D'Ann Rochon (1955-2022), a life of passion for plant virology.

D'Ann Rochon passed away on November 29 2022. She is remembered for her outstanding contributions to the field of plant virology, her strong commitment to high quality science and her dedication to the training and mentorship of the next generation of scientists. She was a research scientist for Agriculture and Agri-Food Canada and an Adjunct Professor for the University of British Columbia.

Plant-biomass-based hybrid seed wraps mitigate yield and post-harvest losses among smallholder farmers in sub-Saharan Africa.

Sustainable practices that reduce food loss are essential for enhancing global food security. We report a 'wrap and plant' seed treatment platform to protect crops from soil-borne pathogens. Developed from the abundantly available wastes of banana harvest and recycled old, corrugated cardboard boxes via chemical-free pulping, these paper-like biodegradable seed wraps exhibit tunable integrity and bioavailability of loaded moieties.

Characterization and Aggressiveness of Take-All Root Rot Pathogens Isolated from Symptomatic Bermudagrass Putting Greens.

Take-all root rot is a disease of ultradwarf bermudagrass putting greens caused by (Gg), sp. (Gx), (Ggram), (Cc), and (Mc). Many etiological and epidemiological components of this disease remain unknown.

PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression.

Polycyclic aromatic hydrocarbons (PAHs) are among the most widespread natural and anthropogenic pollutants, and some PAHs are proven developmental toxicants. We chemically characterized clean and heavily polluted sites and exposed fish embryos to PAH polluted sediment extracts during four critical developmental stages. Embryos were collected from Fundulus heteroclitus populations inhabiting the clean and heavily polluted Superfund estuary.

A CRISPR/dCas9 toolkit for functional analysis of maize genes.

Background: The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9).

Results: In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts.

Recent advances in biodegradable matrices for active ingredient release in crop protection: Towards attaining sustainability in agriculture.

Climate changes, emerging species of plant pests, and deficits of clean water and arable land have made availability of food to the ever-increasing global population a challenge. Excessive use of synthetic pesticides to meet ever-increasing production needs has resulted in development of resistance in pest populations, as well as significant ecotoxicity, which has directly and indirectly impacted all life-forms on earth. To meet the goal of providing safe, sufficient, and high-quality food globally with minimal environmental impact, one strategy is to focus on targeted delivery of pesticides using eco-friendly and biodegradable carriers that are derived from naturally available materials.

Tailored Lignocellulose-Based Biodegradable Matrices with Effective Cargo Delivery for Crop Protection.

Controlled release and targeted delivery of agrochemicals are crucial for achieving effective crop protection with minimal damage to the environment. This work presents an innovative and cost-effective approach to fabricate lignocellulose-based biodegradable porous matrices capable of slow and sustained release of the loaded molecules for effective crop protection. The matrix exhibits tunable physicochemical properties which, when coupled with our unique "wrap-and-plant" concept, help to utilize it as a defense against soil-borne pests while providing controlled release of crop protection moieties.

Relationships of virus titers and transmission rates among sympatric and allopatric virus isolates and thrips vectors support local adaptation.

Plant viruses rely on insect vectors for transmission among plant hosts, but many of the specifics of virus-vector interactions are not fully understood. Thrips tabaci, which transmits Tomato spotted wilt virus (TSWV) in a persistent and propagative manner, varies greatly in its ability to transmit different isolates of TSWV. Similarly, TSWV isolates are transmitted at different efficiencies by different populations of T.

Localization of viral and host RNA within soybean cyst nematode via fluorescence in situ hybridization.

Nematode-infecting RNA viruses have recently been discovered via transcriptome sequencing. In soybean cyst nematode (SCN; Heterodera glycines), seven single-stranded RNA viruses have been identified from transcriptome data and experimentally confirmed with qRT-PCR and Sanger sequencing. Presently, there is still much unknown about the relationship between these viruses and the nematode host.

Electropermeabilization-based fluorescence hybridization of whole-mount plant parasitic nematode specimens.

A fluorescence hybridization (FISH) protocol was developed for nematodes in which nucleic acid probes are introduced within the organism electroporation. This modification of existing FISH protocols removes numerous chemical wash steps, and thus, reduces protocol time and specimen loss while improving hybridization sensitivity. The presented work is optimized for juveniles of soybean cyst nematode (SCN; ) and has been used to identify both host and associated-microbial (viral) targets.

Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes.

Members of the family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the family have single-stranded RNA (ssRNA) genomes with T=3 icosahedral protein shells with a maximum diameter of ∼340 Å. Each capsid protein is comprised of three domains: R (RNA binding), S (shell), and P (protruding).

Quantitative Real-Time PCR Analysis of Individual Flue-Cured Tobacco Seeds and Seedlings Reveals Seed Transmission of Tobacco Mosaic Virus.

Tobacco mosaic virus (TMV) is an extensively studied RNA virus known to infect tobacco () and other solanaceous crops. TMV has been classified as a seedborne virus in tobacco, with infection of developing seedlings thought to occur from contact with the TMV-infected seed coat. The mechanism of TMV transmission through seed was studied in seed of the K 326 cultivar of flue-cured tobacco.

