Journal articles: 'Genome release'

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Škubník, Karel, Lukáš Sukeník, David Buchta, Tibor Füzik, Michaela Procházková, Jana Moravcová, Lenka Šmerdová, Antonín Přidal, Robert Vácha, and Pavel Plevka. "Capsid opening enables genome release of iflaviruses." Science Advances 7, no. 1 (January 2021): eabd7130. http://dx.doi.org/10.1126/sciadv.abd7130.

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The family Iflaviridae includes economically important viruses of the western honeybee such as deformed wing virus, slow bee paralysis virus, and sacbrood virus. Iflaviruses have nonenveloped virions and capsids organized with icosahedral symmetry. The genome release of iflaviruses can be induced in vitro by exposure to acidic pH, implying that they enter cells by endocytosis. Genome release intermediates of iflaviruses have not been structurally characterized. Here, we show that conformational changes and expansion of iflavirus RNA genomes, which are induced by acidic pH, trigger the opening of iflavirus particles. Capsids of slow bee paralysis virus and sacbrood virus crack into pieces. In contrast, capsids of deformed wing virus are more flexible and open like flowers to release their genomes. The large openings in iflavirus particles enable the fast exit of genomes from capsids, which decreases the probability of genome degradation by the RNases present in endosomes.

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Mullapudi, Edukondalu, Jiří Nováček, Lenka Pálková, Pavel Kulich, A. Michael Lindberg, Frank J. M. van Kuppeveld, and Pavel Plevka. "Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3." Journal of Virology 90, no. 17 (June 8, 2016): 7628–39. http://dx.doi.org/10.1128/jvi.00746-16.

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ABSTRACTIn order to initiate an infection, viruses need to deliver their genomes into cells. This involves uncoating the genome and transporting it to the cytoplasm. The process of genome delivery is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the uncoating of the nonenveloped human cardiovirus Saffold virus 3 (SAFV-3) of the familyPicornaviridae. SAFVs cause diseases ranging from gastrointestinal disorders to meningitis. We present a structure of a native SAFV-3 virion determined to 2.5 Å by X-ray crystallography and an 11-Å-resolution cryo-electron microscopy reconstruction of an “altered” particle that is primed for genome release. The altered particles are expanded relative to the native virus and contain pores in the capsid that might serve as channels for the release of VP4 subunits, N termini of VP1, and the RNA genome. Unlike in the related enteroviruses, pores in SAFV-3 are located roughly between the icosahedral 3- and 5-fold axes at an interface formed by two VP1 and one VP3 subunit. Furthermore, in native conditions many cardioviruses contain a disulfide bond formed by cysteines that are separated by just one residue. The disulfide bond is located in a surface loop of VP3. We determined the structure of the SAFV-3 virion in which the disulfide bonds are reduced. Disruption of the bond had minimal effect on the structure of the loop, but it increased the stability and decreased the infectivity of the virus. Therefore, compounds specifically disrupting or binding to the disulfide bond might limit SAFV infection.IMPORTANCEA capsid assembled from viral proteins protects the virus genome during transmission from one cell to another. However, when a virus enters a cell the virus genome has to be released from the capsid in order to initiate infection. This process is not well understood for nonenveloped viruses. We address this gap in our current knowledge by studying the genome release ofHuman Saffold virus 3. Saffold viruses cause diseases ranging from gastrointestinal disorders to meningitis. We show that before the genome is released, the Saffold virus 3 particle expands, and holes form in the previously compact capsid. These holes serve as channels for the release of the genome and small capsid proteins VP4 that in related enteroviruses facilitate subsequent transport of the virus genome into the cell cytoplasm.

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Kalynych, Sergei, Tibor Füzik, Antonín Přidal, Joachim de Miranda, and Pavel Plevka. "Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism." Proceedings of the National Academy of Sciences 114, no. 3 (January 4, 2017): 598–603. http://dx.doi.org/10.1073/pnas.1616562114.

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Viruses from the familyIflaviridaeare insect pathogens. Many of them, including slow bee paralysis virus (SBPV), cause lethal diseases in honeybees and bumblebees, resulting in agricultural losses. Iflaviruses have nonenveloped icosahedral virions containing single-stranded RNA genomes. However, their genome release mechanism is unknown. Here, we show that low pH promotes SBPV genome release, indicating that the virus may use endosomes to enter host cells. We used cryo-EM to study a heterogeneous population of SBPV virions at pH 5.5. We determined the structures of SBPV particles before and after genome release to resolutions of 3.3 and 3.4 Å, respectively. The capsids of SBPV virions in low pH are not expanded. Thus, SBPV does not appear to form “altered” particles with pores in their capsids before genome release, as is the case in many related picornaviruses. The egress of the genome from SBPV virions is associated with a loss of interpentamer contacts mediated by N-terminal arms of VP2 capsid proteins, which result in the expansion of the capsid. Pores that are 7 Å in diameter form around icosahedral threefold symmetry axes. We speculate that they serve as channels for the genome release. Our findings provide an atomic-level characterization of the genome release mechanism of iflaviruses.

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Dalrymple, B. P. "Harnessing the bovine genome sequence for the Australian cattle and sheep industries." Australian Journal of Experimental Agriculture 45, no. 8 (2005): 1011. http://dx.doi.org/10.1071/ea05043.

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Genomics is an emerging science and the release of the human and mouse genomes has significantly altered our picture of the information content of mammalian genomes. A smaller number of protein coding genes, and a larger number of genes that do not appear to encode protein products, the so-called non-coding RNAs (ncRNAs), have been identified. The first 2 drafts of the bovine genome sequence have been released, and work to utilise the framework of the bovine genome to facilitate ovine genomics is underway. In anticipation of the requirement for a detailed analysis of the ruminant genomes, their transcriptomes, interactomes, regulomes and similar, we have been developing the informatics platform for the analysis and integration of genome sequences and expression data for cattle and sheep. This resource will enable us to utilise the ruminant datasets and integrate them with equivalent data from other mammals for the advancement of animal scientific research for applications in the cattle and sheep industries in Australia.

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Contreras, J. L. "Prepublication Data Release, Latency, and Genome Commons." Science 329, no. 5990 (July 22, 2010): 393–94. http://dx.doi.org/10.1126/science.1189253.

