@article{dye_muga_mwangi_hoyer_ly_rosado_sharpee_mware_wambugu_labadie_et al._2023, title={Cassava begomovirus species diversity changes during plant vegetative cycles}, volume={14}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2023.1163566}, DOI={10.3389/fmicb.2023.1163566}, abstractNote={Cassava is a root crop important for global food security and the third biggest source of calories on the African continent. Cassava production is threatened by Cassava mosaic disease (CMD), which is caused by a complex of single-stranded DNA viruses (family: Geminiviridae, genus: Begomovirus) that are transmitted by the sweet potato whitefly (Bemisia tabaci). Understanding the dynamics of different cassava mosaic begomovirus (CMB) species through time is important for contextualizing disease trends. Cassava plants with CMD symptoms were sampled in Lake Victoria and coastal regions of Kenya before transfer to a greenhouse setting and regular propagation. The field-collected and greenhouse samples were sequenced using Illumina short-read sequencing and analyzed on the Galaxy platform. In the field-collected samples, African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Kenya virus (EACMKV), and East African cassava mosaic virus-Uganda variant (EACMV-Ug) were detected in samples from the Lake Victoria region, while EACMV and East African mosaic Zanzibar virus (EACMZV) were found in the coastal region. Many of the field-collected samples had mixed infections of EACMV and another begomovirus. After 3 years of regrowth in the greenhouse, only EACMV-like viruses were detected in all samples. The results suggest that in these samples, EACMV becomes the dominant virus through vegetative propagation in a greenhouse. This differed from whitefly transmission results. Cassava plants were inoculated with ACMV and another EACMV-like virus, East African cassava mosaic Cameroon virus (EACMCV). Only ACMV was transmitted by whiteflies from these plants to recipient plants, as indicated by sequencing reads and copy number data. These results suggest that whitefly transmission and vegetative transmission lead to different outcomes for ACMV and EACMV-like viruses.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Dye, Anna E. and Muga, Brenda and Mwangi, Jenniffer and Hoyer, J. Steen and Ly, Vanessa and Rosado, Yamilex and Sharpee, William and Mware, Benard and Wambugu, Mary and Labadie, Paul and et al.}, year={2023}, month={May} }
 @article{kennedy_sharpee_jacobson_wambugu_mware_hanley-bowdoin_2023, title={Genome segment ratios change during whitefly transmission of two bipartite cassava mosaic begomoviruses}, volume={13}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/s41598-023-37278-8}, DOI={10.1038/s41598-023-37278-8}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Kennedy, George G. and Sharpee, William and Jacobson, Alana L. and Wambugu, Mary and Mware, Benard and Hanley-Bowdoin, Linda}, year={2023}, month={Jun} }
 @article{rajabu_dallas_chiunga_de leon_ateka_tairo_ndunguru_ascencio-ibanez_hanley-bowdoin_2023, title={SEGS-1 a cassava genomic sequence increases the severity of African cassava mosaic virus infection in <i>Arabidopsis</i> thaliana}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1250105}, abstractNote={Cassava is a major crop in Sub-Saharan Africa, where it is grown primarily by smallholder farmers. Cassava production is constrained by Cassava mosaic disease (CMD), which is caused by a complex of cassava mosaic begomoviruses (CMBs). A previous study showed that SEGS-1 (sequences enhancing geminivirus symptoms), which occurs in the cassava genome and as episomes during viral infection, enhances CMD symptoms and breaks resistance in cassava. We report here that SEGS-1 also increases viral disease severity in Arabidopsis thaliana plants that are co-inoculated with African cassava mosaic virus (ACMV) and SEGS-1 sequences. Viral disease was also enhanced in Arabidopsis plants carrying a SEGS-1 transgene when inoculated with ACMV alone. Unlike cassava, no SEGS-1 episomal DNA was detected in the transgenic Arabidopsis plants during ACMV infection. Studies using Nicotiana tabacum suspension cells showed that co-transfection of SEGS-1 sequences with an ACMV replicon increases viral DNA accumulation in the absence of viral movement. Together, these results demonstrated that SEGS-1 can function in a heterologous host to increase disease severity. Moreover, SEGS-1 is active in a host genomic context, indicating that SEGS-1 episomes are not required for disease enhancement.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Rajabu, Cyprian A. and Dallas, Mary M. and Chiunga, Evangelista and De Leon, Leandro and Ateka, Elijah M. and Tairo, Fred and Ndunguru, Joseph and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2023}, month={Oct} }
 @article{aimone_hoyer_dye_deppong_duffy_carbone_hanley-bowdoin_2022, title={An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing}, volume={300}, ISSN={["1879-0984"]}, url={http://dx.doi.org/10.1016/j.jviromet.2021.114405}, DOI={10.1016/j.jviromet.2021.114405}, abstractNote={The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.}, journal={JOURNAL OF VIROLOGICAL METHODS}, publisher={Elsevier BV}, author={Aimone, Catherine D. and Hoyer, J. Steen and Dye, Anna E. and Deppong, David O. and Duffy, Siobain and Carbone, Ignazio and Hanley-Bowdoin, Linda}, year={2022}, month={Feb} }
 @article{peng_dallas_ascencio-ibanez_hoyer_legg_hanley-bowdoin_grieve_yin_2022, title={Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-06372-8}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Peng, Yao and Dallas, Mary M. and Ascencio-Ibanez, Jose T. and Hoyer, J. Steen and Legg, James and Hanley-Bowdoin, Linda and Grieve, Bruce and Yin, Hujun}, year={2022}, month={Feb} }
 @article{mclaughlin_hanley-bowdoin_kennedy_jacobson_2022, title={Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts}, volume={12}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-022-24880-5}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={McLaughlin, Autumn A. and Hanley-Bowdoin, Linda and Kennedy, George G. and Jacobson, Alana L.}, year={2022}, month={Nov} }
 @article{aimone_de leon_dallas_ndunguru_ascencio-ibanez_hanley-bowdoin_2021, title={A New Type of Satellite Associated with Cassava Mosaic Begomoviruses}, volume={95}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00432-21}, abstractNote={Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase.}, number={21}, journal={JOURNAL OF VIROLOGY}, author={Aimone, Catherine D. and De Leon, Leandro and Dallas, Mary M. and Ndunguru, Joseph and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2021}, month={Nov} }
 @article{wang_gong_wu_huang_ismayil_zhang_li_gu_ludman_fatyol_et al._2021, title={A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants}, volume={29}, ISSN={["1934-6069"]}, DOI={10.1016/j.chom.2021.07.003}, abstractNote={RNA interference (RNAi) is an across-kingdom gene regulatory and defense mechanism. However, little is known about how organisms sense initial cues to mobilize RNAi. Here, we show that wounding to Nicotiana benthamiana cells during virus intrusion activates RNAi-related gene expression through calcium signaling. A rapid wound-induced elevation in calcium fluxes triggers calmodulin-dependent activation of calmodulin-binding transcription activator-3 (CAMTA3), which activates RNA-dependent RNA polymerase-6 and Bifunctional nuclease-2 (BN2) transcription. BN2 stabilizes mRNAs encoding key components of RNAi machinery, notably AGONAUTE1/2 and DICER-LIKE1, by degrading their cognate microRNAs. Consequently, multiple RNAi genes are primed for combating virus invasion. Calmodulin-, CAMTA3-, or BN2-knockdown/knockout plants show increased susceptibility to geminivirus, cucumovirus, and potyvirus. Notably, Geminivirus V2 protein can disrupt the calmodulin-CAMTA3 interaction to counteract RNAi defense. These findings link Ca2+ signaling to RNAi and reveal versatility of host antiviral defense and viral counter-defense.}, number={9}, journal={CELL HOST & MICROBE}, author={Wang, Yunjing and Gong, Qian and Wu, Yuyao and Huang, Fan and Ismayil, Asigul and Zhang, Danfeng and Li, Huangai and Gu, Hanqing and Ludman, Marta and Fatyol, Karoly and et al.}, year={2021}, month={Sep}, pages={1393-+} }
 @article{mickelson-young_wear_song_zynda_hanley-bowdoin_thompson_2021, title={A protocol for genome-wide analysis of DNA replication timing in intact root tips}, journal={Methods in Molecular Biology series}, author={Mickelson-Young, Leigh and Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and Hanley-Bowdoin, Linda and Thompson, William F.}, year={2021} }
 @article{borges_donoghue_leblanc_wear_tanurdzic_berube_brooks_thompson_hanley-bowdoin_martienssen_2021, title={Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation}, volume={31}, ISBN={1879-0445}, url={https://doi.org/10.1016/j.cub.2020.10.098}, DOI={10.1016/j.cub.2020.10.098}, abstractNote={5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.}, number={3}, journal={CURRENT BIOLOGY}, publisher={Elsevier BV}, author={Borges, Filipe and Donoghue, Mark T. A. and LeBlanc, Chantal and Wear, Emily E. and Tanurdzic, Milos and Berube, Benjamin and Brooks, Ashley and Thompson, William F. and Hanley-Bowdoin, Linda and Martienssen, Robert A.}, year={2021}, pages={591-+} }
 @article{aimone_lavington_hoyer_deppong_mickelson-young_jacobson_kennedy_carbone_hanley-bowdoin_duffy_2021, title={Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation}, volume={102}, ISSN={0022-1317 1465-2099}, url={http://dx.doi.org/10.1099/jgv.0.001622}, DOI={10.1099/jgv.0.001622}, abstractNote={Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5′ intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.}, number={7}, journal={Journal of General Virology}, publisher={Microbiology Society}, author={Aimone, Catherine D. and Lavington, Erik and Hoyer, J. Steen and Deppong, David O. and Mickelson-Young, Leigh and Jacobson, Alana and Kennedy, George G. and Carbone, Ignazio and Hanley-Bowdoin, Linda and Duffy, Siobain}, year={2021}, month={Jul} }
 @article{shen_hanley-bowdoin_2021, title={SnRK1: a versatile plant protein kinase that limits geminivirus infection}, volume={47}, ISSN={["1879-6265"]}, DOI={10.1016/j.coviro.2020.12.002}, abstractNote={Geminiviruses are a family of single-stranded DNA viruses that infect many plant species and cause serious diseases in important crops. The plant protein kinase, SnRK1, has been implicated in host defenses against geminiviruses. Overexpression of SnRK1 makes plants more resistant to geminivirus infection, and knock-down of SnRK1 increases susceptibility to geminivirus infection. GRIK, the SnRK1 activating kinase, is upregulated by geminivirus infection, while the viral C2 protein inhibits the SnRK1 activity. SnRK1 also directly phosphorylates geminivirus proteins to reduce infection. These data suggest that SnRK1 is involved in the co-evolution of plant hosts and geminiviruses.}, journal={CURRENT OPINION IN VIROLOGY}, author={Shen, Wei and Hanley-Bowdoin, Linda}, year={2021}, month={Apr}, pages={18–24} }
 @article{he_wang_yin_fiallo-oliv_liu_hanley-bowdoin_wang_2020, title={A plant DNA virus replicates in the salivary glands of its insect vector via recruitment of host DNA synthesis machinery}, volume={117}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1820132117}, abstractNote={Significance}, number={29}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={He, Ya-Zhou and Wang, Yu-Meng and Yin, Tian-Yan and Fiallo-Oliv, Elvira and Liu, Yin-Quan and Hanley-Bowdoin, Linda and Wang, Xiao-Wei}, year={2020}, month={Jul}, pages={16928–16937} }
