 or 18. EMBO J. 1991;10:4129–35.Hartley KA, Alexander KA. Human tata binding protein inhibits human papillomavirus type 11 DNA replication by antagonizing e1-e2 protein complex formation on the viral origin of replication. J Virol. 2002;76:5014–23.Ilves I, Kadaja M, Ustav M. Two separate replication modes of the bovine papillomavirus bpv1 origin of replication that have different sensitivity to p53. Virus Res. 2003;96:75–84.Narahari J, Fisk JC, Melendy T, Roman A. Interactions of the cellular ccaat displacement protein and human papillomavirus e2 protein with the viral origin of replication can regulate DNA replication. Virology. 2006;350:302–11.Barrow-Laing L, Chen W, Roman A. Low- and high-risk human papillomavirus e7 proteins regulate p130 differently. Virology. 2010;400:233–9.White EA, Sowa ME, Tan MJ, Jeudy S, Hayes SD, Santha S, et al. Systematic identification of interactions between host cell proteins and e7 oncoproteins from diverse human papillomaviruses. Proc Natl Acad Sci U S A. 2012;109:E260–7.Nomine Y, Masson M, Charbonnier S, Zanier K, Ristriani T, Deryckere F, et al. Structural and functional analysis of e6 oncoprotein: Insights in the molecular pathways of human papillomavirus-mediated pathogenesis. Mol Cell. 2006;21:665–78.Zanier K, ould M’hamed ould Sidi A, Boulade-Ladame C, Rybin V, Chappelle A, Atkinson A, et al. Solution structure analysis of the hpv16 e6 oncoprotein reveals a self-association mechanism required for e6-mediated degradation of p53. Structure. 2012;20:604–17.Briddon RW, Patil BL, Bagewadi B, Nawaz-ul-Rehman MS, Fauquet CM. Distinct evolutionary histories of the DNA-a and DNA-b components of bipartite begomoviruses. BMC Evol Biol. 2010;10:97.Chen JM, Sun YX, Chen JW, Liu S, Yu JM, Shen CJ, et al. Panorama phylogenetic diversity and distribution of type a influenza viruses based on their six internal gene sequences. J Virol. 2009;6:137

    The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

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    INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

    Study of molar mass of industrial gelatins by AsFlFFF-UV/MALS and chemometric approach

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    Industrial gelatins have different physicochemical properties that mainly depend of the raw materials origin and the extraction conditions. These properties are closely related to the molar mass distribution of these gelatins. Several methods exist to characterize molar mass distribution of polymer, including the Asymmetrical Flow Field Flow Fractionation method. The goal of this study is to analyze the relationship between physicochemical properties and the gelatins molar mass distribution obtained by Asymmetrical Flow Field Flow Fractionation. In this study, 49 gelatins samples extracted from pig skin are characterized in terms of gel strength and viscosity and their molar mass distribution are analyzed by Asymmetrical Flow Field Flow Fractionation coupled to an Ultraviolet and Multi Angle Light Scattering detector. This analytical method is an interesting tool for studying, simultaneously, the primary chains and the high-molar-mass fraction corresponding to the polymer chains. Correlation analysis between molar mass distribution data from the different fractions highlights the importance of high molar mass polymer chains to explain the gel strength and viscosity of gelatins. These results are confirmed by an additional chemometric approach based on the UV absorbance of gelatin fractograms to predict gel strength (rÂČCal = 0.85) and viscosity (rÂČCal = 0.79). ****Related forthcoming publication will be available soon***

    Retalho em ilha de tubarĂŁo: uma tĂ©cnica cirĂșrgica reconstrutiva de defeitos localizados na ĂĄrea nasal alar/perialar. Um procedimento simples Shark island pedicle flap for repairing of basal cell carcinoma localized in nasal ala-perialar region: a simple procedure

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    O Carcinoma Basocelular Ă© a neoplasia cutĂąnea mais frequente. Os autores descrevem uma tĂ©cnica realizada unicamente num tempo operatĂłrio para correção de defeitos na asa do nariz apĂłs excisĂŁo tumoral. Esta tĂ©cnica simples permite a correção cirĂșrgica de defeitos nesta localização possibilitando a reconstrução da anatomia local e a preservação das unidades cosmĂ©ticas, sem a necessidade de enxerto<br>Basal Cell Carcinoma is the most common skin cancer. We describe a single-staged technique for correction of nasal ala defect after the excision of a basal cell carcinoma. This technique allows correction of surgical defects of the ala rebuilding the original anatomy, maintaining cosmetic units, without need for a graf

    Microstructure of LiCoO2 with and without "AIPO(4)" nanoparticle coating: Combined STEM and XPS studies

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    "AlPO 4"-coated LiCoO 2 was shown to exhibit markedly improved capacity retention relative to bare LiCO 2 upon cycling to 4.7 V, Scanning and transmission electron microscopy imaging showed that the coating thickness of "AlPOV 4"-coated LiCoO 2 varied from ??? 10 to ??? 100 nm. Energy-dispersive X-ray mapping revealed that the coating was not single-phase "AlPO 4", rather consisting of P-rich thick regions (???100 nm) and Al-rich thin regions (???10 nm). Detailed X-ray photoelectron spectroscopy (XPS) studies of the "AlPO 4"-coated LiCoO 2 in comparison to bare LiCoO 2 and various reference compounds such as Li 2CO 3, Li 3PO 4, and AlPO4 indicate that (1) AlPO 4 is absent on the surface; (2) the surface consisted of Li 3PO 4 and heavily Al substituted LiAl yCo 1-yO 2, which may result from AlPO 4 nanoparticles reacting with bare LiCoO 2 during the coating heat treatment at 700??C; and (3) the amount of surface Li 2CO 3 is markedly reduced in the coated sample relative to the bare LiCoO 2. The existence of Li 3PO 4 in "AlPO 4"-coated LiCoO 2 was confirmed with X-ray powder diffraction. The coating microstructure of "AlPO 4"- coated LICoO 2 is proposed, and the mechanisms of enhancement in the cycling and thermal characteristics by particle surface microstructure are discussed in detail.close524
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