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Hrebík, Dominik, Tibor Füzik, Mária Gondová, Lenka Šmerdová, Athanassios Adamopoulos, Ondrej Šedo, Zbyněk Zdráhal, and Pavel Plevka. "ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating." Proceedings of the National Academy of Sciences 118, no. 19 (May 4, 2021): e2024251118. http://dx.doi.org/10.1073/pnas.2024251118.

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Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14–ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA–VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid–RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.

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Eissenberg, Joel C. "In Our Image: The Ethics of CRISPR Genome Editing." Biomolecular Concepts 12, no. 1 (January 1, 2021): 1–7. http://dx.doi.org/10.1515/bmc-2021-0001.

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Abstract The advent of genome editing technology promises to transform human health, livestock and agriculture, and to eradicate pest species. This transformative power demands urgent scrutiny and resolution of the ethical conflicts attached to the creation and release of engineered genomes. Here, I discuss the ethics surrounding the transformative CRISPR/Cas9-mediated genome editing technology in the contexts of human genome editing to eradicate genetic disease and of gene drive technology to eradicate animal vectors of human disease.

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Kahn, P. "Human Genome Project: Sequencers Split Over Data Release." Science 271, no. 5257 (March 29, 1996): 1798b—1799. http://dx.doi.org/10.1126/science.271.5257.1798b.

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Sukeník, Lukáš, Pavel Plevka, and Robert Vacha. "Pathways of Genome Release Determined by Virion Properties." Biophysical Journal 120, no. 3 (February 2021): 208a. http://dx.doi.org/10.1016/j.bpj.2020.11.1414.

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Jiang, Bingfu, and Eberhard Hildt. "Intracellular Trafficking of HBV Particles." Cells 9, no. 9 (September 2, 2020): 2023. http://dx.doi.org/10.3390/cells9092023.

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The human hepatitis B virus (HBV), that is causative for more than 240 million cases of chronic liver inflammation (hepatitis), is an enveloped virus with a partially double-stranded DNA genome. After virion uptake by receptor-mediated endocytosis, the viral nucleocapsid is transported towards the nuclear pore complex. In the nuclear basket, the nucleocapsid disassembles. The viral genome that is covalently linked to the viral polymerase, which harbors a bipartite NLS, is imported into the nucleus. Here, the partially double-stranded DNA genome is converted in a minichromosome-like structure, the covalently closed circular DNA (cccDNA). The DNA virus HBV replicates via a pregenomic RNA (pgRNA)-intermediate that is reverse transcribed into DNA. HBV-infected cells release apart from the infectious viral parrticle two forms of non-infectious subviral particles (spheres and filaments), which are assembled by the surface proteins but lack any capsid and nucleic acid. In addition, naked capsids are released by HBV replicating cells. Infectious viral particles and filaments are released via multivesicular bodies; spheres are secreted by the classic constitutive secretory pathway. The release of naked capsids is still not fully understood, autophagosomal processes are discussed. This review describes intracellular trafficking pathways involved in virus entry, morphogenesis and release of (sub)viral particles.

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Morales, Mónica, Miguel A. Ramírez, María J. Cano, Mario Párraga, Joaquín Castilla, Luis I. Pérez-Ordoyo, Juan M. Torres, and Juan Bárcena. "Genome Comparison of a Nonpathogenic Myxoma Virus Field Strain with Its Ancestor, the Virulent Lausanne Strain." Journal of Virology 83, no. 5 (December 17, 2008): 2397–403. http://dx.doi.org/10.1128/jvi.02189-08.

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ABSTRACT One of the best-studied examples of host-virus coevolution is the release of myxoma virus (MV) for biological control of European rabbits in Australia and Europe. To investigate the genetic basis of MV adaptation to its new host, we sequenced the genome of 6918, an attenuated Spanish field strain, and compared it with that of Lausanne, the strain originally released in Europe in 1952. Although isolated 43 years apart, the genomes were highly conserved (99.95% identical). Only 32 of the 159 MV predicted proteins revealed amino acid changes. Four genes (M009L, M036L, M135R, and M148R) in 6918 were disrupted by frameshift mutations.

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Romeo, Orazio, Alessia Marchetta, Domenico Giosa, Letterio Giuffrè, Clara Urzì, and Filomena De Leo. "Whole Genome Sequencing and Comparative Genome Analysis of the Halotolerant Deep Sea Black Yeast Hortaea werneckii." Life 10, no. 10 (October 2, 2020): 229. http://dx.doi.org/10.3390/life10100229.

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Hortaea werneckii, an extreme halotolerant black yeast in the order of Capnodiales, was recently isolated from different stations and depths in the Mediterranean Sea, where it was shown to be the dominant fungal species. In order to explore the genome characteristics of these Mediterranean isolates, we carried out a de-novo sequencing of the genome of one strain isolated at a depth of 3400 m (MC873) and a re-sequencing of one strain taken from a depth of 2500 m (MC848), whose genome was previously sequenced but was highly fragmented. A comparative phylogenomic analysis with other published H. werneckii genomes was also carried out to investigate the evolution of the strains from the deep sea in this environment. A high level of genome completeness was obtained for both genomes, for which genome duplication and an extensive level of heterozygosity (~4.6%) were observed, supporting the recent hypothesis that a genome duplication caused by intraspecific hybridization occurred in most H. werneckii strains. Phylogenetic analyses showed environmental and/or geographical specificity, suggesting a possible evolutionary adaptation of marine H. werneckii strains to the deep sea environment. We release high-quality genome assemblies from marine H. werneckii strains, which provides additional data for further genomics analysis, including niche adaptation, fitness and evolution studies.

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Marshall, E. "GENOME SEQUENCING:Clinton and Blair Back Rapid Release of Data." Science 287, no. 5460 (March 17, 2000): 1903a—1903. http://dx.doi.org/10.1126/science.287.5460.1903a.

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Pope, Samuel M. "Impact of Gene Editing Tools, Like CRISPR/Cas9, on the Public Health Response to Disease Outbreaks." Disaster Medicine and Public Health Preparedness 11, no. 2 (September 19, 2016): 155–59. http://dx.doi.org/10.1017/dmp.2016.123.

