scholarly journals Role of Nucleotides Immediately Flanking the Transcription-Regulating Sequence Core in Coronavirus Subgenomic mRNA Synthesis

2005 ◽  
Vol 79 (4) ◽  
pp. 2506-2516 ◽  
Author(s):  
Isabel Sola ◽  
José L. Moreno ◽  
Sonia Zúñiga ◽  
Sara Alonso ◽  
Luis Enjuanes
Keyword(s):  
Reverse Genetics ◽  
The Body ◽  
Transmissible Gastroenteritis Virus ◽  
Template Switching ◽  
Regulation Of Transcription ◽  
Strand Transfer ◽  
Base Pairing ◽  
Transmissible Gastroenteritis ◽  
Definition Of ◽  
Duplex Formation

ABSTRACT The generation of subgenomic mRNAs in coronavirus involves a discontinuous mechanism of transcription by which the common leader sequence, derived from the genome 5′ terminus, is fused to the 5′ end of the mRNA coding sequence (body). Transcription-regulating sequences (TRSs) precede each gene and include a conserved core sequence (CS) surrounded by relatively variable sequences (5′ TRS and 3′ TRS). Regulation of transcription in coronaviruses has been studied by reverse-genetics analysis of the sequences immediately flanking a unique CS in the Transmissible gastroenteritis virus genome (CS-S2), located inside the S gene, that does not lead to detectable amounts of the corresponding mRNA, in spite of its canonical sequence. The transcriptional inactivity of CS-S2 was genome position independent. The presence of a canonical CS was not sufficient to drive transcription, but subgenomic synthesis requires a minimum base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) provided by the CS and its adjacent nucleotides. A good correlation was observed between the free energy of TRS-L and cTRS-B duplex formation and the levels of subgenomic mRNA S2, demonstrating that base pairing between the leader and body beyond the CS is a determinant regulation factor in coronavirus transcription. In TRS mutants with increasing complementarity between TRS-L and cTRS-B, a tendency to reach a plateau in ΔG values was observed, suggesting that a more precise definition of the TRS limits might be proposed, specifically that it consists of the central CS and around 4 nucleotides flanking 5′ and 3′ the CS. Sequences downstream of the CS exert a stronger influence on the template-switching decision according to a model of polymerase strand transfer and template switching during minus-strand synthesis.

scholarly journals Identification of a Coronavirus Transcription Enhancer

2008 ◽  
Vol 82 (8) ◽  
pp. 3882-3893 ◽  
Author(s):  
José L. Moreno ◽  
Sonia Zúñiga ◽  
Luis Enjuanes ◽  
Isabel Sola
Keyword(s):  
The Body ◽  
N Gene ◽  
Regulation Mechanism ◽  
Mrna Levels ◽  
Base Pairing ◽  
Long Distance ◽  
Complementary Sequence ◽  
Transmissible Gastroenteritis ◽  
Rna Interaction ◽  
Duplex Formation

ABSTRACT Coronavirus (CoV) transcription includes a discontinuous mechanism during the synthesis of sub-genome-length minus-strand RNAs leading to a collection of mRNAs in which the 5′ terminal leader sequence is fused to contiguous genome sequences. It has been previously shown that transcription-regulating sequences (TRSs) preceding each gene regulate transcription. Base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) in the nascent RNA is a determinant factor during CoV transcription. In fact, in transmissible gastroenteritis CoV, a good correlation has been observed between subgenomic mRNA (sg mRNA) levels and the free energy (ΔG) of TRS-L and cTRS-B duplex formation. The only exception was sg mRNA N, the most abundant sg mRNA during viral infection in spite of its minimum ΔG associated with duplex formation. We postulated that additional factors should regulate transcription of sg mRNA N. In this report, we have described a novel transcription regulation mechanism operating in CoV by which a 9-nucleotide (nt) sequence located 449 nt upstream of the N gene TRS core sequence (CS-N) interacts with a complementary sequence just upstream of CS-N, specifically increasing the accumulation of sg mRNA N. Alteration of this complementarity in mutant replicon genomes showed a correlation between the predicted stability of the base pairing between 9-nt sequences and the accumulation of sg mRNA N. This interaction is exclusively conserved in group 1a CoVs, the only CoV subgroup in which the N gene is not the most 3′ gene in the viral genome. This is the first time that a long-distance RNA-RNA interaction regulating transcriptional activity specifically enhancing the transcription of one gene has been described to occur in CoVs.

scholarly journals The N-Terminal Domain of Spike Protein Is Not the Enteric Tropism Determinant for Transmissible Gastroenteritis Virus in Piglets

