@article{sohail_pirzada_guenther_barbieri_sit_menegatti_crook_opperman_khan_2023, title={Cellulose Acetate-Stabilized Pickering Emulsions: Preparation, Rheology, and Incorporation of Agricultural Active Ingredients}, volume={11}, ISSN={["2168-0485"]}, url={https://doi.org/10.1021/acssuschemeng.3c02428}, DOI={10.1021/acssuschemeng.3c02428}, abstractNote={We report the use of cellulose acetate (CA) nanoparticles (NPs) to produce oil in water Pickering emulsions. The CA NP can emulsify various oils and form stable emulsions at concentrations as low as 0.5 wt %. Rheological and microscopic analyses show evidence of interconnected NP aggregate networks between droplets. Yield stress measurements display evidence of “double” yielding. We postulate that the presence of the NP aggregates provides a secondary network between droplet clusters resulting in such behavior. We demonstrate the suitability of the emulsions as agriculture formulations by incorporating an agrochemical, abamectin (Abm), and a plant-growth-promoting microbe (PGPM) in the emulsions. Release assays exhibit sustained Abm release, promising higher efficacy at lower usage volumes. Incorporation of nonsporulating PGPM Pseudomonas simiae in the emulsions shows significantly higher microbe viability compared to controls after 70 days of storage. By demonstrating the application of CA NPs as a sustainable Pickering emulsifier, this study introduces the use of CA as a platform technology for the delivery of diverse agriculture cargos. A comprehensive evaluation of the system is articulated in a fundamental microstructure analysis and a demonstration of practical on-site attributes, including shelf-life stability and functional performance, verified through bioassays and plant growth studies.}, number={42}, journal={ACS SUSTAINABLE CHEMISTRY & ENGINEERING}, author={Sohail, Mariam and Pirzada, Tahira and Guenther, Richard and Barbieri, Eduardo and Sit, Tim and Menegatti, Stefano and Crook, Nathan and Opperman, Charles H. and Khan, Saad A.}, year={2023}, month={Sep}, pages={15178–15191} }
 @article{sanfacon_alam_ghoshal_ghoshal_hui_jackson_kakani_morris_nagy_simon_et al._2023, title={D'Ann Rochon (1955-2022), a life of passion for plant virology}, volume={587}, ISSN={["1089-862X"]}, DOI={10.1016/j.virol.2023.109874}, abstractNote={D'Ann Rochon passed away on November 29th 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. Her research program provided new insights on the infection cycle of tombusviruses and related viruses, including ground-breaking research on the structure of virus particles, the mechanisms of virus transmission by fungal zoospores, and the complexity of plant-virus interactions. She also developed diagnostic antibodies for plum pox virus and little cherry virus 2 that have had a significant impact on the management of these viruses.}, journal={VIROLOGY}, author={Sanfacon, Helene and Alam, Syed Benazir and Ghoshal, Basudev and Ghoshal, Kankana and Hui, Elizabeth and Jackson, Andrew O. and Kakani, Kishore and Morris, T. Jack and Nagy, Peter D. and Simon, Anne E. and et al.}, year={2023}, month={Oct} }
 @article{pirzada_affokpon_guenther_mathew_agate_blevins_byrd_sit_koenning_davis_et al._2023, title={Plant-biomass-based hybrid seed wraps mitigate yield and post-harvest losses among smallholder farmers in sub-Saharan Africa}, volume={4}, ISSN={2662-1355}, url={http://dx.doi.org/10.1038/s43016-023-00695-z}, DOI={10.1038/s43016-023-00695-z}, abstractNote={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. These wraps were used for nematode control on yam (Dioscorea cayenensis-rotundata) seed pieces in Benin, a major producer of this staple crop in the sub-Saharan African 'yam belt'. Our seed wraps loaded with ultra-low-volume abamectin (1/100 ≤ commercial formulation) consistently controlled yam nematode (Scutellonema bradys) populations while considerably increasing the yield at various locations over 2015-2018. Substantial reduction in post-harvest tuber weight loss and cracking was observed after 3 and 5 months of storage, contributing to increased value, nutrition and stakeholders' preference for the wrap and plant treatment.}, number={2}, journal={Nature Food}, publisher={Springer Science and Business Media LLC}, author={Pirzada, Tahira and Affokpon, Antoine and Guenther, Richard H. and Mathew, Reny and Agate, Sachin and Blevins, Aitana and Byrd, Medwick V. and Sit, Tim L. and Koenning, Stephen R. and Davis, Eric L. and et al.}, year={2023}, month={Feb}, pages={148–159} }
 @article{stephens_gannon_cubeta_sit_kerns_2022, title={Characterization and Aggressiveness of Take-All Root Rot Pathogens Isolated from Symptomatic Bermudagrass Putting Greens}, volume={112}, ISSN={["1943-7684"]}, DOI={10.1094/PHYTO-05-21-0215-R}, abstractNote={Take-all root rot is a disease of ultradwarf bermudagrass putting greens caused by Gaeumannomyces graminis (Gg), Gaeumannomyces sp. (Gx), Gaeumannomyces graminicola (Ggram), Candidacolonium cynodontis (Cc), and Magnaporthiopsis cynodontis (Mc). Many etiological and epidemiological components of this disease remain unknown. Improving pathogen identification and our understanding of the aggressiveness of these pathogens along with growth at different temperatures will advance our knowledge of disease development to optimize management strategies. Take-all root rot pathogens were isolated from symptomatic bermudagrass root and stolon pieces from 16 different golf courses. Isolates of Gg, Gx, Ggram, Cc, and Mc were used to inoculate 'Champion' bermudagrass in an in planta aggressiveness assay. Each pathogen was also evaluated at 10, 15, 20, 25, 30, and 35C to determine growth temperature optima. Infected plant tissue was used to develop a real-time PCR high resolution melt assay for pathogen detection. This assay was able to differentiate each pathogen directly from infected plant tissue using a single primer pair. In general, Ggram, Gg, and Gx were the most aggressive while Cc and Mc exhibited moderate aggressiveness. Pathogens were more aggressive when incubated at 30C compared to 20C. While they grew optimally between 24.4 and 27.8C, pathogens exhibited limited growth at 35C and no growth at 10C. These data provide important information on this disease and its causal agents that may improve take-all root rot management.}, number={4}, journal={PHYTOPATHOLOGY}, author={Stephens, Cameron M. and Gannon, Travis W. and Cubeta, Marc A. and Sit, Tim L. and Kerns, James P.}, year={2022}, month={Apr}, pages={811–819} }
 @article{dedehouanou_affokpon_2022, title={Comprehensive Perception Approach of Adoption: Innovative Wrap & Plant Technology for Nematodes Management on Yam}, volume={9}, url={http://dx.doi.org/10.14738/assrj.94.12225}, DOI={10.14738/assrj.94.12225}, abstractNote={ABSTRACT 
A new agricultural practice, wrap & plant technology, was experimented in yam fields on three different sites in the centre-north of Benin. These sites were "Savalou", site 1, "Savè", site 2 and “Glazoué”, site 3. The research sought to highlight the perception of various actors from the vegetative to the culinary phases. Two improved practices were introduced: treatment A (wrapping of seed yam cv. Klatchi with banana-fibre paper, impregnated with micro-doses of abamectin), treatment B (wrapping of seed yam of cv. Klatchi using banana-fibre paper alone). On the basis of a Comparative Appraisal Index (CBI), that is, the practice introduced was well appreciated by enumerators if the difference in perception scores of characteristics was greater than zero. In terms of results, treatment A seemed to be the most popular practice on sites 1 and 2. On site 3, treatment B seemed to substitute for A. While in the first two sites, the sensory characteristics of dishes and the agro-morphological descriptors constituted a main component of favourable perception, the descriptors from agro-morphological and harvest phases were very much important at site 3. In terms of the decision to adopt a treatment, it depended significantly amongst other socioeconomic characteristics of the respondents on the sex, number of years of experience, membership in an association, level of education, other income generating activity and the site. For future expansion of introduced practices, agricultural research needs to address socioeconomic characteristics and to improve agro-morphological descriptors. 
Key-words: Abamectin, actors, Dioscorea spp., nematode management, sensory selectivity, Benin}, number={4}, journal={Advances in Social Sciences Research Journal}, publisher={Scholar Publishing}, author={Dedehouanou, Houinsou and Affokpon, Antoine}, year={2022}, month={Apr}, pages={355–368} }
 @article{dedehouanou_2022, title={Wrap & Plant Plant Technology: An Innovative and Cost-Effective Method for Seed Yam Treatment for Nematode Control in Fields}, volume={9}, url={http://dx.doi.org/10.14738/assrj.95.12240}, DOI={10.14738/assrj.95.12240}, abstractNote={ABSTRACT 
In West Africa, seed yam represents an important source of nematode inoculums in yam fields and a major cause of the disease perpetuation. To enhance nematode control on yam (Dioscorea spp.), a pilot participatory field evaluation was conducted in Benin on nematode control potential of abamectin-treated banana paper (treatment A) using seed wrap method. An additional seed yam wrapped with untreated paper (treatment B) is also considered. Both treatments A & B are then compared to unwrapped seed yam representing the farmers’ practice (FP). In each field, plots are arranged in a randomized complete block design with five replicates. The effects of seed yam treatment on nematode control in fields, gustatory qualities of yam tubers, and both social and profitability studies of the technology were assessed. In the present paper, only the study related to the profitability based on the Net Margin (NM) and the ratio Cost/Profit is presented. Results reveal advantages of treatments A and B over (FP). In fact, production statistics from treatments A and B are significantly higher than those from (FP). Based on the "willingness to pay" approach, the profitability study shows that treatment A has a Net Margin of approximately 153.7% that of (FP). Concerning the ratio Cost/Profit, 100 FCFA (West African CFA franc) spent in yam production using this new technology generates around 79.3 FCFA against 59.9 FCFA for (FP). Despite the success of this pilot study, input prices must be monitored before scaling up this innovation to the other agro-ecological regions of Benin. 