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AbstractThe purpose of this communication is to explore the implications of genome editing techniques, such as CRISPR/Cas9, on public health–related responses to outbreaks of disease. The recent commercialization of genome editing techniques makes the creation and release of genetically altered pathogens a much easier task, increasing the possibility to the point of needing discussion. Three areas need to be addressed: predictions concerning potential genetic alterations, predictions and implications concerning the release of genetically altered pathogens, and the short- and long-term implications of the release of genetically altered pathogens. Full discourse on these topics among professionals in the area of public health will help to combat harm from the use of any genetically altered biologic weapons. The topics covered here include a review of the CRISPR/Cas9 gene editing technique, including a discussion of which possibilities utilize genome editing. We then address predictions about the application of gene alterations in the context of bioweapons. We discuss a few basic concepts about the evolution of an intentionally released genetically altered organism based on circumstances and patterns gleaned from observing nature in the hope that this will aid in the public health response to bioterrorism attack. (Disaster Med Public Health Preparedness. 2017;11:155–159)

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Valentin, Guignon, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Conte Matthieu, and Rouard Mathieu. "GreenPhylDB v5: a comparative pangenomic database for plant genomes." Nucleic Acids Research 49, no. D1 (November 25, 2020): D1464—D1471. http://dx.doi.org/10.1093/nar/gkaa1068.

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Abstract Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

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Plevka, Pavel, Pei-Yin Lim, Rushika Perera, Jane Cardosa, Ampa Suksatu, Richard J. Kuhn, and Michael G. Rossmann. "Neutralizing antibodies can initiate genome release from human enterovirus 71." Proceedings of the National Academy of Sciences 111, no. 6 (January 27, 2014): 2134–39. http://dx.doi.org/10.1073/pnas.1320624111.

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Lok, Shee-Mei, Joshua M. Costin, Yancey M. Hrobowski, Andrew R. Hoffmann, Dawne K. Rowe, Petra Kukkaro, Heather Holdaway, et al. "Release of Dengue Virus Genome Induced by a Peptide Inhibitor." PLoS ONE 7, no. 11 (November 30, 2012): e50995. http://dx.doi.org/10.1371/journal.pone.0050995.

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Ojala, Päivi M., Beate Sodeik, Melanie W. Ebersold, Ulrike Kutay, and Ari Helenius. "Herpes Simplex Virus Type 1 Entry into Host Cells: Reconstitution of Capsid Binding and Uncoating at the Nuclear Pore Complex In Vitro." Molecular and Cellular Biology 20, no. 13 (July 1, 2000): 4922–31. http://dx.doi.org/10.1128/mcb.20.13.4922-4931.2000.

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ABSTRACT During entry, herpes simplex virus type 1 (HSV-1) releases its capsid and the tegument proteins into the cytosol of a host cell by fusing with the plasma membrane. The capsid is then transported to the nucleus, where it docks at the nuclear pore complexes (NPCs), and the viral genome is rapidly released into the nucleoplasm. In this study, capsid association with NPCs and uncoating of the viral DNA were reconstituted in vitro. Isolated capsids prepared from virus were incubated with cytosol and purified nuclei. They were found to bind to the nuclear pores. Binding could be inhibited by pretreating the nuclei with wheat germ agglutinin, anti-NPC antibodies, or antibodies against importin β. Furthermore, in the absence of cytosol, purified importin β was both sufficient and necessary to support efficient capsid binding to nuclei. Up to 60 to 70% of capsids interacting with rat liver nuclei in vitro released their DNA if cytosol and metabolic energy were supplied. Interaction of the capsid with the nuclear pore thus seemed to trigger the release of the viral genome, implying that components of the NPC play an active role in the nuclear events during HSV-1 entry into host cells.

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Kienberger, Ferry, Rong Zhu, Rosita Moser, Dieter Blaas, and Peter Hinterdorfer. "Monitoring RNA Release from Human Rhinovirus by Dynamic Force Microscopy." Journal of Virology 78, no. 7 (April 1, 2004): 3203–9. http://dx.doi.org/10.1128/jvi.78.7.3203-3209.2004.

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ABSTRACT Human rhinoviruses were imaged under physiological conditions by dynamic force microscopy. Topographical images revealed various polygonal areas on the surfaces of the 30-nm viral particles. RNA release was initiated by exposure to a low-pH buffer. The lengths of the RNAs that were released but still connected to the virus capsid varied between 40 and 330 nm, whereas RNA molecules that were completely released from the virus were observed with lengths up to 1 μm. Fork-like structure elements with 30-nm extensions were sometimes resolved at one end of the RNA molecules. They possibly correspond to the characteristic multi-stem-loop conformation, the internal ribosomal entry site, located at the 5′ region of the genome. This study demonstrates that dynamic force microscopy can be used to study viral RNA release in situ under physiological conditions.

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Shustov, Alexandr V., Peter W. Mason, and Ilya Frolov. "Production of Pseudoinfectious Yellow Fever Virus with a Two-Component Genome." Journal of Virology 81, no. 21 (August 22, 2007): 11737–48. http://dx.doi.org/10.1128/jvi.01112-07.

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ABSTRACT Application of genetically modified, deficient-in-replication flaviviruses that are incapable of developing productive, spreading infection is a promising means of designing safe and effective vaccines. Here we describe a two-component genome yellow fever virus (YFV) replication system in which each of the genomes encodes complete sets of nonstructural proteins that form the replication complex but expresses either only capsid or prM/E instead of the entire structural polyprotein. Upon delivery to the same cell, these genomes produce together all of the viral structural proteins, and cells release a combination of virions with both types of genomes packaged into separate particles. In tissue culture, this modified YFV can be further passaged at an escalating scale by using a high multiplicity of infection (MOI). However, at a low MOI, only one of the genomes is delivered into the cells, and infection cannot spread. The replicating prM/E-encoding genome produces extracellular E protein in the form of secreted subviral particles that are known to be an effective immunogen. The presented strategy of developing viruses defective in replication might be applied to other flaviviruses, and these two-component genome viruses can be useful for diagnostic or vaccine applications, including the delivery and expression of heterologous genes. In addition, the achieved separation of the capsid-coding sequence and the cyclization signal in the YFV genome provides a new means for studying the mechanism of the flavivirus packaging process.

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Ortega-Esteban, Alvaro, Kai Bodensiek, Carmen San Martín, Maarit Suomalainen, Urs F. Greber, Pedro J. de Pablo, and Iwan A. T. Schaap. "Fluorescence Tracking of Genome Release during Mechanical Unpacking of Single Viruses." ACS Nano 9, no. 11 (September 24, 2015): 10571–79. http://dx.doi.org/10.1021/acsnano.5b03020.