 @article{wheeler_brooks_concia_vera_wear_leblanc_ramu_vaughn_bass_martienssen_et al._2020, title={Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin(1)([OPEN])}, volume={183}, ISSN={["1532-2548"]}, DOI={10.1104/pp.19.01520}, abstractNote={DNA replication initiation sites in plants associate most strongly with AT-rich and highly accessible chromatin, and not with genes or a particular epigenetic signature. The selection and firing of DNA replication origins play key roles in ensuring that eukaryotes accurately replicate their genomes. This process is not well documented in plants due in large measure to difficulties in working with plant systems. We developed a new functional assay to label and map very early replicating loci that must, by definition, include at least a subset of replication origins. Arabidopsis (Arabidopsis thaliana) cells were briefly labeled with 5-ethynyl-2′-deoxy-uridine, and nuclei were subjected to two-parameter flow sorting. We identified more than 5500 loci as initiation regions (IRs), the first regions to replicate in very early S phase. These were classified as strong or weak IRs based on the strength of their replication signals. Strong initiation regions were evenly spaced along chromosomal arms and depleted in centromeres, while weak initiation regions were enriched in centromeric regions. IRs are AT-rich sequences flanked by more GC-rich regions and located predominantly in intergenic regions. Nuclease sensitivity assays indicated that IRs are associated with accessible chromatin. Based on these observations, initiation of plant DNA replication shows some similarity to, but is also distinct from, initiation in other well-studied eukaryotic systems.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Wheeler, Emily and Brooks, Ashley M. and Concia, Lorenzo and Vera, Daniel L. and Wear, Emily E. and LeBlanc, Chantal and Ramu, Umamaheswari and Vaughn, Matthew W. and Bass, Hank W. and Martienssen, Robert A. and et al.}, year={2020}, month={May}, pages={206–220} }
 @article{wear_song_zynda_mickelson-young_leblanc_lee_deppong_allen_martienssen_vaughn_et al._2020, title={Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots}, volume={16}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1008623}, abstractNote={Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.}, number={10}, journal={PLOS GENETICS}, author={Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and Mickelson-Young, Leigh and LeBlanc, Chantal and Lee, Tae-Jin and Deppong, David O. and Allen, George C. and Martienssen, Robert A. and Vaughn, Matthew W. and et al.}, year={2020}, month={Oct} }
 @article{ismayil_yang_haxim_wang_li_han_wang_zheng_wei_nagalakshmi_et al._2020, title={Cotton leaf curl Multan virus beta C1 Protein Induces Autophagy by Disrupting the Interaction of Autophagy-Related Protein 3 with Glyceraldehyde-3-Phosphate Dehydrogenases([OPEN])}, volume={32}, ISBN={1532-298X}, DOI={10.1105/tpc.19.00759}, abstractNote={Abstract}, number={4}, journal={PLANT CELL}, author={Ismayil, Asigul and Yang, Meng and Haxim, Yakupjan and Wang, Yunjing and Li, Jinlin and Han, Lu and Wang, Yan and Zheng, Xiyin and Wei, Xiang and Nagalakshmi, Ugrappa and et al.}, year={2020}, month={Apr}, pages={1124–1135} }
 @article{hoyer_fondong_dallas_aimone_deppong_duffy_hanley-bowdoin_2020, title={Deeply Sequenced Infectious Clones of Key Cassava Begomovirus Isolates from Cameroon}, volume={9}, ISSN={["2576-098X"]}, DOI={10.1128/MRA.00802-20}, abstractNote={We deeply sequenced two pairs of widely used infectious clones (4 plasmids) of the bipartite begomoviruses African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV). The ACMV clones were quite divergent from published sequences. Raw reads, consensus plasmid sequences, and the infectious clones themselves are all publicly available.}, number={46}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Hoyer, J. Steen and Fondong, Vincent N. and Dallas, Mary M. and Aimone, Catherine Doyle and Deppong, David O. and Duffy, Siobain and Hanley-Bowdoin, Linda}, year={2020}, month={Nov} }
 @article{wang_wu_gong_ismayil_yuan_lian_jia_han_deng_hong_et al._2019, title={Geminiviral V2 Protein Suppresses Transcriptional Gene Silencing through Interaction with AGO4}, volume={93}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.01675-18}, abstractNote={
            In plants, the RNA-directed DNA methylation (RdDM) pathway is a natural antiviral defense mechanism against geminiviruses. However, how geminiviruses counter RdDM-mediated defense is largely unknown. Our findings reveal that
            Cotton leaf curl Multan virus
            V2 contributes to viral infection by interaction with NbAGO4 to suppress RNA-directed DNA methylation-mediated transcriptional gene silencing in plants. Our work provides the first evidence that a geminiviral protein is able to directly target core RdDM components to counter RdDM-mediated TGS antiviral defense in plants, which extends our current understanding of viral counters to host antiviral defense.
          }, number={6}, journal={JOURNAL OF VIROLOGY}, author={Wang, Yunjing and Wu, Yuyao and Gong, Qian and Ismayil, Asigul and Yuan, Yuxiang and Lian, Bi and Jia, Qi and Han, Meng and Deng, Haiteng and Hong, Yiguo and et al.}, year={2019}, month={Mar} }
 @inbook{mbewe_hanley-bowdoin_ndunguru_duffy_2018, place={St. Paul, MN}, title={Cassava viruses – host jumps, virus recombination, spread in plant material}, booktitle={Emerging Plant Diseases and Global Food Security}, publisher={APS Press}, author={Mbewe, W. and Hanley-Bowdoin, L. and Ndunguru, J. and Duffy, S.}, editor={Records, A. and Ristaino, J.Editors}, year={2018} }
 @article{turpin_vera_savadel_lung_wear_mickelson-young_thompson_hanley-bowdoin_dennis_zhang_et al._2018, title={Chromatin structure profile data from DNS-seq: Differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L)}, volume={20}, ISSN={["2352-3409"]}, DOI={10.1016/j.dib.2018.08.015}, abstractNote={Presented here are data from Next-Generation Sequencing of differential micrococcal nuclease digestions of formaldehyde-crosslinked chromatin in selected tissues of maize (Zea mays) inbred line B73. Supplemental materials include a wet-bench protocol for making DNS-seq libraries, the DNS-seq data processing pipeline for producing genome browser tracks. This report also includes the peak-calling pipeline using the iSeg algorithm to segment positive and negative peaks from the DNS-seq difference profiles. The data repository for the sequence data is the NCBI SRA, BioProject Accession PRJNA445708.}, journal={DATA IN BRIEF}, author={Turpin, Zachary M. and Vera, Daniel L. and Savadel, Savannah D. and Lung, Pei-Yau and Wear, Emily E. and Mickelson-Young, Leigh and Thompson, William F. and Hanley-Bowdoin, Linda and Dennis, Jonathan H. and Zhang, Jinfeng and et al.}, year={2018}, month={Oct}, pages={358–363} }
 @article{ismayil_haxim_wang_li_qian_han_chen_jia_yihao liu_zhu_et al._2018, title={Cotton Leaf Curl Multan virus C4 protein suppresses both transcriptional and post-transcriptional gene silencing by interacting with SAM synthetase}, volume={14}, ISSN={1553-7374}, url={http://dx.doi.org/10.1371/journal.ppat.1007282}, DOI={10.1371/journal.ppat.1007282}, abstractNote={Gene silencing is a natural antiviral defense mechanism in plants. For effective infection, plant viruses encode viral silencing suppressors to counter this plant antiviral response. The geminivirus-encoded C4 protein has been identified as a gene silencing suppressor, but the underlying mechanism of action has not been characterized. Here, we report that Cotton Leaf Curl Multan virus (CLCuMuV) C4 protein interacts with S-adenosyl methionine synthetase (SAMS), a core enzyme in the methyl cycle, and inhibits SAMS enzymatic activity. By contrast, an R13A mutation in C4 abolished its capacity to interact with SAMS and to suppress SAMS enzymatic activity. Overexpression of wild-type C4, but not mutant C4R13A, suppresses both transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS). Plants infected with CLCuMuV carrying C4R13A show decreased levels of symptoms and viral DNA accumulation associated with enhanced viral DNA methylation. Furthermore, silencing of NbSAMS2 reduces both TGS and PTGS, but enhanced plant susceptibility to two geminiviruses CLCuMuV and Tomato yellow leaf curl China virus. These data suggest that CLCuMuV C4 suppresses both TGS and PTGS by inhibiting SAMS activity to enhance CLCuMuV infection in plants.}, number={8}, journal={PLOS Pathogens}, publisher={Public Library of Science (PLoS)}, author={Ismayil, Asigul and Haxim, Yakupjan and Wang, Yunjing and Li, Huangai and Qian, Lichao and Han, Ting and Chen, Tianyuan and Jia, Qi and Yihao Liu, Alexander and Zhu, Songbiao and et al.}, editor={Dinesh-Kumar, Savithramma P.Editor}, year={2018}, month={Aug}, pages={e1007282} }
 @article{caldo_shen_xu_hanley-bowdoin_chen_weselake_lemieux_2018, title={Diacylglycerol acyltransferase 1 is activated by phosphatidate and inhibited by SnRK1-catalyzed phosphorylation}, volume={96}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.14029}, abstractNote={Summary}, number={2}, journal={PLANT JOURNAL}, author={Caldo, Kristian Mark P. and Shen, Wei and Xu, Yang and Hanley-Bowdoin, Linda and Chen, Guanqun and Weselake, Randall J. and Lemieux, M. Joanne}, year={2018}, month={Oct}, pages={287–299} }
 @article{concia_brooks_wheeler_zynda_wear_leblanc_song_lee_pascuzzi_martienssen_et al._2018, title={Genome-Wide Analysis of the Arabidopsis Replication Timing Program}, volume={176}, ISSN={["1532-2548"]}, url={http://europepmc.org/abstract/med/29301956}, DOI={10.1104/pp.17.01537}, abstractNote={The Arabidopsis genome replicates in two noninteracting compartments during early/mid and late S phase. Eukaryotes use a temporally regulated process, known as the replication timing program, to ensure that their genomes are fully and accurately duplicated during S phase. Replication timing programs are predictive of genomic features and activity and are considered to be functional readouts of chromatin organization. Although replication timing programs have been described for yeast and animal systems, much less is known about the temporal regulation of plant DNA replication or its relationship to genome sequence and chromatin structure. We used the thymidine analog, 5-ethynyl-2′-deoxyuridine, in combination with flow sorting and Repli-Seq to describe, at high-resolution, the genome-wide replication timing program for Arabidopsis (Arabidopsis thaliana) Col-0 suspension cells. We identified genomic regions that replicate predominantly during early, mid, and late S phase, and correlated these regions with genomic features and with data for chromatin state, accessibility, and long-distance interaction. Arabidopsis chromosome arms tend to replicate early while pericentromeric regions replicate late. Early and mid-replicating regions are gene-rich and predominantly euchromatic, while late regions are rich in transposable elements and primarily heterochromatic. However, the distribution of chromatin states across the different times is complex, with each replication time corresponding to a mixture of states. Early and mid-replicating sequences interact with each other and not with late sequences, but early regions are more accessible than mid regions. The replication timing program in Arabidopsis reflects a bipartite genomic organization with early/mid-replicating regions and late regions forming separate, noninteracting compartments. The temporal order of DNA replication within the early/mid compartment may be modulated largely by chromatin accessibility.}, number={3}, journal={PLANT PHYSIOLOGY}, author={Concia, Lorenzo and Brooks, Ashley M. and Wheeler, Emily and Zynda, Gregory J. and Wear, Emily E. and LeBlanc, Chantal and Song, Jawon and Lee, Tae-Jin and Pascuzzi, Pete E. and Martienssen, Robert A. and et al.}, year={2018}, month={Mar}, pages={2166–2185} }