Key-words: Nematode control, Dioscorea spp., cost effectiveness, input prices, Wrap & plant technology, Benin}, number={5}, journal={Advances in Social Sciences Research Journal}, publisher={Scholar Publishing}, author={Dedehouanou, Houinsou}, year={2022}, month={May}, pages={39–59} }
 @article{ochola_cortada_mwaura_tariku_christensen_ng'ang'a_hassanali_pirzada_khan_pal_et al._2022, title={Wrap-and-plant technology to manage sustainably potato cyst nematodes in East Africa}, volume={2}, ISSN={["2398-9629"]}, url={https://doi.org/10.1038/s41893-022-00852-5}, DOI={10.1038/s41893-022-00852-5}, abstractNote={Abstract Renewable eco-friendly options for crop protection are fundamental in achieving sustainable agriculture. Here, we demonstrate the use of a biodegradable lignocellulosic banana-paper matrix as a seed wrap for the protection of potato plants against potato cyst nematode (PCN), Globodera rostochiensis . Potato cyst nematodes are devastating quarantine pests of potato globally. In East Africa, G. rostochiensis has recently emerged as a serious threat to potato production. Wrapping seed potatoes within the lignocellulose banana-paper matrix substantially reduced G. rostochiensis field inoculum and increased potato yields by up to fivefold in Kenya, relative to farmer practice, whether or not impregnated with ultra-low doses of the nematicide abamectin (ABM). Markedly, ABM-treated banana paper at ~1,000 times lower than conventional recommendations reduced PCN inoculum. Assays and analyses revealed that the lignocellulose matrix disrupts parasite–host chemical signalling by adsorbing critical PCN hatching and infective juvenile host location chemicals present in potato root exudate. Recovery experiments confirmed adsorption of these host location chemicals. Our study demonstrates the use of waste organic material to sustainably manage PCN, and potentially other crop root pests, while increasing potato yields.}, journal={NATURE SUSTAINABILITY}, author={Ochola, Juliet and Cortada, Laura and Mwaura, Onesmus and Tariku, Meklit and Christensen, Shawn A. and Ng'ang'a, Margaret and Hassanali, Ahmed and Pirzada, Tahira and Khan, Saad and Pal, Lokendra and et al.}, year={2022}, month={Feb} }
 @article{kraft_sit_diepenbrock_ashrafi_aryal_fernandez_burrack_2021, title={Detection of Fruit Meals Within Laboratory-Raised and Field-Trapped Adult Drosophila suzukii (Diptera: Drosophilidae) Guts}, volume={9}, ISSN={2296-701X}, url={http://dx.doi.org/10.3389/fevo.2021.719645}, DOI={10.3389/fevo.2021.719645}, abstractNote={The feeding habits of adult Brachycera are understudied and may provide important context for understanding invasive pest biology, as with the polyphagous small fruit pest Drosophila suzukii. We developed molecular methods to study adult D. suzukii gut content in order to understand its feeding habits. We designed and verified two primer pairs specific for either blueberries or blackberries and used a qPCR melt curve analysis to determine whether we can detect the presence or absence of berry feeding by adult flies. In a laboratory assay, the blueberry fly meal DNA can be detected for longer periods than the blackberry meal DNA. Generally, female gut contents are less variable than male gut contents. We also tested recently emerged flies that were not fed as adults but developed as larvae in either blueberries or blackberries. Some adult flies from each fruit had detectable fruit DNA in their gut, which could be due to pupal meconium feeding after emergence. Next, we aimed to test the primers in the field to develop techniques to track fruit feeding by D. suzukii in its natural field environment. First, to identify the most appropriate collection method, we determined how long we could detect fruit DNA, using previously developed primers within D. suzukii gut preserved in four types of trap fluid in the laboratory. The likelihood of detecting blackberry DNA differed by day, trap fluid, and between sexes. For the blueberry primer, the possibility of detecting blueberry DNA differed by trap fluid only. Based on those results, we used RV antifreeze with a Scentry SWD lure in field trials at two research station locations, one containing blackberries and one with blueberries. We established transects away from each fruit planting and collected up to 120 total flies at each point along transects. There were no significant differences in the number of flies containing berry DNA among collection points along the transect in both locations. These results suggest that adult flies move between crop and non-crop habitats and may not be highly dependent on fruit food resources.}, journal={Frontiers in Ecology and Evolution}, publisher={Frontiers Media SA}, author={Kraft, Laura J. and Sit, Tim L. and Diepenbrock, Lauren M. and Ashrafi, Hamid and Aryal, Rishi and Fernandez, Gina E. and Burrack, Hannah J.}, year={2021}, month={Aug} }
 @article{bozinovic_shea_feng_hinton_sit_oleksiak_2021, title={PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0249432}, abstractNote={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. Embryos of parents from the clean sites are sensitive to PAH pollutants while those of parents from the heavily polluted site are resistant. Chemical analysis of embryos suggests PAH accumulation and pollution-induced toxicity among sensitive embryos during development that ultimately kills all sensitive embryos before hatching, while remarkably, the resistant embryos develop normally. The adverse effects on sensitive embryos are manifested as developmental delays, reduced heart rates, and severe heart, liver, and kidney morphological abnormalities. Gene expression analysis of early somitogenesis, heartbeat initiation, late organogenesis, and pre-hatching developmental stages reveals genes whose expression significantly differs between sensitive and resistant embryo populations and helps to explain mechanisms of sensitivity and resistance to polluted environments during vertebrate animal development.}, number={4}, journal={PLOS ONE}, author={Bozinovic, Goran and Shea, Damian and Feng, Zuying and Hinton, David and Sit, Tim and Oleksiak, Marjorie F.}, year={2021}, month={Apr} }
 @article{gentzel_park_bellizzi_xiao_gadhave_murphree_yang_lamantia_redinbaugh_balint-kurti_et al._2020, title={A CRISPR/dCas9 toolkit for functional analysis of maize genes}, volume={16}, ISSN={1746-4811}, url={http://dx.doi.org/10.1186/s13007-020-00675-5}, DOI={10.1186/s13007-020-00675-5}, abstractNote={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).In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression.We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.}, number={1}, journal={Plant Methods}, publisher={Springer Science and Business Media LLC}, author={Gentzel, Irene N. and Park, Chan Ho and Bellizzi, Maria and Xiao, Guiqing and Gadhave, Kiran R. and Murphree, Colin and Yang, Qin and LaMantia, Jonathan and Redinbaugh, Margaret G. and Balint-Kurti, Peter and et al.}, year={2020}, month={Oct} }
 @article{ruark-seward_davis_sit_2020, title={Localization of viral and host RNA within soybean cyst nematode via fluorescence in situ hybridization}, volume={211}, ISSN={["1090-2449"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85082019323&partnerID=MN8TOARS}, DOI={10.1016/j.exppara.2020.107866}, abstractNote={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. In this study, we localize three viruses within the soybean cyst nematode: SCN socyvirus-1 (SbCNV-1), SCN nyami-like virus (NLV), and SCN bunya-like virus (BLV). To visually locate the viruses, whole-mount fluorescence in situ hybridization (FISH) methodology was developed for SCN pre-parasitic second-stage juveniles (ppJ2s). Two SCN populations with differing viral titers (LY1 and MM21) were used as a comparison for viral probe fluorescence intensity. Viral RNAs for all three viruses were abundant in cells throughout the SCN ppJ2 body of the high titer (LY1) population but absent within the majority of the intestinal tract. A significant reduction in viral fluorescence intensity was observed in a similar body pattern in ppJ2 of the low-titer (MM21) SCN, highlighting the specificity of the FISH method. As controls, viral RNAs were colocalized with host mRNA glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for full body localization and a secretory ubiquitin protein (4G06) expressed specifically within the subventral esophageal glands. In addition, viral replication was confirmed in SCN eggs and ppJ2s via qRT-PCR detection of the anti-genomic RNA strands.}, journal={EXPERIMENTAL PARASITOLOGY}, publisher={Elsevier BV}, author={Ruark-Seward, Casey L. and Davis, Eric L. and Sit, Tim L.}, year={2020}, month={Apr} }
 @article{sherman_guenther_reade_rochon_sit_smith_2020, title={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}, volume={94}, ISSN={["1098-5514"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077664748&partnerID=MN8TOARS}, DOI={10.1128/JVI.01439-19}, abstractNote={Members of the Tombusviridae family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the “arm,” seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle. ABSTRACT Members of the Tombusviridae family have highly similar structures, and yet there are important differences among them in host, transmission, and capsid stabilities. Viruses in the Tombusviridae 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). Between the R domain and S domain is the “arm” region that studies have shown to play a critical role in assembly. To better understand how the details of structural differences and similarities influence the Tombusviridae viral life cycles, the structures of cucumber leaf spot virus (CLSV; genus Aureusvirus) and red clover necrotic mosaic virus (RCNMV; genus Dianthovirus) were determined to resolutions of 3.2 Å and 2.9 Å, respectively, with cryo-electron microscopy and image reconstruction methods. While the shell domains had homologous structures, the stabilizing interactions at the icosahedral 3-fold axes and the R domains differed greatly. The heterogeneity in the R domains among the members of the Tombusviridae family is likely correlated with differences in the sizes and characteristics of the corresponding genomes. We propose that the changes in the R domain/RNA interactions evolved different arm domain interactions at the β-annuli. For example, RCNMV has the largest genome and it appears to have created the necessary space in the capsid by evolving the shortest R domain. The resulting loss in RNA/R domain interactions may have been compensated for by increased intersubunit β-strand interactions at the icosahedral 3-fold axes. Therefore, the R and arm domains may have coevolved to package different genomes within the conserved and rigid shell. IMPORTANCE Members of the Tombusviridae family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the “arm,” seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.}, number={2}, journal={JOURNAL OF VIROLOGY}, publisher={American Society for Microbiology}, author={Sherman, Michael B. and Guenther, Richard and Reade, Ron and Rochon, D'Ann and Sit, Tim and Smith, Thomas J.}, editor={Parrish, Colin R.Editor}, year={2020}, month={Jan} }
