@article{maurastoni_han_whitfield_rotenberg_2023, title={A call to arms: novel strategies for thrips and tospovirus control}, volume={57}, ISSN={["2214-5753"]}, DOI={10.1016/j.cois.2023.101033}, abstractNote={Thrips and the tospoviruses they transmit are some of the most significant threats to food and ornamental crop production globally. Control of the insect and virus is challenging and new strategies are needed. Characterizing the thrips-virus interactome provides new targets for disrupting the transmission cycle. Viral and insect determinants of vector competence are being defined, including the viral attachment protein and its structure as well as thrips proteins that interact with and respond to tospovirus infection. Additional thrips control strategies such as RNA interference need further refinement and field-applicable delivery systems, but they show promise for the knockdown of essential genes for thrips survival and virus transmission. The identification of a toxin that acts to deter thrips oviposition on cotton also presents new opportunities for control of this important pest.}, journal={CURRENT OPINION IN INSECT SCIENCE}, author={Maurastoni, Marlonni and Han, Jinlong and Whitfield, Anna E. and Rotenberg, Dorith}, year={2023}, month={Jun} }
 @article{lee_hossain_jamalzadegan_liu_wang_saville_shymanovich_paul_rotenberg_whitfield_et al._2023, title={Abaxial leaf surface-mounted multimodal wearable sensor for continuous plant physiology monitoring}, volume={9}, ISSN={["2375-2548"]}, DOI={10.1126/sciadv.ade2232}, abstractNote={Wearable plant sensors hold tremendous potential for smart agriculture. We report a lower leaf surface-attached multimodal wearable sensor for continuous monitoring of plant physiology by tracking both biochemical and biophysical signals of the plant and its microenvironment. Sensors for detecting volatile organic compounds (VOCs), temperature, and humidity are integrated into a single platform. The abaxial leaf attachment position is selected on the basis of the stomata density to improve the sensor signal strength. This versatile platform enables various stress monitoring applications, ranging from tracking plant water loss to early detection of plant pathogens. A machine learning model was also developed to analyze multichannel sensor data for quantitative detection of tomato spotted wilt virus as early as 4 days after inoculation. The model also evaluates different sensor combinations for early disease detection and predicts that minimally three sensors are required including the VOC sensors.}, number={15}, journal={SCIENCE ADVANCES}, author={Lee, Giwon and Hossain, Oindrila and Jamalzadegan, Sina and Liu, Yuxuan and Wang, Hongyu and Saville, Amanda C. and Shymanovich, Tatsiana and Paul, Rajesh and Rotenberg, Dorith and Whitfield, Anna E. and et al.}, year={2023}, month={Apr} }
 @article{bailey_kondragunta_choi_han_rotenberg_ullman_benoit_2023, title={Dehydration yields distinct transcriptional shifts associated with glycogen metabolism and increases feeding in the western flower thrips, <i>Frankliniella occidentalis</i>}, volume={11}, ISSN={["1570-7458"]}, DOI={10.1111/eea.13387}, abstractNote={Abstract}, journal={ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA}, author={Bailey, Samuel T. and Kondragunta, Alekhya and Choi, Hyojin A. and Han, Jinlong and Rotenberg, Dorith and Ullman, Diane E. and Benoit, Joshua B.}, year={2023}, month={Nov} }
 @article{lahre_shekasteband_meadows_whitfield_rotenberg_2023, title={First Report of Resistance-Breaking Variants of Tomato Spotted Wilt Virus (TSWV) Infecting Tomatoes with the Sw-5 Resistance Gene in North Carolina}, volume={1}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-11-22-2637-PDN}, DOI={10.1094/PDIS-11-22-2637-PDN}, abstractNote={Widespread use of tomato cultivars with the Sw-5 resistance gene has led to the emergence of resistance-breaking (RB) strains of tomato spotted wilt virus across the globe. In June of 2022, tomato spotted wilt (TSW) symptoms were observed at two farms (A and B, within 15 miles of each other) in Rowan County, NC on several commercial TSW resistant tomato cultivars (all heterozygous for the Sw-5 gene). At farm A, ~10% of plants had symptomatic foliage with ~30% of fruit with symptoms, while at farm B, up to 50% of plants had symptomatic foliage with ~80% of fruit with symptoms. Visual symptoms included stunting, severe leaf curling and bronzing, necrotic lesions on leaves, petioles and stems, and concentric ring spots on fruit (Supplementary Fig. 1). TSWV ImmunoStrips (AgDia, Elkhart, IN) and reverse-transcription (RT)-PCR with NSm primers (di Rienzo et al 2018) confirmed the presence of TSWV in 12 symptomatic plants sampled across the two farms. Primers designed to detect Impatiens necrotic spot virus, groundnut ringspot virus, tomato chlorotic spot virus, tomato chlorosis virus, alfalfa mosaic virus, and tomato necrotic streak virus (ilarvirus, Badillo et al., 2016) failed to generate amplicons of the expected size from cDNA generated from these field samples. The amplicons from full-length NSm cDNA were sequenced from independent, single-leaflet isolates from the TSWV-positive plants (three from farm A, nine from farm B) with the expectation of finding an amino acid (aa) substitution associated with the Sw-5 RB phenotype identified previously in CA (C118Y, Batuman et al. 2017) or Spain (C118Y and T120N, Lopez et al. 2011). All three nucleotide sequences from farm A contained the NSm C118Y substitution reported in CA. All three sequences were 99% identical (including the C118Y mutation) to NCBI GenBank accession KU179600.1, a TSWV isolate collected from GA in 2014 with no cultivar information reported. The nine nucleotide sequences from farm B contained neither of the two previously reported aa substitutions associated with the RB phenotype. Instead, all contained a D122G substitution within a conserved region of the TSWV NSm protein reported to be involved in direct interaction with the Sw-5 protein (Zhu et al 2017). Likewise, Huang et al (2021) generated a D122A mutation in TSWV-NSm, resulting in failure to elicit a Sw-5 mediated hypersensitive response. Three NSm sequences retrieved from GenBank contained the D122G substitution (AY848921.1, HM015516.1, KU179582.1), however, this mutation was not implicated directly with RB phenotypes (Ciuffo et al., 2005; Lopez et al., 2011; Marshall, 2016). The RB phenotype was confirmed with the NC variants on 'Mountain Merit' (Sw-5) by two means of virus inoculation: mechanical, rub-inoculation with extracted sap from infected plants, and thrips transmission assays with lab colony-maintained, Frankliniella occidentalis, the western flower thrips. Symptomatic leaf tissue obtained from these inoculation assays tested positive for TSWV by DAS-ELISA (AgDia, Elkhart, IN) and RT-PCR with NSm primers, providing definitive evidence of the occurrence of RB-TSWV at both farms, and subsequent sequencing confirmed the C118Y and D122G substitutions. This report warrants further investigation of the putative origins, prevalence and epidemiological implications of RB-TSWV variants in NC tomato production, and the development of new sources of resistance to TSWV.}, number={7}, journal={PLANT DISEASE}, author={Lahre, K. and Shekasteband, R. and Meadows, I. and Whitfield, A. E. and Rotenberg, D.}, year={2023}, month={Jan} }
 @article{whitfield_rotenberg_2023, title={Pests and resistance: The biology and control of supervectors and superpests}, volume={58}, ISSN={["2214-5753"]}, DOI={10.1016/j.cois.2023.101060}, journal={CURRENT OPINION IN INSECT SCIENCE}, author={Whitfield, Anna E. and Rotenberg, Dorith}, year={2023}, month={Aug} }
 @article{rajarapu_ben-mahmoud_benoit_ullman_whitfield_rotenberg_2022, title={Sex-biased proteomic response to tomato spotted wilt virus infection of the salivary glands of Frankliniella occidentalis, the western flower thrips}, volume={149}, ISSN={["1879-0240"]}, DOI={10.1016/j.ibmb.2022.103843}, abstractNote={Successful transmission of tomato spotted wilt virus (TSWV) by Frankliniella occidentalis requires robust infection of the salivary glands (SGs) and virus delivery to plants during salivation. Feeding behavior and transmission efficiency are sexually-dimorphic traits of this thrips vector species. Proteins secreted from male and female SG tissues, and the effect of TSWV infection on the thrips SG proteome are unknown. To begin to discern thrips factors that facilitate virus infection of SGs and transmission by F. occidentalis, we used gel- and label-free quantitative and qualitative proteomics to address two hypotheses: (i) TSWV infection modifies the composition and/or abundance of SG-expressed proteins in adults; and (ii) TSWV has a differential effect on the male and female SG proteome and secreted saliva. Our study revealed a sex-biased SG proteome for F. occidentalis, and TSWV infection modulated the SG proteome in a sex-dependent manner as evident by the number, differential abundance, identities and generalized roles of the proteins. Male SGs exhibited a larger proteomic response to the virus than female SGs. Intracellular processes modulated by TSWV in males indicated perturbation of SG cytoskeletal networks and cell-cell interactions, i.e., basement membrane (BM) and extracellular matrix (ECM) proteins, and subcellular processes consistent with a metabolic slow-down under infection. Several differentially-abundant proteins in infected male SGs play critical roles in viral life cycles of other host-virus pathosystems. In females, TSWV modulated processes consistent with tissue integrity and active translational and transcriptional regulation. A core set of proteins known for their roles in plant cell-wall degradation and protein metabolism were identified in saliva of both sexes, regardless of virus infection status. Saliva proteins secreted by TSWV-infected adults indicated energy generation, consumption and protein turnover, with an enrichment of cytoskeletal/BM/ECM proteins and tricarboxylic acid cycle proteins in male and female saliva, respectively. The nonstructural TSWV protein NSs - a multifunctional viral effector protein reported to target plant defenses against TSWV and thrips - was identified in female saliva. This study represents the first description of the SG proteome and secretome of a thysanopteran and provides many candidate proteins to further unravel the complex interplay between the virus, insect vector, and plant host.}, journal={INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY}, author={Rajarapu, Swapna Priya and Ben-Mahmoud, Sulley and Benoit, Joshua B. and Ullman, Diane E. and Whitfield, Anna E. and Rotenberg, Dorith}, year={2022}, month={Oct} }
 @article{alviar_rotenberg_martin_whitfield_2022, title={The physical interactome between Peregrinus maidis proteins and the maize mosaic virus glycoprotein provides insights into the cellular biology of a rhabdovirus in the insect vector.}, volume={577}, ISSN={["1089-862X"]}, DOI={10.1016/j.virol.2022.10.002}, abstractNote={Rhabdovirus glycoproteins (G) serve multifunctional roles in virus entry, assembly, and exit from animal cells. We hypothesize that maize mosaic virus (MMV) G is required for invasion, infection, and spread in Peregrinus maidis, the planthopper vector. Using a membrane-based yeast two-hybrid assay, we identified 107 P. maidis proteins that physically interacted with MMV G, of which approximately 53% matched proteins with known functions including endocytosis, vesicle-mediated transport, protein synthesis and turnover, nuclear export, metabolism and host defense. Physical interaction networks among conserved proteins indicated a possible cellular coordination of processes associated with MMV G translation, protein folding and trafficking. Non-annotated proteins contained predicted functional sites, including a diverse array of ligand binding sites. Cyclophilin A and apolipophorin III co-immunoprecipitated with MMV G, and each showed different patterns of localization with G in insect cells. This study describes the first protein interactome for a rhabdovirus spike protein and insect vector.}, journal={VIROLOGY}, author={Alviar, Karen B. and Rotenberg, Dorith and Martin, Kathleen M. and Whitfield, Anna E.}, year={2022}, month={Dec}, pages={163–173} }
