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Article ; Online: RNAcanvas: interactive drawing and exploration of nucleic acid structures.

Johnson, Philip Z / Simon, Anne E

2023 Volume 51, Issue W1, Page(s) W501–W508

Abstract: ... as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features ...

Abstract	Two-dimensional drawing of nucleic acid structures, particularly RNA structures, is fundamental to the communication of nucleic acids research. However, manually drawing structures is laborious and infeasible for structures thousands of nucleotides long. RNAcanvas automatically arranges residues into strictly shaped stems and loops while providing robust interactive editing features, including click-and-drag layout adjustment. Drawn elements are highly customizable in a point-and-click manner, including colours, fonts, size and shading, flexible numbering, and outlining of bases. Tertiary interactions can be drawn as draggable, curved lines. Leontis-Westhof notation for depicting non-canonical base-pairs is fully supported, as well as text labels for structural features (e.g. hairpins). RNAcanvas also has many unique features and performance optimizations for large structures that cannot be correctly predicted and require manual refinement based on the researcher's own analyses and expertise. To this end, RNAcanvas has point-and-click structure editing with real-time highlighting of complementary sequences and motif search functionality, novel features that greatly aid in the identification of putative long-range tertiary interactions, de novo analysis of local structures, and phylogenetic comparisons. For ease in producing publication quality figures, drawings can be exported in both SVG and PowerPoint formats. URL: https://rnacanvas.app.
MeSH term(s)	Software ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry ; Base Pairing
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-07-01
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad302
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Article ; Online: Identification of Novel 5' and 3' Translation Enhancers in Umbravirus-Like Coat Protein-Deficient RNA Replicons.

Liu, Jingyuan / Simon, Anne E

Journal of virology

2022 Volume 96, Issue 7, Page(s) e0173621

Abstract: Translation of plant plus-strand RNA viral genomes that lack a 5' cap frequently requires the use of cap-independent translation enhancers (CITEs) located in or near the 3' untranslated region (UTR). 3'CITEs are grouped based on secondary structure and ... ...

Abstract	Translation of plant plus-strand RNA viral genomes that lack a 5' cap frequently requires the use of cap-independent translation enhancers (CITEs) located in or near the 3' untranslated region (UTR). 3'CITEs are grouped based on secondary structure and ability to interact with different translation initiation factors or ribosomal subunits, which assemble a complex at the 3' end that is nearly always transferred to the 5' end via a long-distance kissing-loop interaction between sequences in the 3'CITE and 5' hairpins. We report here the identification of a novel 3'CITE in coat protein-deficient RNA replicons that are related to umbraviruses. Umbra-like associated RNAs (ulaRNAs), such as citrus yellow vein-associated virus (CYVaV), are a new type of subviral RNA that do not encode movement proteins, coat proteins, or silencing suppressors but can independently replicate using their encoded RNA-dependent RNA polymerase. An extended hairpin structure containing multiple internal loops in the 3' UTR of CYVaV is strongly conserved in the most closely related ulaRNAs and structurally resembles an I-shaped structure (ISS) 3'CITE. However, unlike ISS, the CYVaV structure binds to eIF4G and no long-distance interaction is discernible between the CYVaV ISS-like structure and sequences at or near the 5' end. We also report that the ∼30-nucleotide (nt) 5' terminal hairpin of CYVaV and related ulaRNAs can enhance translation of reporter constructs when associated with either the CYVaV 3'CITE or the 3'CITEs of umbravirus pea enation mosaic virus (PEMV2) and even independent of a 3'CITE. These findings introduce a new type of 3'CITE and provide the first information on translation of ulaRNAs.
MeSH term(s)	3' Untranslated Regions/genetics ; Enhancer Elements, Genetic/genetics ; Eukaryotic Initiation Factor-4G/metabolism ; Protein Biosynthesis ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; Replicon/genetics ; Tombusviridae/genetics
Chemical Substances	3' Untranslated Regions ; Eukaryotic Initiation Factor-4G ; RNA, Viral ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01736-21
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Article ; Online: White matter fibre density in the brain's inhibitory control network is associated with falling in low activity older adults.