Plant Virus-Based Nanoparticles for the Delivery of Agronomic Compounds as a Suspension Concentrate.

Nanoparticle formulations of agrichemicals may enhance their performance while simultaneously mitigating any adverse environmental effects. Red clover necrotic mosaic virus (RCNMV) is a soil-transmitted plant virus with many inherent attributes that allow it to function as a plant virus-based nanoparticle (PVN) when loaded with biologically active ingredients. Here we describe how to formulate a PVN loaded with the nematicide abamectin (Abm) beginning with the propagation of the virus through the formulation, deactivation, and characterization of the finished product.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses.

Detecting Specific Resource Use by Drosophila suzukii (Diptera: Drosophilidae) Using Gut Content Analysis.

Drosophila suzukii Matsumura (Diptera: Drosophilidae) is an invasive, highly polyphagous pest of soft-skinned fruits throughout much of the world. A better understanding of the ecology of adult flies, including their nutritional resources, is needed to advance ecologically based management approaches. In this study, we evaluate the capability of polymerase chain reaction-based gut content analysis to detect a known food resource from DNA extracted from laboratory-reared flies.

Novel RNA viruses within plant parasitic cyst nematodes.

The study of invertebrate-and particularly nematode-viruses is emerging with the advancement of transcriptome sequencing. Five single-stranded RNA viruses have now been confirmed within the economically important soybean cyst nematode (SCN; Heterodera glycines). From previous research, we know these viruses to be widespread in greenhouse and field populations of SCN.

Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses.

Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR.

Development of abamectin loaded plant virus nanoparticles for efficacious plant parasitic nematode control.

Plant parasitic nematodes are one of the world's major agricultural pests, causing in excess of $157 billion in worldwide crop damage annually. Abamectin (Abm) is a biological pesticide with a strong activity against a wide variety of plant parasitic nematodes. However, Abm's poor mobility in the soil compromises its nematicide performance because of the limited zone of protection surrounding the growing root system of the plant.

Loading and release mechanism of red clover necrotic mosaic virus derived plant viral nanoparticles for drug delivery of doxorubicin.

Loading and release mechanisms of Red clover necrotic mosaicvirus (RCNMV) derived plant viral nanoparticle (PVN) are shown for controlled delivery of the anticancer drug, doxorubicin (Dox). Previous studies demonstrate that RCNMV's structure and unique response to divalent cation depletion and re-addition enables Dox infusion to the viral capsid through a pore formation mechanism. However, by controlling the net charge of RCNMV outer surface and accessibility of RCNMV interior cavity, tunable release of PVN is possible via manipulation of the Dox loading capacity and binding locations (external surface-binding or internal capsid-encapsulation) with the RCNMV capsid.

Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences.

Background: Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish, Fundulus heteroclitus, inhabiting a clean estuary do not survive when exposed to sediment extract from a site highly contaminated with polycyclic aromatic hydrocarbons (PAHs) while embryos derived from a population inhabiting a PAH polluted estuary are remarkably resistant to the polluted sediment extract.

The red clover necrotic mosaic virus capsid protein N-terminal amino acids possess specific RNA binding activity and are required for stable virion assembly.

The red clover necrotic mosaic virus (RCNMV) bipartite RNA genome is packaged into two virion populations containing either RNA-1 and RNA-2 or multiple copies of RNA-2 only. To understand this distinctive packaging scheme, we investigated the RNA-binding properties of the RCNMV capsid protein (CP). Maltose binding protein-CP fusions exhibited the highest binding affinities for RNA probes containing the RNA-2 trans-activator or the 3' non-coding region from RNA-1.

New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering.

Red clover necrotic mosaic virus (RCNMV) is a 36-nm-diameter, T = 3 icosahedral plant virus with a genome that is split between two single-stranded RNA molecules of approximately 3.9 kb and 1.5 kb, as well as a 400-nucleotide degradation product.

The Red clover necrotic mosaic virus capsid protein N-terminal lysine-rich motif is a determinant of symptomatology and virion accumulation.

The interaction between viral capsid protein (CP) and its cognate viral RNA modulates many steps in the virus infection cycle, such as replication, translation and assembly. The N-terminal 50 amino acids of the Red clover necrotic mosaic virus (RCNMV) CP are rich in basic residues (especially lysine) and are essential for the core functions of the CP, namely RNA binding and virion assembly. To further elucidate additional biological roles for these basic residues, a series of alanine substitution mutations was introduced into infectious clones of RCNMV RNA-1 and assayed for symptomatology, virion formation and systemic infection.

Gene expression throughout a vertebrate's embryogenesis.

Background: Describing the patterns of gene expression during embryonic development has broadened our understanding of the processes and patterns that define morphogenesis. Yet gene expression patterns have not been described throughout vertebrate embryogenesis. This study presents statistical analyses of gene expression during all 40 developmental stages in the teleost Fundulus heteroclitus using four biological replicates per stage.

Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus.

Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell.