The Effect of RNA Inactivator(s) Synthesized from Cu2+ and Hydroquinone on Adenine, Cytosine, Guanine, and Uracil

1984 ◽  
Vol 3 (2) ◽  
pp. 199-205
Author(s):  
Asaad N. Masoud ◽  
Moslih I. Al-Moslih ◽  
George R. Dubes
Keyword(s):  
Significant Loss ◽  
The Other ◽  
Viral Rna ◽  
Rna Genome ◽  
Base Moiety

The RNA inactivator(s) synthesized from Cu2+ and hydroquinone reacts with ail four free bases: adenine, cytosine, guanine, and uracil. After 1 day at 23°C, losses of these bases averaged 66%, 39%, 97%, and 25%, respectively. In the controls with neither Cu2+ nor hydroquinone and with either one without the other, there was no significant loss of any of the bases, except for the possibly significant loss (14%) of adenine after incubation with Cu2+ without hydroquinone. L-Histidine, a chelator of Cu2+, protected all four bases against the inactivation. The hypothesis that the chemical target(s) for the inactivator(s) in monoribonucleotides and in the naked viral RNA genome is the base moiety(ies) is discussed.

scholarly journals Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 565
Author(s):  
Mathieu Gand ◽  
Kevin Vanneste ◽  
Isabelle Thomas ◽  
Steven Van Gucht ◽  
Arnaud Capron ◽  
...  
Keyword(s):  
Performance Evaluation ◽  
Severe Acute Respiratory Syndrome ◽  
In Silico ◽  
The Other ◽  
Viral Rna ◽  
Potential Threat ◽  
The World

For 1 year now, the world is undergoing a coronavirus disease-2019 (COVID-19) pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method for COVID-19 diagnosis is the detection of viral RNA by RT-qPCR with a specific set of primers and probe. It is important to frequently evaluate the performance of these tests and this can be done first by an in silico approach. Previously, we reported some mismatches between the oligonucleotides of publicly available RT-qPCR assays and SARS-CoV-2 genomes collected from GISAID and NCBI, potentially impacting proper detection of the virus. In the present study, 11 primers and probe sets investigated during the first study were evaluated again with 84,305 new SARS-CoV-2 unique genomes collected between June 2020 and January 2021. The lower inclusivity of the China CDC assay targeting the gene N has continued to decrease with new mismatches detected, whereas the other evaluated assays kept their inclusivity above 99%. Additionally, some mutations specific to new SARS-CoV-2 variants of concern were found to be located in oligonucleotide annealing sites. This might impact the strategy to be considered for future SARS-CoV-2 testing. Given the potential threat of the new variants, it is crucial to assess if they can still be correctly targeted by the primers and probes of the RT-qPCR assays. Our study highlights that considering the evolution of the virus and the emergence of new variants, an in silico (re-)evaluation should be performed on a regular basis. Ideally, this should be done for all the RT-qPCR assays employed for SARS-CoV-2 detection, including also commercial tests, although the primer and probe sequences used in these kits are rarely disclosed, which impedes independent performance evaluation.

Disappearance of Meconium Pigment in Placental Specimens on Exposure to Light

2003 ◽  
Vol 127 (6) ◽  
pp. 711-714
Author(s):  
Jacquelyn L. Morhaime ◽  
Kay Park ◽  
Kurt Benirschke ◽  
Rebecca N. Baergen
Keyword(s):  
Neonatal Outcome ◽  
Light Exposure ◽  
Clinical Importance ◽  
Fetal Distress ◽  
Significant Loss ◽  
The Other ◽  
Serial Sections ◽  
Paired Samples ◽  
Weak Expression ◽  
Fluorescent Lighting

Abstract Context.—Meconium discharge has been associated with fetal distress and poor neonatal outcome; thus, its presence is of clinical importance. Objective.—Loss of meconium pigment in histologic sections from light exposure has been described. We sought to confirm this finding and to measure this loss quantitatively. Design.—Sections of umbilical cord, fetal membranes, and fetal surface from 11 grossly meconium-stained placentas were processed swiftly to minimize light exposure. Two serial sections from each block were cut and stained; one set was reviewed immediately, and the other was exposed to 8 hours of direct fluorescent lighting. Each site and exposure was scored for pigment intensity (0, no staining; 1, weak expression; and 2, moderate/strong expression) and number of meconium-laden macrophages per 10 high-power fields (HPF). Results were compared on the same specimen using the χ2 and the paired-samples t test. Results.—The maximum meconium macrophage count was 13.2/10 HPF in the unexposed sections versus 6.1/10 HPF in the exposed sections (P < .001). Unexposed sections varied from 1+ to 2+ intensity, while exposed sections were all 1+ or negative (P < .001). Conclusion.—Exposure to fluorescent laboratory lights for 8 hours resulted in a significant loss in the intensity and number of identifiable meconium macrophages in histologic sections. These findings have important implications in the handling of placental specimens, and we recommend that care be taken to minimize exposure to laboratory lights during processing.

scholarly journals Going beyond Integration: The Emerging Role of HIV-1 Integrase in Virion Morphogenesis

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1005 ◽  
Author(s):  
Jennifer L. Elliott ◽  
Sebla B. Kutluay
Keyword(s):  
Life Cycle ◽  
Viral Genome ◽  
Critical Role ◽  
Viral Rna ◽  
Target Cells ◽  
Host Chromosome ◽  
Virion Morphogenesis ◽  
Rna Genome ◽  
Hiv 1

The HIV-1 integrase enzyme (IN) plays a critical role in the viral life cycle by integrating the reverse-transcribed viral DNA into the host chromosome. This function of IN has been well studied, and the knowledge gained has informed the design of small molecule inhibitors that now form key components of antiretroviral therapy regimens. Recent discoveries unveiled that IN has an under-studied yet equally vital second function in human immunodeficiency virus type 1 (HIV-1) replication. This involves IN binding to the viral RNA genome in virions, which is necessary for proper virion maturation and morphogenesis. Inhibition of IN binding to the viral RNA genome results in mislocalization of the viral genome inside the virus particle, and its premature exposure and degradation in target cells. The roles of IN in integration and virion morphogenesis share a number of common elements, including interaction with viral nucleic acids and assembly of higher-order IN multimers. Herein we describe these two functions of IN within the context of the HIV-1 life cycle, how IN binding to the viral genome is coordinated by the major structural protein, Gag, and discuss the value of targeting the second role of IN in virion morphogenesis.

scholarly journals Roles of Phosphorylation of the Nucleocapsid Protein of Mumps Virus in Regulating Viral RNA Transcription and Replication

2015 ◽  
Vol 89 (14) ◽  
pp. 7338-7347 ◽  
Author(s):  
James Zengel ◽  
Adrian Pickar ◽  
Pei Xu ◽  
Alita Lin ◽  
Biao He
Keyword(s):  
Nucleocapsid Protein ◽  
Rna Synthesis ◽  
Critical Role ◽  
Phosphorylation Site ◽  
Mumps Virus ◽  
Viral Rna ◽  
Human Populations ◽  
Rna Genome ◽  
Major Phosphorylation Site ◽  
Transcription And Replication

ABSTRACTMumps virus (MuV) is a paramyxovirus with a negative-sense nonsegmented RNA genome. The viral RNA genome is encapsidated by the nucleocapsid protein (NP) to form the ribonucleoprotein (RNP), which serves as a template for transcription and replication. In this study, we investigated the roles of phosphorylation sites of NP in MuV RNA synthesis. Using radioactive labeling, we first demonstrated that NP was phosphorylated in MuV-infected cells. Using both liquid chromatography-mass spectrometry (LC-MS) andin silicomodeling, we identified nine putative phosphorylated residues within NP. We mutated these nine residues to alanine. Mutation of the serine residue at position 439 to alanine (S439A) was found to reduce the phosphorylation of NP in transfected cells by over 90%. The effects of these mutations on the MuV minigenome system were examined. The S439A mutant was found to have higher activity, four mutants had lower activity, and four mutants had similar activity compared to wild-type NP. MuV containing the S439A mutation had 90% reduced phosphorylation of NP and enhanced viral RNA synthesis and viral protein expression at early time points after infection, indicating that S439 is the major phosphorylation site of NP and its phosphorylation plays an important role in downregulating viral RNA synthesis.IMPORTANCEMumps virus (MuV), a paramyxovirus, is an important human pathogen that is reemerging in human populations. Nucleocapsid protein (NP) of MuV is essential for viral RNA synthesis. We have identified the major phosphorylation site of NP. We have found that phosphorylation of NP plays a critical role in regulating viral RNA synthesis. The work will lead to a better understanding of viral RNA synthesis and possible novel targets for antiviral drug development.

scholarly journals Real-time audio and visual display of the Coronavirus genome

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark D. Temple
Keyword(s):  
Real Time ◽  
Large Body ◽  
Visual Display ◽  
Viral Rna ◽  
Regulatory Sequences ◽  
Auditory Display ◽  
Rna Motifs ◽  
Rna Sequence ◽  
Rna Genome ◽  
Functional Rna

Abstract Background This paper describes a web based tool that uses a combination of sonification and an animated display to inquire into the SARS-CoV-2 genome. The audio data is generated in real time from a variety of RNA motifs that are known to be important in the functioning of RNA. Additionally, metadata relating to RNA translation and transcription has been used to shape the auditory and visual displays. Together these tools provide a unique approach to further understand the metabolism of the viral RNA genome. This audio provides a further means to represent the function of the RNA in addition to traditional written and visual approaches. Results Sonification of the SARS-CoV-2 genomic RNA sequence results in a complex auditory stream composed of up to 12 individual audio tracks. Each auditory motive is derived from the actual RNA sequence or from metadata. This approach has been used to represent transcription or translation of the viral RNA genome. The display highlights the real-time interaction of functional RNA elements. The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. Functional RNA motifs such as transcription regulatory sequences and stem loop regions have also been sonified. Using the tool, audio can be generated in real-time from either genomic or sub-genomic representations of the RNA. Given the large size of the viral genome, a collection of interactive buttons has been provided to navigate to regions of interest, such as cleavage regions in the polyprotein, untranslated regions or each gene. These tools are available through an internet browser and the user can interact with the data display in real time. Conclusion The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Furthermore, the tool has been used as an algorithmic based audio generator. These audio tracks can be listened to by the general community without reference to the visual display to encourage further inquiry into the science.

