scholarly journals Nidovirus transcription: how to make sense…?

2006 ◽  
Vol 87 (6) ◽  
pp. 1403-1421 ◽  
Author(s):  
Alexander O. Pasternak ◽  
Willy J. M. Spaan ◽  
Eric J. Snijder

Many positive-stranded RNA viruses use subgenomic mRNAs to express part of their genetic information. To produce structural and accessory proteins, members of the order Nidovirales (corona-, toro-, arteri- and roniviruses) generate a 3′ co-terminal nested set of at least three and often seven to nine mRNAs. Coronavirus and arterivirus subgenomic transcripts are not only 3′ co-terminal but also contain a common 5′ leader sequence, which is derived from the genomic 5′ end. Their synthesis involves a process of discontinuous RNA synthesis that resembles similarity-assisted RNA recombination. Most models proposed over the past 25 years assume co-transcriptional fusion of subgenomic RNA leader and body sequences, but there has been controversy over the question of whether this occurs during plus- or minus-strand synthesis. In the latter model, which has now gained considerable support, subgenomic mRNA synthesis takes place from a complementary set of subgenome-size minus-strand RNAs, produced by discontinuous minus-strand synthesis. Sense–antisense base-pairing interactions between short conserved sequences play a key regulatory role in this process. In view of the presumed common ancestry of nidoviruses, the recent finding that ronivirus and torovirus mRNAs do not contain a common 5′ leader sequence is surprising. Apparently, major mechanistic differences must exist between nidoviruses, which raises questions about the functions of the common leader sequence and nidovirus transcriptase proteins and the evolution of nidovirus transcription. In this review, nidovirus transcription mechanisms are compared, the experimental systems used are critically assessed and, in particular, the impact of recently developed reverse genetic systems is discussed.

2020 ◽  
Author(s):  
Aaron R. D’souza ◽  
Amanda Buckingham ◽  
Fanny Salasc ◽  
Carin Ingemarsdotter ◽  
Gennaro Iaconis ◽  
...  

ABSTRACTRecently published transcriptomic data of the SARS-CoV-2 coronavirus show that there is a large variation in the frequency and steady state levels of subgenomic mRNA sequences. This variation is derived from discontinuous subgenomic RNA synthesis where the polymerase switches template from a 3’ proximal genome body sequence to a 5’ untranslated leader sequence. This leads to a fusion between the common 5’ leader sequence and a 3’ proximal body sequence in the RNA product. This process revolves around a common core sequence (CS) that is present at both the template sites that make up the fusion junction. Base-pairing between the leader CS and the nascent complementary minus strand body CS, and flanking regions (together called the transcription regulating sequence, TRS) is vital for this template switching event. However, various factors can influence the site of template switching within the same TRS duplex. Here, we model the duplexes formed between the leader and complementary body TRS regions, hypothesising the role of the stability of the TRS duplex in determining the major sites of template switching for the most abundant mRNAs. We indicate that the stability of secondary structures and the speed of transcription play key roles in determining the probability of template switching in the production of subgenomic RNAs.


2019 ◽  
pp. 33-41
Author(s):  
V. L. Harutyunyan ◽  
S. V. Dokholyan ◽  
A. R. Makaryan

