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[Molecular diagnosis and phylogenetic analysis of the first MERS case in Turkey].

Mikrobiyoloji bulteni

Bayrakdar F, Altaş AB, Korukluoğlu G, Topal S.
PMID: 26313282
Mikrobiyol Bul. 2015 Jul;49(3):414-22. doi: 10.5578/mb.9247.

Coronaviruses (CoV) are enveloped, spherical, single-stranded positive-sense RNA viruses causing mainly respiratory and intestinal infections in animals and humans. Until recently five types of human coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, HCoV-229E, SARS-CoV) have been known, however a novel CoV has...

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Bayrakdar F, Altaş AB, Korukluoğlu G, et al. Türkiye'de tespit edilen ilk MERS olgusunun moleküler tanısı ve fi logenetik analizi. [Molecular diagnosis and phylogenetic analysis of the first MERS case in Turkey]. Mikrobiyol Bul. 2015;49(3):414-22doi: 10.5578/mb.9247.
Bayrakdar, F., Altaş, A. B., Korukluoğlu, G., & Topal, S. (2015). Türkiye'de tespit edilen ilk MERS olgusunun moleküler tanısı ve fi logenetik analizi. [Molecular diagnosis and phylogenetic analysis of the first MERS case in Turkey]. Mikrobiyoloji bulteni, 49(3), 414-22. https://doi.org/10.5578/mb.9247
Bayrakdar, Fatma, et al. "Türkiye'de tespit edilen ilk MERS olgusunun moleküler tanısı ve fi logenetik analizi." [Molecular diagnosis and phylogenetic analysis of the first MERS case in Turkey]. Mikrobiyoloji bulteni vol. 49,3 (2015): 414-22. doi: https://doi.org/10.5578/mb.9247
Bayrakdar F, Altaş AB, Korukluoğlu G, Topal S. Türkiye'de tespit edilen ilk MERS olgusunun moleküler tanısı ve fi logenetik analizi. [Molecular diagnosis and phylogenetic analysis of the first MERS case in Turkey]. Mikrobiyol Bul. 2015 Jul;49(3):414-22. doi: 10.5578/mb.9247. Turkish. PMID: 26313282.
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The role of the priming loop in .

Nature microbiology

Te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E.
PMID: 27274864
Nat Microbiol. 2016 May;1(5). doi: 10.1038/nmicrobiol.2016.29. Epub 2016 Mar 21.

RNA-dependent RNA polymerases (RdRps) are used by RNA viruses to replicate and transcribe their RNA genomes1. They adopt a closed, right-handed fold with conserved subdomains called palm, fingers, and thumb1,2. Conserved RdRp motifs A-F coordinate the viral RNA template,...

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Te Velthuis AJ, Robb NC, Kapanidis AN, et al. The role of the priming loop in . Nat Microbiol. 2016;1(5)doi: 10.1038/nmicrobiol.2016.29.
Te Velthuis, A. J., Robb, N. C., Kapanidis, A. N., & Fodor, E. (2016). The role of the priming loop in . Nature microbiology, 1(5), . https://doi.org/10.1038/nmicrobiol.2016.29
Te Velthuis, Aartjan J W, et al. "The role of the priming loop in ." Nature microbiology vol. 1,5 (2016). doi: https://doi.org/10.1038/nmicrobiol.2016.29
Te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E. The role of the priming loop in . Nat Microbiol. 2016 May;1(5). doi: 10.1038/nmicrobiol.2016.29. Epub 2016 Mar 21. PMID: 27274864; PMCID: PMC4888940.
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Reprint of "Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs.

Virus research

Laske T, Heldt FS, Hoffmann H, Frensing T, Reichl U.
PMID: 27208847
Virus Res. 2016 Jun 15;218:86-95. doi: 10.1016/j.virusres.2016.05.009.

Like many other viral pathogens, influenza A viruses can form defective interfering particles (DIPs). These particles carry a large internal deletion in at least one of their genome segments. Thus, their replication depends on the co-infection of cells by...

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Laske T, Heldt FS, Hoffmann H, et al. Reprint of "Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs. Virus Res. 2016;218:86-95doi: 10.1016/j.virusres.2016.05.009.
Laske, T., Heldt, F. S., Hoffmann, H., Frensing, T., & Reichl, U. (2016). Reprint of "Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs. Virus research, 21886-95. https://doi.org/10.1016/j.virusres.2016.05.009
Laske, Tanja, et al. "Reprint of "Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs." Virus research vol. 218 (2016): 86-95. doi: https://doi.org/10.1016/j.virusres.2016.05.009
Laske T, Heldt FS, Hoffmann H, Frensing T, Reichl U. Reprint of "Modeling the intracellular replication of influenza A virus in the presence of defective interfering RNAs. Virus Res. 2016 Jun 15;218:86-95. doi: 10.1016/j.virusres.2016.05.009. PMID: 27208847.
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Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane.