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CERVINO, A. C. L., N. F. TSINOREMAS, and R. W. HOFFMAN. "A Genome-Wide Study of Lupus: Preliminary Analysis and Data Release." Annals of the New York Academy of Sciences 1110, no. 1 (September 1, 2007): 131–39. http://dx.doi.org/10.1196/annals.1423.015.

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Parker, Michael, Susan J. Bull, Jantina de Vries, Tsiri Agbenyega, Ogobara K. Doumbo, and Dominic P. Kwiatkowski. "Ethical Data Release in Genome-Wide Association Studies in Developing Countries." PLoS Medicine 6, no. 11 (November 24, 2009): e1000143. http://dx.doi.org/10.1371/journal.pmed.1000143.

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Su, Qin, Miguel Sena-Esteves, and Guangping Gao. "Release of the Cloned Recombinant Adenovirus Genome for Rescue and Expansion." Cold Spring Harbor Protocols 2019, no. 5 (May 2019): pdb.prot095539. http://dx.doi.org/10.1101/pdb.prot095539.

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Smit, Samuel J., Melané A. Vivier, and Philip R. Young. "Seeing the Forest through the (Phylogenetic) Trees: Functional Characterisation of Grapevine Terpene Synthase (VviTPS) Paralogues and Orthologues." Plants 10, no. 8 (July 26, 2021): 1520. http://dx.doi.org/10.3390/plants10081520.

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Gene families involved in specialised metabolism play a key role in a myriad of ecophysiological and biochemical functions. The Vitis vinifera sesquiterpene synthases represent the largest subfamily of grapevine terpene synthase (VviTPS) genes and are important volatile metabolites for wine flavour and aroma, as well as ecophysiological interactions. The functional characterisation of VviTPS genes is complicated by a reliance on a single reference genome that greatly underrepresents this large gene family, exacerbated by extensive duplications and paralogy. The recent release of multiple phased diploid grapevine genomes, as well as extensive whole-genome resequencing efforts, provide a wealth of new sequence information that can be utilised to overcome the limitations of the reference genome. A large cluster of sesquiterpene synthases, localised to chromosome 18, was explored by means of comparative sequence analyses using the publicly available grapevine reference genome, three PacBio phased diploid genomes and whole-genome resequencing data from multiple genotypes. Two genes, VviTPS04 and -10, were identified as putative paralogues and/or allelic variants. Subsequent gene isolation from multiple grapevine genotypes and characterisation by means of a heterologous in planta expression and volatile analysis resulted in the identification of genotype-specific structural variations and polymorphisms that impact the gene function. These results present novel insight into how grapevine domestication likely shaped the VviTPS landscape to result in genotype-specific functions.

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Abbas, Ata, Roshan Padmanabhan, Todd Romigh, and Charis Eng. "PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy." Human Molecular Genetics 28, no. 17 (April 17, 2019): 2826–34. http://dx.doi.org/10.1093/hmg/ddz112.

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Abstract Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation and premature termination. Pol II pausing is a phenomenon where Pol II complex pauses within 30–60 nucleotides after initiating the transcription. Negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF) contribute in the establishment of Pol II pausing, and positive transcription elongation factor b releases (P-TEFb) paused complex after phosphorylating DSIF that leads to dissociation of NELF. Pol II pausing is observed in most expressed genes across the metazoan. The precise role of Pol II pausing is not well understood; however, it’s required for integration of signals for gene regulation. In the present study, we investigated the role of phosphatase and tensin homolog (PTEN) in genome-wide transcriptional regulation using PTEN overexpression and PTEN knock-down models. Here we identify that PTEN alters the expression of hundreds of genes, and its restoration establishes genome-wide Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes Pol II occupancy across the genome and possibly impacts Pol II pause duration, release and elongation rate in order to enable precise gene regulation at the genome-wide scale. Our observations demonstrate an imperative role of PTEN in global transcriptional regulation that will provide a new direction to understand PTEN-associated pathologies and its management.

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Meunier, Loïc, Pierre Tocquin, Luc Cornet, Damien Sirjacobs, Valérie Leclère, Maude Pupin, Philippe Jacques, and Denis Baurain. "Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects." Bioinformatics 36, no. 15 (May 16, 2020): 4345–47. http://dx.doi.org/10.1093/bioinformatics/btaa517.

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Abstract Summary To support small and large-scale genome mining projects, we present Post-processing Analysis tooLbox for ANTIsmash Reports (Palantir), a dedicated software suite for handling and refining secondary metabolite biosynthetic gene cluster (BGC) data annotated with the popular antiSMASH pipeline. Palantir provides new functionalities building on NRPS/PKS predictions from antiSMASH, such as improved BGC annotation, module delineation and easy access to sub-sequences at different levels (cluster, gene, module and domain). Moreover, it can parse user-provided antiSMASH reports and reformat them for direct use or storage in a relational database. Availability and implementation Palantir is released both as a Perl API available on CPAN (https://metacpan.org/release/Bio-Palantir) and as a web application (http://palantir.uliege.be). As a practical use case, the web interface also features a database built from the mining of 1616 cyanobacterial genomes, of which 1488 were predicted to encode at least one BGC. Supplementary information Supplementary data are available at Bioinformatics online.

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Bouchemousse, Sarah, Laurent Falquet, and Heinz Müller-Schärer. "Genome Assembly of the Ragweed Leaf Beetle: A Step Forward to Better Predict Rapid Evolution of a Weed Biocontrol Agent to Environmental Novelties." Genome Biology and Evolution 12, no. 7 (May 19, 2020): 1167–73. http://dx.doi.org/10.1093/gbe/evaa102.

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Abstract Rapid evolution of weed biological control agents (BCAs) to new biotic and abiotic conditions is poorly understood and so far only little considered both in pre-release and post-release studies, despite potential major negative or positive implications for risks of nontargeted attacks or for colonizing yet unsuitable habitats, respectively. Provision of genetic resources, such as assembled and annotated genomes, is essential to assess potential adaptive processes by identifying underlying genetic mechanisms. Here, we provide the first sequenced genome of a phytophagous insect used as a BCA, that is, the leaf beetle Ophraella communa, a promising BCA of common ragweed, recently and accidentally introduced into Europe. A total 33.98 Gb of raw DNA sequences, representing ∼43-fold coverage, were obtained using the PacBio SMRT-Cell sequencing approach. Among the five different assemblers tested, the SMARTdenovo assembly displaying the best scores was then corrected with Illumina short reads. A final genome of 774 Mb containing 7,003 scaffolds was obtained. The reliability of the final assembly was then assessed by benchmarking universal single-copy orthologous genes (>96.0% of the 1,658 expected insect genes) and by remapping tests of Illumina short reads (average of 98.6 ± 0.7% without filtering). The number of protein-coding genes of 75,642, representing 82% of the published antennal transcriptome, and the phylogenetic analyses based on 825 orthologous genes placing O. communa in the monophyletic group of Chrysomelidae, confirm the relevance of our genome assembly. Overall, the genome provides a valuable resource for studying potential risks and benefits of this BCA facing environmental novelties.