Simon, Colin / Bolton, David A E / Meaney, James F / Kenny, Rose Anne / Simon, Vivienne A / De Looze, Céline / Knight, Silvin / Ruddy, Kathy L

The European journal of neuroscience

2024

Abstract: Recent research has indicated that the relationship between age-related cognitive decline and falling may be mediated by the individual's capacity to quickly cancel or inhibit a motor response. This longitudinal investigation demonstrates that higher ... ...

Abstract	Recent research has indicated that the relationship between age-related cognitive decline and falling may be mediated by the individual's capacity to quickly cancel or inhibit a motor response. This longitudinal investigation demonstrates that higher white matter fibre density in the motor inhibition network paired with low physical activity was associated with falling in elderly participants. We measured the density of white matter fibre tracts connecting key nodes in the inhibitory control network in a large sample (n = 414) of older adults. We modelled their self-reported frequency of falling over a 4-year period with white matter fibre density in pathways corresponding to the direct and hyperdirect cortical-subcortical loops implicated in the inhibitory control network. Only connectivity between right inferior frontal gyrus and right subthalamic nucleus was associated with falling as measured cross-sectionally. The connectivity was not, however, predictive of future falling when measured 2 and 4 years later. Higher white matter fibre density was associated with falling, but only in combination with low levels of physical activity. No such relationship existed for selected control brain regions that are not implicated in the inhibitory control network. Albeit statistically robust, the direction of this effect was counterintuitive (more dense connectivity associated with falling) and warrants further longitudinal investigation into whether white matter fibre density changes over time in a manner correlated with falling, and mediated by physical activity.
Language	English
Publishing date	2024-04-18
Publishing country	France
Document type	Journal Article
ZDB-ID	645180-9
ISSN	1460-9568 ; 0953-816X
ISSN (online)	1460-9568
ISSN	0953-816X
DOI	10.1111/ejn.16327
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Article ; Online: Oleofoams: The impact of formulating air-in-oil systems from a lipid oxidation perspective.

Ribourg-Birault, Lucie / Meynier, Anne / Vergé, Simon / Sallan, Emeline / Kermarrec, Alice / Falourd, Xavier / Berton-Carabin, Claire / Fameau, Anne-Laure

Current research in food science

2024 Volume 8, Page(s) 100690

Abstract: ... without incorporation of air bubbles (i.e., forming an oleogel), and was somewhat modulated depending on the type ...

Abstract	Air-in-oil foams, or oleofoams, have a great potential for food applications as they can at least partially replace animal or hydrogenated fats, without compromising on textural properties. Yet, there are some challenges to tackle before they can largely be implemented for real-life applications. One of those is the lack of data regarding their oxidative stability. This is an important point to consider, as although using oils rich in polyunsaturated fatty acids (PUFAs) is highly desirable from a nutritional perspective, these fatty acids are particularly prone to oxidation, which leads to major degradations of food quality. This work thus aimed to investigate the oxidative stability of oleofoams prepared with omega-3 PUFA-rich vegetable oils (rapeseed or flaxseed oil) and various types of high melting point lipid-based oleogelators (stearic acid, glyceryl monostearate and stearyl alcohol) when incubated at room temperature. The physical structure and stability of the oleofoams was monitored by various techniques (visual observations, microscopy, DSC, NMR, SAXS and WAXS). Lipid oxidation was assessed by combined measurements of primary (conjugated diene hydroperoxides) and secondary (thiobarbituric acid reactive substances - TBARS) products. We found that the oxidative stability of oleofoams was higher compared to that of the corresponding bulk oil. This protective effect was also found when the oil was simply mixed with the oleogelator without incorporation of air bubbles (i.e., forming an oleogel), and was somewhat modulated depending on the type of oleogelator. These results suggest that oleogelators and the structural changes that they induce limit the cascaded propagation of lipid oxidation in oil-continuous matrices, which is promising in the perspective of future applications.
Language	English
Publishing date	2024-01-29
Publishing country	Netherlands
Document type	Journal Article
ISSN	2665-9271
ISSN (online)	2665-9271
DOI	10.1016/j.crfs.2024.100690
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Article ; Online: Conserved Structure Associated with Different 3'CITEs Is Important for Translation of Umbraviruses.