 @article{ellis_hoak_ellis_brown_sit_wilkinson_reed_welbaum_2020, title={Quantitative Real-Time PCR Analysis of Individual Flue-Cured Tobacco Seeds and Seedlings Reveals Seed Transmission of Tobacco Mosaic Virus}, volume={110}, ISSN={["1943-7684"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077670623&partnerID=MN8TOARS}, DOI={10.1094/PHYTO-06-19-0201-FI}, abstractNote={Tobacco mosaic virus (TMV) is an extensively studied RNA virus known to infect tobacco (Nicotiana tabacum L.) and other Solanaceous crops. TMV has been classified as a seedborne virus in tobacco. The mechanism of TMV transmission through seed was studied in seed of K 326 cultivar of flue-cured tobacco. Cross pollinations were performed to determine effect of parental tissue on TMV infection in seed. Dissection of individual tobacco seed into seed coat, endosperm, and embryo was performed to determine TMV location within a seed, while separation of the developing seedling into seed coat, roots, and cotyledons were conducted to estimate the percent transmission of TMV. A reverse-transcriptase quantitative PCR (RT-qPCR) assay was developed and used to determine TMV concentrations in individual seed harvested from pods that formed on plants from TMV infected and non-infected crosses. Results showed maternal transmission of TMV to tobacco seed and seedlings developed from infected seed, not paternal transmission. RT-qPCR and endpoint PCR assays were also conducted on the separated seed coat, endosperm, and embryo of individual seed, and separated cotyledons, roots, and seed coat of individual seedlings that developed from infected tobacco seed. RT-qPCR and endpoint PCR assay results showed evidence of TMV infection in the endosperm and embryo, as well as in the developing seedling roots and cotyledons within 10 days of initiating seed germination. To our knowledge, this is the first report of TMV being detected in embryos of tobacco seeds, demonstrating that TMV is seedborne and seed-transmitted in flue-cured tobacco.}, number={1}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Ellis, Madeleine D. and Hoak, Jessica M. and Ellis, Bradley W. and Brown, Jessica A. and Sit, Tim L. and Wilkinson, Carol A. and Reed, T. David and Welbaum, Gregory E.}, year={2020}, month={Jan}, pages={194–205} }
 @article{pirzada_farias_mathew_guenther_byrd_sit_pal_opperman_khan_2020, title={Recent Advances in Biodegradable Matrices for Active Ingredient Release in Crop Protection: Towards Attaining Sustainability in Agriculture}, volume={48}, url={http://dx.doi.org/10.1016/j.cocis.2020.05.002}, DOI={10.1016/j.cocis.2020.05.002}, abstractNote={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. Herein, we discuss some of the recent approaches to use biodegradable matrices in crop protection, while exploring their design and efficiency. We summarize by discussing associated challenges with the existing approaches and future trends that can lead the world to more sustainable agricultural practices.}, journal={Current Opinion in Colloid & Interface Science}, author={Pirzada, Tahira and Farias, Barbara V. and Mathew, Reny and Guenther, Richard H. and Byrd, Medwick V. and Sit, Tim L. and Pal, Lokendra and Opperman, Charles H. and Khan, Saad A.}, year={2020}, month={May}, pages={121–136} }
 @article{linak_jacobson_sit_kennedy_2020, title={Relationships of virus titers and transmission rates among sympatric and allopatric virus isolates and thrips vectors support local adaptation}, volume={10}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-020-64507-1}, DOI={10.1038/s41598-020-64507-1}, abstractNote={Abstract 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. tabaci . This study characterizes differences in virus titers in the vector among TSWV isolate- T. tabaci isoline pairings in relation to differences in transmission rates, and demonstrates that although transmission rates were higher for sympatric than allopatric TSWV isolate- T. tabaci isoline pairings, virus titers in the thrips vector were significantly lower in the sympatric pairings. Results further demonstrate that TSWV titers in the vector were unrelated to virus titers in the leaf tissue from which they acquired the virus and provide evidence for the importance of specific vector-virus interactions and local adaptation in determining transmission efficiency of TSWV by T. tabaci .}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Linak, Jessica A. and Jacobson, Alana L. and Sit, Tim L. and Kennedy, George G.}, year={2020}, month={May} }
 @article{pirzada_mathew_guenther_sit_opperman_pal_khan_2020, title={Tailored Lignocellulose-Based Biodegradable Matrices with Effective Cargo Delivery for Crop Protection}, volume={8}, ISSN={2168-0485 2168-0485}, url={http://dx.doi.org/10.1021/acssuschemeng.9b05670}, DOI={10.1021/acssuschemeng.9b05670}, abstractNote={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. The tailored matrix is produced by mechanical treatment of the lignocellulosic fibers obtained from banana plants. The effect of different extents of mechanical treatments of the lignocellulosic fibers on the protective properties of the developed matrices is systematically investigated. While variation in mechanical treatment affects the morphology, strength, and porosity of the matrices, the specific composition and structure of the fibers are also capable of influencing their release profile. To corroborate this hypothesis, the effect of morphology and lignin content changes on the release of rhodamine B and abamectin as model cargos is investigated. These results, compared with those of the matrices developed from non-banana fibrous sources, reveal a unique release profile of the matrices developed from banana fibers, thereby making them strong candidates for crop protection applications.}, number={17}, journal={ACS Sustainable Chemistry & Engineering}, publisher={American Chemical Society (ACS)}, author={Pirzada, Tahira and Mathew, Reny and Guenther, Richard H. and Sit, Tim L. and Opperman, Charles H. and Pal, Lokendra and Khan, Saad A.}, year={2020}, month={Mar}, pages={6590–6600} }
 @article{ruark-seward_davis_sit_2019, title={Electropermeabilization-based fluorescence in situ hybridization of whole-mount plant parasitic nematode specimens}, volume={6}, ISSN={["2215-0161"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85075266069&partnerID=MN8TOARS}, DOI={10.1016/j.mex.2019.11.009}, abstractNote={A fluorescence in situ hybridization (FISH) protocol was developed for nematodes in which nucleic acid probes are introduced within the organism via 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; Heterodera glycines) and has been used to identify both host and associated-microbial (viral) targets. Moreover, through the use of two different long wavelength fluorophores, two probes can be colocalized within one individual. This protocol may be adapted to identify targets-of-interest within other life stages and nematode species.This protocol improves:•Hands-on protocol time (by approximately 1.5 h).•Specimen loss (fewer aspiration steps).•Hybridization (allows colocalization with two nucleic acid probes and increases sensitivity).}, journal={METHODSX}, publisher={Elsevier BV}, author={Ruark-Seward, Casey L. and Davis, Eric L. and Sit, Tim L.}, year={2019}, pages={2720–2728} }
 @article{farias_pirzada_mathew_sit_opperman_khan_2019, title={Electrospun Polymer Nanofibers as Seed Coatings for Crop Protection}, volume={7}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85075621824&partnerID=MN8TOARS}, DOI={10.1021/acssuschemeng.9b05200}, abstractNote={Ineffective delivery of pesticides leads to multiple application cycles of active ingredients (AIs), resulting in increased cost while endangering the environment via soil, water, and air contamina...}, number={24}, journal={ACS Sustainable Chemistry & Engineering}, publisher={American Chemical Society (ACS)}, author={Farias, Barbara V. and Pirzada, Tahira and Mathew, Reny and Sit, Tim L. and Opperman, Charles and Khan, Saad A.}, year={2019}, month={Nov}, pages={19848–19856} }
 @article{steckelberg_akiyama_costantino_sit_nix_kieft_2018, title={A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure}, volume={115}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85048961823&partnerID=MN8TOARS}, DOI={10.1073/pnas.1802429115}, abstractNote={Significance}, number={25}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Steckelberg, Anna-Lena and Akiyama, Benjamin M. and Costantino, David A. and Sit, Tim L. and Nix, Jay C. and Kieft, Jeffrey S.}, year={2018}, month={Jun}, pages={6404–6409} }
 @article{diepenbrock_lundgren_sit_burrack_2018, title={Detecting Specific Resource Use by Drosophila suzukii (Diptera: Drosophilidae) Using Gut Content Analysis}, volume={111}, ISSN={["1938-291X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052551988&partnerID=MN8TOARS}, DOI={10.1093/jee/toy077}, abstractNote={Abstract 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. Using strawberry as a focal host and available DNA primers, we validated that DNA from this host could be detected for up to 7 d post-consumption. With the development of specific primers for additional hosts, we expect that this technique will enable researchers to better understand how D. suzukii adults use, and move between, nutritional resources.}, number={3}, journal={JOURNAL OF ECONOMIC ENTOMOLOGY}, publisher={Oxford University Press (OUP)}, author={Diepenbrock, Lauren M. and Lundgren, Jonathan G. and Sit, Tim L. and Burrack, Hannah J.}, year={2018}, month={Jun}, pages={1496–1500} }