 @article{rajabu_kennedy_ndunguru_ateka_tairo_hanley-bowdoin_ascencio-ibanez_2018, title={Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses}, volume={256}, ISSN={["1879-0984"]}, DOI={10.1016/j.jviromet.2018.03.002}, abstractNote={Geminiviruses are devastating single-stranded DNA viruses that infect a wide variety of crops in tropical and subtropical areas of the world. Tomato, which is a host for more than 100 geminiviruses, is one of the most affected crops. Developing plant models to study geminivirus-host interaction is important for the design of virus management strategies. In this study, “Florida Lanai” tomato was broadly characterized using three begomoviruses (Tomato yellow leaf curl virus, TYLCV; Tomato mottle virus, ToMoV; Tomato golden mosaic virus, TGMV) and a curtovirus (Beet curly top virus, BCTV). Infection rates of 100% were achieved by agroinoculation of TYLCV, ToMoV or BCTV. Mechanical inoculation of ToMoV or TGMV using a microsprayer as well as whitefly transmission of TYLCV or ToMoV also resulted in 100% infection frequencies. Symptoms appeared as early as four days post inoculation when agroinoculation or bombardment was used. Symptoms were distinct for each virus and a range of features, including plant height, flower number, fruit number, fruit weight and ploidy, was characterized. Due to its small size, rapid growth, ease of characterization and maintenance, and distinct responses to different geminiviruses, “Florida Lanai” is an excellent choice for comparing geminivirus infection in a common host.}, journal={JOURNAL OF VIROLOGICAL METHODS}, author={Rajabu, C. A. and Kennedy, G. G. and Ndunguru, J. and Ateka, E. M. and Tairo, F. and Hanley-Bowdoin, L. and Ascencio-Ibanez, J. T.}, year={2018}, month={Jun}, pages={89–99} }
 @article{shen_bobay_greeley_reyes_rajabu_blackburn_dallas_goshe_ascencio-ibanez_hanley-bowdoin_2018, title={Sucrose Nonfermenting 1-Related Protein Kinase 1 Phosphorylates a Geminivirus Rep Protein to Impair Viral Replication and Infection}, volume={178}, ISSN={["1532-2548"]}, DOI={10.1104/pp.18.00268}, abstractNote={Sucrose nonfermenting 1-related protein kinase 1 targets the geminivirus Rep protein to interfere with viral infection. Geminiviruses are single-stranded DNA viruses that infect a wide variety of plants and cause severe crop losses worldwide. The geminivirus replication initiator protein (Rep) binds to the viral replication origin and catalyzes DNA cleavage and ligation to initiate rolling circle replication. In this study, we found that the Tomato golden mosaic virus (TGMV) Rep is phosphorylated at serine-97 by sucrose nonfermenting 1-related protein kinase 1 (SnRK1), a master regulator of plant energy homeostasis and metabolism. Phosphorylation of Rep or the phosphomimic S97D mutation impaired Rep binding to viral DNA. A TGMV DNA-A replicon containing the Rep S97D mutation replicated less efficiently in tobacco (Nicotiana tabacum) protoplasts than in wild-type or Rep phosphorylation-deficient replicons. The TGMV Rep-S97D mutant also was less infectious than the wild-type virus in Nicotiana benthamiana and was unable to infect tomato (Solanum lycopersicum). Nearly all geminivirus Rep proteins have a serine residue at the position equivalent to TGMV Rep serine-97. SnRK1 phosphorylated the equivalent serines in the Rep proteins of Tomato mottle virus and Tomato yellow leaf curl virus and reduced DNA binding, suggesting that SnRK1 plays a key role in combating geminivirus infection. These results established that SnRK1 phosphorylates Rep and interferes with geminivirus replication and infection, underscoring the emerging role for SnRK1 in the host defense response against plant pathogens.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Shen, Wei and Bobay, Benjamin G. and Greeley, Laura A. and Reyes, Maria I. and Rajabu, Cyprian A. and Blackburn, R. Kevin and Dallas, Mary Beth and Goshe, Michael B. and Ascencio-Ibanez, Jose T. and Hanley-Bowdoin, Linda}, year={2018}, month={Sep}, pages={372–389} }
 @article{reyes_flores-vergara_guerra-peraza_rajabu_desai_hiromoto-ruiz_ndunguru_hanley-bowdoin_kjemtrup_ascencio-ibanez_et al._2017, title={A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae}, volume={92}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13716}, abstractNote={Summary}, number={5}, journal={PLANT JOURNAL}, author={Reyes, Maria Ines and Flores-Vergara, Miguel A. and Guerra-Peraza, Orlene and Rajabu, Cyprian and Desai, Jigar and Hiromoto-Ruiz, Yokiko H. and Ndunguru, Joseph and Hanley-Bowdoin, Linda and Kjemtrup, Susanne and Ascencio-Ibanez, Jose T. and et al.}, year={2017}, month={Dec}, pages={796–807} }
 @article{michelmore_coaker_bart_beattie_bent_bruce_cameron_dangl_dinesh-kumar_edwards_et al._2017, title={Foundational and Translational Research Opportunities to Improve Plant Health}, volume={30}, ISSN={0894-0282}, url={http://dx.doi.org/10.1094/mpmi-01-17-0010-cr}, DOI={10.1094/mpmi-01-17-0010-cr}, abstractNote={ The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture. }, number={7}, journal={Molecular Plant-Microbe Interactions}, publisher={Scientific Societies}, author={Michelmore, Richard and Coaker, Gitta and Bart, Rebecca and Beattie, Gwyn and Bent, Andrew and Bruce, Toby and Cameron, Duncan and Dangl, Jeffery and Dinesh-Kumar, Savithramma and Edwards, Rob and et al.}, year={2017}, month={Jul}, pages={515–516} }
 @article{wear_song_zynda_leblanc_lee_mickelson-young_concia_mulvaney_szymanski_allen_et al._2017, title={Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips}, volume={29}, ISSN={["1532-298X"]}, url={http://europepmc.org/abstract/med/28842533}, DOI={10.1105/tpc.17.00037}, abstractNote={The time during S phase at which different maize DNA sequences replicate reveals a complex temporal program influenced by genomic features, transcriptional activity, and chromatin structure. All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.}, number={9}, journal={PLANT CELL}, author={Wear, Emily E. and Song, Jawon and Zynda, Gregory J. and LeBlanc, Chantal and Lee, Tae-Jin and Mickelson-Young, Leigh and Concia, Lorenzo and Mulvaney, Patrick and Szymanski, Eric S. and Allen, George C. and et al.}, year={2017}, month={Sep}, pages={2126–2149} }
 @article{zynda_song_concia_wear_hanley-bowdoin_thompson_vaughn_2017, title={Repliscan: a tool for classifying replication timing regions}, volume={18}, ISSN={["1471-2105"]}, url={http://europepmc.org/abstract/med/28784090}, DOI={10.1186/s12859-017-1774-x}, abstractNote={Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing.To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds.Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.}, journal={BMC BIOINFORMATICS}, author={Zynda, Gregory J. and Song, Jawon and Concia, Lorenzo and Wear, Emily E. and Hanley-Bowdoin, Linda and Thompson, William F. and Vaughn, Matthew W.}, year={2017}, month={Aug}, pages={1–14} }
 @article{mickelson-young_wear_mulvaney_lee_szymanski_allen_hanley-bowdoin_thompson_2016, title={A flow cytometric method for estimating S-phase duration in plants}, volume={67}, ISSN={["1460-2431"]}, url={http://europepmc.org/abstract/med/27697785}, DOI={10.1093/jxb/erw367}, abstractNote={Highlight We estimated S-phase duration for several plant species by following EdU-labeled nuclei from G1 to G2 using bivariate flow cytometry. S-phase duration is relatively consistent over a range of genome sizes.}, number={21}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Mickelson-Young, Leigh and Wear, Emily and Mulvaney, Patrick and Lee, Tae-Jin and Szymanski, Eric S. and Allen, George and Hanley-Bowdoin, Linda and Thompson, William}, year={2016}, month={Nov}, pages={6077–6087} }
 @inbook{wear_concia_brooks_markham_lee_allen_thompson_hanley-bowdoin_2016, title={Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry}, ISBN={9781493931415 9781493931422}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-3142-2_6}, DOI={10.1007/978-1-4939-3142-2_6}, abstractNote={5-Ethynyl-2'-deoxyuridine (EdU) is a nucleoside analog of thymidine that can be rapidly incorporated into replicating DNA in vivo and, subsequently, detected by using "click" chemistry to couple its terminal alkyne group to fluorescent azides such as Alexa Fluor 488. Recently, EdU incorporation followed by coupling with a fluorophore has been used to visualize newly synthesized DNA in a wide range of plant species. One particularly useful application is in flow cytometry, where two-parameter sorting can be employed to analyze different phases of the cell cycle, as defined both by total DNA content and the amount of EdU pulse-labeled DNA. This approach allows analysis of the cell cycle without the need for synchronous cell populations, which can be difficult to obtain in many plant systems. The approach presented here, which was developed for fixed, EdU-labeled nuclei, can be used to prepare analytical profiles as well as to make highly purified preparations of G1, S, or G2/M phase nuclei for molecular or biochemical analysis. We present protocols for EdU pulse labeling, tissue fixation and harvesting, nuclei preparation, and flow sorting. Although developed for Arabidopsis suspension cells and maize root tips, these protocols should be modifiable to many other plant systems.}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Wear, Emily E. and Concia, Lorenzo and Brooks, Ashley M. and Markham, Emily A. and Lee, Tae-Jin and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2016}, pages={69–86} }
 @article{ndunguru_de leon_doyle_sseruwagi_plata_legg_thompson_tohme_aveling_ascencio-ibanez_et al._2016, title={Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease}, volume={90}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02834-15}, abstractNote={ABSTRACT}, number={8}, journal={JOURNAL OF VIROLOGY}, author={Ndunguru, Joseph and De Leon, Leandro and Doyle, Catherine D. and Sseruwagi, Peter and Plata, German and Legg, James P. and Thompson, Graham and Tohme, Joe and Aveling, Theresa and Ascencio-Ibanez, Jose T. and et al.}, year={2016}, month={Apr}, pages={4160–4173} }
 @article{bass_hoffman_lee_wear_joseph_allen_hanley-bowdoin_thompson_2015, title={Defining multiple, distinct, and shared spatiotemporal patterns of DNA replication and endoreduplication from 3D image analysis of developing maize (Zea mays L.) root tip nuclei}, volume={89}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-015-0364-4}, abstractNote={Spatiotemporal patterns of DNA replication have been described for yeast and many types of cultured animal cells, frequently after cell cycle arrest to aid in synchronization. However, patterns of DNA replication in nuclei from plants or naturally developing organs remain largely uncharacterized. Here we report findings from 3D quantitative analysis of DNA replication and endoreduplication in nuclei from pulse-labeled developing maize root tips. In both early and middle S phase nuclei, flow-sorted on the basis of DNA content, replicative labeling was widely distributed across euchromatic regions of the nucleoplasm. We did not observe the perinuclear or perinucleolar replicative labeling patterns characteristic of middle S phase in mammals. Instead, the early versus middle S phase patterns in maize could be distinguished cytologically by correlating two quantitative, continuous variables, replicative labeling and DAPI staining. Early S nuclei exhibited widely distributed euchromatic labeling preferentially localized to regions with weak DAPI signals. Middle S nuclei also exhibited widely distributed euchromatic labeling, but the label was preferentially localized to regions with strong DAPI signals. Highly condensed heterochromatin, including knobs, replicated during late S phase as previously reported. Similar spatiotemporal replication patterns were observed for both mitotic and endocycling maize nuclei. These results revealed that maize euchromatin exists as an intermingled mixture of two components distinguished by their condensation state and replication timing. These different patterns might reflect a previously described genome organization pattern, with "gene islands" mostly replicating during early S phase followed by most of the intergenic repetitive regions replicating during middle S phase.}, number={4-5}, journal={PLANT MOLECULAR BIOLOGY}, author={Bass, Hank W. and Hoffman, Gregg G. and Lee, Tae-Jin and Wear, Emily E. and Joseph, Stacey R. and Allen, George C. and Hanley-Bowdoin, Linda and Thompson, William F.}, year={2015}, month={Nov}, pages={339–351} }
 @misc{bass_wear_lee_hoffman_gumber_allen_thompson_hanley-bowdoin_2014, title={A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development}, volume={65}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/ert470}, abstractNote={The progress of nuclear DNA replication is complex in both time and space, and may reflect several levels of chromatin structure and 3-dimensional organization within the nucleus. To understand the relationship between DNA replication and developmental programmes, it is important to examine replication and nuclear substructure in different developmental contexts including natural cell-cycle progressions in situ. Plant meristems offer an ideal opportunity to analyse such processes in the context of normal growth of an organism. Our current understanding of large-scale chromosomal DNA replication has been limited by the lack of appropriate tools to visualize DNA replication with high resolution at defined points within S phase. In this perspective, we discuss a promising new system that can be used to visualize DNA replication in isolated maize (Zea mays L.) root tip nuclei after in planta pulse labelling with the thymidine analogue, 5-ethynyl-2'-deoxyuridine (EdU). Mixed populations of EdU-labelled nuclei are then separated by flow cytometry into sequential stages of S phase and examined directly using 3-dimensional deconvolution microscopy to characterize spatial patterns of plant DNA replication. Combining spatiotemporal analyses with studies of replication and epigenetic inheritance at the molecular level enables an integrated experimental approach to problems of mitotic inheritance and cellular differentiation.}, number={10}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Bass, Hank W. and Wear, Emily E. and Lee, Tae-Jin and Hoffman, Gregg G. and Gumber, Hardeep K. and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2014}, month={Jun}, pages={2747–2756} }
 @article{pascuzzi_flores-vergara_lee_sosinski_vaughn_hanley-bowdoin_thompson_allen_2014, title={In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts}, volume={26}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.113.121194}, abstractNote={This work uses tiling microarrays to map S/MARs on Arabidopsis chromosome 4. S/MARs were found to be spaced more closely than in the large plant and animal genomes studied to date and preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation. Most S/MARs occur near gene transcription start sites, and these genes show an increased probability of expression. Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function.}, number={1}, journal={PLANT CELL}, author={Pascuzzi, Pete E. and Flores-Vergara, Miguel A. and Lee, Tae-Jin and Sosinski, Bryon and Vaughn, Matthew W. and Hanley-Bowdoin, Linda and Thompson, William F. and Allen, George C.}, year={2014}, month={Jan}, pages={102–120} }
 @article{shen_dallas_goshe_hanley-bowdoin_2014, title={SnRK1 Phosphorylation of AL2 Delays Cabbage Leaf Curl Virus Infection in Arabidopsis}, volume={88}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.00761-14}, abstractNote={ABSTRACT}, number={18}, journal={JOURNAL OF VIROLOGY}, author={Shen, Wei and Dallas, Mary Beth and Goshe, Michael B. and Hanley-Bowdoin, Linda}, year={2014}, month={Sep}, pages={10598–10612} }
 @misc{hanley-bowdoin_bejarano_robertson_mansoor_2013, title={Geminiviruses: masters at redirecting and reprogramming plant processes}, volume={11}, ISSN={["1740-1534"]}, DOI={10.1038/nrmicro3117}, abstractNote={Geminiviruses are important plant pathogens that cause devastating crop losses worldwide. Here, Hanley-Bowdoin and colleagues review how viral proteins interact with cellular machineries and reprogramme cellular control pathways in their plant host to support viral DNA replication, gene expression and trafficking, and to interfere with host defences. The family Geminiviridae is one of the largest and most important families of plant viruses. The small, single-stranded DNA genomes of geminiviruses encode 5–7 proteins that redirect host machineries and processes to establish a productive infection. These interactions reprogramme plant cell cycle and transcriptional controls, inhibit cell death pathways, interfere with cell signalling and protein turnover, and suppress defence pathways. This Review describes our current knowledge of how geminiviruses interact with their plant hosts and the functional consequences of these interactions.}, number={11}, journal={NATURE REVIEWS MICROBIOLOGY}, author={Hanley-Bowdoin, Linda and Bejarano, Eduardo R. and Robertson, Dominique and Mansoor, Shahid}, year={2013}, month={Nov}, pages={777–788} }
 @article{reyes_nash_dallas_ascencio-ibanez_hanley-bowdoin_2013, title={Peptide Aptamers That Bind to Geminivirus Replication Proteins Confer a Resistance Phenotype to Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus Infection in Tomato}, volume={87}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.01095-13}, abstractNote={ABSTRACT}, number={17}, journal={JOURNAL OF VIROLOGY}, author={Reyes, Maria Ines and Nash, Tara E. and Dallas, Mary M. and Ascencio-Ibanez, J. Trinidad and Hanley-Bowdoin, Linda}, year={2013}, month={Sep}, pages={9691–9706} }
 @article{nash_dallas_reyes_buhrman_ascencio-ibanez_hanley-bowdoin_2011, title={Functional Analysis of a Novel Motif Conserved across Geminivirus Rep Proteins}, volume={85}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02143-10}, abstractNote={ABSTRACT}, number={3}, journal={JOURNAL OF VIROLOGY}, author={Nash, Tara E. and Dallas, Mary B. and Reyes, Maria Ines and Buhrman, Gregory K. and Ascencio-Ibanez, J. Trinidad and Hanley-Bowdoin, Linda}, year={2011}, month={Feb}, pages={1182–1192} }
 @article{sanchez-duran_dallas_ascencio-ibanez_reyes_arroyo-mateos_ruiz-albert_hanley-bowdoin_bejarano_2011, title={Interaction between Geminivirus Replication Protein and the SUMO-Conjugating Enzyme Is Required for Viral Infection}, volume={85}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.02566-10}, abstractNote={ABSTRACT}, number={19}, journal={JOURNAL OF VIROLOGY}, author={Sanchez-Duran, Miguel A. and Dallas, Mary B. and Ascencio-Ibanez, Jose T. and Reyes, Maria Ines and Arroyo-Mateos, Manuel and Ruiz-Albert, Javier and Hanley-Bowdoin, Linda and Bejarano, Eduardo R.}, year={2011}, month={Oct}, pages={9789–9800} }
 @article{shen_liu_song_xie_hanley-bowdoin_zhou_2011, title={Tomato SlSnRK1 Protein Interacts with and Phosphorylates beta C1, a Pathogenesis Protein Encoded by a Geminivirus beta-Satellite}, volume={157}, ISSN={["0032-0889"]}, DOI={10.1104/pp.111.184648}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Shen, Qingtang and Liu, Zhou and Song, Fengming and Xie, Qi and Hanley-Bowdoin, Linda and Zhou, Xueping}, year={2011}, month={Nov}, pages={1394–1406} }
 @article{lee_pascuzzi_settlage_shultz_tanurdzic_rabinowicz_menges_zheng_main_murray_et al._2010, title={Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State}, volume={6}, ISSN={1553-7404}, url={http://dx.doi.org/10.1371/journal.pgen.1000982}, DOI={10.1371/journal.pgen.1000982}, abstractNote={DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation of core DNA replication proteins, little is known about replication programs in plants. We used flow cytometry and tiling microarrays to profile DNA replication of Arabidopsis thaliana chromosome 4 (chr4) during early, mid, and late S phase. Replication profiles for early and mid S phase were similar and encompassed the majority of the euchromatin. Late S phase exhibited a distinctly different profile that includes the remaining euchromatin and essentially all of the heterochromatin. Termination zones were consistent between experiments, allowing us to define 163 putative replicons on chr4 that clustered into larger domains of predominately early or late replication. Early-replicating sequences, especially the initiation zones of early replicons, displayed a pattern of epigenetic modifications specifying an open chromatin conformation. Late replicons, and the termination zones of early replicons, showed an opposite pattern. Histone H3 acetylated on lysine 56 (H3K56ac) was enriched in early replicons, as well as the initiation zones of both early and late replicons. H3K56ac was also associated with expressed genes, but this effect was local whereas replication time correlated with H3K56ac over broad regions. The similarity of the replication profiles for early and mid S phase cells indicates that replication origin activation in euchromatin is stochastic. Replicon organization in Arabidopsis is strongly influenced by epigenetic modifications to histones and DNA. The domain organization of Arabidopsis is more similar to that in Drosophila than that in mammals, which may reflect genome size and complexity. The distinct patterns of association of H3K56ac with gene expression and early replication provide evidence that H3K56ac may be associated with initiation zones and replication origins.}, number={6}, journal={PLoS Genetics}, publisher={Public Library of Science (PLoS)}, author={Lee, Tae-Jin and Pascuzzi, Pete E. and Settlage, Sharon B. and Shultz, Randall W. and Tanurdzic, Milos and Rabinowicz, Pablo D. and Menges, Margit and Zheng, Ping and Main, Dorrie and Murray, James A. H. and et al.}, editor={Copenhaver, Gregory P.Editor}, year={2010}, month={Jun}, pages={e1000982} }
 @article{sozzani_maggio_giordo_umana_ascencio-ibañez_hanley-bowdoin_bergounioux_cella_albani_2010, title={The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis}, volume={72}, ISSN={1573-5028}, DOI={10.1007/s11103-009-9577-8}, abstractNote={An emerging view of plant cell cycle regulators, including the E2F transcription factors, implicates them in the integration of cell proliferation and development. Arabidopsis encodes six E2F proteins that can act as activators or repressors of E2F-responsive genes. E2FA, E2FB and E2FC interact with the retinoblastoma-like RBR protein and bind to DNA together with their DP partners. In contrast, E2FD, E2FE and E2FF (also known as DEL2, DEL1 and DEL3) are atypical E2Fs that possess duplicated DNA binding regions, lack trans-activating and RBR-binding domains and are believed to act as transcriptional inhibitors/repressors. E2FE/DEL1 has been shown to inhibit the endocycle and E2FF/DEL3 appears to control cell expansion but the role of E2FD/DEL2 has not been reported so far. In this study, we investigated the expression of E2FD/DEL2 and analysed the accumulation of its product. These studies revealed that E2FD/DEL2 accumulation is subject to negative post-translational regulation mediated by the plant hormone auxin. Moreover, the analysis of mutant and transgenic plants characterized by altered expression of E2FD/DEL2 has revealed that this atypical E2F can affect plant growth by promoting cell proliferation and repressing cell elongation. Overexpression of E2FD/DEL2 increased the expression of E2FA, E2FB and E2FE/DEL1 whereas its inactivation led to the up-regulation of genes encoding repressors of cell division. These results suggest that E2FD/DEL2 is part of a regulatory network that controls the balance between cell proliferation and development in Arabidopsis.}, number={4-5}, journal={Plant Molecular Biology}, author={Sozzani, Rosangela and Maggio, Caterina and Giordo, Roberta and Umana, Elisabetta and Ascencio-Ibañez, Jose Trinidad and Hanley-Bowdoin, Linda and Bergounioux, Catherine and Cella, Rino and Albani, Diego}, year={2010}, month={Mar}, pages={381–395} }