Bera, Sayanta / Ilyas, Muhammad / Mikkelsen, Anna A / Simon, Anne E

Viruses

2023 Volume 15, Issue 3

Abstract: The cap-independent translation of plus-strand RNA plant viruses frequently depends on 3' structures to attract translation initiation factors that bind ribosomal subunits or bind directly to ribosomes. Umbraviruses are excellent models for studying 3' ... ...

Abstract	The cap-independent translation of plus-strand RNA plant viruses frequently depends on 3' structures to attract translation initiation factors that bind ribosomal subunits or bind directly to ribosomes. Umbraviruses are excellent models for studying 3' cap-independent translation enhancers (3'CITEs), as umbraviruses can have different 3'CITEs in the central region of their lengthy 3'UTRs, and most also have a particular 3'CITE (the T-shaped structure or 3'TSS) near their 3' ends. We discovered a novel hairpin just upstream of the centrally located (known or putative) 3'CITEs in all 14 umbraviruses. These CITE-associated structures (CASs) have conserved sequences in their apical loops and at the stem base and adjacent positions. In 11 umbraviruses, CASs are preceded by two small hairpins joined by a putative kissing loop interaction (KL). Converting the conserved 6-nt apical loop to a GNRA tetraloop in opium poppy mosaic virus (OPMV) and pea enation mosaic virus 2 (PEMV2) enhanced translation of genomic (g)RNA, but not subgenomic (sg)RNA reporter constructs, and significantly repressed virus accumulation in
MeSH term(s)	3' Untranslated Regions ; Nucleic Acid Conformation ; Protein Biosynthesis ; Ribosomes/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Tombusviridae/genetics ; Tombusviridae/metabolism ; Subgenomic RNA/genetics
Chemical Substances	3' Untranslated Regions ; RNA, Viral ; Subgenomic RNA
Language	English
Publishing date	2023-02-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15030638
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Article ; Online: Correction to: Universal, School-Based Mental Health Program Implemented among Racially and Ethnically Diverse Youth Yields Equitable Outcomes: Building Resilience for Healthy Kids.

Chandrasekhar, Jessica L / Bowen, Anne E / Heberlein, Erin / Pyle, Emily / Studts, Christina R / Simon, Stacey L / Shomaker, Lauren / Kaar, Jill L

Community mental health journal

2023 Volume 59, Issue 6, Page(s) 1118

Language	English
Publishing date	2023-02-22
Publishing country	United States
Document type	Published Erratum
ZDB-ID	215855-3
ISSN	1573-2789 ; 0010-3853
ISSN (online)	1573-2789
ISSN	0010-3853
DOI	10.1007/s10597-023-01114-0
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Article ; Online: Teleworking, Parenting Stress, and the Health of Mothers and Fathers.

Parker, John James / Garfield, Craig F / Simon, Clarissa D / Bendelow, Anne / Heffernan, Marie E / Davis, Matthew M / Kan, Kristin

JAMA network open

2023 Volume 6, Issue 11, Page(s) e2341844

MeSH term(s)	Female ; Humans ; Male ; Parenting ; Teleworking ; Mothers ; Fathers
Language	English
Publishing date	2023-11-01
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2023.41844
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Article ; Online: Targeting of viral RNAs by Upf1-mediated RNA decay pathways.

May, Jared P / Simon, Anne E

Current opinion in virology

2020 Volume 47, Page(s) 1–8

Abstract: Viral RNAs are susceptible to co-translational RNA decay pathways mediated by the RNA helicase Upstream frameshift 1 (Upf1). Upf1 is a key component in nonsense-mediated decay (NMD), Staufen1-mediated mRNA decay (SMD), and structure-mediated RNA decay ( ... ...