Drug metabolism and disposition: the biological fate of chemicals

Zhuo X, Cantone JL, Wang Y, Leet JE, Drexler DM, Yeung KS, Huang XS, Eastman KJ, Parcella KE, Mosure KW, Soars MG, Kadow JF, Johnson BM.
PMID: 26961241
Drug Metab Dispos. 2016 Aug;44(8):1332-1340. doi: 10.1124/dmd.115.069062. Epub 2016 Mar 09.

During a medicinal chemistry campaign to identify inhibitors of the hepatitis C virus nonstructural protein 5B (RNA-dependent RNA polymerase), a bicyclo[1.1.1]pentane was introduced into the chemical scaffold to improve metabolic stability. The inhibitors bearing this feature, 5-(3-(bicyclo[1.1.1]pentan-1-ylcarbamoyl)-4-fluorophenyl)-2-(4-fluorophenyl)-N-methyl-6-(3,3,3-trifluoropropyl)furo[2,3-b]pyridine-3-carboxamide (1) and...

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Zhuo X, Cantone JL, Wang Y, et al. Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane. Drug Metab Dispos. 2016;44(8):1332-1340doi: 10.1124/dmd.115.069062.
Zhuo, X., Cantone, J. L., Wang, Y., Leet, J. E., Drexler, D. M., Yeung, K. S., Huang, X. S., Eastman, K. J., Parcella, K. E., Mosure, K. W., Soars, M. G., Kadow, J. F., & Johnson, B. M. (2016). Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane. Drug metabolism and disposition: the biological fate of chemicals, 44(8), 1332-1340. https://doi.org/10.1124/dmd.115.069062
Zhuo, Xiaoliang, et al. "Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane." Drug metabolism and disposition: the biological fate of chemicals vol. 44,8 (2016): 1332-1340. doi: https://doi.org/10.1124/dmd.115.069062
Zhuo X, Cantone JL, Wang Y, Leet JE, Drexler DM, Yeung KS, Huang XS, Eastman KJ, Parcella KE, Mosure KW, Soars MG, Kadow JF, Johnson BM. Phosphocholine conjugation: an unexpected in vivo conjugation pathway associated with hepatitis c ns5b inhibitors featuring a bicyclo[1.1.1]pentane. Drug Metab Dispos. 2016 Aug;44(8):1332-1340. doi: 10.1124/dmd.115.069062. Epub 2016 Mar 09. PMID: 26961241.
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Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants.

Advances in bioinformatics

Prabahar A, Swaminathan S, Loganathan A, Jegadeesan R.
PMID: 26557141
Adv Bioinformatics. 2015;2015:198214. doi: 10.1155/2015/198214. Epub 2015 Oct 18.

Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. TMV enters the host cell and produces the capping enzyme RNA polymerase. The viral genome replicates...

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Prabahar A, Swaminathan S, Loganathan A, et al. Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants. Adv Bioinformatics. 2015;2015:198214doi: 10.1155/2015/198214.
Prabahar, A., Swaminathan, S., Loganathan, A., & Jegadeesan, R. (2015). Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants. Advances in bioinformatics, 2015198214. https://doi.org/10.1155/2015/198214
Prabahar, Archana, et al. "Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants." Advances in bioinformatics vol. 2015 (2015): 198214. doi: https://doi.org/10.1155/2015/198214
Prabahar A, Swaminathan S, Loganathan A, Jegadeesan R. Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants. Adv Bioinformatics. 2015;2015:198214. doi: 10.1155/2015/198214. Epub 2015 Oct 18. PMID: 26557141; PMCID: PMC4628775.
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6K2-induced vesicles can move cell to cell during turnip mosaic virus infection.

Frontiers in microbiology

Grangeon R, Jiang J, Wan J, Agbeci M, Zheng H, Laliberté JF.
PMID: 24409170
Front Microbiol. 2013 Dec 04;4:351. doi: 10.3389/fmicb.2013.00351. eCollection 2013.

To successfully infect plants, viruses replicate in an initially infected cell and then move to neighboring cells through plasmodesmata (PDs). However, the nature of the viral entity that crosses over the cell barrier into non-infected ones is not clear....