Lighting up the Native Viral RNA Genome with a Fluorogenic Probe for the Live-Cell Visualization of Virus Infection

2019 ◽  
Vol 141 (13) ◽  
pp. 5182-5191 ◽  
Author(s):  
Xingyu Luo ◽  
Binbin Xue ◽  
Guangfu Feng ◽  
Jiaheng Zhang ◽  
Bin Lin ◽  
...  
Keyword(s):  
Virus Infection ◽  
Live Cell ◽  
Viral Rna ◽  
Fluorogenic Probe ◽  
Rna Genome

Study of the genetic organisation of a plant viral RNA genome by in vitro expression of a full-length DNA copy.

1984 ◽  
Vol 3 (13) ◽  
pp. 3049-3053 ◽  
Author(s):  
P. Vos ◽  
J. Verver ◽  
P. van Wezenbeek ◽  
A. van Kammen ◽  
R. Goldbach
Keyword(s):  
Full Length ◽  
Viral Rna ◽  
In Vitro Expression ◽  
Genetic Organisation ◽  
Rna Genome

Survival of Ostrinia nubilalis (Hübner) After Exposure to Bacillus thuringiensis Berliner Encapsulated in Flour Matrices2

1994 ◽  
Vol 29 (4) ◽  
pp. 496-508 ◽  
Author(s):  
Michael R. McGuire ◽  
Robert L. Gillespie ◽  
Baruch S. Shasha
Keyword(s):  
Bacillus Thuringiensis ◽  
Ostrinia Nubilalis ◽  
European Corn Borer ◽  
Significant Loss ◽  
The Other ◽  
Field Site ◽  
Corn Flour ◽  
Corn Borer ◽  
Natural Infestation ◽  
Corn Plants

Two types of pregelatinized corn flour were used to produce granules containing Bacillus thuringiensis Berliner subsp. kurstaki and various additives for control of the European corn borer, Ostrinia nubilalis (Hübner), in the whorl of corn plants. Laboratory-reared larvae were applied to corn whorls in the greenhouse and field, and a high natural infestation occurred at one field site (Champaign). In the greenhouse and at all three field sites, five of these formulations were just as effective as Dipel 10G, a commercially available B. thuringiensis product, for control of European corn borer larvae. In all greenhouse studies and at one of the three field sites (Champaign), the dose of B. thuringiensis could be reduced by as much as 75% when a phagostimulant was added to flour granules without significant loss of corn borer control. The phagostimulant dose response was not observed at the other two field sites in which larval infestations were relatively low. Flour type had no significant effect on European corn borer control under greenhouse and field conditions. Greenhouse evaluations provided results significantly similar to results from two of the field sites indicating the usefulness of the technique. The data presented highlight the versatility and potential for using novel formulation techniques for enhancing the efficacy of B. thuringiensis.

scholarly journals Homologous Crossovers among Molecules of Brome Mosaic Bromovirus RNA1 or RNA2 Segments In Vivo

2005 ◽  
Vol 79 (9) ◽  
pp. 5732-5742 ◽  
Author(s):  
Anna Urbanowicz ◽  
Magdalena Alejska ◽  
Piotr Formanowicz ◽  
Jacek Błażewicz ◽  
Marek Figlerowicz ◽  
...  
Keyword(s):  
Hot Spot ◽  
Rna Replication ◽  
Viral Rna ◽  
Noncoding Regions ◽  
Genome Variability ◽  
Coding Regions ◽  
Virus Life Cycle ◽  
Brome Mosaic Bromovirus ◽  
Rna Genome

ABSTRACT Previously we demonstrated frequent homologous crossovers among molecules of the RNA3 segment in the tripartite brome mosaic bromovirus (BMV) RNA genome (A. Bruyere, M. Wantroba, S. Flasinski, A. Dzianott, and J. J. Bujarski, J. Virol. 74:4214-4219, 2000). To further our knowledge about mechanisms of viral RNA genome variability, in this paper we have studied homologous recombination in BMV RNA1 and RNA2 components during infection. We have found that basal RNA-RNA crossovers could occur within coding regions of both RNAs, although recombination frequencies slightly varied at different RNA sections. In all cases, the frequencies were much lower than the rate observed for the intercistronic recombination hot spot in BMV RNA3. Probability calculations accounted for at least one homologous crossover per RNA molecule per replication cycle. In addition, we have demonstrated an efficient repair of mutations within the conserved 3′ and 5′ noncoding regions, most likely due to error-prone BMV RNA replication. Overall, our data verify that homologous crossovers are common events a during virus life cycle, and we discuss their importance for viral RNA genetics.

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