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van Lieshout, Natascha, Ate van der Burgt, Michiel E. de Vries, Menno ter Maat, David Eickholt, Danny Esselink, Martijn P. W. van Kaauwen, et al. "Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)." G3: Genes|Genomes|Genetics 10, no. 10 (August 5, 2020): 3489–95. http://dx.doi.org/10.1534/g3.120.401550.

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With the rapid expansion of the application of genomics and sequencing in plant breeding, there is a constant drive for better reference genomes. In potato (Solanum tuberosum), the third largest food crop in the world, the related species S. phureja, designated “DM”, has been used as the most popular reference genome for the last 10 years. Here, we introduce the de novo sequenced genome of Solyntus as the next standard reference in potato genome studies. A true Solanum tuberosum made up of 116 contigs that is also highly homozygous, diploid, vigorous and self-compatible, Solyntus provides a more direct and contiguous reference then ever before available. It was constructed by sequencing with state-of-the-art long and short read technology and assembled with Canu. The 116 contigs were assembled into scaffolds to form each pseudochromosome, with three contigs to 17 contigs per chromosome. This assembly contains 93.7% of the single-copy gene orthologs from the Solanaceae set and has an N50 of 63.7 Mbp. The genome and related files can be found at https://www.plantbreeding.wur.nl/Solyntus/. With the release of this research line and its draft genome we anticipate many exciting developments in (diploid) potato research.

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dos Santos, G., A. J. Schroeder, J. L. Goodman, V. B. Strelets, M. A. Crosby, J. Thurmond, D. B. Emmert, and W. M. Gelbart. "FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations." Nucleic Acids Research 43, no. D1 (November 14, 2014): D690—D697. http://dx.doi.org/10.1093/nar/gku1099.

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Wang, Jian Ben, Daniel E. Nixon, and Michael A. McVoy. "Definition of the Minimal cis-Acting Sequences Necessary for Genome Maturation of the Herpesvirus Murine Cytomegalovirus." Journal of Virology 82, no. 5 (December 19, 2007): 2394–404. http://dx.doi.org/10.1128/jvi.00063-07.

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ABSTRACT Herpesvirus DNA replication proceeds via concatemeric replicative intermediates that are comprised of head-to-tail-linked genomes. Genome maturation is carried out by the terminase, a protein complex that mediates both insertion of concatemer DNA into capsids and its subsequent cleavage to release genomes within these capsids. This cleavage is sequence specific, but the governing cis-acting DNA sequences are only partially characterized. Two highly conserved motifs called pac1 and pac2 lie near the ends of herpesvirus genomes and are known to be critical for genome maturation. However, the potential importance of other sequences has not been fully investigated. We have undertaken to define all of the sequences necessary for efficient genome maturation for a herpesvirus by inserting ectopic cleavage sites into the murine cytomegalovirus genome and assessing their ability to mediate genome maturation. A combination of deletion and substitution mutations revealed that the minimal cleavage site is large (∼180 bp) and complex. Sequences distal of pac1 (relative to the point of cleavage) were dispensable, suggesting that pac1 may be the sole cis-acting element on this side of the cleavage site. In contrast, a region distal to pac2 up to 150 bp from the point of cleavage was essential. Scanning substitutions revealed that the pac2 side of the cleavage site is complex and may contain multiple cis-acting sequence elements in addition to pac2. These results should facilitate the identification of trans-acting factors that bind to these elements and the elucidation of their functions. Such information will be critical for understanding the molecular basis of this complex process.

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PEREZ, Jean-Claude. "WUHAN COVID-19 SYNTHETIC ORIGINS AND EVOLUTION." International Journal of Research -GRANTHAALAYAH 8, no. 2 (May 31, 2020): 285–324. http://dx.doi.org/10.29121/granthaalayah.v8.i2.2020.221.

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The main result of this updated release is the formal proof that 2019-nCoV coronavirus is partially a SYNTHETIC genome. We proof the CONCENTRATION in a small région of wuhan New genome (300bp) of 3 different régions from HIV1 ENVELOPPE gene and 3 others from HIV2 and SIV (ENV and POL RT). All this is remarkable and bears the mark of a desire for organization of a human nature: LOGIC, SYMETRIES. In this article, we demonstrate also that there is a kind of global human hosts adaptation strategy of SARS viruses as well as a strategy of global evolution of the genomes of the different strains of SARS which have emerged, mainly in China, between years 2003 first SARS genomes and the last 2019 COVID-19 Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome. This global strategy, this temporal link, is materialized in our demonstration by highlighting stationary numerical waves controlling the entire sequence of their genomes. Curiously, these digital waves characterizing the 9 SARS genomes studied here are characteristic whole numbers: the "Fibonacci numbers", omnipresent in the forms of Nature, and which our research for several decades has shown strong links with the proportions of nucleotides in DNA. Here we demonstrate that the complexity and fractal multiplicity of these Fibonacci numerical waves increases over the years of the emergence of new SARS strains. We suggest that this increase in the overall organization of the SARS genomes over the years reflects a better adaptation of SARS genomes to the human host. The question of a link with pathogenicity remains open. However, we believe that this overall strategy for the evolution of the SARS genomes ensures greater unity, consistency and integrity of the genome. Finally, we ask ourselves the question of a possible artificial origin of this genome, in particular because of the presence of fragments of HIV1, HIV2 and SIV retroviruses.

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Nováček, Jiří, Marta Šiborová, Martin Benešík, Roman Pantůček, Jiří Doškař, and Pavel Plevka. "Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate." Proceedings of the National Academy of Sciences 113, no. 33 (July 28, 2016): 9351–56. http://dx.doi.org/10.1073/pnas.1605883113.

