Anne E. Simon
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View article: Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila
Identification of the peptide Vulnusin, a wound signal that mediates mechanical-injury-induced nociception in Drosophila Open
Animals can acutely sense a puncture or cut in their skin through nociceptors. However, the molecular identity of such "wound signals" and their receptors on nociceptors remains unknown. In Drosophila larvae, class IV dendritic arborizatio…
View article: Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica)
Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica) Open
Gene expression plasticity is an essential mechanism of physiological acclimation. In adult eastern oysters, Crassostrea virginica (Gmelin, 1791), transcriptomic responses to experimental osmotic stress differ between oyster bed sources wi…
View article: Hairpin inserts in viral genomes are stable when they conform to the thermodynamic properties of viral RNA substructures
Hairpin inserts in viral genomes are stable when they conform to the thermodynamic properties of viral RNA substructures Open
Virus-induced gene silencing (VIGS) allows for the rapid targeting of gene expression and has been instrumental in characterizing plant genes. However, foreign sequences inserted into VIGS vectors are rarely maintained for unknown reasons.…
View article: R2DT: a comprehensive platform for visualizing RNA secondary structure
R2DT: a comprehensive platform for visualizing RNA secondary structure Open
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R…
View article: COLLABORATIVE LEARNING IN ARABIC LANGUAGE LEARNING IN INDONESIA: A SYSTEMATIC LITERATURE REVIEW
COLLABORATIVE LEARNING IN ARABIC LANGUAGE LEARNING IN INDONESIA: A SYSTEMATIC LITERATURE REVIEW Open
The Education 5.0 era requires learners to acquire both language and communication skills. In light of the contemporary demands, collaborative learning is highly recognized as a strong methodology to improve both linguistic and social comp…
View article: Contextual Teaching-Learning dalam Media Digital: Studi pada Channel YouTube 'Arab Podcasts'
Contextual Teaching-Learning dalam Media Digital: Studi pada Channel YouTube 'Arab Podcasts' Open
This study analyzes the application of Contextual Teaching and Learning (CTL) elements in Arabic language learning videos on the Arab Podcast YouTube channel. The research method used is qualitative descriptive with content analysis of vid…
View article: R2DT: a comprehensive platform for visualising RNA secondary structure
R2DT: a comprehensive platform for visualising RNA secondary structure Open
RNA secondary (2D) structure visualisation is an essential tool for understanding RNA function. R2DT is a software package designed to visualise RNA 2D structures in consistent, recognisable, and reproducible layouts. The latest release, R…
View article: Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles
Direct nanopore RNA sequencing of umbra-like virus-infected plants reveals long non-coding RNAs, specific cleavage sites, D-RNAs, foldback RNAs, and temporal- and tissue-specific profiles Open
The traditional view of plus (+)-strand RNA virus transcriptomes is that infected cells contain a limited variety of viral RNAs, such as full-length (+)-strand genomic RNA(s), (–)-strand replication intermediate(s), 3′ co-terminal subgenom…
View article: Expanding the Plant Virome: Umbra-Like Viruses Use Host Proteins for Movement
Expanding the Plant Virome: Umbra-Like Viruses Use Host Proteins for Movement Open
Before the very recent discovery of umbra-like viruses (ULVs), the signature defining feature of all plant RNA viruses was the encoding of specialized RNA-binding movement proteins (MPs) for transiting their RNA genomes through gated plasm…
View article: Umbravirus-like RNA viruses are capable of independent systemic plant infection in the absence of encoded movement proteins
Umbravirus-like RNA viruses are capable of independent systemic plant infection in the absence of encoded movement proteins Open
The signature feature of all plant viruses is the encoding of movement proteins (MPs) that supports the movement of the viral genome into adjacent cells and through the vascular system. The recent discovery of umbravirus-like viruses (ULVs…
View article: -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
-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 Open
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)…
View article: RNAcanvas: interactive drawing and exploration of nucleic acid structures
RNAcanvas: interactive drawing and exploration of nucleic acid structures Open
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 nu…
View article: ADAR1 Biology Can Hinder Effective Antiviral RNA Interference
ADAR1 Biology Can Hinder Effective Antiviral RNA Interference Open
All life at the cellular level has the capacity to induce an antiviral response. Here, we examine the result of imposing the antiviral response of one branch of life onto another and find evidence for conflict.