 @article{han_rotenberg_2021, title={Integration of transcriptomics and network analysis reveals co-expressed genes in Frankliniella occidentalis larval guts that respond to tomato spotted wilt virus infection}, volume={22}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-021-08100-4}, abstractNote={Abstract}, number={1}, journal={BMC GENOMICS}, author={Han, Jinlong and Rotenberg, Dorith}, year={2021}, month={Nov} }
 @article{klobasa_chu_huot_grubbs_rotenberg_whitfield_lorenzen_2021, title={Microinjection of Corn Planthopper, <em>Peregrinus maidis</em>, Embryos for CRISPR/Cas9 Genome Editing}, volume={3}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/62417}, DOI={10.3791/62417}, abstractNote={The corn planthopper, Peregrinus maidis, is a pest of maize and a vector of several maize viruses. Previously published methods describe the triggering of RNA interference (RNAi) in P. maidis through microinjection of double-stranded RNAs (dsRNAs) into nymphs and adults. Despite the power of RNAi, phenotypes generated via this technique are transient and lack long-term Mendelian inheritance. Therefore, the P. maidis toolbox needs to be expanded to include functional genomic tools that would enable the production of stable mutant strains, opening the door for researchers to bring new control methods to bear on this economically important pest. However, unlike the dsRNAs used for RNAi, the components used in CRISPR/Cas9-based genome editing and germline transformation do not easily cross cell membranes. As a result, plasmid DNAs, RNAs, and/or proteins must be microinjected into embryos before the embryo cellularizes, making the timing of injection a critical factor for success. To that end, an agarose-based egg-lay method was developed to allow embryos to be harvested from P. maidis females at relatively short intervals. Herein are provided detailed protocols for collecting and microinjecting precellular P. maidis embryos with CRISPR components (Cas9 nuclease that has been complexed with guide RNAs), and results of Cas9-based gene knockout of a P. maidis eye-color gene, white, are presented. Although these protocols describe CRISPR/Cas9-genome editing in P. maidis, they can also be used for producing transgenic P. maidis via germline transformation by simply changing the composition of the injection solution.}, number={169}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Klobasa, William and Chu, Fu-Chyun and Huot, Ordom and Grubbs, Nathaniel and Rotenberg, Dorith and Whitfield, Anna E. and Lorenzen, Marcé D.}, year={2021}, month={Mar} }
 @article{thomas_dohmen_hughes_murali_poelchau_glastad_anstead_ayoub_batterham_bellair_et al._2020, title={Gene content evolution in the arthropods}, volume={21}, ISSN={["1474-760X"]}, DOI={10.1186/s13059-019-1925-7}, abstractNote={Abstract}, number={1}, journal={GENOME BIOLOGY}, author={Thomas, Gregg W. C. and Dohmen, Elias and Hughes, Daniel S. T. and Murali, Shwetha C. and Poelchau, Monica and Glastad, Karl and Anstead, Clare A. and Ayoub, Nadia A. and Batterham, Phillip and Bellair, Michelle and et al.}, year={2020}, month={Jan} }
 @article{rotenberg_baumann_ben-mahmoud_christiaens_dermauw_ioannidis_jacobs_vargas jentzsch_oliver_poelchau_et al._2020, title={Genome-enabled insights into the biology of thrips as crop pests}, volume={18}, ISSN={["1741-7007"]}, DOI={10.1186/s12915-020-00862-9}, abstractNote={Abstract}, number={1}, journal={BMC BIOLOGY}, author={Rotenberg, Dorith and Baumann, Aaron A. and Ben-Mahmoud, Sulley and Christiaens, Olivier and Dermauw, Wannes and Ioannidis, Panagiotis and Jacobs, Chris G. C. and Vargas Jentzsch, Iris M. and Oliver, Jonathan E. and Poelchau, Monica F. and et al.}, year={2020}, month={Oct} }
 @article{rotenberg_baumann_ben-mahmoud_christiaens_dermauw_ioannidis_jacobs_jentzsch_oliver_poelchau_et al._2020, title={Genome-enabled insights into the biology of thrips as crop pests (vol 18, 142, 2020)}, volume={18}, ISSN={["1741-7007"]}, DOI={10.1186/s12915-020-00915-z}, abstractNote={An amendment to this paper has been published and can be accessed via the original article.}, number={1}, journal={BMC BIOLOGY}, author={Rotenberg, Dorith and Baumann, Aaron A. and Ben-Mahmoud, Sulley and Christiaens, Olivier and Dermauw, Wannes and Ioannidis, Panagiotis and Jacobs, Chris G. C. and Jentzsch, Iris M. Vargas and Oliver, Jonathan E. and Poelchau, Monica F. and et al.}, year={2020}, month={Nov} }
 @article{nachappa_challacombe_margolies_nechols_whitfield_rotenberg_2020, title={Tomato Spotted Wilt Virus Benefits Its Thrips Vector by Modulating Metabolic and Plant Defense Pathways in Tomato}, volume={11}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2020.575564}, abstractNote={Several plant viruses modulate vector fitness and behavior in ways that may enhance virus transmission. Previous studies have documented indirect, plant-mediated effects of tomato spotted wilt virus (TSWV) infection on the fecundity, growth and survival of its principal thrips vector, Frankliniella occidentalis, the western flower thrips. We conducted thrips performance and preference experiments combined with plant gene expression, phytohormone and total free amino acid analyses to determine if systemically-infected tomato plants modulate primary metabolic and defense-related pathways to culminate into a more favorable environment for the vector. In a greenhouse setting, we documented a significant increase in the number of offspring produced by F. occidentalis on TSWV-infected tomato plants compared to mock-inoculated plants, and in choice test assays, females exhibited enhanced settling on TSWV-infected leaves. Microarray analysis combined with phytohormone signaling pathway analysis revealed reciprocal modulation of key phytohormone pathways under dual attack, possibly indicating a coordinated and dampening defense against the vector on infected plants. TSWV infection, alone or in combination with thrips, suppressed genes associated with photosynthesis and chloroplast function thereby significantly impacting primary metabolism of the host plant, and hierarchical cluster and network analyses revealed that many of these genes were co-regulated with phytohormone defense signaling genes. TSWV infection increased expression of genes related to protein synthesis and degradation which was reflected in the increased total free amino acid content in virus-infected plants that harbored higher thrips populations. These results suggest coordinated gene networks that regulate plant primary metabolism and defense responses rendering virus-infected plants more conducive for vector colonization, an outcome that is potentially beneficial to the vector and the virus when considered within the context of the complex transmission biology of TSWV. To our knowledge this is the first study to identify global transcriptional networks that underlie the TSWV-thrips interaction as compared to a single mechanistic approach. Findings of this study increase our fundamental knowledge of host plant-virus-vector interactions and identifies underlying mechanisms of induced host susceptibility to the insect vector.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Nachappa, Punya and Challacombe, Jean and Margolies, David C. and Nechols, James R. and Whitfield, Anna E. and Rotenberg, Dorith}, year={2020}, month={Dec} }
 @article{yao_rotenberg_whitfield_2019, title={Delivery of maize mosaic virus to planthopper vectors by microinjection increases infection efficiency and facilitates functional genomics experiments in the vector}, volume={270}, ISBN={1879-0984}, DOI={10.1016/j.jviromet.2019.05.010}, abstractNote={The corn planthopper, Peregrinus maidis, not only causes direct damage to plants by feeding, but also transmits maize mosaic virus (MMV) to the plant hosts. The virus is transmitted in a propagative manner but the acquisition of MMV by the vector feeding on infected plants can result in low acquisition and inoculation efficiency. Here, we increased the acquisition efficiency by delivering the virus directly into the hemocoel through microinjection, which resulted in efficient virus infection of the insect and transmission to maize. We found that delivery of virus by injection of 10 ng MMV (50 nl, 200 μg/ml virions) into P. maidis resulted in 93% transmission efficiency. In dose-response experiments, MMV abundance in insects and transmission efficiency decreased as the amount of virus inoculum delivered into the hemocoel was reduced. Examination of virus distribution in the vector using immunolabeling and confocal microscopy revealed similar tissue distributions in the injected insects when compared to those of previous studies using feeding on plants for virus acquisition. The utility of virus inoculation by microinjection for functional analysis in virus-vector interaction was explored. Co-microinjection of MMV virions and the dsRNA of PI3Kδ (a transcript that is less abundant in MMV-infected insects), resulted in a reduction in PI3Kδ expression and higher virus titers in P. maidis. These findings demonstrated that virus microinjection is a robust method for obtaining large numbers of infected planthoppers that are competent in transmitting MMV and, in combination with RNAi, could significantly facilitate the functional analysis of P. maidis-MMV interactions.}, journal={JOURNAL OF VIROLOGICAL METHODS}, author={Yao, Jianxiu and Rotenberg, Dorith and Whitfield, Anna E.}, year={2019}, month={Aug}, pages={153–162} }
 @article{badillo-vargas_chen_martin_rotenberg_whitfield_2019, title={Discovery of Novel Thrips Vector Proteins That Bind to the Viral Attachment Protein of the Plant Bunyavirus Tomato Spotted Wilt Virus}, volume={93}, ISSN={["1098-5514"]}, url={https://doi.org/10.1101/416560}, DOI={10.1128/JVI.00699-19}, abstractNote={
            Thrips-transmitted viruses cause devastating losses to numerous food crops worldwide. For negative-sense RNA viruses that infect plants, the arthropod serves as a host as well by supporting virus replication in specific tissues and organs of the vector. The goal of this work was to identify thrips proteins that bind directly to the viral attachment protein and thus may play a role in the infection cycle in the insect. Using the model plant bunyavirus tomato spotted wilt virus (TSWV), and the most efficient thrips vector, we identified and validated six TSWV-interacting proteins from
            Frankliniella occidentalis
            first-instar larvae. Two proteins, an endocuticle structural glycoprotein and cyclophilin, were able to interact directly with the TSWV attachment protein, G
            N
            , in insect cells. The TSWV G
            N
            -interacting proteins provide new targets for disrupting the viral disease cycle in the arthropod vector and could be putative determinants of vector competence.
          }, number={21}, journal={Journal of Virology}, author={Badillo-Vargas, I.E. and Chen, Y. and Martin, K.M. and Rotenberg, D. and Whitfield, A.E.}, year={2019}, pages={e00699–19} }
 @article{chen_dessau_rotenberg_rasmussen_whitfield_2019, title={Entry of bunyaviruses into plants and vectors}, volume={104}, ISBN={["978-0-12-818394-6"]}, ISSN={["1557-8399"]}, DOI={10.1016/bs.aivir.2019.07.001}, abstractNote={The majority of plant-infecting viruses are transmitted by arthropod vectors that deliver them directly into a living plant cell. There are diverse mechanisms of transmission ranging from direct binding to the insect stylet (non-persistent transmission) to persistent-propagative transmission in which the virus replicates in the insect vector. Despite this diversity in interactions, most arthropods that serve as efficient vectors have feeding strategies that enable them to deliver the virus into the plant cell without extensive damage to the plant and thus effectively inoculate the plant. As such, the primary virus entry mechanism for plant viruses is mediated by the biological vector. Remarkably, viruses that are transmitted in a propagative manner (bunyaviruses, rhabdoviruses, and reoviruses) have developed an ability to replicate in hosts from two kingdoms. Viruses in the order Bunyavirales are of emerging importance and with the advent of new sequencing technologies, we are getting unprecedented glimpses into the diversity of these viruses. Plant-infecting bunyaviruses are transmitted in a persistent, propagative manner must enter two unique types of host cells, plant and insect. In the insect phase of the virus life cycle, the propagative viruses likely use typical cellular entry strategies to traverse cell membranes. In this review, we highlight the transmission and entry strategies of three genera of plant-infecting bunyaviruses: orthotospoviruses, tenuiviruses, and emaraviruses.}, journal={VIRUS ENTRY}, author={Chen, Yuting and Dessau, Moshe and Rotenberg, Dorith and Rasmussen, David A. and Whitfield, Anna E.}, year={2019}, pages={65–96} }
 @misc{thomas_dohmen_hughes_murali_poelchau_glastad_anstead_ayoub_batterham_bellair_et al._2018, title={Gene Content Evolution in the Arthropods}, url={http://dx.doi.org/10.1101/382945}, DOI={10.1101/382945}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Thomas, Gregg W.C. and Dohmen, Elias and Hughes, Daniel S.T. and Murali, Shwetha C. and Poelchau, Monica and Glastad, Karl and Anstead, Clare A. and Ayoub, Nadia A. and Batterham, Phillip and Bellair, Michelle and et al.}, year={2018}, month={Aug} }
 @article{rotenberg_whitfield_2018, title={Molecular interactions between tospoviruses and thrips vectors}, volume={33}, ISSN={["1879-6265"]}, DOI={10.1016/j.coviro.2018.11.007}, abstractNote={Thrips-transmitted tospoviruses are an emerging and re-emerging threat to crop production worldwide. Tospoviruses are transstadially transmitted from larval to pupal stages of development, with adults serving as the primary inoculators of plants. A unique feature of the transmission cycle is that adults—while they can acquire virus from plants directly—are competent as vectors only if they acquire virus as larvae. Thrips vectors also serve as hosts for the virus, supporting its replication in midgut tissues and salivary glands. There is a tight link between thrips development and virus dissemination in the insect, and recent transcriptome studies point to stage-specific responses that coincide with localization of the virus in the insect body. Transcriptome sequencing of thrips vectors is leading to identification of virus-responsive thrips genes and possibly new targets to disrupt the virus transmission cycle. Accumulation of thrips-omics resources and advancements in functional biology tools will propel new and exciting molecular studies of thrips-tospoviruses interactions.}, journal={CURRENT OPINION IN VIROLOGY}, author={Rotenberg, Dorith and Whitfield, Anna E.}, year={2018}, month={Dec}, pages={191–197} }
 @article{laney_acosta-leal_rotenberg_2018, title={Optimized Yellow Dwarf Virus Multiplex PCR Assay Reveals a Common Occurrence of Barley yellow dwarf virus-PAS in Kansas Winter Wheat}, volume={19}, ISSN={["1535-1025"]}, DOI={10.1094/PHP-09-17-0056-RS}, abstractNote={ Barley yellow dwarf is an aphid-transmitted virus disease caused by yellow dwarf virus (YDV) species in the family Luteoviridae. Previous partial sequencing efforts conducted in Kansas revealed that Barley yellow dwarf virus-PAS (PAS) occurs in winter wheat fields, and currently available YDV multiplex reverse-transcription PCR (RT-PCR) assays do not detect this species. To enable precise determination of YDV species for research, disease diagnostic, and plant breeding programs, this study enhanced and validated the utility of a multiplex RT-PCR protocol to discriminate six YDV species, including PAS, in archived and fresh field samples. From a representative subset of samples collected from commercial and variety trial locations across nine wheat growing regions of Kansas, PAS and Barley yellow dwarf virus-PAV (PAV) were equally prevalent in single or mixed infections, and other YDVs occurred in mixed infections with PAS and/or PAV in low numbers. The optimized multiplex assay provided robust and specific detection of YDVs and showed promise as a diagnostic tool for determining species occurrence and composition of YDVs in an intensive wheat cropping region of the United States. }, number={1}, journal={PLANT HEALTH PROGRESS}, author={Laney, Alma G. and Acosta-Leal, Rodolfo and Rotenberg, Dorith}, year={2018}, pages={37–43} }
 @article{gamage_rotenberg_schneweis_tsai_dietzgen_2018, title={Transcriptome-wide responses of adult melon thrips (Thrips palmi) associated with capsicum chlorosis virus infection}, volume={13}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0208538}, abstractNote={Thrips palmi is a widely distributed major agricultural pest in the tropics and subtropics, causing significant losses in cucurbit and solanaceous crops through feeding damage and transmission of tospoviruses. Thrips palmi is a vector of capsicum chlorosis virus (CaCV) in Australia. The present understanding of transmission biology and potential effects of CaCV on T. palmi is limited. To gain insights into molecular responses to CaCV infection, we performed RNA-Seq to identify thrips transcripts that are differentially-abundant during virus infection of adults. De-novo assembly of the transcriptome generated from whole bodies of T. palmi adults generated 166,445 contigs, of which ~24% contained a predicted open reading frame. We identified 1,389 differentially-expressed (DE) transcripts, with comparable numbers up- (708) and down-regulated (681) in virus-exposed thrips compared to non-exposed thrips. Approximately 59% of these DE transcripts had significant matches to NCBI non-redundant proteins (Blastx) and Blast2GO identified provisional functional categories among the up-regulated transcripts in virus-exposed thrips including innate immune response-related genes, salivary gland and/or gut-associated genes and vitellogenin genes. The majority of the immune-related proteins are known to serve functions in lysosome activity and melanisation in insects. Most of the up-regulated oral and extra-oral digestion-associated genes appear to be involved in digestion of proteins, lipids and plant cell wall components which may indirectly enhance the likelihood or frequency of virus transmission or may be involved in the regulation of host defence responses. Most of the down-regulated transcripts fell into the gene ontology functional category of ‘structural constituent of cuticle’. Comparison to DE genes responsive to tomato spotted wilt virus in Frankliniella occidentalis indicates conservation of some thrips molecular responses to infection by different tospoviruses. This study assembled the first transcriptome in the genus Thrips and provides important data to broaden our understanding of networks of molecular interactions between thrips and tospoviruses.}, number={12}, journal={PLOS ONE}, author={Gamage, Shirani M. K. Widana and Rotenberg, Dorith and Schneweis, Derek J. and Tsai, Chi-Wei and Dietzgen, Ralf G.}, year={2018}, month={Dec} }
 @misc{rotenberg_martin_whitfield_2017, title={Insight into molecular basis of plant-infecting arbovirus persistence in the vector: Conserved responses to viruses in insects}, url={http://www.elsevierblogs.com/virology/insight-into-molecular-basis-of-plant-infecting-arbovirus-persistence-in-the-vector/}, journal={Virology Highlights Blog}, publisher={Elsevier}, author={Rotenberg, D. and Martin, K. and Whitfield, A.}, year={2017} }
 @article{schneweis_whitfield_rotenberg_2017, title={Thrips developmental stage-specific transcriptome response to tomato spotted wilt virus during the virus infection cycle in Frankliniella occidentalis, the primary vector}, volume={500}, ISSN={0042-6822}, url={http://dx.doi.org/10.1016/j.virol.2016.10.009}, DOI={10.1016/j.virol.2016.10.009}, abstractNote={Tomato spotted wilt virus (TSWV) is transmitted by Frankliniella occidentalis in a circulative-propagative manner. Little is known about thrips vector response to TSWV during the infection process from larval acquisition to adult inoculation of plants. Whole-body transcriptome response to virus infection was determined for first-instar larval, pre-pupal and adult thrips using RNA-Seq. TSWV responsive genes were identified using preliminary sequence of a draft genome of F. occidentalis as a reference and three developmental-stage transcriptomes were assembled. Processes and functions associated with host defense, insect cuticle structure and development, metabolism and transport were perturbed by TSWV infection as inferred by ontologies of responsive genes. The repertoire of genes responsive to TSWV varied between developmental stages, possibly reflecting the link between thrips development and the virus dissemination route in the vector. This study provides the foundation for exploration of tissue-specific expression in response to TSWV and functional analysis of thrips gene function.}, journal={Virology}, publisher={Elsevier BV}, author={Schneweis, Derek J. and Whitfield, Anna E. and Rotenberg, Dorith}, year={2017}, month={Jan}, pages={226–237} }
 @article{shrestha_champagne_culbreath_rotenberg_whitfield_srinivasan_2017, title={Transcriptome changes associated with Tomato spotted wilt virus infection in various life stages of its thrips vector, Frankliniella fusca (Hinds)}, volume={98}, ISSN={0022-1317 1465-2099}, url={http://dx.doi.org/10.1099/jgv.0.000874}, DOI={10.1099/jgv.0.000874}, abstractNote={Persistent propagative viruses maintain intricate interactions with their arthropod vectors. In this study, we investigated the transcriptome-level responses associated with a persistent propagative phytovirus infection in various life stages of its vector using an Illumina HiSeq sequencing platform. The pathosystem components included a Tospovirus, Tomato spotted wilt virus (TSWV), its insect vector, Frankliniella fusca (Hinds), and a plant host, Arachis hypogaea (L.). We assembled (de novo) reads from three developmental stage groups of virus-exposed and non-virus-exposed F. fusca into one transcriptome consisting of 72 366 contigs and identified 1161 differentially expressed (DE) contigs. The number of DE contigs was greatest in adults (female) (562) when compared with larvae (first and second instars) (395) and pupae (pre- and pupae) (204). Upregulated contigs in virus-exposed thrips had blastx annotations associated with intracellular transport and virus replication. Upregulated contigs were also assigned blastx annotations associated with immune responses, including apoptosis and phagocytosis. In virus-exposed larvae, Blast2GO analysis identified functional groups, such as multicellular development with downregulated contigs, while reproduction, embryo development and growth were identified with upregulated contigs in virus-exposed adults. This study provides insights into differences in transcriptome-level responses modulated by TSWV in various life stages of an important vector, F. fusca.}, number={8}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Shrestha, Anita and Champagne, Donald E. and Culbreath, Albert K. and Rotenberg, Dorith and Whitfield, Anna E. and Srinivasan, Rajagopalbabu}, year={2017}, month={Aug}, pages={2156–2170} }
 @article{martin_barandoc-alviar_schneweis_stewart_rotenberg_whitfield_2017, title={Transcriptomic response of the insect vector, Peregrinus maidis, to Maize mosaic rhabdovirus and identification of conserved responses to propagative viruses in hopper vectors}, volume={509}, ISSN={0042-6822}, url={http://dx.doi.org/10.1016/j.virol.2017.05.019}, DOI={10.1016/j.virol.2017.05.019}, abstractNote={Maize mosaic virus (MMV) is a plant-pathogenic rhabdovirus that is transmitted by the corn planthopper, Peregrinus maidis, in a propagative manner. P. maidis supports long-term MMV infections with no negative effects on insect performance. To elucidate whole-body transcriptome responses to virus infection, RNA-Seq was used to examine differential gene expression of virus-infected adult insects, and libraries were prepared from replicated groups of virus-exposed insects and non-exposed insects. From the 68,003 de novo-assembled transcripts, 144 were differentially-expressed (DE) during viral infection with comparable numbers up- and down-regulated. DE transcripts with similarity to genes associated with transposable elements (i.e., RNA-directed DNA polymerases) were enriched and may represent a mechanisim for modulating virus infection. Comparison of the P. maidis DE transcripts to published propagative virus-responsive transcript databases for two other hopper vectors revealed that 16% of the DE transcripts were shared across the three systems and may represent conserved responses to propagative viruses.}, journal={Virology}, publisher={Elsevier BV}, author={Martin, Kathleen M. and Barandoc-Alviar, Karen and Schneweis, Derek J. and Stewart, Catherine L. and Rotenberg, Dorith and Whitfield, Anna E.}, year={2017}, month={Sep}, pages={71–81} }
 @article{barandoc-alviar_ramirez_rotenberg_whitfield_2016, title={Analysis of Acquisition and Titer of Maize Mosaic Rhabdovirus in Its Vector, Peregrinus maidis (Hemiptera: Delphacidae)}, volume={16}, ISSN={1536-2442}, url={http://dx.doi.org/10.1093/jisesa/iev154}, DOI={10.1093/jisesa/iev154}, abstractNote={The corn planthopper, Peregrinus maidis (Ashmead) (Hemiptera: Delphacidae), transmits Maize mosaic rhabdovirus (MMV), an important pathogen of maize and sorghum, in a persistent propagative manner. To better understand the vectorial capacity of P. maidis, we determined the efficiency of MMV acquisition by nymphal and adult stages, and characterized MMV titer through development. Acquisition efficiency, i.e., proportion of insects that acquired the virus, was determined by reverse transcriptase polymerase chain reaction (RT-PCR) and virus titer of individual insects was estimated by quantitative RT-PCR. Acquisition efficiency of MMV differed significantly between nymphs and adults. MMV titer increased significantly over time and throughout insect development from nymphal to adult stage, indication of virus replication in the vector during development. There was a positive association between the vector developmental stage and virus titer. Also, the average titer in male insects was threefold higher than female titers, and this difference persisted up to 30 d post adult eclosion. Overall, our findings indicate that nymphs are more efficient than adults at acquiring MMV and virus accumulated in the vector over the course of nymphal development. Furthermore, sustained infection over the lifespan of P. maidis indicates a potentially high capacity of this vector to transmit MMV.}, number={1}, journal={Journal of Insect Science}, publisher={Oxford University Press (OUP)}, author={Barandoc-Alviar, Karen and Ramirez, Girly M. and Rotenberg, Dorith and Whitfield, Anna E.}, year={2016}, pages={14} }
 @article{rotenberg_bockus_whitfield_hervey_baker_ou_laney_de wolf_appel_2016, title={Occurrence of Viruses and Associated Grain Yields of Paired Symptomatic and Nonsymptomatic Tillers in Kansas Winter Wheat Fields}, volume={106}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto-04-15-0089-r}, DOI={10.1094/phyto-04-15-0089-r}, abstractNote={ Vector-borne virus diseases of wheat are recurrent in nature and pose significant threats to crop production worldwide. In the spring of 2011 and 2012, a state-wide sampling survey of multiple commercial field sites and university-managed Kansas Agricultural Experiment Station variety performance trial locations spanning all nine crop-reporting regions of the state was conducted to determine the occurrence of Barley yellow dwarf virus-PAV (BYDV-PAV), Cereal yellow dwarf virus-RPV, Wheat streak mosaic virus (WSMV), High plains virus, Soilborne wheat mosaic virus, and Wheat spindle streak mosaic virus using enzyme-linked immunosorbent assays (ELISA). As a means of directly coupling tiller infection status with tiller grain yield, multiple pairs of symptomatic and nonsymptomatic plants were selected and individual tillers were tagged for virus species and grain yield determination at the variety performance trial locations. BYDV-PAV and WSMV were the two most prevalent species across the state, often co-occurring within location. Of those BYDV-PAV- or WSMV-positive tillers, 22% and 19%, respectively, were nonsymptomatic, a finding that underscores the importance of sampling criteria to more accurately assess virus occurrence in winter wheat fields. Symptomatic tillers that tested positive for BYDV-PAV produced significantly lower grain yields compared with ELISA-negative tillers in both seasons, as did WSMV-positive tillers in 2012. Nonsymptomatic tillers that tested positive for either of the two viruses in 2011 produced significantly lower grain yields than tillers from nonsymptomatic, ELISA-negative plants, an indication that these tillers were physiologically compromised in the absence of virus-associated symptoms. Overall, the virus survey and tagged paired-tiller sampling strategy revealed effects of virus infection on grain yield of individual tillers of plants grown under field conditions and may provide a complementary approach toward future estimates of the impact of virus incidence on crop health in Kansas. }, number={2}, journal={Phytopathology}, publisher={Scientific Societies}, author={Rotenberg, Dorith and Bockus, William W. and Whitfield, Anna E. and Hervey, Kaylee and Baker, Kara D. and Ou, Zhining and Laney, Alma G. and De Wolf, Erick D. and Appel, Jon A.}, year={2016}, month={Feb}, pages={202–210} }
 @inbook{montero-astúa_stafford-banks_badillo-vargas_rotenberg_ullman_whitfield_2016, place={St. Paul, Minnesota}, title={Tospovirus-thrips biology}, DOI={10.1094/9780890545355.020}, abstractNote={HomeGeneral Plant PathologyVector-Mediated Transmission of Plant PathogensCHAPTER 20: Tospovirus–Thrips Biology PreviousNext CHAPTER 20: Tospovirus–Thrips BiologyMauricio Montero-Astúa, Candice A. Stafford-Banks, Ismael E. Badillo-Vargas, Dorith Rotenberg, Diane E. Ullman, and Anna E. WhitfieldMauricio Montero-AstúaSearch for more papers by this author, Candice A. Stafford-BanksSearch for more papers by this author, Ismael E. Badillo-VargasSearch for more papers by this author, Dorith RotenbergSearch for more papers by this author, Diane E. UllmanSearch for more papers by this author, and Anna E. WhitfieldSearch for more papers by this authorAffiliationsAuthors and Affiliations Published Online:15 Nov 2016https://doi.org/10.1094/9780890545355.020AboutSectionsPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Abstract Since the first description of Tomato spotted wilt virus (TSWV) in 1915, significant progress has been made toward understanding the biology of this virus and its relationship with thrips vectors and plant hosts. In the 1930s, thrips were determined to be vectors of TSWV, revealing a unique requisite that transmission depends on virus acquisition by larval thrips. The emergence of TSWV as a serious threat to hundreds of crops across several continents in the 1980s revived interest in the virus and insect vector, and this interest has since been sustained. TSWV is considered one of the 10 most devastating plant viruses because of the ubiquitous nature of the thrips vector and the extremely wide host range of the virus (more than 1,000 plant species). Molecular characterization of the virus and determination that the virus replicates in the insect vector enabled classification of TSWV in Bunyaviridae, a family composed primarily of animal-infecting viruses. Since the 1990s, the number of tospoviruses has grown to more than 25 described species and the number of vectors to 14, and the interaction between virus and vector has been characterized from the molecular to the ecological levels. The era of molecular virology resulted in elucidation of functions for all tospovirus genes. However, little progress has been made toward determining vector molecular components of transmission. With the combined advances in cell biology and the state-of-the-art genomic tools that are now available, we expect that a deeper understanding of the complex interplay between tospoviruses and hosts in the plant and animal kingdoms will emerge. In this chapter, we highlight past and recent advances in our understanding of the biology of tospoviruses and thrips and the multiple factors that play roles in virus acquisition and transmission. Key concepts included in this chapter: Historical Perspective of Tospovirus–Thrips Interactions Tospovirus Species Thrips Vectors of Tospoviruses Molecular Biology of Virus–Vector Interaction Future Research DetailsFiguresLiterature CitedRelated Vector-Mediated Transmission of Plant PathogensISBN:978-0-89054-535-5 Metrics Pages: 289-308 InformationPDF download}, booktitle={Vector-Mediated Transmission of Plant Pathogens}, publisher={APS Press}, author={Montero-Astúa, M. and Stafford-Banks, C. and Badillo-Vargas, I. and Rotenberg, D. and Ullman, D.E. and Whitfield, A.E.}, editor={Brown, J.K.Editor}, year={2016}, pages={289–309} }
 @article{whitfield_rotenberg_2015, title={Disruption of insect transmission of plant viruses}, volume={8}, ISSN={2214-5745}, url={http://dx.doi.org/10.1016/j.cois.2015.01.009}, DOI={10.1016/j.cois.2015.01.009}, abstractNote={Plant-infecting viruses are transmitted by a diverse array of organisms including insects, mites, nematodes, fungi, and plasmodiophorids. Virus interactions with these vectors are diverse, but there are some commonalities. Generally the infection cycle begins with the vector encountering the virus in the plant and the virus is acquired by the vector. The virus must then persist in or on the vector long enough for the virus to be transported to a new host and delivered into the plant cell. Plant viruses rely on their vectors for breaching the plant cell wall to be delivered directly into the cytosol. In most cases, viral capsid or membrane glycoproteins are the specific viral proteins that are required for transmission and determinants of vector specificity. Specific molecules in vectors also interact with the virus and while there are few-identified to no-identified receptors, candidate recognition molecules are being further explored in these systems. Due to the specificity of virus transmission by vectors, there are defined steps that represent good targets for interdiction strategies to disrupt the disease cycle. This review focuses on new technologies that aim to disrupt the virus–vector interaction and focuses on a few of the well-characterized virus–vector interactions in the field. In closing, we discuss the importance of integration of these technologies with current methods for plant virus disease control.}, journal={Current Opinion in Insect Science}, publisher={Elsevier BV}, author={Whitfield, Anna E and Rotenberg, Dorith}, year={2015}, month={Apr}, pages={79–87} }
 @article{whitfield_falk_rotenberg_2015, title={Insect vector-mediated transmission of plant viruses}, volume={479-480}, ISSN={0042-6822}, url={http://dx.doi.org/10.1016/j.virol.2015.03.026}, DOI={10.1016/j.virol.2015.03.026}, abstractNote={The majority of plant-infecting viruses are transmitted to their host plants by vectors. The interactions between viruses and vector vary in duration and specificity but some common themes in vector transmission have emerged: 1) plant viruses encode structural proteins on the surface of the virion that are essential for transmission, and in some cases additional non-structural helper proteins that act to bridge the virion to the vector binding site; 2) viruses bind to specific sites in or on vectors and are retained there until they are transmitted to their plant hosts; and 3) viral determinants of vector transmission are promising candidates for translational research aimed at disrupting transmission or decreasing vector populations. In this review, we focus on well-characterized insect vector-transmitted viruses in the following genera: Caulimovirus, Crinivirus, Luteovirus, Geminiviridae, Reovirus, Tospovirus, and Tenuivirus. New discoveries regarding these genera have increased our understanding of the basic mechanisms of virus transmission by arthropods, which in turn have enabled the development of innovative strategies for breaking the transmission cycle.}, journal={Virology}, publisher={Elsevier BV}, author={Whitfield, Anna E. and Falk, Bryce W. and Rotenberg, Dorith}, year={2015}, month={May}, pages={278–289} }
 @article{badillo-vargas_rotenberg_schneweis_whitfield_2015, title={RNA interference tools for the western flower thrips, Frankliniella occidentalis}, volume={76}, ISSN={0022-1910}, url={http://dx.doi.org/10.1016/j.jinsphys.2015.03.009}, DOI={10.1016/j.jinsphys.2015.03.009}, abstractNote={The insect order Thysanoptera is exclusively comprised of small insects commonly known as thrips. The western flower thrips, Frankliniella occidentalis, is an economically important pest amongst thysanopterans due to extensive feeding damage and tospovirus transmission to hundreds of plant species worldwide. Geographically-distinct populations of F. occidentalis have developed resistance against many types of traditional chemical insecticides, and as such, management of thrips and tospoviruses are a persistent challenge in agriculture. Molecular methods for defining the role(s) of specific genes in thrips–tospovirus interactions and for assessing their potential as gene targets in thrips management strategies is currently lacking. The goal of this work was to develop an RNA interference (RNAi) tool that enables functional genomic assays and to evaluate RNAi for its potential as a biologically-based approach for controlling F. occidentalis. Using a microinjection system, we delivered double-stranded RNA (dsRNA) directly to the hemocoel of female thrips to target the vacuolar ATP synthase subunit B (V-ATPase-B) gene of F. occidentalis. Gene expression analysis using real-time quantitative reverse transcriptase-PCR (qRT-PCR) revealed significant reductions of V-ATPase-B transcripts at 2 and 3 days post-injection (dpi) with dsRNA of V-ATPase-B compared to injection with dsRNA of GFP. Furthermore, the effect of knockdown of the V-ATPase-B gene in females at these two time points was mirrored by the decreased abundance of V-ATPase-B protein as determined by quantitative analysis of Western blots. Reduction in V-ATPase-B expression in thrips resulted in increased female mortality and reduced fertility, i.e., number of viable offspring produced. Survivorship decreased significantly by six dpi compared to the dsRNA-GFP control group, which continued decreasing significantly until the end of the bioassay. Surviving female thrips injected with dsRNA-V-ATPase-B produced significantly fewer offspring compared to those in the dsRNA-GFP control group. Our findings indicate that an RNAi-based strategy to study gene function in thrips is feasible, can result in quantifiable phenotypes, and provides a much-needed tool for investigating the molecular mechanisms of thrips–tospovirus interactions. To our knowledge, this represents the first report of RNAi for any member of the insect order Thysanoptera and demonstrates the potential for translational research in the area of thrips pest control.}, journal={Journal of Insect Physiology}, publisher={Elsevier BV}, author={Badillo-Vargas, Ismael E. and Rotenberg, Dorith and Schneweis, Brandi A. and Whitfield, Anna E.}, year={2015}, month={May}, pages={36–46} }
 @article{rotenberg_jacobson_schneweis_whitfield_2015, title={Thrips transmission of tospoviruses}, volume={15}, ISSN={1879-6257}, url={http://dx.doi.org/10.1016/j.coviro.2015.08.003}, DOI={10.1016/j.coviro.2015.08.003}, abstractNote={One hundred years ago, the disease tomato spotted wilt was first described in Australia. Since that time, knowledge of this disease caused by Tomato spotted wilt virus (TSWV) and transmitted by thrips (insects in the order Thysanoptera) has revealed a complex relationship between the virus, vector, plant host, and environment. Numerous tospoviruses and thrips vectors have been described, revealing diversity in plant host range and geographical distributions. Advances in characterization of the tripartite interaction between the virus, vector, and plant host have provided insight into molecular and ecological relationships. Comparison to animal-infecting viruses in the family Bunyaviridae has enabled the identification of commonalities between tospoviruses and other bunyaviruses in transmission by arthropod vectors and molecular interactions with hosts. This review provides a special emphasis on TSWV and Frankliniella occidentalis, the model tospovirus-thrips pathosystem. However, other virus-vector combinations are also of importance and where possible, comparisons are made between different viruses and thrips vectors.}, journal={Current Opinion in Virology}, publisher={Elsevier BV}, author={Rotenberg, Dorith and Jacobson, Alana L and Schneweis, Derek J and Whitfield, Anna E}, year={2015}, month={Dec}, pages={80–89} }
 @article{stafford-banks_rotenberg_johnson_whitfield_ullman_2014, title={Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0094447}, DOI={10.1371/journal.pone.0094447}, abstractNote={Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande) (the western flower thrips) is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina) technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E−6) to known proteins, whereas a high percentage (61.24%) of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome) against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways) of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the viruses they transmit.}, number={4}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Stafford-Banks, Candice A. and Rotenberg, Dorith and Johnson, Brian R. and Whitfield, Anna E. and Ullman, Diane E.}, editor={Wang, Xiao-WeiEditor}, year={2014}, month={Apr}, pages={e94447} }
 @article{montero-astúa_rotenberg_leach-kieffaber_schneweis_park_park_german_whitfield_2014, title={Disruption of Vector Transmission by a Plant-Expressed Viral Glycoprotein}, volume={27}, ISSN={0894-0282}, url={http://dx.doi.org/10.1094/mpmi-09-13-0287-fi}, DOI={10.1094/mpmi-09-13-0287-fi}, abstractNote={ Vector-borne viruses are a threat to human, animal, and plant health worldwide, requiring the development of novel strategies for their control. Tomato spotted wilt virus (TSWV) is one of the 10 most economically significant plant viruses and, together with other tospoviruses, is a threat to global food security. TSWV is transmitted by thrips, including the western flower thrips, Frankliniella occidentalis. Previously, we demonstrated that the TSWV glycoprotein GN binds to thrips vector midguts. We report here the development of transgenic plants that interfere with TSWV acquisition and transmission by the insect vector. Tomato plants expressing GN-S protein supported virus accumulation and symptom expression comparable with nontransgenic plants. However, virus titers in larval insects exposed to the infected transgenic plants were three-log lower than insects exposed to infected nontransgenic control plants. The negative effect of the GN-S transgenics on insect virus titers persisted to adulthood, as shown by four-log lower virus titers in adults and an average reduction of 87% in transmission efficiencies. These results demonstrate that an initial reduction in virus infection of the insect can result in a significant decrease in virus titer and transmission over the lifespan of the vector, supportive of a dose-dependent relationship in the virus–vector interaction. These findings demonstrate that plant expression of a viral protein can be an effective way to block virus transmission by insect vectors. }, number={3}, journal={Molecular Plant-Microbe Interactions}, publisher={Scientific Societies}, author={Montero-Astúa, Mauricio and Rotenberg, Dorith and Leach-Kieffaber, Alexandria and Schneweis, Brandi A. and Park, Sunghun and Park, Jungeun K. and German, Thomas L. and Whitfield, Anna E.}, year={2014}, month={Mar}, pages={296–304} }
 @article{whitfield_rotenberg_german_2014, title={Plant pest destruction goes viral}, volume={32}, ISSN={1087-0156 1546-1696}, url={http://dx.doi.org/10.1038/nbt.2787}, DOI={10.1038/nbt.2787}, number={1}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Whitfield, Anna E and Rotenberg, Dorith and German, Thomas L}, year={2014}, month={Jan}, pages={65–66} }
 @article{yao_rotenberg_afsharifar_barandoc-alviar_whitfield_2013, title={Development of RNAi Methods for Peregrinus maidis, the Corn Planthopper}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0070243}, DOI={10.1371/journal.pone.0070243}, abstractNote={The corn planthopper, Peregrinus maidis, is a major pest of agronomically-important crops. Peregrinus maidis has a large geographical distribution and transmits Maize mosaic rhabdovirus (MMV) and Maize stripe tenuivirus (MSpV). The objective of this study was to develop effective RNAi methods for P. maidis. Vacuolar-ATPase (V-ATPase) is an essential enzyme for hydrolysis of ATP and for transport of protons out of cells thereby maintaining membrane ion balance, and it has been demonstrated to be an efficacious target for RNAi in other insects. In this study, two genes encoding subunits of P. maidis V-ATPase (V-ATPase B and V-ATPase D) were chosen as RNAi target genes. The open reading frames of V-ATPase B and D were generated and used for constructing dsRNA fragments. Experiments were conducted using oral delivery and microinjection of V-ATPase B and V-ATPase D dsRNA to investigate the effectiveness of RNAi in P. maidis. Real-time quantitative reverse transcriptase-PCR (qRT-PCR) analysis indicated that microinjection of V-ATPase dsRNA led to a minimum reduction of 27-fold in the normalized abundance of V-ATPase transcripts two days post injection, while ingestion of dsRNA resulted in a two-fold reduction after six days of feeding. While both methods of dsRNA delivery resulted in knockdown of target transcripts, the injection method was more rapid and effective. The reduction in V-ATPase transcript abundance resulted in observable phenotypes. Specifically, the development of nymphs injected with 200 ng of either V-ATPase B or D dsRNA was impaired, resulting in higher mortality and lower fecundity than control insects injected with GFP dsRNA. Microscopic examination of these insects revealed that female reproductive organs did not develop normally. The successful development of RNAi in P. maidis to target specific genes will enable the development of new insect control strategies and functional analysis of vital genes and genes associated with interactions between P. maidis and MMV.}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Yao, Jianxiu and Rotenberg, Dorith and Afsharifar, Alireza and Barandoc-Alviar, Karen and Whitfield, Anna E.}, editor={Jurat-Fuentes, Juan LuisEditor}, year={2013}, month={Aug}, pages={e70243} }
 @article{nachappa_margolies_nechols_whitfield_rotenberg_2013, title={Tomato Spotted Wilt Virus Benefits a Non-Vector Arthropod, Tetranychus Urticae, by Modulating Different Plant Responses in Tomato}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0075909}, DOI={10.1371/journal.pone.0075909}, abstractNote={The interaction between plant viruses and non-vector arthropod herbivores is poorly understood. However, there is accumulating evidence that plant viruses can impact fitness of non-vector herbivores. In this study, we used oligonucleotide microarrays, phytohormone, and total free amino acid analyses to characterize the molecular mechanisms underlying the interaction between Tomato spotted wilt virus (TSWV) and a non-vector arthropod, twospotted spider mite ( Tetranychusurticae ), on tomato plants, Solanum lycopersicum . Twospotted spider mites showed increased preference for and fecundity on TSWV-infected plants compared to mock-inoculated plants. Transcriptome profiles of TSWV-infected plants indicated significant up-regulation of salicylic acid (SA)-related genes, but no apparent down-regulation of jasmonic acid (JA)-related genes which could potentially confer induced resistance against TSM. This suggests that there was no antagonistic crosstalk between the signaling pathways to influence the interaction between TSWV and spider mites. In fact, SA- and JA-related genes were up-regulated when plants were challenged with both TSWV and the herbivore. TSWV infection resulted in down-regulation of cell wall-related genes and photosynthesis-associated genes, which may contribute to host plant susceptibility. There was a three-fold increase in total free amino acid content in virus-infected plants compared to mock-inoculated plants. Total free amino acid content is critical for arthropod nutrition and may, in part, explain the apparent positive indirect effect of TSWV on spider mites. Taken together, these data suggest that the mechanism(s) of increased host suitability of TSWV-infected plants to non-vector herbivores is complex and likely involves several plant biochemical processes.}, number={9}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Nachappa, Punya and Margolies, David C. and Nechols, James R. and Whitfield, Anna E. and Rotenberg, Dorith}, editor={Ballhorn, DanielEditor}, year={2013}, month={Sep}, pages={e75909} }
 @article{johnson_nechols_cloyd_rotenberg_kennelly_2012, title={Effect of Light Intensity on Brassica rapa Chemistry and Plutella xylostella (Lepidoptera: Plutellidae) Life History Traits.}, volume={47}, ISSN={0749-8004}, url={http://dx.doi.org/10.18474/0749-8004-47.4.327}, DOI={10.18474/0749-8004-47.4.327}, abstractNote={Abstract Greenhouse studies were conducted to examine the effects of light intensity on pac choi (Brassica rapa L. var. chinensis cv. ‘Mei Qing Choi’) and the corresponding plant-mediated effects of light intensity on the diamondback moth (Plutella xylostella L.). Plants with and without diamondback moth larvae were exposed either to ambient light or shade in 4 experiments conducted at different times of the year, resulting in a range of light intensities. The plant parameters measured were shoot biomass, primary nutrients, and phenolic content of leaves; for diamondback moth, larval consumption, cohort development, and male and female body weights were measured. In the light treatments, plants tended to have higher levels of phenolics and exhibited greater shoot biomass with higher carbon:nitrogen ratios under ambient versus shade. However, diamondback moth responses were not correlated with any plant responses, with one exception. Higher concentrations of ferulic acid under higher light intensities were associated with lower adult male body weights. Larval consumption was not different among the 4 months. However, cohort development was more rapid on plants during August, which had higher light intensities, compared with July, where light intensity was lower. Based on the responses measured, growing pac choi in the greenhouse under different light intensities is unlikely to affect diamondback moths through changes in pac choi chemistry unless decreased male body weight confers a fitness cost. However, plant-mediated effects associated with changes in light intensity on P. xylostella survival should be evaluated.}, number={4}, journal={Journal of Entomological Science}, publisher={Georgia Entomological Society}, author={Johnson, W.A. and Nechols, J.R. and Cloyd, R.A. and Rotenberg, D. and Kennelly, M.M.}, year={2012}, month={Oct}, pages={327–349} }
 @article{johnson_cloyd_nechols_williams_nelson_rotenberg_kennelly_2012, title={Effect of Nitrogen Source on Pac Choi (Brassica rapa L.) Chemistry and Interactions with the Diamondback Moth (Plutella xylostella L.)}, volume={47}, ISSN={0018-5345 2327-9834}, url={http://dx.doi.org/10.21273/hortsci.47.10.1457}, DOI={10.21273/hortsci.47.10.1457}, abstractNote={Two greenhouse studies were conducted to examine effects of nitrogen source on primary and secondary metabolism of pac choi (Brassica rapa L. subsp. chinensis cv. Mei Qing Choi) and diamondback moth (Plutella xylostella L.) consumption, development, survival, and body weight. Applications of a liquid organic source of nitrogen (fish hydrolysate fertilizer) were compared with a conventional fertilizer to determine whether nitrogen source directly impacts pac choi chemistry (elemental composition and phenolics) and biomass and indirectly affects diamondback moth fitness parameters. There was no significant effect of fertility treatment on pac choi chemistry or biomass with the exception of percent leaf phosphorus, which was significantly higher in the conventional fertility treatment, and p-coumarin, which was significantly higher in the organic fertility treatment. Diamondback moth also affected plant chemistry. Both calcium (Ca) and magnesium (Mg) were significantly higher in plants infested with larvae compared with uninfested plants. Fertilizer affected diamondback moth fitness with percent survival and cohort development significantly reduced on pac choi associated with the organic fertilizer. However, pac choi receiving the organic treatment was similar in regard to primary nutrients and secondary compounds compared with plants that received a conventional fertilizer.}, number={10}, journal={HortScience}, publisher={American Society for Horticultural Science}, author={Johnson, Wendy A. and Cloyd, Raymond A. and Nechols, James R. and Williams, Kimberly A. and Nelson, Nathan O. and Rotenberg, Dorith and Kennelly, Megan M.}, year={2012}, month={Oct}, pages={1457–1465} }
 @article{jacobson_johnston_rotenberg_whitfield_booth_vargo_kennedy_2012, title={Genome size and ploidy of Thysanoptera}, volume={22}, ISSN={0962-1075}, url={http://dx.doi.org/10.1111/j.1365-2583.2012.01165.x}, DOI={10.1111/j.1365-2583.2012.01165.x}, abstractNote={Abstract}, number={1}, journal={Insect Molecular Biology}, publisher={Wiley}, author={Jacobson, A. L. and Johnston, J. S. and Rotenberg, D. and Whitfield, A. E. and Booth, W. and Vargo, E. L. and Kennedy, G. G.}, year={2012}, month={Nov}, pages={12–17} }
 @article{badillo-vargas_rotenberg_schneweis_hiromasa_tomich_whitfield_2012, title={Proteomic Analysis of Frankliniella occidentalis and Differentially Expressed Proteins in Response to Tomato Spotted Wilt Virus Infection}, volume={86}, ISSN={0022-538X 1098-5514}, url={http://dx.doi.org/10.1128/jvi.00285-12}, DOI={10.1128/jvi.00285-12}, abstractNote={ABSTRACT}, number={16}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={Badillo-Vargas, I. E. and Rotenberg, D. and Schneweis, D. J. and Hiromasa, Y. and Tomich, J. M. and Whitfield, A. E.}, year={2012}, month={Jun}, pages={8793–8809} }
 @article{whitfield_rotenberg_aritua_hogenhout_2011, title={Analysis of expressed sequence tags from Maize mosaic rhabdovirus-infected gut tissues of Peregrinus maidis reveals the presence of key components of insect innate immunity}, volume={20}, ISSN={0962-1075}, url={http://dx.doi.org/10.1111/j.1365-2583.2010.01060.x}, DOI={10.1111/j.1365-2583.2010.01060.x}, abstractNote={The corn planthopper, Peregrinus maidis, causes direct feeding damage to plants and transmits Maize mosaic rhabdovirus (MMV) in a persistent‐propagative manner. MMV must cross several insect tissue layers for successful transmission to occur, and the gut serves as an important barrier for rhabdovirus transmission. In order to facilitate the identification of proteins that may interact with MMV either by facilitating acquisition or responding to virus infection, we generated and analysed the gut transcriptome of P. maidis. From two normalized cDNA libraries, we generated a P. maidis gut transcriptome composed of 20 771 expressed sequence tags (ESTs). Assembly of the sequences yielded 1860 contigs and 14 032 singletons, and biological roles were assigned to 5793 (36%). Comparison of P. maidis ESTs with other insect amino acid sequences revealed that P. maidis shares greatest sequence similarity with another hemipteran, the brown planthopper Nilaparvata lugens. We identified 202 P. maidis transcripts with putative homology to proteins associated with insect innate immunity, including those implicated in the Toll, Imd, JAK/STAT, Jnk and the small‐interfering RNA‐mediated pathways. Sequence comparisons between our P. maidis gut EST collection and the currently available National Center for Biotechnology Information EST database collection for Ni. lugens revealed that a pathogen recognition receptor in the Imd pathway, peptidoglycan recognition protein‐long class (PGRP‐LC), is present in these two members of the family Delphacidae; however, these recognition receptors are lacking in the model hemipteran Acyrthosiphon pisum. In addition, we identified sequences in the P. maidis gut transcriptome that share significant amino acid sequence similarities with the rhabdovirus receptor molecule, acetylcholine receptor (AChR), found in other hosts. This EST analysis sheds new light on immune response pathways in hemipteran guts that will be useful for further dissecting innate defence response pathways to rhabdovirus infection.}, number={2}, journal={Insect Molecular Biology}, publisher={Wiley}, author={Whitfield, A. E. and Rotenberg, D. and Aritua, V. and Hogenhout, S. A.}, year={2011}, month={Jan}, pages={225–242} }
 @article{rotenberg_whitfield_2010, title={Analysis of expressed sequence tags for Frankliniella occidentalis, the western flower thrips}, volume={19}, DOI={10.1111/j.1365-2583.2010.01012.x}, abstractNote={Abstract}, number={4}, journal={Insect Molecular Biology}, author={Rotenberg, D. and Whitfield, A.E.}, year={2010}, pages={537–551} }
 @article{rotenberg_krishna kumar_ullman_montero-astúa_willis_german_whitfield_2009, title={Variation in Tomato spotted wilt virus Titer in Frankliniella occidentalis and Its Association with Frequency of Transmission}, volume={99}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto-99-4-0404}, DOI={10.1094/phyto-99-4-0404}, abstractNote={ Tomato spotted wilt virus (TSWV) is transmitted in a persistent propagative manner by Frankliniella occidentalis, the western flower thrips. While it is well established that vector competence depends on TSWV acquisition by young larvae and virus replication within the insect, the biological factors associated with frequency of transmission have not been well characterized. We hypothesized that the number of transmission events by a single adult thrips is determined, in part, by the amount of virus harbored (titer) by the insect. Transmission time-course experiments were conducted using a leaf disk assay to determine the efficiency and frequency of TSWV transmission following 2-day inoculation access periods (IAPs). Virus titer in individual adult thrips was determined by real-time quantitative reverse transcriptase-PCR (qRT-PCR) at the end of the experiments. On average, 59% of adults transmitted the virus during the first IAP (2 to 3 days post adult-eclosion). Male thrips were more efficient at transmitting TSWV multiple times compared with female thrips of the same cohort. However, females harbored two to three times more copies of TSWV-N RNA per insect, indicating that factors other than absolute virus titer in the insect contribute to a successful transmission event. Examination of virus titer in individual insects at the end of the third IAP (7 days post adult-eclosion) revealed significant and consistent positive associations between frequency of transmission and virus titer. Our data support the hypothesis that a viruliferous thrips is more likely to transmit multiple times if it harbors a high titer of virus. This quantitative relationship provides new insights into the biological parameters that may influence the spread of TSWV by thrips. }, number={4}, journal={Phytopathology}, publisher={Scientific Societies}, author={Rotenberg, Dorith and Krishna Kumar, Nallur K. and Ullman, Diane E. and Montero-Astúa, Mauricio and Willis, David K. and German, Thomas L. and Whitfield, Anna E.}, year={2009}, month={Apr}, pages={404–410} }
 @article{whitfield_kumar_rotenberg_ullman_wyman_zietlow_willis_german_2008, title={A Soluble Form of the Tomato spotted wilt virus (TSWV) Glycoprotein GN (GN-S) Inhibits Transmission of TSWV by Frankliniella occidentalis}, volume={98}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto-98-1-0045}, DOI={10.1094/phyto-98-1-0045}, abstractNote={ Tomato spotted wilt virus (TSWV) is an economically important virus that is transmitted in a persistent propagative manner by its thrips vector, Frankliniella occidentalis. Previously, we found that a soluble form of the envelope glycoprotein GN (GN-S) specifically bound thrips midguts and reduced the amount of detectable virus inside midgut tissues. The aim of this research was to (i) determine if GN-S alters TSWV transmission by thrips and, if so, (ii) determine the duration of this effect. In one study, insects were given an acquisition access period (AAP) with GN-S mixed with purified virus and individual insects were assayed for transmission. We found that GN-S reduced the percent of transmitting adults by eightfold. In a second study, thrips were given an AAP on GN-S protein and then placed on TSWV-infected plant material. Individual insects were assayed for transmission over three time intervals of 2 to 3, 4 to 5, and 6 to 7 days post-adult eclosion. We observed a significant reduction in virus transmission that persisted to the same degree throughout the time course. Real-time reverse transcription polymerase chain reaction analysis of virus titer in individual insects revealed that the proportion of thrips infected with virus was reduced threefold when insects were preexposed to the GN-S protein as compared to no exposure to protein, and nontransmitters were not infected with virus. These results demonstrate that thrips transmission of a tospovirus can be reduced by exogenous viral glycoprotein. }, number={1}, journal={Phytopathology}, publisher={Scientific Societies}, author={Whitfield, A. E. and Kumar, N. K. K. and Rotenberg, D. and Ullman, D. E. and Wyman, E. A. and Zietlow, C. and Willis, D. K. and German, T. L.}, year={2008}, month={Jan}, pages={45–50} }
 @article{rotenberg_joshi_benitez_chapin_camp_zumpetta_osborne_dick_gardener_2007, title={Farm Management Effects on Rhizosphere Colonization by Native Populations of 2,4-Diacetylphloroglucinol-Producing Pseudomonas spp. and Their Contributions to Crop Health}, volume={97}, ISSN={0031-949X}, url={http://dx.doi.org/10.1094/phyto-97-6-0756}, DOI={10.1094/phyto-97-6-0756}, abstractNote={ Analyses of multiple field experiments indicated that the incidence and relative abundance of root-colonizing phlD+ Pseudomonas spp. were influenced by crop rotation, tillage, organic amendments, and chemical seed treatments in subtle but reproducible ways. In no-till corn plots, 2-year rotations with soybean resulted in plants with approximately twofold fewer phlD+ pseudomonads per gram of root, but 3-year rotations with oat and hay led to population increases of the same magnitude. Interestingly, tillage inverted these observed effects of cropping sequence in two consecutive growing seasons, indicating a complex but reproducible interaction between rotation and tillage on the rhizosphere abundance of 2,4-diacetlyphloroglucinol (DAPG) producers. Amending conventionally managed sweet corn plots with dairy manure compost improved plant health and also increased the incidence of root colonization when compared with nonamended plots. Soil pH was negatively correlated to rhizosphere abundance of phlD+ pseudomonads in no-till and nonamended soils, with the exception of the continuous corn treatments. Chemical seed treatments intended to control fungal pathogens and insect pests on corn also led to more abundant populations of phlD in different tilled soils. However, increased root disease severity generally was associated with elevated levels of root colonization by phlD+ pseudomonads in no-till plots. Interestingly, within a cropping sequence treatment, correlations between the relative abundance of phlD and crop stand or yield were generally positive on corn, and the strength of those correlations was greater in plots experiencing more root disease pressure. In contrast, such correlations were generally negative in soybean, a difference that may be partially explained by difference in application of N fertilizers and soil pH. Our findings indicate that farming practices can alter the relative abundance and incidence of phlD+ pseudomonads in the rhizosphere and that practices that reduce root disease severity (i.e., rotation, tillage, and chemical seed treatment) are not universally linked to increased root colonization by DAPG-producers. }, number={6}, journal={Phytopathology}, publisher={Scientific Societies}, author={Rotenberg, Dorith and Joshi, Raghavendra and Benitez, Maria-Soledad and Chapin, Laura Gutierrez and Camp, Amara and Zumpetta, Clara and Osborne, Adam and Dick, Warren A. and Gardener, Brian B. McSpadden}, year={2007}, month={Jun}, pages={756–766} }
 @article{benítez_tustas_rotenberg_kleinhenz_cardina_stinner_miller_mcspadden gardener_2007, title={Multiple statistical approaches of community fingerprint data reveal bacterial populations associated with general disease suppression arising from the application of different organic field management strategies}, volume={39}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2007.03.028}, DOI={10.1016/j.soilbio.2007.03.028}, abstractNote={Multiple statistical analyses of terminal restriction fragment length polymorphism (T-RFLP) data were used to screen and identify bacterial populations involved in general disease suppression in an organically managed soil. Prior to sampling three different management strategies (i.e. mixed hay (H), tilled fallowing and open-field vegetables production) were used during the transition from conventional to organic farming, with and without compost amendment. The H transition strategy consistently led to the lowest damping-off disease incidence on two different crops in separate greenhouse and field experiments. Bacterial population structure in bulk soil and the rhizosphere of both crops was characterized using T-RFLP analyses of amplified 16S rDNA sequences. First, principal component analysis (PCA) revealed changes in the relative abundance of bacterial terminal restriction fragments (TRF) in response to transition strategy and/or compost amendment in eight different experimental contexts. In each context, a different subset of TRF substantially contributed to the variation along the first two principal components. However, terminal restriction fragment M148 contributed significantly to the observed variation in 6 out of the 8 experiments, and moderately in the remaining 2 experiments. As a second approach, nonparametric analyses of variance revealed that the relative abundance of TRF differed among treatments. While the responsive subsets identified varied somewhat by experimental context, M137, M139 and M141 were more abundant in samples from the H transition strategy in multiple experimental contexts. Subsequent correlation analyses revealed that TRF associated with disease suppressive treatments (i.e. H with and without compost) were frequently negatively correlated with damping-off disease incidence. As a group, these TRF were disproportionately associated with lower disease levels further indicating their role in disease suppression. Interestingly, in silico analysis of the bacterial 16S rDNA sequence database revealed that the TRF identified in this study (e.g. M137, M139, M141, and M148) might correspond to well-characterized genera of bacterial biological control agents.}, number={9}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Benítez, María-Soledad and Tustas, Fulya Baysal and Rotenberg, Dorith and Kleinhenz, Mathew D. and Cardina, John and Stinner, Deborah and Miller, Sally A. and McSpadden Gardener, Brian B.}, year={2007}, month={Sep}, pages={2289–2301} }
 @article{rotenberg_wells_chapman_whitfield_goodman_cooperband_2007, title={Soil properties associated with organic matter-mediated suppression of bean root rot in field soil amended with fresh and composted paper mill residuals}, volume={39}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2007.06.011}, DOI={10.1016/j.soilbio.2007.06.011}, abstractNote={The ability of an organic amendment to suppress soil-borne disease is mediated by the complex interactions between biotic and abiotic soil factors. Various microbiological and physicochemical soil properties were measured in field soils with histories of receiving 4 or 5 years of spring additions of paper mill residuals (PMR), PMR composted alone (PMRC), PMR composted with bark (PMRB), or no amendment under a conventionally managed vegetable crop rotation. The objectives of this study were to (i) determine the residual and re-amendment effects of the organic materials on root rot disease severity; (ii) determine the influence of amendment type on the structure of bacterial communities associated with snap bean roots grown in these soils; and (iii) quantify the relative contributions of microbiological and physicochemical properties to root rot suppression in the field and greenhouse. While all amendment types significantly suppressed root rot disease compared to non-amended soils in both environments, only soils amended with PMR or PMRB sustained suppressive conditions 1 year after the most recent amendment event. Disease severity was inversely related to microbial activity (fluorescein diacetate assay) in recently amended soils only. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16s rRNA gene was performed to obtain bacterial profiles. Principal component analysis (PCA) of terminal restriction fragments (TRFs) revealed general differences in bacterial community composition (PC1) among amendment types, and specific TRFs contributed to these differences. Correlation and multiple regression analyses of the measured soil variables revealed that the composition of root-associated bacterial communities and the amount of particulate organic matter—carbon in bulk soils imparted independent and relatively equal contributions to the variation in disease severity documented in the field and greenhouse. Together, our findings provide evidence that disease suppression induced by annual PMR inputs was mediated by their differential effects on bacterial communities and the amount and quality of organic matter in these soils.}, number={11}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Rotenberg, Dorith and Wells, Ana Jiménez and Chapman, Elisabeth J. and Whitfield, Anna E. and Goodman, Robert M. and Cooperband, Leslie R.}, year={2007}, month={Nov}, pages={2936–2948} }
 @article{rotenberg_thompson_german_willis_2006, title={Methods for effective real-time RT-PCR analysis of virus-induced gene silencing}, volume={138}, ISSN={0166-0934}, url={http://dx.doi.org/10.1016/j.jviromet.2006.07.017}, DOI={10.1016/j.jviromet.2006.07.017}, abstractNote={We applied real-time RT-PCR to the analysis of Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) of the phytoene desaturase (PDS) gene in Nicotiana benthamiana and tomato. Using a combination of direct measurement and mathematical assessment, we evaluated three plant genes, ubiquitin (ubi3), elongation factor-1 alpha (EF-1), and actin, for use as internal reference transcripts and found that EF-1 and ubi3 were least variable under our experimental conditions. Primer sets designed to amplify the 5' or 3' regions of endogenous PDS transcripts in tomato yielded similar reductions in transcript levels indicating a uniform VIGS-mediated degradation of target RNA. By measuring the ratio of the abundance of the PDS insert transcript to the TRV coat protein RNA, we established that the PDS insert within TRV was stable in both hosts. VIGS in N. benthamiana resulted in complete photo-bleaching of all foliar tissue compared to chimeric bleaching in tomato. PDS transcript levels were decreased eleven- and seven-fold in photobleached leaves of N. benthamiana and tomato, respectively, while sampling tomato leaflets on the basis of age rather than visible bleaching resulted in only a 17% reduction in PDS coupled with a large leaf-to-leaf variation. There was a significant inverse relationship (r2=76%, P=0.01) between the relative abundance of CP RNA and the amount of PDS transcript in rTRV::tPDS-infected tomato suggesting that virus spread and accumulation are required precursors for successful VIGS in this host.}, number={1-2}, journal={Journal of Virological Methods}, publisher={Elsevier BV}, author={Rotenberg, Dorith and Thompson, Thea S. and German, Thomas L. and Willis, David K.}, year={2006}, month={Dec}, pages={49–59} }
 @article{rotenberg_cooperband_stone_2005, title={Dynamic relationships between soil properties and foliar disease as affected by annual additions of organic amendment to a sandy-soil vegetable production system}, volume={37}, ISSN={0038-0717}, url={http://dx.doi.org/10.1016/j.soilbio.2004.12.006}, DOI={10.1016/j.soilbio.2004.12.006}, abstractNote={Additions of organic amendments to agricultural soils can lead to improved soil quality and reduced severity of crop diseases. However, the relationship between disease severity and soil properties as affected by repeated additions of these amendments is poorly understood. The primary objectives of this study were to (i) resolve multivariate relationships between soil properties and foliar disease severity and (ii) identify soil properties that contribute to disease severity in an intensive irrigated vegetable production system receiving annual additions of fresh and composted paper mill residuals (PMR). Foliar diseases caused by Pseudomonas syringae pv. syringae on snap bean (bacterial brown spot) and P. s. pv. lachrymans on cucumber (angular leaf spot) are the focus of this report. The experiment consisted of a 3-year crop rotation of potato (1998 and 2001), snap bean (1999 and 2002), and cucumber (2000). Treatments included a non-amended fertilizer control and two rates of fresh PMR, PMR composted alone (PMRC), and PMR composted with bark (PMRB). Soil measures included total soil carbon (TC) and nitrogen (TN), particulate organic matter carbon (POMC) and nitrogen (POMN), volumetric soil moisture (VM) and in situ NO3-N. Multiple regression (MR) and principal component analyses (PCA) were conducted to identify key soil properties that influenced the amount of disease. On average, the amount of TC in plots amended with PMR composts increased 77–178% from 1999 to 2002 compared to the non-amended soils. In 1999, a year in which compost additions reduced the amount of bacterial brown spot of bean, TC explained 42% of the total variation in disease severity in the best MR model. Midseason TN alone was inversely related to angular leaf spot incidence in 2000, while POMN explained 51% of the variation in the best MR model for that year. In 2002, a year in which PMRC-amended soils exacerbated brown spot symptoms, midseason quantities of TN explained 80% of the variation in disease severity. Unique to 2002, NO3-N alone positively correlated with disease severity. Overall, the influence of soil carbon on disease severity was displaced by the increasing importance of TN and NO3-N, indicating a transition from a C-dependent to an N-dependent system.}, number={7}, journal={Soil Biology and Biochemistry}, publisher={Elsevier BV}, author={Rotenberg, Dorith and Cooperband, Leslie and Stone, Alexandra}, year={2005}, month={Jul}, pages={1343–1357} }
 @article{newman_rotenberg_cooperband_2005, title={PAPER MILL RESIDUALS AND COMPOST EFFECTS ON PARTICULATE ORGANIC MATTER AND RELATED SOIL FUNCTIONS IN A SANDY SOIL}, volume={170}, ISSN={0038-075X}, url={http://dx.doi.org/10.1097/01.ss.0000190506.33675.e6}, DOI={10.1097/01.ss.0000190506.33675.e6}, abstractNote={Amending sandy soils with paper mill residuals (PMR) and/or PMR composts should build soil organic matter pools, thereby increasing carbon and nutrient availability for biologically mediated soil functions. We investigated the effects of PMR and PMR composts on total and particulate organic matter (POM) and their relationships with plant available water (PAW) and mineral nitrogen. From 1998 to 2001, we applied PMR, PMR composted alone (PMR-C), and PMR composted with bark (PMR-B) annually at two agronomic rates to sandy soils in a 3-year vegetable rotation of potato, snap bean, and cucumber. After 4 years, all PMR amendments increased total soil C and N (TC, TN), POM-C, and POM-N 2- to 4-fold, relative to a nonamended control. After 3 years of annual amendment additions, the soil achieved an elevated steady state of POM-C, indicating a net balance between C-input and C-decay. Either TC or POM-C explained greater than 50% of the variation in PAW in years 2 through 4, indicating the functional similarities between the two carbon pools. The first sign of a significant but weak relationship between mineral N and POM-N (R2 = 15%) or TN (R2 = 34%) occurred during the final year of study. Annual additions of PMR and PMR composts produced sustained increases in labile soil C and N pools; however, increases in these OM pools did not translate into short-term nutrient availability in these sandy soils.}, number={10}, journal={Soil Science}, publisher={Ovid Technologies (Wolters Kluwer Health)}, author={Newman, C. M. and Rotenberg, D. and Cooperband, L. R.}, year={2005}, month={Oct}, pages={788–801} }
 @article{rotenberg_macguidwin_saeed_rouse_2004, title={Interaction of spatially separated Pratylenchus penetrans and Verticillium dahliae on potato measured by impaired photosynthesis}, volume={53}, ISSN={0032-0862 1365-3059}, url={http://dx.doi.org/10.1111/j.0032-0862.2004.01005.x}, DOI={10.1111/j.0032-0862.2004.01005.x}, abstractNote={Experiments were conducted under growth‐chamber conditions to determine if Pratylenchus penetrans systemically alters light use efficiency (LUE) of Russet Burbank potato infected by Verticillium dahliae. Pathogen separation was achieved by inoculating potato roots with the nematode prior to injecting fungal conidia into the stem vasculature. Treatments were P. penetrans alone, V. dahliae alone, nematode and fungus together, and a no‐pathogen control. Gas exchange was repeatedly and nondestructively measured on the fifth‐youngest leaf with a Li‐Cor LI‐6200 portable photosynthesis system. By 16 and 20 days after stem injection with the fungus, LUE was synergistically impaired in jointly infected plants. Transpiration in plants infected with both pathogens was significantly reduced. However, the combined effect of nematode and fungus was synergistic in one experiment and additive in the other. Stems were destructively harvested when LUE was synergistically impaired. Coinfected potato plants contained more colony‐forming units (CFU) of V. dahliae in stem sap than those infected by the fungus alone in one experiment. Evidence is provided that infection of Russet Burbank roots by P. penetrans systemically affects disease physiology associated with stem vascular infection by V. dahliae. The findings indicate that the role of the nematode in the fungus/host interaction is more than simply to facilitate extravascular and/or vascular entry of the fungus into potato roots.}, number={3}, journal={Plant Pathology}, publisher={Wiley}, author={Rotenberg, D. and MacGuidwin, A. E. and Saeed, I. A. M. and Rouse, D. I.}, year={2004}, month={Jun}, pages={294–302} }
 @article{stone_vallad_cooperband_rotenberg_darby_james_stevenson_goodman_2003, title={Effect of Organic Amendments on Soilborne and Foliar Diseases in Field-Grown Snap Bean and Cucumber}, volume={87}, ISSN={0191-2917}, url={http://dx.doi.org/10.1094/pdis.2003.87.9.1037}, DOI={10.1094/pdis.2003.87.9.1037}, abstractNote={ Several paper mills in Wisconsin have programs for spreading paper mill residuals (PMR) on land. A growing number of vegetable farmers recognize the agronomic benefits of PMR applications, but there have been no investigations on the use of PMR for control of vegetable crop diseases. Our objective was to determine the effect of PMR amendments on soilborne and foliar diseases of cucumber and snap bean grown on a sandy soil. Raw PMR, PMR composted without bulking agent (PMRC), or PMR composted with bark (PMRBC) were applied annually in a 3-year rotation of potato, snap bean, and pickling cucumber. Several naturally occurring diseases were evaluated in the field, along with in situ field bioassays. All amendments suppressed cucumber damping-off and Pythium blight and foliar brown spot of snap bean. Both composts reduced the incidence of angular leaf spot in cucumber. In a separate field experiment planted with snap bean for two consecutive years, all amendments reduced common root rot severity in the second year. In a greenhouse experiment, the high rate of PMRBC suppressed anthracnose of snap bean. These results suggest that the application of raw and composted PMR to sandy soils has the potential to control several soilborne and foliar diseases. }, number={9}, journal={Plant Disease}, publisher={Scientific Societies}, author={Stone, A. G. and Vallad, G. E. and Cooperband, L. R. and Rotenberg, D. and Darby, H. M. and James, R. V. and Stevenson, W. R. and Goodman, R. M.}, year={2003}, month={Sep}, pages={1037–1042} }