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Bacteriophages from the family Myoviridae use double-layered contractile tails to infect bacteria. Contraction of the tail sheath enables the tail tube to penetrate through the bacterial cell wall and serve as a channel for the transport of the phage genome into the cytoplasm. However, the mechanisms controlling the tail contraction and genome release of phages with “double-layered” baseplates were unknown. We used cryo-electron microscopy to show that the binding of the Twort-like phage phi812 to the Staphylococcus aureus cell wall requires a 210° rotation of the heterohexameric receptor-binding and tripod protein complexes within its baseplate about an axis perpendicular to the sixfold axis of the tail. This rotation reorients the receptor-binding proteins to point away from the phage head, and also results in disruption of the interaction of the tripod proteins with the tail sheath, hence triggering its contraction. However, the tail sheath contraction of Myoviridae phages is not sufficient to induce genome ejection. We show that the end of the phi812 double-stranded DNA genome is bound to one protein subunit from a connector complex that also forms an interface between the phage head and tail. The tail sheath contraction induces conformational changes of the neck and connector that result in disruption of the DNA binding. The genome penetrates into the neck, but is stopped at a bottleneck before the tail tube. A subsequent structural change of the tail tube induced by its interaction with the S. aureus cell is required for the genome’s release.

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Lee, Jin-Ching, Hong-Hwa Chen, and Yu-Chan Chao. "Persistent Baculovirus Infection Results from Deletion of the Apoptotic Suppressor Gene p35." Journal of Virology 72, no. 11 (November 1, 1998): 9157–65. http://dx.doi.org/10.1128/jvi.72.11.9157-9165.1998.

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ABSTRACT Infection with the wild-type baculovirus Autographa californica multiple nuclear polyhedrosis virus (AcMNPV) results in complete death of Spodoptera frugiperda (Sf) cells. However, infection of Sf cells with AcMNPV carrying a mutation or deletion of the apoptotic suppressor gene p35 allowed the cloning of surviving Sf cells that harbored persistent viral genomes. Persistent infection established with the virus with p35 mutated or deleted was blocked by stable transfection of p35 in the host genome or by insertion of the inhibitor of apoptosis (iap) gene into the viral genome. These artificially established persistently virus-infected cells became resistant to subsequent viral challenge, and some of the cell lines carried large quantities of viral DNA capable of early gene expression. Continuous release of viral progenies was evident in some of the persistently virus-infected cells, and transfection of p35 further stimulated viral activation of the persistent cells, including the reactivation of viruses in those cell lines without original continuous virus release. These results have demonstrated the successful establishment of persistent baculovirus infections under laboratory conditions and that their establishment may provide a novel continuous, nonlytic baculovirus expression system in the future.

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Li, Cuiping, Dongmei Tian, Bixia Tang, Xiaonan Liu, Xufei Teng, Wenming Zhao, Zhang Zhang, and Shuhui Song. "Genome Variation Map: a worldwide collection of genome variations across multiple species." Nucleic Acids Research 49, no. D1 (November 10, 2020): D1186—D1191. http://dx.doi.org/10.1093/nar/gkaa1005.

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Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. It aims to collect and integrate genome variations for a wide range of species, accepts submissions of different variation types from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Compared with the previous version, particularly, a total of 22 species, 115 projects, 55 935 samples, 463 429 609 variants, 66 220 associations and 56 submissions (as of 7 September 2020) were newly added in the current version of GVM. In the current release, GVM houses a total of ∼960 million variants from 41 species, including 13 animals, 25 plants and 3 viruses. Moreover, it incorporates 64 819 individual genotypes and 260 393 manually curated high-quality genotype-to-phenotype associations. Since its inception, GVM has archived genomic variation data of 43 754 samples submitted by worldwide users and served >1 million data download requests. Collectively, as a core resource in the National Genomics Data Center, GVM provides valuable genome variations for a diversity of species and thus plays an important role in both functional genomics studies and molecular breeding.

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Tang, Haibao, Vivek Krishnakumar, Shelby Bidwell, Benjamin Rosen, Agnes Chan, Shiguo Zhou, Laurent Gentzbittel, et al. "An improved genome release (version Mt4.0) for the model legume Medicago truncatula." BMC Genomics 15, no. 1 (2014): 312. http://dx.doi.org/10.1186/1471-2164-15-312.

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Bell, J. William. "Our Genome in Common: Genomic Data Release Policies and the Academic Librarian." portal: Libraries and the Academy 3, no. 2 (2003): 293–306. http://dx.doi.org/10.1353/pla.2003.0025.

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Toropova, Katerina, Peter G. Stockley, and Neil A. Ranson. "Visualising a Viral RNA Genome Poised for Release from Its Receptor Complex." Journal of Molecular Biology 408, no. 3 (May 2011): 408–19. http://dx.doi.org/10.1016/j.jmb.2011.02.040.

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Howe, Kevin L., Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, et al. "Ensembl 2021." Nucleic Acids Research 49, no. D1 (November 2, 2020): D884—D891. http://dx.doi.org/10.1093/nar/gkaa942.

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Abstract The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.

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Tello-Ruiz, Marcela K., Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, et al. "Gramene 2021: harnessing the power of comparative genomics and pathways for plant research." Nucleic Acids Research 49, no. D1 (November 10, 2020): D1452—D1463. http://dx.doi.org/10.1093/nar/gkaa979.

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Abstract Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. The resource is committed to open access and reproducible science based on the FAIR data principles. Since the last NAR update, we made nine releases; doubled the genome portal's content; expanded curated genes, pathways and expression sets; and implemented the Domain Informational Vocabulary Extraction (DIVE) algorithm for extracting gene function information from publications. The current release, #63 (October 2020), hosts 93 reference genomes—over 3.9 million genes in 122 947 families with orthologous and paralogous classifications. Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of gene–gene interactions. Gramene integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused journals using DIVE. We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome.

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Hauck, Bernd, Wei Zhao, Katherine High, and Weidong Xiao. "Intracellular Viral Processing, Not Single-Stranded DNA Accumulation, Is Crucial for Recombinant Adeno-Associated Virus Transduction." Journal of Virology 78, no. 24 (December 15, 2004): 13678–86. http://dx.doi.org/10.1128/jvi.78.24.13678-13686.2004.