 @article{shen_reyes_hanley-bowdoin_2009, title={Arabidopsis Protein Kinases GRIK1 and GRIK2 Specifically Activate SnRK1 by Phosphorylating Its Activation Loop}, volume={150}, ISSN={["1532-2548"]}, DOI={10.1104/pp.108.132787}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Shen, Wei and Reyes, Maria Ines and Hanley-Bowdoin, Linda}, year={2009}, month={Jun}, pages={996–1005} }
 @article{shultz_lee_allen_thompson_hanley-bowdoin_2009, title={Dynamic Localization of the DNA Replication Proteins MCM5 and MCM7 in Plants}, volume={150}, ISSN={["1532-2548"]}, DOI={10.1104/pp.109.136614}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Shultz, Randall W. and Lee, Tae-Jin and Allen, George C. and Thompson, William F. and Hanley-Bowdoin, Linda}, year={2009}, month={Jun}, pages={658–669} }
 @inbook{lopez-ochoa_nash_ramirez-prado_hanley-bowdoin_2009, title={Isolation of Peptide Aptamers to Target Protein Function}, ISBN={9781934115893 9781597455572}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-59745-557-2_19}, DOI={10.1007/978-1-59745-557-2_19}, abstractNote={Peptide aptamers are small recombinant proteins typically inserted into a supportive protein scaffold. These short peptide domains can bind to their target proteins with high specificity and affinity, often resulting in an altered target protein. We describe high-throughput protocols that facilitate the selection and characterization of peptide aptamers from yeast dihybrid libraries. These protocols include the preparation and evaluation of the bait fusion and the peptide aptamer screen. They also include confirmation of interaction specificity as well as isolation and sequencing of peptide inserts. Once the amino acid sequence is determined, we describe a protocol for aligning and comparing short peptide sequences and assessing the statistical significance of the alignments.}, booktitle={Methods in Molecular Biology}, publisher={Humana Press}, author={Lopez-Ochoa, Luisa and Nash, Tara E. and Ramirez-Prado, Jorge and Hanley-Bowdoin, Linda}, year={2009}, pages={333–360} }
 @misc{ascencio-ibanez_sozzani_lee_chu_wolfinger_cella_hanley-bowdoin_2008, title={Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection}, volume={148}, number={1}, journal={Plant Physiology}, author={Ascencio-Ibanez, J. T. and Sozzani, R. and Lee, T. J. and Chu, T. M. and Wolfinger, R. D. and Cella, R. and Hanley-Bowdoin, L.}, year={2008}, pages={436–454} }
 @article{jordan_shen_hanley-bowdoin_robertson_2007, title={Geminivirus-induced gene silencing of the tobacco retinoblastoma-related gene results in cell death and altered development}, volume={65}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-007-9206-3}, abstractNote={The retinoblastoma-related protein (RBR) is required for cell cycle control and differentiation and is expressed throughout the life of plants and animals. In this study, the tomato golden mosaic virus (TGMV) geminivirus vector was used to silence NbRBR1 in Nicotiana benthamiana by microprojectile bombardment into fully developed leaves. Similar to previous results using agroinoculation of a tobacco rattle virus silencing vector [Park et al. (Plant J 42:153, 2005)], developmental defects caused by disruptions in cell size and number were seen in new growth. Leaf midvein cross-sections showed tissue-specific differences in size, cell number, and cell morphology. While cortical cell numbers decreased, size increased to maintain overall shape. In contrast, xylem parenchyma cells increased approximately three fold but remained small. Normally straight flowers often curved up to 360 degrees without a significant change in size. However, the most striking phenotype was cell death in mature cells after a delay of 3-4 weeks. Trypan blue staining confirmed cell death and demonstrated that cell death was absent in similarly treated leaves of wild type TGMV-inoculated plants. Quantitative RT-PCR confirmed that the mature TGMV:RBR-inoculated leaves still maintained reduced accumulation of RBR transcript at 4 weeks compared to controls. The results suggest that either inappropriate activation of the cell cycle is lethal in plants or that RBR has other functions, unrelated to the cell cycle. The results also demonstrate that continual transcription of RBR is necessary for cell survival.}, number={1-2}, journal={PLANT MOLECULAR BIOLOGY}, author={Jordan, Chad V. and Shen, Wei and Hanley-Bowdoin, Linda K. and Robertson, Dominique}, year={2007}, month={Sep}, pages={163–175} }
 @misc{shultz_tatineni_hanley-bowdoin_thompson_2007, title={Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice(1[W][OA])}, volume={144}, number={4}, journal={Plant Physiology}, author={Shultz, R. W. and Tatineni, V. M. and Hanley-Bowdoin, L. and Thompson, W. F.}, year={2007}, pages={1697–1714} }
 @article{arguello-astorga_ascencio-ibanez_dallas_orozco_hanley-bowdoin_2007, title={High-frequency reversion of geminivirus replication protein mutants during infection}, volume={81}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00925-07}, abstractNote={ABSTRACT}, number={20}, journal={JOURNAL OF VIROLOGY}, author={Arguello-Astorga, Gerardo and Ascencio-Ibanez, J. Trinidad and Dallas, Mary Beth and Orozco, Beverly M. and Hanley-Bowdoin, Linda}, year={2007}, month={Oct}, pages={11005–11015} }
 @article{shen_hanley-bowdoin_2006, title={Geminivirus infection up-regulates the expression of two Arabidopsis protein kinases related to yeast SNF1-and mammalian AMPK-activating kinases}, volume={142}, ISSN={["1532-2548"]}, DOI={10.1104/pp.106.088476}, abstractNote={Geminivirus Rep-interacting kinase 1 (GRIK1) and GRIK2 constitute a small protein kinase family in Arabidopsis (Arabidopsis thaliana). An earlier study showed that a truncated version of GRIK1 binds to the geminivirus replication protein AL1. We show here both full-length GRIK1 and GRIK2 interact with AL1 in yeast two-hybrid studies. Using specific antibodies, we showed that both Arabidopsis kinases are elevated in infected leaves. Immunoblot analysis of healthy plants revealed that GRIK1 and GRIK2 are highest in young leaf and floral tissues and low or undetectable in mature tissues. Immunohistochemical staining showed that the kinases accumulate in the shoot apical meristem, leaf primordium, and emerging petiole. Unlike the protein patterns, GRIK1 and GRIK2 transcript levels only show a small increase during infection and do not change significantly during development. Treating healthy seedlings and infected leaves with the proteasome inhibitor MG132 resulted in higher GRIK1 and GRIK2 protein levels, whereas treatment with the translation inhibitor cycloheximide reduced both kinases, demonstrating that their accumulation is modulated by posttranscriptional processes. Phylogenetic comparisons indicated that GRIK1, GRIK2, and related kinases from Medicago truncatula and rice (Oryza sativa) are most similar to the yeast kinases PAK1, TOS3, and ELM1 and the mammalian kinase CaMKK, which activate the yeast kinase SNF1 and its mammalian homolog AMPK, respectively. Complementation studies using a PAK1/TOS3/ELM1 triple mutant showed that GRIK1 and GRIK2 can functionally replace the yeast kinases, suggesting that the Arabidopsis kinases mediate one or more processes during early plant development and geminivirus infection by activating SNF1-related kinases.}, number={4}, journal={PLANT PHYSIOLOGY}, author={Shen, Wei and Hanley-Bowdoin, Linda}, year={2006}, month={Dec}, pages={1642–1655} }
 @article{lopez-ochoa_ramirez-prado_hanley-bowdoin_2006, title={Peptide aptamers that bind to a geminivirus replication protein interfere with viral replication in plant cells}, volume={80}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.02698-05}, abstractNote={ABSTRACT}, number={12}, journal={JOURNAL OF VIROLOGY}, author={Lopez-Ochoa, Luisa and Ramirez-Prado, Jorge and Hanley-Bowdoin, Linda}, year={2006}, month={Jun}, pages={5841–5853} }
 @article{shultz_settlage_hanley-bowdoin_thompson_2005, title={A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue}, volume={23}, ISSN={["0735-9640"]}, DOI={10.1007/BF02788888}, number={4}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Shultz, RW and Settlage, SB and Hanley-Bowdoin, L and Thompson, WF}, year={2005}, month={Dec}, pages={405–409} }
 @article{settlage_see_hanley-bowdoin_2005, title={Geminivirus C3 protein: Replication enhancement and protein interactions}, volume={79}, ISSN={["1098-5514"]}, DOI={10.1128/jvi.79.15.9885-9895.2005}, abstractNote={ABSTRACT}, number={15}, journal={JOURNAL OF VIROLOGY}, author={Settlage, SB and See, RG and Hanley-Bowdoin, L}, year={2005}, month={Aug}, pages={9885–9895} }
 @article{arguello-astorga_lopez-ochoa_kong_orozco_settlage_hanley-bowdoin_2004, title={A novel motif in geminivirus replication proteins interacts with the plant retinoblastoma-related protein}, volume={78}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.78.9.4817-4826.2004}, abstractNote={ABSTRACT}, number={9}, journal={JOURNAL OF VIROLOGY}, author={Arguello-Astorga, G and Lopez-Ochoa, L and Kong, LJ and Orozco, BM and Settlage, SB and Hanley-Bowdoin, L}, year={2004}, month={May}, pages={4817–4826} }
 @article{lee_shultz_hanley-bowdoin_thompson_2004, title={Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis}, volume={22}, ISSN={["1572-9818"]}, DOI={10.1007/BF02773136}, number={3}, journal={PLANT MOLECULAR BIOLOGY REPORTER}, author={Lee, TJ and Shultz, RW and Hanley-Bowdoin, L and Thompson, WF}, year={2004}, month={Sep}, pages={259–267} }
 @misc{hanley-bowdoin_orozco_kong_gruissem_2004, title={Geminivirus resistant transgenic plants}, volume={6,800,793}, number={2004 Oct. 5}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Hanley-Bowdoin, L. and Orozco, B. M. and Kong, L. J. and Gruissem, W.}, year={2004} }
 @misc{hanley-bowdoin_settlage_2004, title={Geminivirus resistant transgenic plants expressing a mutant geminivirus AL3/C3 coding sequence}, volume={6,747,188}, number={2004 June 8}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Hanley-Bowdoin, L. and Settlage, S.}, year={2004} }
 @article{castillo_kong_hanley-bowdoin_bejarano_2004, title={Interaction between a geminivirus replication protein and the plant sumoylation system}, volume={78}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.78.6.2758-2769.2004}, abstractNote={ABSTRACT}, number={6}, journal={JOURNAL OF VIROLOGY}, author={Castillo, AG and Kong, LJ and Hanley-Bowdoin, L and Bejarano, ER}, year={2004}, month={Mar}, pages={2758–2769} }
 @misc{hanley-bowdoin_settlage_robertson_2004, title={Reprogramming plant gene expression: a prerequisite to geminivirus DNA replication}, volume={5}, ISSN={["1364-3703"]}, DOI={10.1111/J.1364-3703.2004.00214.X}, abstractNote={SUMMARY}, number={2}, journal={MOLECULAR PLANT PATHOLOGY}, author={Hanley-Bowdoin, L and Settlage, SB and Robertson, D}, year={2004}, month={Mar}, pages={149–156} }
