scholarly journals Characterization of Mollivirus kamchatka, the first modern representative of the proposed Molliviridae family of giant viruses

2019 ◽  
Author(s):  
Eugene Christo-Foroux ◽  
Jean-Marie Alempic ◽  
Audrey Lartigue ◽  
Sebastien Santini ◽  
Karine Labadie ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Plant Diseases ◽  
Close Relative ◽  
Homologous Proteins ◽  
New Era ◽  
Environmental Virology ◽  
Double Stranded Dna ◽  
Giant Viruses ◽  
Incomplete Picture

AbstractMicrobes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing researches in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky river in Kamchatka. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleo-cytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6-μm in diameter) encloses a 648-kb GC-rich double stranded DNA genome coding for 480 proteins of which 61 % are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92 % identical residues in average) despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to the virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry.ImportanceVirology has long been viewed through the prism of human, cattle or plant diseases leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under light microscopy (i.e., >0.3μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenomes analyses have shown the presence of giant viruses in most terrestrial and aquatic environments including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year old arctic permafrost.

scholarly journals Characterization of Mollivirus kamchatka, the First Modern Representative of the Proposed Molliviridae Family of Giant Viruses

2020 ◽  
Vol 94 (8) ◽  
Author(s):  
Eugene Christo-Foroux ◽  
Jean-Marie Alempic ◽  
Audrey Lartigue ◽  
Sebastien Santini ◽  
Karine Labadie ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Plant Diseases ◽  
Close Relative ◽  
Homologous Proteins ◽  
New Era ◽  
Environmental Virology ◽  
Double Stranded Dna ◽  
Giant Viruses ◽  
Incomplete Picture

ABSTRACT Microbes trapped in permanently frozen paleosoils (permafrost) are the focus of increasing research in the context of global warming. Our previous investigations led to the discovery and reactivation of two Acanthamoeba-infecting giant viruses, Mollivirus sibericum and Pithovirus sibericum, from a 30,000-year old permafrost layer. While several modern pithovirus strains have since been isolated, no contemporary mollivirus relative was found. We now describe Mollivirus kamchatka, a close relative to M. sibericum, isolated from surface soil sampled on the bank of the Kronotsky River in Kamchatka, Russian Federation. This discovery confirms that molliviruses have not gone extinct and are at least present in a distant subarctic continental location. This modern isolate exhibits a nucleocytoplasmic replication cycle identical to that of M. sibericum. Its spherical particle (0.6 μm in diameter) encloses a 648-kb GC-rich double-stranded DNA genome coding for 480 proteins, of which 61% are unique to these two molliviruses. The 461 homologous proteins are highly conserved (92% identical residues, on average), despite the presumed stasis of M. sibericum for the last 30,000 years. Selection pressure analyses show that most of these proteins contribute to virus fitness. The comparison of these first two molliviruses clarify their evolutionary relationship with the pandoraviruses, supporting their provisional classification in a distinct family, the Molliviridae, pending the eventual discovery of intermediary missing links better demonstrating their common ancestry. IMPORTANCE Virology has long been viewed through the prism of human, cattle, or plant diseases, leading to a largely incomplete picture of the viral world. The serendipitous discovery of the first giant virus visible under a light microscope (i.e., >0.3 μm in diameter), mimivirus, opened a new era of environmental virology, now incorporating protozoan-infecting viruses. Planet-wide isolation studies and metagenome analyses have shown the presence of giant viruses in most terrestrial and aquatic environments, including upper Pleistocene frozen soils. Those systematic surveys have led authors to propose several new distinct families, including the Mimiviridae, Marseilleviridae, Faustoviridae, Pandoraviridae, and Pithoviridae. We now propose to introduce one additional family, the Molliviridae, following the description of M. kamchatka, the first modern relative of M. sibericum, previously isolated from 30,000-year-old arctic permafrost.