The presented study discusses the issues of applying the Common Customs Tariff (CCT) rates of the Eurasian Economic Union (EAEU) on rough diamonds and the impact thereof on the exports of stones cut and polished inArmeniaand then exported toRussia.Aim. The study aims to identify the possible strategies Armenian diamond cutting and polishing companies could adopt as a response to the application of the CCT rates on rough diamonds and how it would affect exports to various destinations, namely to Russia.Tasks. The authors analyze the current state of the gems and jewelry sector and substantiate the need to either integrate it into the jewelry manufacturing sector or to apply various strategies to facilitate exports to either Russia or other destinations in the medium term in response to the application of the CCT rates.Methods. This study uses general scientific methods of cognition, including analytical and methodological approaches and elements of forecasting. Possible strategies the Armenian diamond cutting and polishing companies could adopt in the medium term in response to the application of the EAEU CCT rates are determined using the analytical research method, forecasts in the context of the developments in the Armenian gem processing and jewelry market and global trends, statistical data on the imports and exports of cut and polished gems and jewelry for 2014–2018 published by the UN Comtrade Statistics.Results. Statistics on the exports of processed diamonds from 2014 to 2018 highlights the issue associated with the loss of competitiveness suffered by Armenian companies (mainly in comparison with Indian diamond cutters). The major global trends in the diamond cutting and polishing business indicate that it could be virtually impossible for Armenian cutters and polishers to compete with Indian companies in the medium term if they do not comes to investing in new technology to achieve operational efficiency. For these companies, it is important not to lose the Russian market due to an increase in the tariff rate and concentrate on the processing of gems that are larger than 1 carat. Another strategy to avoid an increase in the customs tariff rates would depend on the Armenian government’s ability to negotiate with Russia in respect of direct imports of diamond stones from Russian manufactures. Two other options for Armenian cutters involve focusing on cutting and polishing of rubies, sapphires, emeralds, etc. or integrating into the jewelry sector either by being the primary supplier or by considering this business as a channel to sell processed diamond stones by setting up their own jewelry manufacturing companies.Conclusions. With CCT going into effect in January 2021 and India’s dominant role in the diamond cutting and polishing business, Armenia needs to carefully consider all of the strategies the Armenian companies could adopt, as discussed above. As a member state of the EAEU, Armenia freely exports to Russia, however, further exports to Russia would depend on Armenia’s ability to ensure that cost-effective operations are in place, or to concentrate on the processing of precious gems rather than diamonds, or to switch to the manufacturing of jewelry items as a major export item.Practical Implication. The findings of this study could be of interest to the Ministry of Economy of the Republic of Armenia and Business Armenia that could be used in elaborating the strategy for the development of Armenian gems and jewelry sector of the economy.


2020 ◽  
Vol 26 (4) ◽  
pp. 358-365
Author(s):  
V. L. Harutyunyan ◽  
S. V. Dokholyan ◽  
A. R. Makaryan

1985 ◽  
Vol 17 (6-7) ◽  
pp. 1187-1198 ◽  
Author(s):  
G. Mance ◽  
A. R. O'Donnell

This paper discusses the derivation of environmental quality standards for coastal waters and the difficulties of using such standards for controlling industrial discharges. Attention is focused on the common List II substances, copper, chromium, lead, nickel, zinc and arsenic - and their effects on marine life. The adequacy of existing toxicity data is discussed and it is concluded that long exposure tests are required to provide information on sublethal effects. Such data are currently limited. It is also important that consideration be given to the effects that reducing salinities and increasing temperatures have in increasing the toxicity of these substances. The complexity of interpreting the results of laboratory toxicity data to coastal waters is discussed with reference to a study of the impact of an industrial discharge.


2020 ◽  
Vol 12 (17) ◽  
pp. 17374-17379
Author(s):  
W.G.D. Chathuranga ◽  
K. Kariyawasam ◽  
Anslem De Silva ◽  
W.A.Priyanka P. De Silva

We investigated the impact of dipteran predators on eggs in foam nests of the Common Hour-glass Tree Frog Polypedates cruciger Blyth, 1852 (Anura: Rhacophoridae) in central Sri Lanka.  Foam nests (n=24) of P. cruciger were examined at their natural breeding habitats and infected (n=8) and uninfected spawns (n=16) were identified.  Emerging tadpoles were collected in a water container hung under each spawn and the average number of tadpoles (N) hatched from infected spawns (N=0) was compared with that of uninfected spawns (N=354 ± 67).  Three severely infected spawns were brought to the laboratory and the fly larvae were reared until they metamorphosed to adults.  Morphological and molecular identification of the flies confirmed them as belonging to Caiusa testacea Senior-White, 1923 of the family Calliphoridae.  The infected spawns were completely destroyed and an estimated average of 400 P. cruciger eggs per spawn were lost.  The results revealed a high impact of Caiusa testacea on egg and embryo mortality of P. cruciger.


Author(s):  
Thomas A Lewis

Abstract As a discipline, the academic study of religion is strikingly fragmented, with little engagement or shared criteria of excellence across subfields. Although important recent developments have expanded the traditions and peoples studied as well as the methods used, the current extent of fragmentation limits the impact of this diversification and pluralization. At a moment when the global pandemic is catalyzing profound pressures on our universities and disciplines, this fragmentation makes it difficult to articulate to the public, to non-religious studies colleagues, and to students why the study of religion matters. We therefore too often fall back on platitudes. I argue for a revitalized methods and theories conversation that connects us even as it bears our arguments and disagreements about what we do and how. Courses in methods and theories in the study of religion represent the most viable basis we have for bringing the academic study of religion into the common conversation or argument that constitutes a discipline without sacrificing our pluralism.


2021 ◽  
Vol 10 (6) ◽  
pp. 1239
Author(s):  
Alexandru Cojocaru ◽  
Emilia Burada ◽  
Adrian-Tudor Bălșeanu ◽  
Alexandru-Florian Deftu ◽  
Bogdan Cătălin ◽  
...  

As the average age and life expectancy increases, the incidence of both acute and chronic central nervous system (CNS) pathologies will increase. Understanding mechanisms underlying neuroinflammation as the common feature of any neurodegenerative pathology, we can exploit the pharmacology of cell specific ion channels to improve the outcome of many CNS diseases. As the main cellular player of neuroinflammation, microglia play a central role in this process. Although microglia are considered non-excitable cells, they express a variety of ion channels under both physiological and pathological conditions that seem to be involved in a plethora of cellular processes. Here, we discuss the impact of modulating microglia voltage-gated, potential transient receptor, chloride and proton channels on microglial proliferation, migration, and phagocytosis in neurodegenerative diseases.


2021 ◽  
Vol 10 (8) ◽  
pp. 1740
Author(s):  
Marion Bareille ◽  
Michaël Hardy ◽  
Jonathan Douxfils ◽  
Stéphanie Roullet ◽  
Dominique Lasne ◽  
...  

Infection by SARS-CoV-2 is associated with a high risk of thrombosis. The laboratory documentation of hypercoagulability and impaired fibrinolysis remains a challenge. Our aim was to assess the potential usefulness of viscoelastometric testing (VET) to predict thrombotic events in COVID-19 patients according to the literature. We also (i) analyzed the impact of anticoagulation and the methods used to neutralize heparin, (ii) analyzed whether maximal clot mechanical strength brings more information than Clauss fibrinogen, and (iii) critically scrutinized the diagnosis of hypofibrinolysis. We performed a systematic search in PubMed and Scopus databases until December 31st, 2020. VET methods and parameters, and patients’ features and outcomes were extracted. VET was performed for 1063 patients (893 intensive care unit (ICU) and 170 non-ICU, 44 studies). There was extensive heterogeneity concerning study design, VET device used (ROTEM, TEG, Quantra and ClotPro) and reagents (with non-systematic use of heparin neutralization), timing of assay, and definition of hypercoagulable state. Notably, only 4 out of 25 studies using ROTEM reported data with heparinase (HEPTEM). The common findings were increased clot mechanical strength mainly due to excessive fibrinogen component and impaired to absent fibrinolysis, more conspicuous in the presence of an added plasminogen activator. Only 4 studies out of the 16 that addressed the point found an association of VETs with thrombotic events. So-called functional fibrinogen assessed by VETs showed a variable correlation with Clauss fibrinogen. Abnormal VET pattern, often evidenced despite standard prophylactic anticoagulation, tended to normalize after increased dosing. VET studies reported heterogeneity, and small sample sizes do not support an association between the poorly defined prothrombotic phenotype of COVID-19 and thrombotic events.


2010 ◽  
Vol 11 (6) ◽  
pp. 656-670
Author(s):  
Kate Sutherland

Professor Joseph Weiler will soon stand trial for criminal libel in France for refusing to remove a book review from a website associated with an academic journal for which he serves as editor. His case has disturbing implications for all those who write, edit, and publish critical scholarly work. In this article, I explore those implications for Canadian scholars at home and as members of a global scholarly community. I assess the likelihood of success of a similar complaint under Canadian defamation law, and I consider the impact of libel chill and libel tourism. I conclude that although the defendant in such a case would have a good chance of prevailing under Canadian law through the defense of fair comment, a threat to academic freedom remains that requires action on the part of individuals and institutions committed to its preservation and enhancement.


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