 @article{kong_hanley-bowdoin_2002, title={A geminivirus replication protein interacts with a protein kinase and a motor protein that display different expression patterns during plant development and infection}, volume={14}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.003681}, abstractNote={The geminivirus protein AL1 initiates viral DNA replication, regulates its own expression, and induces plant gene transcription. To better understand how AL1 interacts with host proteins during these processes, we used yeast two-hybrid library screening and a baculovirus protein interaction system to identify plant proteins that interact with AL1. These studies identified a Ser/Thr kinase, a kinesin, and histone H3 as AL1 partners. The kinase is autophosphorylated and can phosphorylate common kinase substrates in vitro. The kinesin is phosphorylated in insect cells by a cyclin-dependent kinase. Immunostaining of Nicotiana benthamiana and Arabidopsis showed that kinase protein levels and subcellular location are regulated during plant development and geminivirus infection. By contrast, the kinesin is ubiquitous even though it is associated with the spindle apparatus in mitotic cells. Together, our results establish that AL1 interacts with host proteins involved in plant cell division and development. Possible functions of these host factors in healthy and geminivirus-infected plants are discussed.}, number={8}, journal={PLANT CELL}, author={Kong, LJ and Hanley-Bowdoin, L}, year={2002}, month={Aug}, pages={1817–1832} }
 @article{nagara_hanley-bowdoin_robertson_2002, title={Host DNA replication is induced by geminivirus infection of differentiated plant cells}, volume={14}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.005777}, abstractNote={The geminivirus Tomato golden mosaic virus (TGMV) replicates in differentiated plant cells using host DNA synthesis machinery. We used 5-bromo-2-deoxyuridine (BrdU) incorporation to examine DNA synthesis directly in infected Nicotiana benthamiana plants to determine if viral reprogramming of host replication controls had an impact on host DNA replication. Immunoblot analysis revealed that up to 17-fold more BrdU was incorporated into chromosomal DNA of TGMV-infected versus mock-infected, similarly treated healthy leaves. Colocalization studies of viral DNA and BrdU demonstrated that BrdU incorporation was specific to infected cells and was associated with both host and viral DNA. TGMV and host DNA synthesis were inhibited differentially by aphidicolin but were equally sensitive to hydroxyurea. Short BrdU labeling times resulted in some infected cells showing punctate foci associated with host DNA. Longer periods showed BrdU label uniformly throughout host DNA, some of which showed condensed chromatin, only in infected nuclei. By contrast, BrdU associated with viral DNA was centralized and showed uniform, compartmentalized labeling. Our results demonstrate that chromosomal DNA is replicated in TGMV-infected cells.}, number={12}, journal={PLANT CELL}, author={Nagara, S and Hanley-Bowdoin, L and Robertson, D}, year={2002}, month={Dec}, pages={2995–3007} }
 @article{egelkrout_mariconti_settlage_cella_robertson_hanley-bowdoin_2002, title={Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development}, volume={14}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.006403}, abstractNote={E2F transcription factors regulate genes expressed at the G1/S boundary of the cell division cycle in higher eukaryotes. Although animal E2F proteins and their target promoters have been studied extensively, little is known about how these factors regulate plant promoters. An earlier study identified two E2F consensus binding sites in the promoter of a Nicotiana benthamiana gene encoding proliferating cell nuclear antigen (PCNA) and showed that the proximal element (E2F2) is required for the full repression of PCNA expression in mature leaves. In this study, we examined the distal element (E2F1) and how it interacts with the E2F2 site to regulate the PCNA promoter. Gel shift assays using plant nuclear extracts or purified Arabidopsis E2F and DP proteins showed that different complexes bind to the two E2F sites. Mutation of the E2F1 site or both sites differentially altered PCNA promoter function in transgenic plants. As reported previously for the E2F2 mutation, the E2F1 and E2F1+2 mutations partially relieved the repression of the PCNA promoter in mature leaves. In young tissues, the E2F1 mutation resulted in a threefold reduction in PCNA promoter activity, whereas the E2F1+2 mutation had no detectable effect. The activity of E2F1+2 mutants was indistinguishable from that of E2F2 mutants. These results demonstrate that both E2F elements contribute to the repression of the PCNA promoter in mature leaves, whereas the E2F1 site counters the repression activity of the E2F2 element in young leaves.}, number={12}, journal={PLANT CELL}, author={Egelkrout, EM and Mariconti, L and Settlage, SB and Cella, R and Robertson, D and Hanley-Bowdoin, L}, year={2002}, month={Dec}, pages={3225–3236} }
 @article{settlage_miller_gruissem_hanley-bowdoin_2001, title={Dual interaction of a geminivirus replication accessory factor with a viral replication protein and a plant cell cycle regulator}, volume={279}, ISSN={["0042-6822"]}, DOI={10.1006/viro.2000.0719}, abstractNote={Geminiviruses replicate their small, single-stranded DNA genomes through double-stranded DNA intermediates in plant nuclei using host replication machinery. Like most dicot-infecting geminiviruses, tomato golden mosaic virus encodes a protein, AL3 or C3, that greatly enhances viral DNA accumulation through an unknown mechanism. Earlier studies showed that AL3 forms oligomers and interacts with the viral replication initiator AL1. Experiments reported here established that AL3 also interacts with a plant homolog of the mammalian tumor suppressor protein, retinoblastoma (pRb). Analysis of truncated AL3 proteins indicated that pRb and AL1 bind to similar regions of AL3, whereas AL3 oligomerization is dependent on a different region of the protein. Analysis of truncated AL1 proteins located the AL3-binding domain between AL1 amino acids 101 and 180 to a region that also includes the AL1 oligomerization domain and the catalytic site for initiation of viral DNA replication. Interestingly, the AL3-binding domain was fully contiguous with the domain that mediates AL1/pRb interactions. The potential significance of AL3/pRb binding and the coincidence of the domains responsible for AL3, AL1, and pRb interactions are discussed.}, number={2}, journal={VIROLOGY}, author={Settlage, SB and Miller, AB and Gruissem, W and Hanley-Bowdoin, L}, year={2001}, month={Jan}, pages={570–576} }
 @article{egelkrout_robertson_hanley-bowdoin_2001, title={Proliferating cell nuclear antigen transcription is repressed through an E2F consensus element and activated by geminivirus infection in mature leaves}, volume={13}, ISSN={["1531-298X"]}, DOI={10.1105/tpc.13.6.1437}, abstractNote={The geminivirus tomato golden mosaic virus (TGMV) amplifies its DNA genome in differentiated plant cells that lack detectable levels of DNA replication enzymes. Earlier studies showed that TGMV induces the accumulation of proliferating cell nuclear antigen (PCNA), the processivity factor for DNA polymerase delta, in mature cells of Nicotiana benthamiana. We sought to determine if PCNA protein accumulation reflects transcriptional activation of the host gene. RNA gel blot analysis detected an approximately 1200-nucleotide PCNA transcript in young leaves. The same RNA was found in mature leaves of infected but not healthy plants. Reporter gene analysis showed that a 633-bp promoter fragment of the N. benthamiana PCNA gene supports high levels of expression in cultured cells and in young but not mature leaves of healthy transgenic plants. In contrast, PCNA promoter activity was detected in both young and mature leaves of TGMV-infected plants. Developmental studies established a strong relationship between symptom severity, viral DNA accumulation, PCNA promoter activity, and endogenous PCNA mRNA levels. Mutation of an E2F consensus element in the PCNA promoter had no effect on its activity in young leaves but increased transcription in healthy mature leaves. Unlike the wild-type PCNA promoter, TGMV infection had no detectable effect on the activity of the mutant E2F promoter. Together, these results demonstrate that geminivirus infection induces the accumulation of a host replication factor by activating transcription of its gene in mature tissues, most likely by overcoming E2F-mediated repression.}, number={6}, journal={PLANT CELL}, author={Egelkrout, EM and Robertson, D and Hanley-Bowdoin, L}, year={2001}, month={Jun}, pages={1437–1452} }
 @article{peele_jordan_muangsan_turnage_egelkrout_eagle_hanley-bowdoin_robertson_2001, title={Silencing of a meristematic gene using geminivirus-derived vectors}, volume={27}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313x.2001.01080.x}, abstractNote={Summary}, number={4}, journal={PLANT JOURNAL}, author={Peele, C and Jordan, CV and Muangsan, N and Turnage, M and Egelkrout, E and Eagle, P and Hanley-Bowdoin, L and Robertson, D}, year={2001}, month={Aug}, pages={357–366} }
 @article{kong_orozco_roe_nagar_ou_feiler_durfee_miller_gruissem_robertson_et al._2000, title={A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants}, volume={19}, ISSN={["0261-4189"]}, DOI={10.1093/emboj/19.13.3485}, abstractNote={Geminiviruses replicate in nuclei of mature plant cells after inducing the accumulation of host DNA replication machinery. Earlier studies showed that the viral replication factor, AL1, is sufficient for host induction and interacts with the cell cycle regulator, retinoblastoma (pRb). Unlike other DNA virus proteins, AL1 does not contain the pRb binding consensus, LXCXE, and interacts with plant pRb homo logues (pRBR) through a novel amino acid sequence. We mapped the pRBR binding domain of AL1 between amino acids 101 and 180 and identified two mutants that are differentially impacted for AL1–pRBR interactions. Plants infected with the E‐N140 mutant, which is wild‐type for pRBR binding, developed wild‐type symptoms and accumulated viral DNA and AL1 protein in epidermal, mesophyll and vascular cells of mature leaves. Plants inoculated with the KEE146 mutant, which retains 16% pRBR binding activity, only developed chlorosis along the veins, and viral DNA, AL1 protein and the host DNA synthesis factor, proliferating cell nuclear antigen, were localized to vascular tissue. These results established the importance of AL1–pRBR interactions during geminivirus infection of plants.}, number={13}, journal={EMBO JOURNAL}, author={Kong, LJ and Orozco, BM and Roe, JL and Nagar, S and Ou, S and Feiler, HS and Durfee, T and Miller, AB and Gruissem, W and Robertson, D and et al.}, year={2000}, month={Jul}, pages={3485–3495} }
 @article{bass_nagar_hanley-bowdoin_robertson_2000, title={Chromosome condensation induced by geminivirus infection of mature plant cells}, volume={113}, number={7}, journal={Journal of Cell Science}, author={Bass, H. W. and Nagar, S. and Hanley-Bowdoin, L. and Robertson, D.}, year={2000}, pages={1149–1160} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_2000, title={Geminiviruses - Models for plant DNA replication, transcription and cell cycle regulation ([correction to] vol 35, pg 105, 2000)}, volume={35}, number={4}, journal={Critical Reviews in Biochemistry and Molecular Biology}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={2000}, pages={U4} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_2000, title={Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation}, volume={35}, number={2}, journal={Critical Reviews in Biochemistry and Molecular Biology}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={2000}, pages={105–140} }