 @article{ruark_gardner_mitchum_davis_sit_2018, title={Novel RNA viruses within plant parasitic cyst nematodes}, volume={13}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85042946067&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0193881}, abstractNote={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. Several of the SCN viruses were also confirmed within clover (H. trifolii) and beet (H. schachtii) cyst nematodes. In the presented study, we sequenced the transcriptomes of several inbred SCN populations and identified two previously undiscovered viral-like genomes. Both of these proposed viruses are negative-sense RNA viruses and have been named SCN nyami-like virus (NLV) and SCN bunya-like virus (BLV). Finally, we analyzed publicly available transcriptome data of two potato cyst nematode (PCN) species, Globodera pallida and G. rostochiensis. From these data, a third potential virus was discovered and called PCN picorna-like virus (PLV). PCN PLV is a positive-sense RNA virus, and to the best of our knowledge, is the first virus described within PCN. The presence of these novel viruses was confirmed via qRT-PCR, endpoint PCR, and Sanger sequencing with the exception of PCN PLV due to quarantine restrictions on the nematode host. While much work needs to be done to understand the biological and evolutionary significance of these viruses, they offer insight into nematode ecology and the possibility of novel nematode management strategies.}, number={3}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Ruark, Casey L. and Gardner, Michael and Mitchum, Melissa G. and Davis, Eric L. and Sit, Tim L.}, editor={Melcher, UlrichEditor}, year={2018}, month={Mar} }
 @article{guenther_lommel_opperman_sit_2018, title={Plant Virus-Based Nanoparticles for the Delivery of Agronomic Compounds as a Suspension Concentrate}, volume={1776}, ISBN={["978-1-4939-7806-9"]}, ISSN={["1940-6029"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85048246738&partnerID=MN8TOARS}, DOI={10.1007/978-1-4939-7808-3_13}, abstractNote={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.}, journal={VIRUS-DERIVED NANOPARTICLES FOR ADVANCED TECHNOLOGIES: METHODS AND PROTOCOLS}, publisher={Springer New York}, author={Guenther, Richard H. and Lommel, Steven A. and Opperman, Charles H. and Sit, Tim L.}, year={2018}, pages={203–214} }
 @article{ruark_koenning_davis_opperman_lommel_mitchum_sit_2017, title={Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses}, volume={12}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85011268632&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0171514}, abstractNote={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. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation.}, number={1}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Ruark, Casey L. and Koenning, Stephen R. and Davis, Eric L. and Opperman, Charles H. and Lommel, Steven A. and Mitchum, Melissa G. and Sit, Tim L.}, editor={Rao, A.L.N.Editor}, year={2017}, month={Jan} }
 @article{cao_guenther_sit_lommel_opperman_willoughby_2016, title={Development of abamectin loaded lignocellulosic matrices for the controlled release of nematicide for crop protection}, volume={23}, ISSN={["1572-882X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84955651797&partnerID=MN8TOARS}, DOI={10.1007/s10570-015-0817-6}, number={1}, journal={CELLULOSE}, publisher={Springer Science and Business Media LLC}, author={Cao, Jing and Guenther, Richard H. and Sit, Tim L. and Lommel, Steven A. and Opperman, Charles H. and Willoughby, Julie A.}, year={2016}, month={Feb}, pages={673–687} }
 @article{cao_guenther_sit_lommel_opperman_willoughby_2015, title={Development of Abamectin Loaded Plant Virus Nanoparticles for Efficacious Plant Parasitic Nematode Control}, volume={7}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/ACSAMI.5B00940}, DOI={10.1021/acsami.5b00940}, abstractNote={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. In this study, we manipulated Abm's soil physical chemistry by encapsulating Abm within the Red clover necrotic mosaic virus (RCNMV) to produce a plant virus nanoparticle (PVN) delivery system for Abm. The transmission electron microscopic and dynamic light scattering characterization of Abm-loaded PVN (PVN(Abm)) indicated the resultant viral capsid integrity and morphology comparable to native RCNMV. In addition, the PVN(Abm) significantly increased Abm's soil mobility while enabling a controlled release strategy for Abm's bioavailability to nematodes. As a result, PVN(Abm) enlarged the zone of protection from Meloidogyne hapla root knot nematodes in the soil as compared to treating with free Abm molecules. Tomato seedlings treated with PVN(Abm) had healthier root growth and a reduction in root galling demonstrating the success of this delivery system for the increased efficacy of Abm to control nematode damage in crops.}, number={18}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Cao, Jing and Guenther, Richard H. and Sit, Tim L. and Lommel, Steven A. and Opperman, Charles H. and Willoughby, Julie A.}, year={2015}, month={May}, pages={9546–9553} }
 @article{sit_lommel_2015, title={Tombusviridae}, DOI={10.1002/9780470015902.a0000756.pub3}, abstractNote={Abstract The Tombusviridae is a relatively large and diverse family of plant viruses that have small single‐stranded, positive‐sense, RNA (ribonucleic acid) genomes which have been grouped together owing to the high degree of sequence identity displayed by their RNA ‐dependent RNA polymerases. Tombusvirid virion structures, gene expression strategies, replication, RNA recombination, virus movement and the support of satellite viruses/defective‐interfering RNAs have been particularly well characterised. All genera (with the exception of the Umbraviruses ) produce spherical virions with capsid proteins that can be subdivided by the presence (or absence) of a C ‐terminal protruding domain. Transmission of several members by fungal zoospores in a species‐specific manner has been reported while aphid transmission of Umbraviruses is completely dependent on a helper virus from the Luteoviridae . The virions of several members have been utilised for biotechnology purposes. Key Concepts Various genera most likely arose through RNA recombination. Tombusviridae species replicate to high titres within their host cells. RNA genomes are small with a limited number of gene products that serve multiple functions. RNA–RNA interactions control gene expression in several genera. Viral‐encoded suppressors of RNA silencing act at several different stages in the response cascade. Virions (if present) are non‐enveloped and extremely stable. Several members are transmitted through soil by specific fungal zoospores.}, journal={eLS}, author={Sit, Tim L and Lommel, Steven A}, year={2015}, month={Nov} }
 @article{cao_guenther_sit_opperman_lommel_willoughby_2014, title={Loading and Release Mechanism of Red Clover Necrotic Mosaic Virus Derived Plant Viral Nanoparticles for Drug Delivery of Doxorubicin}, volume={10}, ISSN={["1613-6829"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84919761332&partnerID=MN8TOARS}, DOI={10.1002/smll.201400558}, abstractNote={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. Bimodal release kinetics is achieved via a rapid release of surface‐Dox followed by a slow release of encapsulated Dox. Moreover, the rate of Dox release and the amount of released Dox increases with an increase in environmental pH or a decrease in concentration of divalent cations. This pH‐responsive Dox release from PVN is controlled by Fickian diffusion kinetics where the release rate is dependent on the location of the bound or loaded active molecule. In summary, controllable release of Dox‐loaded PVNs is imparted by 1) formulation conditions and 2) driven by the capsid's pH‐ and ion‐ responsive functions in a given environment.}, number={24}, journal={SMALL}, publisher={Wiley}, author={Cao, Jing and Guenther, Richard H. and Sit, Tim L. and Opperman, Charles H. and Lommel, Steven A. and Willoughby, Julie A.}, year={2014}, month={Dec}, pages={5126–5136} }
 @article{bozinovic_sit_giulio_wills_oleksiak_2013, title={Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84887326217&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-14-779}, abstractNote={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. We exposed embryos from these two populations to surrogate model PAHs and analyzed changes in gene expression, morphology, and cardiac physiology in order to better understand sensitivity and adaptive resistance mechanisms mediating PAH exposure during development.The synergistic effects of two model PAHs, an aryl hydrocarbon receptor (AHR) agonist (β-naphthoflavone) and a cytochrome P4501A (CYP1A) inhibitor (α-naphthoflavone), caused significant developmental delays, impaired cardiac function, severe morphological alterations and failure to hatch, leading to the deaths of reference embryos; resistant embryos were mostly unaffected. Unexpectedly, patterns of gene expression among normal and moderately deformed embryos were similar, and only severely deformed embryos showed a contrasting pattern of gene expression. Given the drastic morphological differences between reference and resistant embryos, a surprisingly low percentage of genes, 2.24% of 6,754 analyzed, show statistically significant differences in transcript levels during late organogenesis between the two embryo populations.Our study demonstrates important contrasts in responses between reference and resistant natural embryo populations to synergistic effects of surrogate model PAHs that may be important in adaptive mechanisms mediating PAH effects during fish embryo development. These results suggest that statistically significant changes in gene expression of relatively few genes contribute to the phenotypic changes and large morphological differences exhibited by reference and resistant populations upon exposure to PAH pollutants. By correlating cardiac physiology and morphology with changes in gene expression patterns of reference and resistant embryos, we provide additional evidence for acquired resistance among embryos whose parents live at heavily contaminated sites.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Bozinovic, Goran and Sit, Tim L and Giulio, Richard Di and Wills, Lauren F and Oleksiak, Marjorie F}, year={2013}, pages={779} }
 @article{martin_he_meilleur_guenther_sit_lommel_heller_2013, title={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}, volume={158}, ISSN={["0304-8608"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84880793442&partnerID=MN8TOARS}, DOI={10.1007/s00705-013-1650-6}, number={8}, journal={ARCHIVES OF VIROLOGY}, publisher={Springer Science and Business Media LLC}, author={Martin, Stanton L. and He, Lilin and Meilleur, Flora and Guenther, Richard H. and Sit, Tim L. and Lommel, Steven A. and Heller, William T.}, year={2013}, month={Aug}, pages={1661–1669} }
 @article{park_sit_kim_lommel_2013, title={The red clover necrotic mosaic virus capsid protein N-terminal amino acids possess specific RNA binding activity and are required for stable virion assembly}, volume={176}, ISSN={["0168-1702"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84881374230&partnerID=MN8TOARS}, DOI={10.1016/j.virusres.2013.05.014}, abstractNote={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. Other viral and non-viral RNA probes displayed CP binding but to a much lower degree. Deletion of the highly basic N-terminal 50 residues abolished CP binding to viral RNA transcripts. In planta studies of select CP deletion mutants within this N-terminal region revealed that it was indispensable for stable virion formation and the region spanning CP residues 5–15 is required for systemic movement. Thus, the N-terminal region of the CP is involved in both producing two virion populations due to its RNA binding properties and virion stability.}, number={1-2}, journal={VIRUS RESEARCH}, publisher={Elsevier BV}, author={Park, Sang-Ho and Sit, Tim L. and Kim, Kook-Hyung and Lommel, Steven A.}, year={2013}, month={Sep}, pages={107–118} }
 @article{park_sit_kim_lommel_2012, title={The Red clover necrotic mosaic virus capsid protein N-terminal lysine-rich motif is a determinant of symptomatology and virion accumulation}, volume={13}, ISSN={["1364-3703"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84864388918&partnerID=MN8TOARS}, DOI={10.1111/j.1364-3703.2011.00784.x}, abstractNote={SUMMARY}, number={7}, journal={MOLECULAR PLANT PATHOLOGY}, publisher={Wiley}, author={Park, Sang-Ho and Sit, Tim L. and Kim, Kook-Hyung and Lommel, Steven A.}, year={2012}, month={Sep}, pages={744–754} }
 @article{sit_lommel_2011, title={Dianthovirus}, DOI={10.1007/978-0-387-95919-1_310}, journal={The Springer Index of Viruses}, publisher={Springer New York}, author={Sit, Tim L. and Lommel, Steven A.}, year={2011}, pages={1895–1900} }
 @article{bozinovic_sit_hinton_oleksiak_2011, title={Gene expression throughout a vertebrate's embryogenesis}, volume={12}, ISSN={["1471-2164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79952053301&partnerID=MN8TOARS}, DOI={10.1186/1471-2164-12-132}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, publisher={Springer Science and Business Media LLC}, author={Bozinovic, Goran and Sit, Tim L. and Hinton, David E. and Oleksiak, Marjorie F.}, year={2011}, month={Feb} }
 @article{martin_guenther_sit_swartz_meilleur_lommel_rose_section_2010, title={Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus}, volume={66}, ISSN={["2053-230X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-78149304361&partnerID=MN8TOARS}, DOI={10.1107/s1744309110032483}, abstractNote={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. The crystals diffracted to better than 4 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 Å in the analysis presented here.}, number={11}, journal={ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS}, author={Martin, S.L. and Guenther, R.H. and Sit, T.L. and Swartz, P.D. and Meilleur, Flora and Lommel, S.A. and Rose, Robert and Section, F.}, year={2010}, month={Nov}, pages={1458–1462} }
 @article{sit_lommel_2010, title={Tombusviridae}, DOI={10.1002/9780470015902.a0000756.pub2}, abstractNote={Abstract The Tombusviridae is a relatively large and diverse family of soil‐borne viruses that have single‐stranded, positive‐sense, RNA ( ribonucleic acid ) genomes and that share morphological, structural, molecular and genetic features. Their high titres, compact genomes and extremely stable virions lend to their attractiveness as research subjects. Indeed, the Tombusviridae are a particularly well‐characterized family of viruses in the areas of virus structure, gene expression strategies, virus movement, the support of satellite viruses and defective‐interfering RNAs as well as RNA recombination. Although the RNA‐dependent RNA polymerases share a great deal of sequence identity, the capsid proteins can be separated by the presence (or absence) of a C ‐terminal protruding domain which gives the virions a bumpy appearance in electron micrographs. Transmission of several members by fungal zoospores in a species‐specific manner has been reported. The virions of several members have been utilized for biotechnology purposes. Key Concepts: Virions are nonenveloped and extremely stable. Tombusviridae species replicate to high titres within their host cells. RNA genomes are small with a limited number of gene products that serve multiple functions. RNA–RNA interactions control gene expression in several genera. Viral‐encoded suppressors of RNA silencing act at several different stages in the response cascade. Several members transmitted through soil by specific fungal zoospores.}, journal={Encyclopedia of Life Sciences}, author={Sit, Tim L and Lommel, Steven A}, year={2010}, month={Apr} }
 @article{basnayake_sit_lommel_2009, title={The Red clover necrotic mosaic virus origin of assembly is delimited to the RNA-2 trans-activator}, volume={384}, ISSN={["0042-6822"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-58549086327&partnerID=MN8TOARS}, DOI={10.1016/j.virol.2008.11.005}, abstractNote={The bipartite RNA genome of Red clover necrotic mosaic virus (RCNMV) is encapsidated into icosahedral virions that exist as two populations: i) virions that co-package both genomic RNAs and ii) virions packaging multiple copies of RNA-2. To elucidate the packaging mechanism, we sought to identify the RCNMV origin of assembly sequence (OAS). RCNMV RNA-1 cannot package in the absence of RNA-2 suggesting that it does not contain an independent packaging signal. A 209 nt RNA-2 element expressed from the Tomato bushy stunt virus CP subgenomic promoter is co-assembled with genomic RNA-1 into virions. Deletion mutagenesis delimited the previously characterized 34 nt trans-activator (TA) as the minimal RCNMV OAS. From this study we hypothesize that RNA-1 must be base-paired with RNA-2 at the TA to initiate co-packaging. The addition of viral assembly illustrates the critical importance of the multifunctional TA element as a key regulatory switch in the RCNMV life cycle.}, number={1}, journal={VIROLOGY}, publisher={Elsevier BV}, author={Basnayake, Veronica R. and Sit, Tim L. and Lommel, Steven A.}, year={2009}, month={Feb}, pages={169–178} }
 @article{powers_sit_qu_morris_kim_lommel_2008, title={A versatile assay for the identification of RNA silencing suppressors based on complementation of viral movement}, volume={21}, ISSN={["1943-7706"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-47549110190&partnerID=MN8TOARS}, DOI={10.1094/MPMI-21-7-0879}, abstractNote={ The cell-to-cell movement of Turnip crinkle virus (TCV) in Nicotiana benthamiana requires the presence of its coat protein (CP), a known suppressor of RNA silencing. RNA transcripts of a TCV construct containing a reporter gene (green fluorescent protein) (TCV-sGFP) in place of the CP open reading frame generated foci of three to five cells. TCV CP delivered in trans by Agrobacterium tumefaciens infiltration potentiated movement of TCV-sGFP and increased foci diameter, on average, by a factor of four. Deletion of the TCV movement proteins in TCV-sGFP (construct TCVΔ92-sGFP) abolished the movement complementation ability of TCV CP. Other known suppressors of RNA silencing from a wide spectrum of viruses also complemented the movement of TCV-sGFP when delivered in trans by Agrobacterium tumefaciens. These include suppressors from nonplant viruses with no known plant movement function, demonstrating that this assay is based solely on RNA silencing suppression. While the TCV-sGFP construct is primarily used as an infectious RNA transcript, it was also subcloned for direct expression from Agrobacterium tumefaciens for simple quantification of suppressor activity based on fluorescence levels in whole leaves. Thus, this system provides the flexibility to assay for suppressor activity in either the cytoplasm or nucleus, depending on the construct employed. }, number={7}, journal={MOLECULAR PLANT-MICROBE INTERACTIONS}, publisher={Scientific Societies}, author={Powers, Jason G. and Sit, Tim L. and Qu, Feng and Morris, T. Jack and Kim, Kook-Hyung and Lommel, Steven A.}, year={2008}, month={Jul}, pages={879–890} }
 @article{powers_sit_heinsohn_george_kim_lommel_2008, title={The Red clover necrotic mosaic virus RNA-2 encoded movement protein is a second suppressor of RNA silencing}, volume={381}, ISSN={["0042-6822"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-54549091972&partnerID=MN8TOARS}, DOI={10.1016/j.virol.2008.09.004}, abstractNote={The replication complex of Red clover necrotic mosaic virus (RCNMV) has been shown to possess silencing suppression activity. Here a newly developed viral-based assay for the identification of silencing suppression activity was used to provide evidence for a second, mechanistically distinct method of silencing suppression provided for by the RCNMV movement protein (MP). This new assay relies on Turnip crinkle virus with its capsid protein replaced with green fluorescent protein to act as a reporter (TCV-sGFP). In the presence of a protein with silencing suppression activity TCV-sGFP readily moves from cell-to-cell, but in the absence of such a protein TCV-sGFP is confined to small foci of infection. This TCV-sGFP assay was used to identify MP as a suppressor of RNA silencing, to delimit essential amino acids for this activity and uncouple silencing and movement functions.}, number={2}, journal={VIROLOGY}, publisher={Elsevier BV}, author={Powers, Jason G. and Sit, Tim L. and Heinsohn, Curtis and George, Carol G. and Kim, Kook-Hyung and Lommel, Steven A.}, year={2008}, month={Nov}, pages={277–286} }
 @article{lommel_sit_2008, title={Tombusviruses}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85069936114&partnerID=MN8TOARS}, DOI={10.1016/b978-012374410-4.00382-4}, journal={Encyclopedia of Virology}, publisher={Elsevier}, author={Lommel, S.A. and Sit, T.L.}, year={2008}, pages={145–151} }
 @article{tompkins_sit_wallace_2008, title={Unique transcription start sites and distinct promoter regions differentiate the pregnane X receptor (PXR) isoforms PXR 1 and PXR 2}, volume={36}, ISSN={["1521-009X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-42449091555&partnerID=MN8TOARS}, DOI={10.1124/dmd.107.018317}, abstractNote={The pregnane X receptor (PXR) is known as the xenosensing receptor responsible for coordinated regulation of metabolic genes in response to diverse xenobiotic challenges. In particular, the ability of the PXR to regulate CYP3A4, the enzyme capable of metabolizing more than 60% of all pharmaceuticals, defines its metabolic importance. Currently the list of PXR ligands and target genes is extensive, yet investigations into the regulation and expression of PXRs are few. After an initial review of available sequence data, we discovered discrepancies in the 5′ untranslated region (UTR) and transcriptional start site (TSS) characterizations of the human PXR gene and subsequently endeavored to define TSSs and proximal promoters for isoforms PXR 1 and PXR 2. Reverse transcriptase-polymerase chain reaction and primer extension experiments performed on RNA from human liver identified two TSSs for each receptor isoform. These results extended the 5′UTR sequence of each isoform and defined new proximal promoters for both. Candidate response elements for liver-enriched transcription factors and other receptors were found in both proximal promoters. Quantitative PCR from human liver illustrated a highly variable expression profile for total PXRs; yet PXR 2 expression represented a consistent 2 to 5% of total PXR expression, despite the observed variability. Transfection experiments demonstrated that PXR 1 and PXR 2 had comparable abilities to transcriptionally activate the CYP3A4 promoter. Collectively, comparable function, consistent expression, and independent regulation suggest that PXR 2 is capable of contributing to the cumulative function of PXRs and should be included in the larger investigations of PXR expression and regulation.}, number={5}, journal={DRUG METABOLISM AND DISPOSITION}, publisher={American Society for Pharmacology & Experimental Therapeutics (ASPET)}, author={Tompkins, Leslie M. and Sit, Tim L. and Wallace, Andrew D.}, year={2008}, month={May}, pages={923–929} }
 @article{franzen_belyea_gilvey_davis_chaudhary_sit_lommel_2006, title={Proximal cavity, distal histidine, and substrate hydrogen-bonding mutations modulate the activity of Amphitrite ornata dehaloperoxidase}, volume={45}, ISSN={["0006-2960"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33746584767&partnerID=MN8TOARS}, DOI={10.1021/bi060020z}, abstractNote={Dehaloperoxidase (DHP) from Amphitrite ornata is the first globin that has peroxidase activity that approaches that of heme peroxidases. The substrates 2,4,6-tribromophenol (TBP) and 2,4,6-trichlorophenol are oxidatively dehalogenated by DHP to form 2,6-dibromo-1,4-benzoquinone and 2,6-dichloro-1,4-benzoquinone, respectively. There is a well-defined internal substrate-binding site above the heme, a feature not observed in other globins or peroxidases. Given that other known heme peroxidases act on the substrate at the heme edge there is great interest in understanding the possible modes of substrate binding in DHP. Stopped-flow studies (Belyea, J., Gilvey, L. B., Davis, M. F., Godek, M., Sit, T. L., Lommel, S. A., and Franzen, S. (2005) Biochemistry 44, 15637-15644) show that substrate binding must precede the addition of H2O2. This observation suggests that the mechanism of DHP relies on H2O2 activation steps unlike those of other known peroxidases. In this study, the roles of the distal histidine (H55) and proximal histidine (H89) were probed by the creation of site-specific mutations H55R, H55V, H55V/V59H, and H89G. Of these mutants, only H55R shows significant enzymatic activity. H55R is 1 order of magnitude less active than wild-type DHP and has comparable activity to sperm whale myoglobin. The role of tyrosine 38 (Y38), which hydrogen bonds to the hydroxyl group of the substrate, was probed by the mutation Y38F. Surprisingly, abolishing this hydrogen bond increases the activity of the enzyme for the substrate TBP. However, it may open a pathway for the escape of the one-electron product, the phenoxy radical leading to polymeric products.}, number={30}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Franzen, Stefan and Belyea, Jennifer and Gilvey, Lauren B. and Davis, Michael F. and Chaudhary, Chelsea E. and Sit, Tim L. and Lommel, Steven A.}, year={2006}, month={Aug}, pages={9085–9094} }
 @article{sherman_guenther_tama_sit_brooks_mikhailov_orlova_baker_lommel_2006, title={Removal of divalent cations induces structural transitions in Red clover necrotic mosaic virus, revealing a potential mechanism for RNA release}, volume={80}, ISSN={["1098-5514"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33750318283&partnerID=MN8TOARS}, DOI={10.1128/JVI.01137-06}, abstractNote={ABSTRACT}, number={21}, journal={JOURNAL OF VIROLOGY}, publisher={American Society for Microbiology}, author={Sherman, Michael B. and Guenther, Richard H. and Tama, Florence and Sit, Tim L. and Brooks, Charles L. and Mikhailov, Albert M. and Orlova, Elena V. and Baker, Timothy S. and Lommel, Steven A.}, year={2006}, month={Nov}, pages={10395–10406} }
 @article{basnayake_sit_lommel_2006, title={The genomic RNA packaging scheme of Red clover necrotic mosaic virus}, volume={345}, ISSN={["0042-6822"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-31944440651&partnerID=MN8TOARS}, DOI={10.1016/j.virol.2005.10.017}, abstractNote={Red clover necrotic mosaic virus (RCNMV) is a small icosahedral plant virus with a bipartite RNA genome. While the RCNMV genome consists of two RNAs, it has not been definitively established whether these RNAs are co-packaged into a single virion or packaged individually into separate virions. Biochemical evidence exists to support both hypotheses. To determine the genomic RNA complement within RCNMV, virions were subjected to heat treatments and UV crosslinking. A stable RNA-1:RNA-2 heterodimer was formed with both treatments establishing that RCNMV genomic RNAs are co-packaged into a single virion. Furthermore, RNA-2 homodimer and homotrimers were also observed indicating that some virions contain multiple copies of RNA-2 exclusively. These results indicate that RCNMV virions consist of two distinct populations: (i) virions containing both genomic RNAs; and (ii) virions with multiple copies of RNA-2. This type of hybrid packaging arrangement was unexpected and appears to be unique among the multipartite RNA viruses.}, number={2}, journal={VIROLOGY}, publisher={Elsevier BV}, author={Basnayake, VR and Sit, TL and Lommel, SA}, year={2006}, month={Feb}, pages={532–539} }
 @article{tremblay_vaewhongs_turner_sit_lommel_2005, title={Cell wall localization of Red clover necrotic mosaic virus movement protein is required for cell-to-cell movement}, volume={333}, ISSN={["0042-6822"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-13644249879&partnerID=MN8TOARS}, DOI={10.1016/j.virol.2004.12.019}, abstractNote={The Red clover necrotic mosaic virus movement protein (MP) is essential for cell-to-cell movement. Eight previously characterized alanine-scanning mutants of the MP were fused to the green fluorescent protein (GFP) and expressed from viral infectious transcripts. Inoculated plants were assayed for movement and intracellular accumulation of MP by confocal laser-scanning microscopy. A strict correlation was observed between the targeting to the cell wall (presumably the plasmodesmata) and cell-to-cell movement. Complementation of dysfunctional MP mutants with either wild-type MP or other null mutants in some cases rescued intracellular targeting and movement. The data suggest the presence of distinct domains in the MP for virus movement (near residues 27–31), complementarity (near residues 122 and 128), and intracellular localization (near residue 161). These data support a model of MP interacting cooperatively with itself to bind viral RNA, localize to and modify plasmodesmata and effect virus movement.}, number={1}, journal={VIROLOGY}, publisher={Elsevier BV}, author={Tremblay, D and Vaewhongs, AA and Turner, KA and Sit, TL and Lommel, SA}, year={2005}, month={Mar}, pages={10–21} }
 @article{belyea_gilvey_davis_godek_sit_lommel_franzen_2005, title={Enzyme function of the globin dehaloperoxidase from Amphitrite ornata is activated by substrate binding}, volume={44}, ISSN={["0006-2960"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-28544440508&partnerID=MN8TOARS}, DOI={10.1021/bi051731k}, abstractNote={Amphitrite ornata dehaloperoxidase (DHP) is a heme enzyme with a globin structure, which is capable of oxidizing para-halogenated phenols to the corresponding quinones. Cloning, high-level expression, and purification of recombinant DHP are described. Recombinant DHP was assayed by stopped-flow experiments for its ability to oxidatively debrominate 2,4,6-tribromophenol (TBP). The enzymatic activity of the ferric form of recombinant DHP is intermediate between that of a typical peroxidase (horseradish peroxidase) and a typical globin (horse heart myoglobin). The present study shows that, unlike other known peroxidases, DHP activity requires the addition of substrate, TBP, prior to the cosubstrate, peroxide. The presence of a substrate-binding site in DHP is consistent with a two-electron oxidation mechanism and an obligatory order for activation of the enzyme by addition of the substrate prior to the cosubstrate.}, number={48}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Belyea, J and Gilvey, LB and Davis, MF and Godek, M and Sit, TL and Lommel, SA and Franzen, S}, year={2005}, month={Dec}, pages={15637–15644} }