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Grangeon R, Jiang J, Wan J, et al. 6K2-induced vesicles can move cell to cell during turnip mosaic virus infection. Front Microbiol. 2013;4:351doi: 10.3389/fmicb.2013.00351.
Grangeon, R., Jiang, J., Wan, J., Agbeci, M., Zheng, H., & Laliberté, J. F. (2013). 6K2-induced vesicles can move cell to cell during turnip mosaic virus infection. Frontiers in microbiology, 4351. https://doi.org/10.3389/fmicb.2013.00351
Grangeon, Romain, et al. "6K2-induced vesicles can move cell to cell during turnip mosaic virus infection." Frontiers in microbiology vol. 4 (2013): 351. doi: https://doi.org/10.3389/fmicb.2013.00351
Grangeon R, Jiang J, Wan J, Agbeci M, Zheng H, Laliberté JF. 6K2-induced vesicles can move cell to cell during turnip mosaic virus infection. Front Microbiol. 2013 Dec 04;4:351. doi: 10.3389/fmicb.2013.00351. eCollection 2013. PMID: 24409170; PMCID: PMC3885808.
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Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase.

PeerJ

Ma MY, Lan XR, Niu DK.
PMID: 27547574
PeerJ. 2016 Jul 26;4:e2272. doi: 10.7717/peerj.2272. eCollection 2016.

The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent...

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Ma MY, Lan XR, Niu DK. Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ. 2016;4:e2272doi: 10.7717/peerj.2272.
Ma, M. Y., Lan, X. R., & Niu, D. K. (2016). Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ, 4e2272. https://doi.org/10.7717/peerj.2272
Ma, Ming-Yue, et al. "Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase." PeerJ vol. 4 (2016): e2272. doi: https://doi.org/10.7717/peerj.2272
Ma MY, Lan XR, Niu DK. Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ. 2016 Jul 26;4:e2272. doi: 10.7717/peerj.2272. eCollection 2016. PMID: 27547574; PMCID: PMC4974935.
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Structure-guided design of small-molecule therapeutics against RSV disease.

Expert opinion on drug discovery

Cox R, Plemper RK.
PMID: 27046051
Expert Opin Drug Discov. 2016;11(6):543-556. doi: 10.1517/17460441.2016.1174212. Epub 2016 Apr 21.

INTRODUCTION: In the United States, respiratory syncytial virus (RSV) is responsible for the majority of infant hospitalizations resulting from viral infections, as well as a leading source of pneumonia and bronchiolitis in young children and the elderly. In the...

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Cox R, Plemper RK. Structure-guided design of small-molecule therapeutics against RSV disease. Expert Opin Drug Discov. 2016;11(6):543-556doi: 10.1517/17460441.2016.1174212.
Cox, R., & Plemper, R. K. (2016). Structure-guided design of small-molecule therapeutics against RSV disease. Expert opinion on drug discovery, 11(6), 543-556. https://doi.org/10.1517/17460441.2016.1174212
Cox, Robert, and Plemper, Richard K. "Structure-guided design of small-molecule therapeutics against RSV disease." Expert opinion on drug discovery vol. 11,6 (2016): 543-556. doi: https://doi.org/10.1517/17460441.2016.1174212
Cox R, Plemper RK. Structure-guided design of small-molecule therapeutics against RSV disease. Expert Opin Drug Discov. 2016;11(6):543-556. doi: 10.1517/17460441.2016.1174212. Epub 2016 Apr 21. PMID: 27046051; PMCID: PMC5074927.
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Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence.

Frontiers in microbiology

Momose F, Morikawa Y.
PMID: 27014212
Front Microbiol. 2016 Mar 08;7:288. doi: 10.3389/fmicb.2016.00288. eCollection 2016.

The RNA-dependent RNA polymerase (RdRp) of influenza A virus consists of three subunits, PB2, PB1, and PA, and catalyses both viral RNA genome replication and transcription. Cotransfection of four monocistronic expression vectors for these subunits and nucleoprotein with an...