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 313 ◽  
Author(s):  
Gang Wang ◽  
Rui Liang ◽  
Ziwei Liu ◽  
Zhou Shen ◽  
Jiale Shi ◽  
...  
Keyword(s):  
Recombinant Virus ◽  
Reverse Genetics ◽  
Clinical Signs ◽  
Etiologic Agent ◽  
Spike Protein ◽  
Transmissible Gastroenteritis Virus ◽  
Spike Gene ◽  
Terminal Domain ◽  
Gastroenteritis Virus ◽  
Transmissible Gastroenteritis

Transmissible gastroenteritis virus (TGEV) is the etiologic agent of transmissible gastroenteritis in pigs, and the N-terminal domain of TGEV spike protein is generally recognized as both the virulence determinant and enteric tropism determinant. Here, we assembled a full-length infectious cDNA clone of TGEV in a bacterial artificial chromosome. Using a novel approach, the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems efficiently and rapidly rescued another recombinant virus with a 224-amino-acid deletion in the N-terminal domain of the TGEV Spike gene (S_NTD224), which is analogous to the N-terminal domain of porcine respiratory coronavirus. S_NTD224 notably affected the TGEV growth kinetics in PK-15 cells but was not essential for recombinant virus survival. In animal experiments with 13 two-day-old piglets, the TGEV recombinant viruses with/without S_NTD224 deletion induced obvious clinical signs and mortality. Together, our results directly demonstrated that S_NTD224 of TGEV mildly influenced TGEV virulence but was not the enteric tropism determinant and provide new insights for the development of a new attenuated vaccine against TGEV. Importantly, the optimized reverse genetics platform used in this study will simplify the construction of mutant infectious clones and help accelerate progress in coronavirus research.

scholarly journals Sequence Motifs Involved in the Regulation of Discontinuous Coronavirus Subgenomic RNA Synthesis

2004 ◽  
Vol 78 (2) ◽  
pp. 980-994 ◽  
Author(s):  
Sonia Zúñiga ◽  
Isabel Sola ◽  
Sara Alonso ◽  
Luis Enjuanes
Keyword(s):  
Reverse Genetics ◽  
Virus Genome ◽  
Site Directed Mutagenesis ◽  
Template Switching ◽  
Sequence Motifs ◽  
Base Pairing ◽  
Subgenomic Rna ◽  
High Base ◽  
Template Switch ◽  
Conserved Core

ABSTRACT Coronavirus transcription leads to the synthesis of a nested set of mRNAs with a leader sequence derived from the 5′ end of the genome. The mRNAs are produced by a discontinuous transcription in which the leader is linked to the mRNA coding sequences. This process is regulated by transcription-regulating sequences (TRSs) preceding each mRNA, including a highly conserved core sequence (CS) with high identity to sequences present in the virus genome and at the 3′ end of the leader (TRS-L). The role of TRSs was analyzed by reverse genetics using a full-length infectious coronavirus cDNA and site-directed mutagenesis of the CS. The canonical CS-B was nonessential for the generation of subgenomic mRNAs (sgmRNAs), but its presence led to transcription levels at least 103-fold higher than those in its absence. The data obtained are compatible with a transcription mechanism including three steps: (i) formation of 5′-3′ complexes in the genomic RNA, (ii) base-pairing scanning of the nascent negative RNA strand by the TRS-L, and (iii) template switching during synthesis of the negative strand to complete the negative sgRNA. This template switch takes place after copying the CS sequence and was predicted in silico based on high base-pairing score between the nascent negative RNA strand and the TRS-L and minimum ΔG.

Derrida on Pornography: Putting (It) Up for Sale

Derrida Today ◽  
2013 ◽  
Vol 6 (1) ◽  
pp. 97-114 ◽  
Author(s):  
Christopher Morris
Keyword(s):  
Cultural Studies ◽  
English Translation ◽  
The Body ◽  
The Past ◽  
French Original ◽  
Definition Of ◽  
Critical Discourses ◽  
Academic Debate

Over the past thirty years, academic debate over pornography in the discourses of feminism and cultural studies has foundered on questions of the performative and of the word's definition. In the polylogue of Droit de regards, pornography is defined as la mise en vente that is taking place in the act of exegesis in progress. (Wills's idiomatic English translation includes an ‘it’ that is absent in the French original). The definition in Droit de regards alludes to the word's etymology (writing by or about prostitutes) but leaves the referent of the ‘sale’ suspended. Pornography as la mise en vente boldly restates the necessary iterability of the sign and anticipates two of Derrida's late arguments: that there is no ‘the’ body and that performatives may be powerless. Deriving a definition of pornography from a truncated etymology exemplifies the prosthesis of origin and challenges other critical discourses to explain how pornography can be understood as anything more than ‘putting (it) up for sale’.