View article: Conserved Structure Associated with Different 3′CITEs Is Important for Translation of Umbraviruses
Conserved Structure Associated with Different 3′CITEs Is Important for Translation of Umbraviruses Open
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 fo…
View article: Data set for Mikkelsen et al
Data set for Mikkelsen et al Open
Dataset of in vitro translation assays for ribosomal frameshifting
View article: Novel 3′ Proximal Replication Elements in Umbravirus Genomes
Novel 3′ Proximal Replication Elements in Umbravirus Genomes Open
The 3′ untranslated regions (UTRs) of positive-strand RNA plant viruses commonly contain elements that promote viral replication and translation. The ~700 nt 3′UTR of umbravirus pea enation mosaic virus 2 (PEMV2) contains three 3′ cap-inde…
View article: Identification of Novel 5′ and 3′ Translation Enhancers in Umbravirus-Like Coat Protein-Deficient RNA Replicons
Identification of Novel 5′ and 3′ Translation Enhancers in Umbravirus-Like Coat Protein-Deficient RNA Replicons Open
Umbra-like associated RNAs (ulaRNAs) are a recently discovered type of subviral RNA that use their encoded RNA-dependent RNA polymerase for replication but do not encode any coat proteins, movement proteins, or silencing suppressors yet ca…
View article: Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer
Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer Open
Canonical eukaryotic mRNA translation requires 5′cap recognition by initiation factor 4E (eIF4E). In contrast, many positive-strand RNA virus genomes lack a 5′cap and promote translation by non-canonical mechanisms. Among plant viruses, PT…
View article: Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)
Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV) Open
Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucl…
View article: Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs
Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs Open
We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (R…
View article: <i>Opium Poppy Mosaic Virus</i> Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3′ CITE
<i>Opium Poppy Mosaic Virus</i> Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3′ CITE Open
Opium poppy mosaic virus (OPMV) is an umbravirus in the family Tombusviridae . We determined that OPMV accumulates two similarly sized subgenomic RNAs (sgRNAs), with the smaller known to code for proteins expressed from overlapping open re…
View article: In Tribute to Michael Goodin
In Tribute to Michael Goodin Open
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 [...]
View article: The Multifunctional Long-Distance Movement Protein of <i>Pea Enation Mosaic Virus 2</i> Protects Viral and Host Transcripts from Nonsense-Mediated Decay
The Multifunctional Long-Distance Movement Protein of <i>Pea Enation Mosaic Virus 2</i> Protects Viral and Host Transcripts from Nonsense-Mediated Decay Open
Nonsense-mediated decay (NMD) represents an RNA regulatory pathway that degrades both natural and faulty messenger RNAs with long 3′ untranslated regions. NMD targets diverse families of RNA viruses, requiring that viruses counteract the N…
View article: RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences
RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences Open
RNA structure prediction programs remain imperfect and many substructures are still identified by manual exploration, which is most efficiently conducted within an RNA structure drawing program. However, most nucleic acid structure drawing…
View article: RNA virus evasion of nonsense-mediated decay
RNA virus evasion of nonsense-mediated decay Open
Nonsense-mediated decay (NMD) is a host RNA control pathway that removes aberrant transcripts with long 3' untranslated regions (UTRs) due to premature termination codons (PTCs) that arise through mutation or defective splicing. To maximiz…
View article: Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA
Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA Open
Translation commencing at closely spaced initiation codons is common in RNA viruses with limited genome space. In the subgenomic RNA (sgRNA) of Pea enation mosaic virus 2, two closely spaced, out-of-frame start codons direct synthesis of m…