Abstract	Viral RNAs are susceptible to co-translational RNA decay pathways mediated by the RNA helicase Upstream frameshift 1 (Upf1). Upf1 is a key component in nonsense-mediated decay (NMD), Staufen1-mediated mRNA decay (SMD), and structure-mediated RNA decay (SRD) pathways, among others. Diverse families of viruses have features that predispose them to Upf1 targeting, but have evolved means to escape decay through the action of cis-acting or trans-acting viral factors. Studies aimed at understanding how viruses are subjected to and circumvent NMD have increased our understanding of NMD target selection of host mRNAs. This review focuses on the knowledge gained from studying NMD in viral systems as well as related Upf1-dependent pathways and how these pathways restrict virus replication.
MeSH term(s)	3' Untranslated Regions ; Animals ; Host-Pathogen Interactions ; Humans ; Nonsense Mediated mRNA Decay ; RNA Helicases/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; RNA-Binding Proteins/metabolism ; Trans-Activators/metabolism ; Viral Proteins/metabolism ; Viruses/classification ; Viruses/genetics ; Viruses/metabolism
Chemical Substances	3' Untranslated Regions ; RNA, Messenger ; RNA, Viral ; RNA-Binding Proteins ; Trans-Activators ; Viral Proteins ; RNA Helicases (EC 3.6.4.13)
Language	English
Publishing date	2020-12-17
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2611378-8
ISSN	1879-6265 ; 1879-6257
ISSN (online)	1879-6265
ISSN	1879-6257
DOI	10.1016/j.coviro.2020.11.002
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Article ; Online: In Tribute to Michael Goodin.

Verchot, Jeanmarie / Jackson, Andrew O / Simon, Anne E

Viruses

2021 Volume 13, Issue 1

Abstract: It is with great sadness and sympathy for his family and the plant virology community that we convey the passing of Michael Goodin unexpectedly in December 2020 [ ... ]. ...

Abstract	It is with great sadness and sympathy for his family and the plant virology community that we convey the passing of Michael Goodin unexpectedly in December 2020 [...].
Language	English
Publishing date	2021-01-08
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13010078
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Article ; Online: -1 Programmed ribosomal frameshifting in Class 2 umbravirus-like RNAs uses multiple long-distance interactions to shift between active and inactive structures and destabilize the frameshift stimulating element.

Mikkelsen, Anna A / Gao, Feng / Carino, Elizabeth / Bera, Sayanta / Simon, Anne E

Nucleic acids research

2023 Volume 51, Issue 19, Page(s) 10700–10718

Abstract: Plus-strand RNA viruses frequently employ -1 programmed ribosomal frameshifting (-1 PRF) to maximize their coding capacity. Ribosomes can frameshift at a slippery sequence if progression is impeded by a frameshift stimulating element (FSE), which is ... ...

Abstract	Plus-strand RNA viruses frequently employ -1 programmed ribosomal frameshifting (-1 PRF) to maximize their coding capacity. Ribosomes can frameshift at a slippery sequence if progression is impeded by a frameshift stimulating element (FSE), which is generally a stable, complex, dynamic structure with multiple conformations that contribute to the efficiency of -1 PRF. As FSE are usually analyzed separate from the viral genome, little is known about cis-acting long-distance interactions. Using full-length genomic RNA of umbravirus-like (ula)RNA citrus yellow vein associated virus (CY1) and translation in wheat germ extracts, six tertiary interactions were found associated with the CY1 FSE that span nearly three-quarters of the 2.7 kb genomic RNA. All six tertiary interactions are conserved in other Class 2 ulaRNAs and two are conserved in all ulaRNAs. Two sets of interactions comprise local and distal pseudoknots that involve overlapping FSE nucleotides and thus are structurally incompatible, suggesting that Class 2 FSEs assume multiple conformations. Importantly, two long-distance interactions connect with sequences on opposite sides of the critical FSE central stem, which would unzip the stem and destabilize the FSE. These latter interactions could allow a frameshifting ribosome to translate through a structurally disrupted upstream FSE that no longer blocks ribosome progression.
MeSH term(s)	Frameshifting, Ribosomal ; Tombusviridae/genetics ; RNA, Viral/metabolism ; Nucleic Acid Conformation ; Frameshift Mutation
Chemical Substances	RNA, Viral
Language	English
Publishing date	2023-09-23
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad744
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