scholarly journals Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses

2021 ◽  
pp. 104063872110021
Author(s):  
Giovani Trevisan ◽  
Leticia C. M. Linhares ◽  
Kent J. Schwartz ◽  
Eric R. Burrough ◽  
Edison de S. Magalhães ◽  
...  
Keyword(s):  
Seasonal Pattern ◽  
Laboratory Data ◽  
Information Management System ◽  
Transmissible Gastroenteritis Virus ◽  
Test Results ◽  
Diarrhea Virus ◽  
Oral Fluids ◽  
Transmissible Gastroenteritis ◽  
Technology Processes ◽  
Laboratory Information Management

Every day, thousands of samples from diverse populations of animals are submitted to veterinary diagnostic laboratories (VDLs) for testing. Each VDL has its own laboratory information management system (LIMS), with processes and procedures to capture submission information, perform laboratory tests, define the boundaries of test results (i.e., positive or negative), and report results, in addition to internal business and accounting applications. Enormous quantities of data are accumulated and stored within VDL LIMSs. There is a need for platforms that allow VDLs to exchange and share portions of laboratory data using standardized, reliable, and sustainable information technology processes. Here we report concepts and applications for standardization and aggregation of data from swine submissions to multiple VDLs to detect and monitor porcine enteric coronaviruses by RT-PCR. Oral fluids, feces, and fecal swabs were the specimens submitted most frequently for enteric coronavirus testing. Statistical algorithms were used successfully to scan and monitor the overall and state-specific percentage of positive submissions. Major findings revealed a consistently recurrent seasonal pattern, with the highest percentage of positive submissions detected during December–February for porcine epidemic diarrhea virus, porcine deltacoronavirus, and transmissible gastroenteritis virus (TGEV). After 2014, very few submissions tested positive for TGEV. Monitoring VDL data proactively has the potential to signal and alert stakeholders early of significant changes from expected detection. We demonstrate the importance of, and applications for, data organized and aggregated by using LOINC and SNOMED CTs, as well as the use of customized messaging to allow inter-VDL exchange of information.

scholarly journals Zur exakten Behandlung von kollektiven Rotationen Teil A: Theorie / On the Exact Treatment of Collective Rotations Part A: Theory

1973 ◽  
Vol 28 (2) ◽  
pp. 206-215
Author(s):  
Hanns Ruder
Keyword(s):  
Coordinate System ◽  
Perturbation Expansion ◽  
Rotational Energy ◽  
The Body ◽  
System A ◽  
N Body Problem ◽  
Definition Of ◽  
Fixed System ◽  
Body Fixed Coordinate System ◽  
Groundstate Energy

Basic in the treatment of collective rotations is the definition of a body-fixed coordinate system. A kinematical method is derived to obtain the Hamiltonian of a n-body problem for a given definition of the body-fixed system. From this exact Hamiltonian, a consequent perturbation expansion in terms of the total angular momentum leads to two exact expressions: one for the collective rotational energy which has to be added to the groundstate energy in this order of perturbation and a second one for the effective inertia tensor in the groundstate. The discussion of these results leads to two criteria how to define the best body-fixed coordinate system, namely a differential equation and a variational principle. The equivalence of both is shown.

scholarly journals Spiritual nursing care: A concept analysis

Curationis ◽  
2012 ◽  
Vol 35 (1) ◽  
Author(s):  
Lydia V. Monareng
Keyword(s):  
Nursing Care ◽  
Concept Analysis ◽  
Operational Definition ◽  
The Body ◽  
Empirical Literature ◽  
Spiritual Needs ◽  
Optimal Care ◽  
Health Crisis ◽  
Group Interviews ◽  
Definition Of

Although the concept ‘spiritual nursing care’ has its roots in the history of the nursing profession, many nurses in practice have difficulty integrating the concept into practice. There is an ongoing debate in the empirical literature about its definition, clarity and application in nursing practice. The study aimed to develop an operational definition of the concept and its application in clinical practice. A qualitative study was conducted to explore and describe how professional nurses render spiritual nursing care. A purposive sampling method was used to recruit the sample. Individual and focus group interviews were audio-taped and transcribed verbatim. Trustworthiness was ensured through strategies of truth value, applicability, consistency and neutrality. Data were analysed using the NUD*IST power version 4 software, constant comparison, open, axial and selective coding. Tech’s eight steps of analysis were also used, which led to the emergence of themes, categories and sub-categories. Concept analysis was conducted through a comprehensive literature review and as a result ‘caring presence’ was identified as the core variable from which all the other characteristics of spiritual nursing care arise. An operational definition of spiritual nursing care based on the findings was that humane care is demonstrated by showing caring presence, respect and concern for meeting the needs not only of the body and mind of patients, but also their spiritual needs of hope and meaning in the midst of health crisis, which demand equal attention for optimal care from both religious and nonreligious nurses.

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