 @article{orozco_kong_batts_elledge_hanley-bowdoin_2000, title={The multifunctional character of a geminivirus replication protein is reflected by its complex oligomerization properties}, volume={275}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.275.9.6114}, abstractNote={Tomato golden mosaic virus (TGMV), a member of the geminivirus family, encodes one essential replication protein, AL1, and recruits the rest of the DNA replication apparatus from its plant host. TGMV AL1 is an oligomeric protein that binds double-stranded DNA and catalyzes cleavage and ligation of single-stranded DNA. The oligomerization domain, which is required for DNA binding, maps to a region that displays strong sequence and structural homology to other geminivirus Rep proteins. To assess the importance of conserved residues, we generated a series of site-directed mutations and analyzed their impact on AL1 function in vitro and in vivo. Two-hybrid experiments revealed that mutation of amino acids 157–159 inhibited AL1-AL1 interactions, whereas mutations at nearby residues reduced complex stability. Changes at positions 157–159 also disrupted interaction between the full-length mutant protein and a glutathione S-transferase-AL1 oligomerization domain fusion in insect cells. The mutations had no detectable effect on oligomerization when both proteins contained full-length AL1 sequences, indicating that AL1 complexes can be stabilized by amino acids outside of the oligomerization domain. Nearly all of the oligomerization domain mutants were inhibited or severely attenuated in their ability to support AL1-directed viral DNA replication. In contrast, the same mutants were enhanced for AL1-mediated transcriptional repression. The replication-defective AL1 mutants also interfered with replication of a TGMV A DNA encoding wild type AL1. Full-length mutant AL1 was more effective in the interference assays than truncated proteins containing the oligomerization domain. Together, these results suggested that different AL1 complexes mediate viral replication and transcriptional regulation and that replication interference involves multiple domains of the AL1 protein.}, number={9}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Orozco, BM and Kong, LJ and Batts, LA and Elledge, S and Hanley-Bowdoin, L}, year={2000}, month={Mar}, pages={6114–6122} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_1999, title={Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation {review}}, volume={18}, DOI={10.1080/07352689991309162}, abstractNote={Geminiviruses have small, single-stranded DNA genomes that replicate through double-stranded intermediates in the nuclei of infected plant cells. Viral double-stranded DNA also assembles into minichromosomes and is transcribed in infected cells. Geminiviruses encode only a few proteins for their replication and transcription and rely on host enzymes for these processes. However, most plant cells, which have exited the cell cycle and undergone differentiation, do not contain the replicative enzymes necessary for viral DNA synthesis. To overcome this barrier, geminiviruses induce the accumulation of DNA replication machinery in mature plant cells, most likely by modifying cell cycle and transcriptional controls. In animals, several DNA viruses depend on host replication and transcription machinery and can alter their hosts to create an environment that facilitates efficient viral replication. Analysis of these viruses and their proteins has contributed significantly to our understanding of DNA replication, transcription, and cell cycle regulation in mammalian cells. Geminiviruses have the same potential for plant systems. Plants offer many advantages for these types of studies, including ease of transformation, well-defined cell populations and developmental programs, and greater tolerance of cell cycle perturbation and polyploidy. Our knowledge of the molecular and cellular events that mediate geminivirus infection has increased significantly during recent years. The goal of this review is to summarize recent research addressing geminivirus DNA replication and its integration with transcriptional and cell cycle regulatory processes.}, number={1}, journal={Critical Reviews in Plant Sciences}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={1999}, pages={71–106} }
 @article{orozco_hanley-bowdoin_1998, title={Conserved sequence and structural motifs contribute to the DNA binding and cleavage activities of a geminivirus replication protein}, volume={273}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.273.38.24448}, abstractNote={Tomato golden mosaic virus (TGMV), a member of the geminivirus family, has a single-stranded DNA genome that replicates through a rolling circle mechanism in nuclei of infected plant cells. TGMV encodes one essential replication protein, AL1, and recruits the rest of the DNA replication apparatus from its host. AL1 is a multifunctional protein that binds double-stranded DNA, catalyzes cleavage and ligation of single-stranded DNA, and forms oligomers. Earlier experiments showed that the region of TGMV AL1 necessary for DNA binding maps to the N-terminal 181 amino acids of the protein and overlaps the DNA cleavage (amino acids 1–120) and oligomerization (amino acids 134–181) domains. In this study, we generated a series of site-directed mutations in conserved sequence and structural motifs in the overlapping DNA binding and cleavage domains and analyzed their impact on AL1 function in vivo and in vitro. Only two of the fifteen mutant proteins were capable of supporting viral DNA synthesis in tobacco protoplasts. In vitroexperiments demonstrated that a pair of predicted α-helices with highly conserved charged residues are essential for DNA binding and cleavage. Three sequence motifs conserved among geminivirus AL1 proteins and initiator proteins from other rolling circle systems are also required for both activities. We used truncated AL1 proteins fused to a heterologous dimerization domain to show that the DNA binding domain is located between amino acids 1 and 130 and that binding is dependent on protein dimerization. In contrast, AL1 monomers were sufficient for DNA cleavage and ligation. Together, these results established that the conserved motifs in the AL1 N terminus contribute to DNA binding and cleavage with both activities displaying nearly identical amino acid requirements. However, DNA binding was readily distinguished from cleavage and ligation by its dependence on AL1/AL1 interactions.}, number={38}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Orozco, BM and Hanley-Bowdoin, L}, year={1998}, month={Sep}, pages={24448–24456} }
 @article{orozco_gladfelter_settlage_eagle_gentry_hanley-bowdoin_1998, title={Multiple cis elements contribute to geminivirus origin function}, volume={242}, ISSN={["0042-6822"]}, DOI={10.1006/viro.1997.9013}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules which are dissimilar in sequence except for a highly conserved 200-bp common region that includes the origin for rolling circle replication. To better characterize the plus-strand origin, we analyzed the capacities of various TGMV common region sequences to support episomal replication in tobacco protoplasts when the viral replication proteins AL1 and AL3 were supplied in trans. These experiments demonstrated that the minimal origin is located in 89-bp common region fragment that includes the known AL1 binding motif and a hairpin structure containing the DNA cleavage site. Analyses of mutant origin sequences identified two additional cis elements--one that is required for origin activity and a second that greatly enhances replication. In contrast, a conserved partial copy of the AL1 binding site did not contribute to origin function. Mutational analysis of the functional AL1 binding site showed that both spacing and sequence of this motif are important for replication in vivo and AL1/DNA binding in vitro. Spacing changes between the AL1 binding site and hairpin also negatively impacted TGMV origin function in a position-dependent manner. Together, these results demonstrated that the organization of TGMV plus-strand origin is complex, involving multiple cis elements that are likely to interact with each other during initiation of replication.}, number={2}, journal={VIROLOGY}, author={Orozco, BM and Gladfelter, HJ and Settlage, SB and Eagle, PA and Gentry, RN and Hanley-Bowdoin, L}, year={1998}, month={Mar}, pages={346–356} }
 @article{eagle_hanley-bowdoin_1997, title={CIS elements that contribute to geminivirus transcriptional regulation and the efficiency of DNA replication}, volume={71}, number={9}, journal={Journal of Virology}, author={Eagle, P. A. and Hanley-Bowdoin, L. K.}, year={1997}, pages={6947–6955} }
 @article{orozco_miller_settlage_hanley-bowdoin_1997, title={Functional domains of a geminivirus replication protein}, volume={272}, DOI={10.1074/jbc.272.15.9840}, abstractNote={Tomato golden mosaic virus, a member of the geminivirus family, has a single-stranded DNA genome that is replicated and transcribed in infected plant cells through the concerted action of viral and host factors. One viral protein, AL1, contributes to both processes by binding to a directly repeated, double-stranded DNA sequence located in the overlapping (+) strand origin of replication and AL1 promoter. The AL1 protein, which occurs as a multimeric complex in solution, also catalyzes DNA cleavage during initiation of rolling circle replication. To identify the tomato golden mosaic virus AL1 domains that mediate protein oligomerization, DNA binding, and DNA cleavage, a series of truncated AL1 proteins were produced in a baculovirus expression system and assayed for each activity. These experiments localized the AL1 oligomerization domain between amino acids 121 and 181, the DNA binding domain between amino acids 1 and 181, and the DNA cleavage domain between amino acids 1 and 120. Deletion of the first 29 amino acids of AL1 abolished DNA binding and DNA cleavage, demonstrating that an intact N terminus is required for both activities. The observation that the DNA binding domain includes the oligomerization domain suggested that AL1-AL1 protein interaction may be a prerequisite for DNA binding but not for DNA cleavage. The significance of these results for AL1 function during geminivirus replication and transcription is discussed.}, number={15}, journal={Journal of Biological Chemistry}, author={Orozco, B. M. and Miller, A. B. and Settlage, S. B. and Hanley-Bowdoin, Linda}, year={1997}, pages={9840–9846} }
 @article{ach_durfee_miller_taranto_hanleybowdoin_zambryski_gruissem_1997, title={RRB1 and RRB2 encode maize retinoblastoma-related proteins that interact with a plant D-type cyclin and geminivirus replication protein}, volume={17}, ISSN={["0270-7306"]}, DOI={10.1128/MCB.17.9.5077}, abstractNote={Unlike mammalian and yeast cells, little is known about how plants regulate G1 progression and entry into the S phase of the cell cycle. In mammalian cells, a key regulator of this process is the retinoblastoma tumor suppressor protein (RB). In contrast, G1 control in Saccharomyces cerevisiae does not utilize an RB-like protein. We report here the cloning of cDNAs from two Zea mays genes, RRB1 and RRB2, that encode RB-related proteins. Further, RRB2 transcripts are alternatively spliced to yield two proteins with different C termini. At least one RRB gene is expressed in all the tissues examined, with the highest levels seen in the shoot apex. RRB1 is a 96-kDa nuclear protein that can physically interact with two mammalian DNA tumor virus oncoproteins, simian virus 40 large-T antigen and adenovirus E1A, and with a plant D-type cyclin. These associations are abolished by mutation of a conserved cysteine residue in RRB1 that is also essential for RB function. RRB1 binding potential is also sensitive to deletions in the conserved A and B domains, although differences exist in these effects compared to those of human RB. RRB1 can also bind to the AL1 protein from tomato golden mosaic virus (TGMV), a protein which is essential for TGMV DNA replication. These results suggest that G1 regulation in plant cells is controlled by a mechanism which is much more similar to that found in mammalian cells than that in yeast.}, number={9}, journal={MOLECULAR AND CELLULAR BIOLOGY}, author={Ach, RA and Durfee, T and Miller, AB and Taranto, P and HanleyBowdoin, L and Zambryski, PC and Gruissem, W}, year={1997}, month={Sep}, pages={5077–5086} }