 @article{turner_sit_callaway_allen_lommel_2004, title={Red clover necrotic mosaic virus replication proteins accumulate at the endoplasmic reticulum}, volume={320}, ISSN={["0042-6822"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1542285421&partnerID=MN8TOARS}, DOI={10.1016/j.virol.2003.12.006}, abstractNote={Red clover necrotic mosaic virus (RCNMV) encodes N-terminally overlapping proteins of 27 and 88 kDa (p27 and p88) known to be required for replication. Green fluorescent protein (GFP) fusions were used to visualize the location of p27 and p88 within Nicotiana benthamiana cells. GFP:p27 fusions localized to the endoplasmic reticulum (ER), co-localized with ER-targeted yellow fluorescent protein and caused membrane restructuring and proliferation. Cellular fractionation of virus-inoculated N. benthamiana leaves confirmed the association of p27 with ER membranes. GFP:p88 fusions also localized to the ER and co-localized with GFP:p27. Both fusion proteins co-localize to the cortical and cytoplasmic ER and were associated with invaginations of the nuclear envelope. Independent accumulation in, and perturbation of, the ER suggests that p27 and p88 function together in the replication complex. This is the first report of a member of the Tombusviridae replicating in association with the ER.}, number={2}, journal={VIROLOGY}, publisher={Elsevier BV}, author={Turner, KA and Sit, TL and Callaway, AS and Allen, NS and Lommel, SA}, year={2004}, month={Mar}, pages={276–290} }
 @article{guenther_sit_gracz_dolan_townsend_liu_newman_agris_lommel_2004, title={Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus}, volume={32}, ISSN={["1362-4962"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3042761419&partnerID=MN8TOARS}, DOI={10.1093/nar/gkh585}, abstractNote={The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.}, number={9}, journal={NUCLEIC ACIDS RESEARCH}, publisher={Oxford University Press (OUP)}, author={Guenther, RH and Sit, TL and Gracz, HS and Dolan, MA and Townsend, HL and Liu, GH and Newman, WH and Agris, PF and Lommel, SA}, year={2004}, month={May}, pages={2819–2828} }
 @article{sit_haikal_callaway_lommel_2001, title={A single amino acid mutation in the Carnation ringspot virus capsid protein allows virion formation but prevents systemic infection}, volume={75}, ISSN={["0022-538X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034853341&partnerID=MN8TOARS}, DOI={10.1128/JVI.75.19.9538-9542.2001}, abstractNote={ABSTRACT}, number={19}, journal={JOURNAL OF VIROLOGY}, publisher={American Society for Microbiology}, author={Sit, TL and Haikal, PR and Callaway, AS and Lommel, SA}, year={2001}, month={Oct}, pages={9538–9542} }
 @article{reade_delroux_macdonald_sit_lommel_rochon_2001, title={Spontaneous deletion enhances movement of a cucumber necrosis virus based chimera expressing the red clover necrotic mosaic virus movement protein gene +}, volume={2}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035026811&partnerID=MN8TOARS}, DOI={10.1046/j.1364-3703.2001.00045.x}, abstractNote={Summary The 35-kDa movement protein (MP) gene of red clover necrotic mosaic virus (RCNMV) and 3' flanking sequence were inserted in a cucumber necrosis virus (CNV) deletion mutant lacking a large portion of the coding region for the MP. Nicotiana benthamiana plants inoculated with chimeric synthetic transcripts of the resulting hybrid cDNA clone (M5/RM2) developed both local and systemic symptoms and accumulated high levels of chimeric viral RNA. Reverse transcriptase polymerase chain reaction (RT-PCR) and sequence analysis of viral RNA extracted from systemically infected leaves of four different plants revealed that in each plant a large portion (305, 308, 315 or 127 nts) of the 3' terminus of the inserted sequence spontaneously deleted during infection. In three of the deletion derivatives, the truncated RCNMV MP open reading frame (ORF) was fused in-frame with the remaining portion of the 3' terminal region of CNV MP ORF. The movement efficiencies of M5/RM2, a cloned copy of one of the deletion derivatives (ClM5/RM2dd1), and a stop codon mutant of ClM5/RM2dd1 (ClM5/RM2dd1stop), which prevents translational fusion to the CNV MP, were compared and it was determined that deletion of RCNMV MP sequences in conjunction with fusion to CNV MP sequences increases the movement efficiency of the chimeric virus genome. Absence of the C-terminal region of the RCNMV MP in RCNMV RNA-2 abolished RCNMV movement. However, movement could be complemented in trans if cells were coinoculated with ClM5/RM2dd1. Complementation of RCNMV movement did not occur using ClM5/RM2dd1stop, suggesting a role for appended CNV MP sequences in movement of the RCNMV genome. The ability of the CNV replicase to delete unnecessary or deleterious RCNMV sequences and to append the required CNV MP sequences reinforces the role of RNA recombination in the adaptation and evolution of viral genomes.}, number={1}, journal={Molecular Plant Pathology}, publisher={Wiley}, author={Reade, Ron and Delroux, Karine and Macdonald, Kim and Sit, Tim L. and Lommel, Steven A. and Rochon, D'Ann}, year={2001}, month={Jan}, pages={13–25} }
 @misc{callaway_giesman-cookmeyer_gillock_sit_lommel_2001, title={The multifunctional capsid proteins of plant RNA viruses}, volume={39}, ISSN={["1545-2107"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0034799288&partnerID=MN8TOARS}, DOI={10.1146/annurev.phyto.39.1.419}, abstractNote={▪ Abstract  This article summarizes studies of viral coat (capsid) proteins (CPs) of RNA plant viruses. In addition, we discuss and seek to interpret the knowledge accumulated to date. CPs are named for their primary function; to encapsidate viral genomic nucleic acids. However, encapsidation is only one feature of an extremely diverse array of structural, functional, and ecological roles played during viral infection and spread. Herein, we consider the evolution of viral CPs and their multitude of interactions with factors encoded by the virus, host plant, or viral vector (biological transmission agent) that influence the infection and epidemiological facets of plant disease. In addition, applications of today's understanding of CPs in the protection of crops from viral infection and use in the manufacture of valuable compounds are considered.}, number={1}, journal={ANNUAL REVIEW OF PHYTOPATHOLOGY}, publisher={Annual Reviews}, author={Callaway, A and Giesman-Cookmeyer, D and Gillock, ET and Sit, TL and Lommel, SA}, year={2001}, pages={419-+} }
 @article{giesman-cookmeyer_sit_lommel_2001, title={Tombusviridae}, DOI={10.1038/npg.els.0000756}, abstractNote={Abstract The family Tombusviridae is a relatively large and diverse family of viruses that have single‐stranded, positive‐sense, RNA genomes and that share morphological, structural, molecular and genetic features. It is a particularly well‐characterized family of viruses in the areas of virus structure, gene expression strategies, virus movement and the support of satellite viruses and defective‐interfering RNAs.}, journal={Encyclopedia of Life Sciences}, author={Giesman-Cookmeyer, Donna and Sit, Tim L and Lommel, Steven A}, year={2001}, month={Aug} }
 @article{sit_vaewhongs_lommel_1998, title={RNA-mediated trans-activation of transcription from a viral RNA}, volume={281}, ISSN={["0036-8075"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032493916&partnerID=MN8TOARS}, DOI={10.1126/science.281.5378.829}, abstractNote={The red clover necrotic mosaic virus genome is composed of two single-stranded RNA components, RNA-1 and RNA-2. The viral capsid protein is translated from a subgenomic RNA (sgRNA) that is transcribed from genomic RNA-1. Here, a 34-nucleotide sequence in RNA-2 is shown to be required for transcription of sgRNA. Mutations that prevent base-pairing between the RNA-1 subgenomic promoter and the 34-nucleotide trans-activator prevent expression of a reporter gene. A model is proposed in which direct binding of RNA-2 to RNA-1 trans-activates sgRNA synthesis. This RNA-mediated regulation of transcription is unusual among RNA viruses, which typically rely on protein regulators.}, number={5378}, journal={SCIENCE}, publisher={American Association for the Advancement of Science (AAAS)}, author={Sit, TL and Vaewhongs, AA and Lommel, SA}, year={1998}, month={Aug}, pages={829–832} }
 @misc{lommel_sit_1998, title={Trans-activation of transcription from viral RNA}, volume={6,433,248}, number={1998 Jun 01}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Lommel, S. A. and Sit, T. L.}, year={1998} }
 @article{sit_johnston_borg_frison_mclean_rochon_1995, title={Mutational analysis of the cucumber necrosis virus coat protein gene}, volume={206}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028854860&partnerID=MN8TOARS}, DOI={10.1016/s0042-6822(95)80017-4}, abstractNote={A series of frameshift, deletion, and inversion mutations were made in the coat protein (CP) gene of the icosahedralcucumber necrosis tombusvirus (CNV) to investigate the role of the CP protruding (P) domain in the production of virus particles and, also, to investigate the basis for the accumulation of CP deletion derivatives previously reported in plants inoculated with PD(−), a P-domainless CNV CP mutant. P-domainless coat protein subunit could be detected in extracts of CP mutant-infected plants; however, virus-like particles could not, suggesting that the P domain is essential for tombusvirus particle assembly and/or stability. In addition, each of the P-domain mutants analyzed invariably produced coat protein deletion derivatives in infected plants whereas shell domain mutants rarely produced deletion derivatives. Finally, P-domain inversion and deletion mutants accumulated deletion derivatives very rapidly in comparison to P-domain frameshift mutants. Protoplast studies show that PD(−) RNA inoculum does not undergo further deletion in infected protoplasts, suggesting that PD(−) CP deletion derivatives preferentially accumulate in plants because they have a greater capacity for cell-to-cell movement.}, number={1}, journal={Virology}, publisher={Elsevier BV}, author={Sit, Tim L. and Johnston, Julie C. and Borg, Melanie G. Ter and Frison, Emile and McLean, Morven A. and Rochon, D'Ann}, year={1995}, month={Jan}, pages={38–48} }