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ABSTRACT Adeno-associated virus (AAV) is a unique gene transfer vector which takes approximately 4 to 6 weeks to reach its expression plateau. The mechanism for this slow-rise expression profile was proposed to be inefficient second-strand DNA synthesis from the input single-stranded (ss) DNA viral genome. In order to clarify the status of ss AAV genomes, we generated AAV vectors labeled with bromodeoxyuridine (BrdU), a nucleotide analog that can be incorporated into the AAV genome and packaged into infectious virions. Since BrdU-DNA can be detected only by an anti-BrdU antibody when DNA is in an ss form, not in a double-stranded (ds) form, ss AAV genomes with BrdU can be readily tracked in situ. Although ss AAV DNA was abundant by Southern blot analysis, free ss AAV genomes were not detectable after AAV transduction by this new detection method. Further Southern blot analysis of viral DNA and virions revealed that ss AAV DNA was protected within virions. Extracted cellular fractions demonstrated that viral particles in host cells remained infectious. In addition, a significant amount of AAV genomes was degraded after AAV transduction. Therefore, we conclude that the amount of free ss DNA is not abundant during AAV transduction. AAV transduction is limited by the steps that affect AAV ss DNA release (i.e., uncoating) before second-strand DNA synthesis can occur. AAV ss DNA released from viral uncoating is either converted into ds DNA efficiently or degraded by cellular DNA repair mechanisms as damaged DNA. This study elucidates a mechanism that can be exploited to develop new strategies to improve AAV vector transduction efficiency.

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Cleemput, Sara, Wim Dumon, Vagner Fonseca, Wasim Abdool Karim, Marta Giovanetti, Luiz Carlos Alcantara, Koen Deforche, and Tulio de Oliveira. "Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes." Bioinformatics 36, no. 11 (February 28, 2020): 3552–55. http://dx.doi.org/10.1093/bioinformatics/btaa145.

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Abstract Summary Genome detective is a web-based, user-friendly software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent viruses that have caused large outbreaks, such as Zika and Yellow Fever Virus in Brazil. Here, we present the Genome Detective Coronavirus Typing Tool that can accurately identify the novel severe acute respiratory syndrome (SARS)-related coronavirus (SARS-CoV-2) sequences isolated in China and around the world. The tool can accept up to 2000 sequences per submission and the analysis of a new whole-genome sequence will take approximately 1 min. The tool has been tested and validated with hundreds of whole genomes from 10 coronavirus species, and correctly classified all of the SARS-related coronavirus (SARSr-CoV) and all of the available public data for SARS-CoV-2. The tool also allows tracking of new viral mutations as the outbreak expands globally, which may help to accelerate the development of novel diagnostics, drugs and vaccines to stop the COVID-19 disease. Availability and implementation https://www.genomedetective.com/app/typingtool/cov Contact koen@emweb.be or deoliveira@ukzn.ac.za Supplementary information Supplementary data are available at Bioinformatics online.

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Otto, Thomas D., Ulrike Böhme, Mandy Sanders, Adam J. Reid, Ellen I. Bruske, Craig W. Duffy, Pete C. Bull, et al. "Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres." Wellcome Open Research 3 (May 3, 2018): 52. http://dx.doi.org/10.12688/wellcomeopenres.14571.1.

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Background: Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal var genes clusters. Results: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates. We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa. Conclusions: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.

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Agirre, J., G. Goret, M. LeGoff, R. Sánchez-Eugenia, G. A. Marti, J. Navaza, D. M. A. Guérin, and E. Neumann. "Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly." Journal of General Virology 94, no. 5 (May 1, 2013): 1058–68. http://dx.doi.org/10.1099/vir.0.048553-0.

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Triatoma virus (TrV) is a member of the insect virus family Dicistroviridae and consists of a small, non-enveloped capsid that encloses its positive-sense ssRNA genome. Using cryo-transmission electron microscopy and three-dimensional reconstruction techniques combined with fitting of the available crystallographic models, this study analysed the capsids corresponding to mature and several RNA-empty TrV particles. After genome release, the resulting reconstruction of the empty capsids displayed no prominent conformational changes with respect to the full virion capsid. The results showed that RNA delivery led to empty capsids with an apparent overall intact protein shell and suggested that, in a subsequent step, empty capsids disassemble into small symmetrical particles. Contrary to what is observed upon genome release in mammalian picornaviruses, the empty TrV capsid maintained a protein shell thickness and size identical to that in full virions.

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Meiser, Johannes, Sergey Tumanov, Oliver Maddocks, Christiaan Fred Labuschagne, Dimitris Athineos, Niels Van Den Broek, Gillian M. Mackay, et al. "Serine one-carbon catabolism with formate overflow." Science Advances 2, no. 10 (October 2016): e1601273. http://dx.doi.org/10.1126/sciadv.1601273.

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Serine catabolism to glycine and a one-carbon unit has been linked to the anabolic requirements of proliferating mammalian cells. However, genome-scale modeling predicts a catabolic role with one-carbon release as formate. We experimentally prove that in cultured cancer cells and nontransformed fibroblasts, most of the serine-derived one-carbon units are released from cells as formate, and that formate release is dependent on mitochondrial reverse 10-CHO-THF synthetase activity. We also show that in cancer cells, formate release is coupled to mitochondrial complex I activity, whereas in nontransformed fibroblasts, it is partially insensitive to inhibition of complex I activity. We demonstrate that in mice, about 50% of plasma formate is derived from serine and that serine starvation or complex I inhibition reduces formate synthesis in vivo. These observations transform our understanding of one-carbon metabolism and have implications for the treatment of diabetes and cancer with complex I inhibitors.

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Pascoal, Túlio, Jérémie Decouchant, Antoine Boutet, and Paulo Esteves-Verissimo. "DyPS: Dynamic, Private and Secure GWAS." Proceedings on Privacy Enhancing Technologies 2021, no. 2 (January 29, 2021): 214–34. http://dx.doi.org/10.2478/popets-2021-0025.

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Abstract Genome-Wide Association Studies (GWAS) identify the genomic variations that are statistically associated with a particular phenotype (e.g., a disease). The confidence in GWAS results increases with the number of genomes analyzed, which encourages federated computations where biocenters would periodically share the genomes they have sequenced. However, for economical and legal reasons, this collaboration will only happen if biocenters cannot learn each others’ data. In addition, GWAS releases should not jeopardize the privacy of the individuals whose genomes are used. We introduce DyPS, a novel framework to conduct dynamic privacy-preserving federated GWAS. DyPS leverages a Trusted Execution Environment to secure dynamic GWAS computations. Moreover, DyPS uses a scaling mechanism to speed up the releases of GWAS results according to the evolving number of genomes used in the study, even if individuals retract their participation consent. Lastly, DyPS also tolerates up to all-but-one colluding biocenters without privacy leaks. We implemented and extensively evaluated DyPS through several scenarios involving more than 6 million simulated genomes and up to 35,000 real genomes. Our evaluation shows that DyPS updates test statistics with a reasonable additional request processing delay (11% longer) compared to an approach that would update them with minimal delay but would lead to 8% of the genomes not being protected. In addition, DyPS can result in the same amount of aggregate statistics as a static release (i.e., at the end of the study), but can produce up to 2.6 times more statistics information during earlier dynamic releases. Besides, we show that DyPS can support a larger number of genomes and SNP positions without any significant performance penalty.