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Momose F, Morikawa Y. Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence. Front Microbiol. 2016;7:288doi: 10.3389/fmicb.2016.00288.
Momose, F., & Morikawa, Y. (2016). Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence. Frontiers in microbiology, 7288. https://doi.org/10.3389/fmicb.2016.00288
Momose, Fumitaka, and Morikawa, Yuko. "Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence." Frontiers in microbiology vol. 7 (2016): 288. doi: https://doi.org/10.3389/fmicb.2016.00288
Momose F, Morikawa Y. Polycistronic Expression of the Influenza A Virus RNA-Dependent RNA Polymerase by Using the Thosea asigna Virus 2A-Like Self-Processing Sequence. Front Microbiol. 2016 Mar 08;7:288. doi: 10.3389/fmicb.2016.00288. eCollection 2016. PMID: 27014212; PMCID: PMC4782009.
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Correction to Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase.

Journal of medicinal chemistry

Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS.
PMID: 28339203
J Med Chem. 2017 Apr 13;60(7):3219. doi: 10.1021/acs.jmedchem.7b00427. Epub 2017 Mar 24.

No abstract available.

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Sofia MJ, Chang W, Furman PA, et al. Correction to Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase. J Med Chem. 2017;60(7):3219doi: 10.1021/acs.jmedchem.7b00427.
Sofia, M. J., Chang, W., Furman, P. A., Mosley, R. T., & Ross, B. S. (2017). Correction to Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase. Journal of medicinal chemistry, 60(7), 3219. https://doi.org/10.1021/acs.jmedchem.7b00427
Sofia, Michael J, et al. "Correction to Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase." Journal of medicinal chemistry vol. 60,7 (2017): 3219. doi: https://doi.org/10.1021/acs.jmedchem.7b00427
Sofia MJ, Chang W, Furman PA, Mosley RT, Ross BS. Correction to Nucleoside, Nucleotide, and Non-Nucleoside Inhibitors of Hepatitis C Virus NS5B RNA-Dependent RNA-Polymerase. J Med Chem. 2017 Apr 13;60(7):3219. doi: 10.1021/acs.jmedchem.7b00427. Epub 2017 Mar 24. PMID: 28339203.
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Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach.

In silico pharmacology

Oany AR, Sharmin T, Chowdhury AS, Jyoti TP, Hasan MA.
PMID: 26820892
In Silico Pharmacol. 2015 Dec;3(1):7. doi: 10.1186/s40203-015-0011-4. Epub 2015 Aug 08.

PURPOSE: Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has...

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Oany AR, Sharmin T, Chowdhury AS, et al. Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach. In Silico Pharmacol. 2015;3(1):7doi: 10.1186/s40203-015-0011-4.
Oany, A. R., Sharmin, T., Chowdhury, A. S., Jyoti, T. P., & Hasan, M. A. (2015). Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach. In silico pharmacology, 3(1), 7. https://doi.org/10.1186/s40203-015-0011-4
Oany, Arafat Rahman, et al. "Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach." In silico pharmacology vol. 3,1 (2015): 7. doi: https://doi.org/10.1186/s40203-015-0011-4
Oany AR, Sharmin T, Chowdhury AS, Jyoti TP, Hasan MA. Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach. In Silico Pharmacol. 2015 Dec;3(1):7. doi: 10.1186/s40203-015-0011-4. Epub 2015 Aug 08. PMID: 26820892; PMCID: PMC4529428.
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Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element.

Pharmaceuticals (Basel, Switzerland)

Marton S, Berzal-Herranz B, Garmendia E, Cueto FJ, Berzal-Herranz A.
PMID: 24288042
Pharmaceuticals (Basel). 2011 Dec 28;5(1):49-60. doi: 10.3390/ph5010049.

Hepatitis C virus (HCV) replication is dependent on the existence of several highly conserved functional genomic RNA domains. The cis-acting replication element (CRE), located within the 3' end of the NS5B coding region of the HCV genome, has been...

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Marton S, Berzal-Herranz B, Garmendia E, et al. Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element. Pharmaceuticals (Basel). 2011;5(1):49-60doi: 10.3390/ph5010049.
Marton, S., Berzal-Herranz, B., Garmendia, E., Cueto, F. J., & Berzal-Herranz, A. (2011). Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element. Pharmaceuticals (Basel, Switzerland), 5(1), 49-60. https://doi.org/10.3390/ph5010049
Marton, Soledad, et al. "Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element." Pharmaceuticals (Basel, Switzerland) vol. 5,1 (2011): 49-60. doi: https://doi.org/10.3390/ph5010049
Marton S, Berzal-Herranz B, Garmendia E, Cueto FJ, Berzal-Herranz A. Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element. Pharmaceuticals (Basel). 2011 Dec 28;5(1):49-60. doi: 10.3390/ph5010049. PMID: 24288042; PMCID: PMC3763624.
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