 @article{rochon_finnen_sit_1994, title={Coat protein of cucumber necrosis virus is not required for efficient generation or accumulation of defective interfering RNAs}, volume={75}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028022814&partnerID=MN8TOARS}, DOI={10.1099/0022-1317-75-9-2505}, abstractNote={It is generally assumed that defective interfering (DI) forms of viruses are encapsidated in structural proteins encoded by the helper virus. Virion RNA extracts from cucumber necrosis virus (CNV) infections showing high levels of cellular DI RNAs contain barely detectable levels of DI RNAs, suggesting that DI RNAs are encapsidated very inefficiently. In addition, accumulation of CNV DI RNAs occurs at equal efficiency in coinoculated plants using either synthetic wild-type CNV genomic RNA as helper or a mutant of CNV which lacks the coat protein-coding sequence. Together this shows that the CNV coat protein is not required for efficient accumulation of CNV DI RNA in plants. Factors that could account for the high level of CNV DI RNAs in plants are discussed.}, number={9}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Rochon, D. M. and Finnen, R. L. and Sit, T. L.}, year={1994}, month={Sep}, pages={2505–2508} }
 @article{sit_leclerc_abou-haidar_1994, title={The Minimal 5′ Sequence for in Vitro Initiation of Papaya Mosaic Potexvirus Assembly}, volume={199}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028222193&partnerID=MN8TOARS}, DOI={10.1006/viro.1994.1118}, abstractNote={The minimal 5' initiation of assembly sequence for papaya mosaic virus (PMV) has been determined by the generation of successive 3' deletion clones from a full-length cDNA copy of the PMV genome followed by in vitro assembly of RNA transcripts. Sequences closest to the 5' terminus were cloned into plasmid vectors with synthetic complementary oligonucleotides representing viral sequences. The in vitro initiation sequence has been narrowed down to 38-47 nucleotides at the 5' terminus which are capable of initiation alone or in conjunction with homologous or heterologous sequences. The minimum initiation sequence is rich in adenosine and cytidine and very poor in uridine nucleotides and lacks any discernible secondary structure.}, number={1}, journal={Virology}, publisher={Elsevier BV}, author={Sit, Tim L. and Leclerc, Denis and Abou-Haidar, Mounir O.}, year={1994}, month={Feb}, pages={238–242} }
 @article{taylor_toy_sit_bognar_1993, title={Cloning and sequence determination of the valS gene, encoding valyl-tRNA synthetase in Lactobacillus casei.}, volume={175}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0027221497&partnerID=MN8TOARS}, DOI={10.1128/jb.175.8.2475-2478.1993}, abstractNote={The DNA sequence of the valS gene from Lactobacillus casei and the predicted amino acid sequence of its valyl-tRNA synthetase product have been determined. An open reading frame coding for a protein of 901 amino acids was found. A clone containing the intact L. casei valS gene functionally complemented the temperature-sensitive growth of the valS mutant strain 236c of Escherichia coli. The valS gene and the downstream folylpolyglutamate synthetase gene are transcribed in the same direction but are separated by a putative transcription terminator.}, number={8}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Taylor, B V and Toy, J and Sit, T L and Bognar, A L}, year={1993}, pages={2475–2478} }
 @article{sit_abouhaidar_1993, title={Infectious RNA transcripts derived from cloned cDNA of papaya mosaic virus: effect of mutations to the capsid and polymerase proteins}, volume={74}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0027302566&partnerID=MN8TOARS}, DOI={10.1099/0022-1317-74-6-1133}, abstractNote={Genomic length cDNAs of papaya mosaic virus (PMV) RNA were generated utilizing reverse transcriptase (RNase H-) for first strand synthesis, Sequenase for second strand synthesis and primers specific for the 5' and 3' termini of the viral genome. These cDNAs were cloned into plasmid pUC18 and infectious RNA transcripts were synthesized in vitro from a bacteriophage T7 RNA polymerase promoter incorporated into the 5' specific primer. The infectivity of transcripts was 16% that of native PMV RNA. Increasing the poly(A) tail length from A24 to A71 produced a 43% increase in infectivity. Transcripts synthesized with or without an m7GpppG cap structure were biologically active although uncapped transcripts were much less infectious. The addition of up to 2434 non-viral nucleotides at the 3' end of transcripts decreased but did not abolish infectivity. Insertions of two amino acid residues within the polymerase coding region inactivated viral transcripts. A single amino acid deletion within the capsid protein (CP) produced local lesions of a reduced size as compared to native PMV RNA. Viral particles could not be observed in crude extracts from lesions produced by this deletion mutant suggesting that it exists as a naked RNA species within the host. Mutations to the CP suggest that it is required not only for viral assembly but also for some other unidentified function(s) during the replication cycle.}, number={6}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Sit, T. L. and AbouHaidar, M. G.}, year={1993}, month={Jun}, pages={1133–1140} }
 @article{sit_white_holy_padmanabhan_eweida_hiebert_mackie_abouhaidar_1990, title={Complete nucleotide sequence of clover yellow mosaic virus RNA}, volume={71}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0024992259&partnerID=MN8TOARS}, DOI={10.1099/0022-1317-71-9-1913}, abstractNote={The entire genomic RNA of clover yellow mosaic virus was sequenced from cDNA clones and run-off cDNA transcripts. The genomic RNA is 7015 nucleotides in length [excluding a 3' poly(A) tail], with six open reading frames (ORFs) greater than 150 nucleotides in length. The first five ORFs encode proteins of Mr 191K, 26K, 12K, 6.5K and 28K, respectively. The sixth ORF lies completely within ORF1 and codes for a protein of Mr 14K. The capsid protein coding region (Mr 23K) is found within ORF5 which encodes the Mr 28K protein. Proteins encoded by ORFs 1 to 3 and ORF5 show strong homology with proteins of other potexviruses, especially papaya mosaic virus.}, number={9}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Sit, T. L. and White, K. A. and Holy, S. and Padmanabhan, U. and Eweida, M. and Hiebert, M. and Mackie, G. A. and AbouHaidar, M. G.}, year={1990}, month={Sep}, pages={1913–1920} }
 @article{eweida_sit_sira_abouhaidar_1989, title={Highly sensitive and specific non-radioactive biotinylated probes for dot-blot, Southern and colony hybridizations}, volume={26}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0024426306&partnerID=MN8TOARS}, DOI={10.1016/0166-0934(89)90072-4}, abstractNote={We describe a simple method for the incorporation of biotin into nucleic acid probes. This method has been improved and optimized to produce biotinylated DNA probes for the detection of DNA by dot-blot, Southern and colony hybridization techniques. The sensitivity of this method has been particularly improved to allow detection of DNA quantities under one femtogram. Probes prepared by this method are highly specific for target DNA even in crude bacterial lysates.}, number={1}, journal={Journal of Virological Methods}, publisher={Elsevier BV}, author={Eweida, M. and Sit, T.L. and Sira, S. and AbouHaidar, M.G.}, year={1989}, month={Oct}, pages={35–43} }
 @article{eweida_sit_abouhaidar_1989, title={Molecular cloning of the genome of the carlavirus potato virus S: biotinylated RNA transcripts for virus detection in crude potato extracts}, volume={115}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84984155243&partnerID=MN8TOARS}, DOI={10.1111/j.1744-7348.1989.tb03384.x}, abstractNote={Summary 
 
A cDNA library of potato virus S (PVS) in plasmid pBS+was produced. Insert sizes of two selected overlapping cDNA clones were 1.6 and 4.0 kbp which represent about 75% of the genomic length. Restriction enzyme mapping, hybridisation and in vitro transcription were used to determine the sense and orientation of the inserts in relation to native PVS RNA. The 4.0 kbp insert was used to produce biotinylated DNA or RNA probes for the detection of PVS and its RNA in infected potato plants. In dot-blot hybridisation biotinylated probes were highly specific with virtually no background coloration. As little as 20 femtograms of PVS RNA could be easily detected in crude plant extracts.}, number={2}, journal={Annals of Applied Biology}, publisher={Wiley}, author={EWEIDA, M. and SIT, T. L. and ABOUHAIDAR, M. G.}, year={1989}, month={Oct}, pages={253–261} }
 @article{sit_abouhaidar_holy_1989, title={Nucleotide Sequence of Papaya Mosaic Virus RNA}, volume={70}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0024730334&partnerID=MN8TOARS}, DOI={10.1099/0022-1317-70-9-2325}, abstractNote={The RNA genome of papaya mosaic virus is 6656 nucleotides long [excluding the poly(A) tail] with six open reading frames (ORFs) more than 200 nucleotides long. The four nearest the 5' end each overlap with adjacent ORFs and could code for proteins with Mr 176307, 26248, 11949 and 7224 (ORFs 1 to 4). The fifth ORF produces the capsid protein of Mr 23043 and the sixth ORF, located completely within ORF1, could code for a protein with Mr 14113. The translation products of ORFs 1 to 3 show strong similarity with those of other potexviruses but the ORF 4 protein has only limited similarity with the other potexvirus ORF 4 proteins of 7K to 11K.}, number={9}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Sit, T. L. and Abouhaidar, M. G. and Holy, S.}, year={1989}, month={Sep}, pages={2325–2331} }