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Bauer, D. W., D. Li, J. Huffman, F. L. Homa, K. Wilson, J. C. Leavitt, S. R. Casjens, J. Baines, and A. Evilevitch. "Exploring the Balance between DNA Pressure and Capsid Stability in Herpesviruses and Phages." Journal of Virology 89, no. 18 (July 1, 2015): 9288–98. http://dx.doi.org/10.1128/jvi.01172-15.

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ABSTRACTWe have recently shown in both herpesviruses and phages that packaged viral DNA creates a pressure of tens of atmospheres pushing against the interior capsid wall. For the first time, using differential scanning microcalorimetry, we directly measured the energy powering the release of pressurized DNA from the capsid. Furthermore, using a new calorimetric assay to accurately determine the temperature inducing DNA release, we found a direct influence of internal DNA pressure on the stability of the viral particle. We show that the balance of forces between the DNA pressure and capsid strength, required for DNA retention between rounds of infection, is conserved between evolutionarily diverse bacterial viruses (phages λ and P22), as well as a eukaryotic virus, human herpes simplex 1 (HSV-1). Our data also suggest that the portal vertex in these viruses is the weakest point in the overall capsid structure and presents the Achilles heel of the virus's stability. Comparison between these viral systems shows that viruses with higher DNA packing density (resulting in higher capsid pressure) have inherently stronger capsid structures, preventing spontaneous genome release prior to infection. This force balance is of key importance for viral survival and replication. Investigating the ways to disrupt this balance can lead to development of new mutation-resistant antivirals.IMPORTANCEA virus can generally be described as a nucleic acid genome contained within a protective protein shell, called the capsid. For many double-stranded DNA viruses, confinement of the large DNA molecule within the small protein capsid results in an energetically stressed DNA state exerting tens of atmospheres of pressures on the inner capsid wall. We show that stability of viral particles (which directly relates to infectivity) is strongly influenced by the state of the packaged genome. Using scanning calorimetry on a bacterial virus (phage λ) as an experimental model system, we investigated the thermodynamics of genome release associated with destabilizing the viral particle. Furthermore, we compare the influence of tight genome confinement on the relative stability for diverse bacterial and eukaryotic viruses. These comparisons reveal an evolutionarily conserved force balance between the capsid stability and the density of the packaged genome.

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Persinoti, Gabriela F., Douglas A. A. Paixão, Timothy D. H. Bugg, and Fabio M. Squina. "Genome Sequence of Lysinibacillus sphaericus, a Lignin-Degrading Bacterium Isolated from Municipal Solid Waste Soil." Genome Announcements 6, no. 18 (May 3, 2018): e00353-18. http://dx.doi.org/10.1128/genomea.00353-18.

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ABSTRACT We report here the draft genome sequence of Lysinibacillus sphaericus strain A1, a potential lignin-degrading bacterium isolated from municipal solid waste (MSW) soil and capable of enhancing gas release from lignocellulose-containing soil.

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TAILLEFER, EDDY, and JONATHAN MILLER. "EXHAUSTIVE COMPUTATION OF EXACT DUPLICATIONS VIA SUPER AND NON-NESTED LOCAL MAXIMAL REPEATS." Journal of Bioinformatics and Computational Biology 12, no. 01 (January 28, 2014): 1350018. http://dx.doi.org/10.1142/s0219720013500182.

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We propose and implement a method to obtain all duplicated sequences (repeats) from a chromosome or whole genome. Unlike existing approaches our method makes it possible to simultaneously identify and classify repeats into super, local, and non-nested local maximal repeats. Computation verification demonstrates that maximal repeats for a genome of several gigabases can be identified in a reasonable time, enabling us to identified these maximal repeats for any sequenced genome. The algorithm used for the identification relies on enhanced suffix array data structure to achieve practical space and time efficiency, to identify and classify the maximal repeats, and to perform further post-processing on the identified duplicated sequences. The simplicity and effectiveness of the implementation makes the method readily extendible to more sophisticated computations. Maxmers can be exhaustively accounted for in few minutes for genome sequences of dozen megabases in length and in less than a day or two for genome sequences of few gigabases in length. One application of duplicated sequence identification is to the study of duplicated sequence length distributions, which our found to exhibit for large lengths a persistent power-law behavior. Variation of estimated exponents of this power law are studied among different species and successive assembly release versions of the same species. This makes the characterization of the power-law regime of sequenced genomes via maximal repeats identification and classification, an important task for the derivation of models that would help us to elucidate sequence duplication and genome evolution.

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Levy, Hazel C., Mihnea Bostina, David J. Filman, and James M. Hogle. "Catching a Virus in the Act of RNA Release: a Novel Poliovirus Uncoating Intermediate Characterized by Cryo-Electron Microscopy." Journal of Virology 84, no. 9 (February 24, 2010): 4426–41. http://dx.doi.org/10.1128/jvi.02393-09.

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ABSTRACT Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes associated with the release of the RNA genome, we have used cryo-electron microscopy to characterize the structure of the 80S “empty” particles of poliovirus that are thought to represent the final product of the cell entry pathway. Using two-dimensional classification methods, we show that preparations of 80S particles contain at least two structures, which might represent snapshots from a continuous series of conformers. Using three-dimensional reconstruction methods, we have solved the structure of two distinct forms at subnanometric resolution, and we have built and refined pseudoatomic models into the reconstructions. The reconstructions and the derived models demonstrate that the two structural forms are both slightly expanded, resulting in partial disruption of interprotomer interfaces near their particle 2-fold axes, which may represent the site where RNA is released. The models demonstrate that each of the two 80S structures has undergone a unique set of movements of the capsid proteins, associated with rearrangement of flexible loops and amino-terminal extensions that participate in contacts between protomers, between pentamers, and with the viral RNA.

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Journal articles on the topic 'Genome release'

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