Optical Absorption Spectroscopy of DNA-Wrapped HiPco Carbon Nanotubes

2019 ◽  
Vol 943 ◽  
pp. 95-99
Author(s):  
Li Jun Wang ◽  
Kazuo Umemura
Keyword(s):  
Carbon Nanotubes ◽  
Aqueous Solution ◽  
Optical Absorption ◽  
Absorption Spectroscopy ◽  
Near Infrared ◽  
Nir Spectroscopy ◽  
Optical Characterization ◽  
Optical Absorption Spectroscopy ◽  
Double Stranded Dna

Optical absorption spectroscopy provides evidence for individually dispersed carbon nanotubes. A common method to disperse SWCNTs into aqueous solution is to sonicate the mixture in the presence of a double-stranded DNA (dsDNA). In this paper, optical characterization of dsDNA-wrapped HiPco carbon nanotubes (dsDNA-SWCNT) was carried out using near infrared (NIR) spectroscopy and photoluminescence (PL) experiments. The findings suggest that SWCNT dispersion is very good in the environment of DNA existing. Additionally, its dispersion depends on dsDNA concentration.

scholarly journals Characterization of a Novel Thermobifida fusca Bacteriophage P318

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1042
Author(s):  
Cheepudom ◽  
Lin ◽  
Lee ◽  
Meng
Keyword(s):  
Plant Cell Wall ◽  
Hydrolytic Enzymes ◽  
Thermobifida Fusca ◽  
Genome Replication ◽  
Putative Orfs ◽  
Base Pairs ◽  
Double Stranded Dna ◽  
Virion Morphogenesis ◽  
Genome Information

Thermobifida fusca is of biotechnological interest due to its ability to produce an array of plant cell wall hydrolytic enzymes. Nonetheless, only one T. fusca bacteriophage with genome information has been reported to date. This study was aimed at discovering more relevant bacteriophages to expand the existing knowledge of phage diversity for this host species. With this end in view, a thermostable T. fusca bacteriophage P318, which belongs to the Siphoviridae family, was isolated and characterized. P318 has a double-stranded DNA genome of 48,045 base pairs with 3′-extended COS ends, on which 52 putative ORFs are organized into clusters responsible for the order of genome replication, virion morphogenesis, and the regulation of the lytic/lysogenic cycle. In comparison with T. fusca and the previously discovered bacteriophage P1312, P318 has a much lower G+C content in its genome except at the region encompassing ORF42, which produced a protein with unknown function. P1312 and P318 share very few similarities in their genomes except for the regions encompassing ORF42 of P318 and ORF51 of P1312 that are homologous. Thus, acquisition of ORF42 by lateral gene transfer might be an important step in the evolution of P318.

Operating Temperature Analysis of LED with Cylindrical Cu Slug

2014 ◽  
Vol 487 ◽  
pp. 145-148 ◽  
Author(s):  
Rajendaran Vairavan ◽  
Zaliman Sauli ◽  
Vithyacharan Retnasamy
Keyword(s):  
Natural Convection ◽  
Operating Temperature ◽  
Simulation Method ◽  
Input Power ◽  
Junction Temperature ◽  
Temperature Analysis ◽  
Light Emitting ◽  
New Era ◽  
Lighting Systems

High power light emitting diodes is the new era of lighting due to momentous supremacy in terms of lighting efficacy over traditional lighting systems. The reliability of LED is dependent on its junction temperature. This study confers on the thermal and stress characterization of LED chip with copper cylindrical heat slug through simulation method. The simulation characterization was carried out with Ansys version 11 at ambient temperature of 25°C under natural convection condition. The LED package was powered with input powers of 0.1 W, 0.5 W and 1W .Results indicated that input power influences the junction temperature and stress of LED chip.

scholarly journals Analysis of Ribonucleotide 5′-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Gaofei Lu ◽  
Gregory R. Bluemling ◽  
Paul Collop ◽  
Michael Hager ◽  
Damien Kuiper ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Zika Virus ◽  
Nonstructural Protein ◽  
Rna Dependent Rna Polymerase ◽  
Antiviral Compounds ◽  
Double Stranded Dna ◽  
Virus Rna ◽  
Potential Inhibitors

ABSTRACT Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn2+ is required for enzymatic activity, while Mg2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5′-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2′-C-methyl- and 2′-C-ethynyl-substituted analog 5′-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.

scholarly journals Structural studies on M. tuberculosis O6-methylguanine methyltransferase

2014 ◽  
Vol 70 (a1) ◽  
pp. C832-C832
Author(s):  
Menico Rizzi ◽  
Riccardo Miggiano ◽  
Samarpita Lahiri ◽  
Giuseppe Perugino ◽  
Maria Ciaramella ◽  
...  
Keyword(s):  
Excision Repair ◽  
Single Step ◽  
Double Stranded Dna ◽  
Nucleotide Excision ◽  
Enzymatic Systems ◽  
Methylguanine Methyltransferase ◽  
Mutagenic Effects ◽  
Wild Type Form

Mycobacterium tuberculosis (MTB) is an extremely well adapted human pathogen capable to survive for decades inside the hostile environment represented by the host's infected macrophages despite exposure to multiple potential DNA-damaging stresses. In order to maintain a remarkable low level of genetic diversity, MTB deploys different strategies of DNA repair, including multi-enzymatic systems, such as Nucleotide Excision Repair, and single-step repair. In particular, to counteract the mutagenic effects of DNA alkylation, MTB performs the direct alkylated-base reversal by sacrificing one molecule of a DNA-protein alkyltransferase, such as O6-methylguanine methyltransferase (OGT; orf: Rv1316c). We present here the biochemical and structural characterization of recombinant mycobacterial OGT (MtOGT) in its wild-type form along with its mutated variants mimicking the ones occurring in relevant clinical strains (i.e. MtOGT-T15S and MtOGT-R37L). Our studies reveal that MtOGT-R37L is severely impaired in its activity as consequence of its ten-fold lower affinity for modified double-stranded DNA (dsDNA) (1). Further investigations on a new structure-based panel of OGT versions, designed to explore different molecular environment at position 37, allowed us a better understanding of the functional role of the MtOGT Arg37-bearing loop during catalysis. Moreover, we solved the crystal structure of MtOGT in covalent complex with modified dsDNA that reveals an unprecedented MtOGT::DNA architecture, suggesting that the MtOGT monomer performing the catalysis needs assisting unreacted subunits during cooperative DNA binding. This work is supported by European Community FP7 program SYSTEMTB (Health-F4-2010-241587)

scholarly journals Personalized Medicine in Cancer

2015 ◽  
Vol 32 (3) ◽  
pp. 153-163
Author(s):  
Md Mizanur Rahman
Keyword(s):  
Personalized Medicine ◽  
Single Gene ◽  
Biomedical Science ◽  
Practical Application ◽  
Molecular Alteration ◽  
New Era ◽  
Patients With Cancer ◽  
The Past ◽  
Molecular Aspects

Current and emerging biomedical science efforts are driven by determining how to improve clini-cal outcomes for patients. High-throughput tech-nology has revolutionized the area of transla-tional research, confirming the high complexity and heterogeneity of common diseases, partic-ularly cancer. Therefore, moving from ‘classic’ single-gene-based molecular investigation to molecular network research might result in dis-covering clinical implications faster and more efficiently .Molecular characterization of tumour cells enables refinement of classifications for many cancers and can sometimes guide treatment. Malignant diseases are no longer classified only by tumour site and histology but are separated into various homogenous molecular subtypes, distinguished by a presumed key molecular alteration. Therapies for patients with cancer have changed gradually over the past decade, moving away from the administration of broadly acting cytotoxic drugs towards the use of more-specific therapies that are targeted to each tumour. To facilitate this shift, tests need to be developed to identify those individuals who require therapy and those who are most likely to benefit from certain therapies. In particular, tests that predict the clinical outcome for patients on the basis of the genes expressed by their tumours are likely to increasingly affect patient management, heralding a new era of personalized medicine. In this review a brief discussion on definition and molecular aspects of personalized medicine and its practical application for the management of common solid cancers are highlighted.J Bangladesh Coll Phys Surg 2014; 32: 153-163

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

Characterization of two Salmonella newport bacteriophages

1979 ◽  
Vol 25 (9) ◽  
pp. 1063-1072 ◽  
Author(s):  
N. Moazamie ◽  
H.-W. Ackermann ◽  
M. R. V. Murthy
Keyword(s):  
Molecular Weight ◽  
Melting Point ◽  
Acid Hydrolysis ◽  
Phage Particle ◽  
Size Classes ◽  
Salmonella Newport ◽  
Double Stranded Dna

Salmonella newport phages 16–19 and 7–11 have very long heads and are members of two rare and so far little-known phage groups. Both produce various morphological aberrations. Preparations of phage 7–11 contain numerous polyheads and about 0.4% short heads belonging to nine size classes. In addition, one giant phage particle was observed. The head of phage 7–11 seems to be an icosahedron which became elongated by adding successive rows of subunits. Phages 16–19 and 7–11 have buoyant densities in CsCl of 1.43 and 1.48 g/mL and particle weights of 103 and 204 × 106 respectively. Both viruses contain double-stranded DNA, internal proteins, and sugars. Phage 16–19 contains 46.5% DNA of 35 × 106 molecular weight, and glucose. Phage 7–11 contains 47.5% DNA of 108 × 106 molecular weight, and mannose. Base compositions of phage and S. newport DNAs were determined from buoyant densities, melting point, and acid hydrolysis. Phage 16–19 contains 5.4% 5-methylcytosine.

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