 @article{gladfelter_eagle_fontes_batts_hanley-bowdoin_1997, title={Two domains of the AL1 protein mediate geminivirus origin recognition}, volume={239}, ISSN={["0042-6822"]}, DOI={10.1006/viro.1997.8869}, abstractNote={The geminiviruses tomato golden mosaic virus (TGMV) and bean golden mosaic virus (BGMV) have bipartite genomes. Their A and B DNA components contain cis-acting sequences that function as origins of replication, while their A components encode the trans-acting replication proteins--AL1 and AL3. Earlier experiments demonstrated that virus-specific interactions between the cis- and trans-acting functions are required for TGMV and BGMV replication and that the AL1 proteins of the two viruses specifically bind their respective origins. In the current study, characterization of AL1 and AL3 proteins produced from plant expression cassettes in transient replication assays revealed that interaction between AL1 and the origin is responsible for virus-specific replication. The AL3 protein does not contribute to specificity but can be preferred by its cognate AL1 protein when replication is impaired. Analysis of chimeric proteins showed that two regions of AL1 act as specificity determinants during replication. The first domain is located between amino acids 1 and 116 and recognizes the AL1 origin binding site. The second region, which is between amino acids 121 and 209, is not dependent on the known AL1 DNA binding site. Analysis of wild type and chimeric proteins in transient transcription assays showed that AL1 also represses its own promoter in a virus-specific manner. Transcriptional specificity is conferred primarily by AL1 amino acids 1-93 with amino acids 121-209 making a smaller contribution. Together, these results demonstrated that the virus-specific interactions of AL1 during replication and transcription are complex, involving at least two discreet domains of the protein.}, number={1}, journal={VIROLOGY}, author={Gladfelter, HJ and Eagle, PA and Fontes, EPB and Batts, L and Hanley-Bowdoin, L}, year={1997}, month={Dec}, pages={186–197} }
 @article{orozco_hanley-bowdoin_1996, title={A DNA structure is required for geminivirus replication origin function.}, volume={70}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.70.1.148-158.1996}, DOI={10.1128/jvi.70.1.148-158.1996}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two single-stranded circular DNAs, A and B, that replicate through a rolling-circle mechanism in nuclei of infected plant cells. The TGMV origin of replication is located in a conserved 5' intergenic region and includes at least two functional elements: the origin recognition site of the essential viral replication protein, AL1, and a sequence motif with the potential to form a hairpin or cruciform structure. To address the role of the hairpin motif during TGMV replication, we constructed a series of B-component mutants that resolved sequence changes from structural alterations of the motif. Only those mutant B DNAs that retained the capacity to form the hairpin structure replicated to wild-type levels in tobacco protoplasts when the viral replication proteins were provided in trans from a plant expression cassette. In contrast, the same B DNAs replicated to significantly lower levels in transient assays that included replicating, wild-type TGMV A DNA. These data established that the hairpin structure is essential for TGMV replication, whereas its sequence affects the efficiency of replication. We also showed that TGMV AL1 functions as a site-specific endonuclease in vitro and mapped the cleavage site to the loop of the hairpin. In vitro cleavage analysis of two TGMV B mutants with different replication phenotypes indicated that there is a correlation between the two assays for origin activity. These results suggest that the in vivo replication results may reflect structural and sequence requirements for DNA cleavage during initiation of rolling-circle replication.}, number={1}, journal={Journal of virology}, publisher={American Society for Microbiology}, author={Orozco, B M and Hanley-Bowdoin, L}, year={1996}, pages={148–158} }
 @inbook{hanley-bowdoin_eagle_orozco_robertson_settlage_1996, place={St. Paul, MN}, title={Geminivirus Replication}, booktitle={Biology of Plant-Microbe Interactions}, publisher={International Society of Molecular Plant-Microbe Interactions}, author={Hanley-Bowdoin, L. and Eagle, P.A. and Orozco, B.M. and Robertson, D. and Settlage, S.B.}, editor={Stacey, G. and Mullin, B. and Gresshoff, P.M.Editors}, year={1996}, pages={287–292} }
 @article{settlage_miller_hanley-bowdoin_1996, title={Interactions between geminivirus replication proteins.}, volume={70}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.70.10.6790-6795.1996}, DOI={10.1128/jvi.70.10.6790-6795.1996}, abstractNote={Geminiviruses are small DNA viruses that replicate in the nuclei of infected plant cells. The closely related geminiviruses tomato golden mosaic virus and bean golden mosaic virus each encode a protein, AL1, that catalyzes the initiation of rolling-circle replication. Both viruses also specify a second replication protein, AL3, that greatly enhances the level of viral DNA accumulation. Using recombinant proteins produced in a baculovirus expression system, we showed that AL1 copurifies with a protein fusion of glutathione S-transferase (GST) and AL1, independent of the GST domain. Similarly, authentic AL3 cofractionates with a GST-AL3 fusion protein. These results demonstrated that both AL1 and AL3 form oligomers. Immunoprecipitation of protein extracts from insect cells expressing both AL1 and AL3 showed that the two proteins also complex with each other. None of the protein interactions displayed virus specificity; the tomato and bean golden mosaic virus proteins complexed with each other. The addition of heterologous replication proteins had no effect on the efficiency of geminivirus replication in transient-replication assays, suggesting that heteroprotein complexes might be functional. The significance of these protein interactions is discussed with respect to geminivirus replication in plant cells.}, number={10}, journal={Journal of virology}, publisher={American Society for Microbiology}, author={Settlage, S B and Miller, A B and Hanley-Bowdoin, L}, year={1996}, pages={6790–6795} }
 @article{nagar_pedersen_carrick_hanley-bowdoin_robertson_1995, title={A geminivirus induces expression of a host DNA synthesis protein in terminally differentiated plant cells.}, volume={7}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.7.6.705}, DOI={10.1105/tpc.7.6.705}, abstractNote={Geminiviruses are plant DNA viruses that replicate through DNA intermediates in plant nuclei. The viral components required for replication are known, but no host factors have yet been identified. We used immunolocalization to show that the replication proteins of the geminivirus tomato golden mosaic virus (TGMV) are located in nuclei of terminally differentiated cells that have left the cell cycle. In addition, TGMV infection resulted in a significant accumulation of the host DNA synthesis protein proliferating cell nuclear antigen (PCNA). PCNA, an accessory factor for DNA polymerase delta, was not present at detectable levels in healthy differentiated cells. The TGMV replication protein AL1 was sufficient to induce accumulation of PCNA in terminally differentiated cells of transgenic plants. Analysis of the mechanism(s) whereby AL1 induces the accumulation of host replication machinery in quiescent plant cells will provide a unique opportunity to study plant DNA synthesis.}, number={6}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Nagar, S and Pedersen, T J and Carrick, K M and Hanley-Bowdoin, L and Robertson, D}, year={1995}, month={Jun}, pages={705–719} }
 @article{eagle_orozco_hanley-bowdoin_1994, title={A DNA sequence required for geminivirus replication also mediates transcriptional regulation.}, volume={6}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.6.8.1157}, DOI={10.1105/tpc.6.8.1157}, abstractNote={Tomato golden mosaic virus (TGMV), a member of the geminivirus family, requires a single virus-encoded protein for DNA replication. We show that the TGMV replication protein, AL1, also acts during transcription to specifically repress the activity of its promoter. An earlier study established that AL1 binds to a 13-bp sequence (5'-GGTAGTAAGGTAG) that is essential for activity of the TGMV replication origin. Analysis of AL1 binding site mutants in transient expression assays demonstrated that the same site, which is located between the transcription start site and TATA box in the AL1 promoter, also mediates transcriptional repression. These experiments revealed that the repeated motifs in the AL1 binding site contribute differentially to repression, as has been observed previously for AL1-DNA binding and viral replication. Introduction of the AL1 binding site into the 35S promoter of the cauliflower mosaic virus was sufficient to confer AL1-mediated repression to the heterologous promoter. Analysis of a truncated AL1 promoter and of mutant AL1 proteins showed that repression does not require a replication-competent template or a replication-competent AL1 protein. Transient expression studies using two different Nicotiana cell lines revealed that, although the two lines replicate plasmids containing the TGMV origin similarly, they support very different levels of AL1-mediated repression. These results suggest that geminivirus transcriptional repression and replication may be independent processes.}, number={8}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Eagle, P A and Orozco, B M and Hanley-Bowdoin, L}, year={1994}, month={Aug}, pages={1157–1170} }
 @article{fontes_gladfelter_schaffer_petty_hanley-bowdoin_1994, title={Geminivirus replication origins have a modular organization.}, volume={6}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.6.3.405}, DOI={10.1105/tpc.6.3.405}, abstractNote={Tomato golden mosaic virus (TGMV) and bean golden mosaic virus (BGMV) are closely related geminiviruses with bipartite genomes. The A and B DNA components of each virus have cis-acting sequences necessary for replication, and their A components encode trans-acting factors are required for this process. We showed that virus-specific interactions between the cis- and trans-acting functions are required for TGMV and BGMV replication in tobacco protoplasts. We also demonstrated that, similar to the essential TGMV AL1 replication protein, BGMV AL1 binds specifically to its origin in vitro and that neither TGMV nor BGMV AL1 proteins bind to the heterologous origin. The in vitro AL1 binding specificities of the B components were exchanged by site-directed mutagenesis, but the resulting mutants were not replicated by either A component. These results showed that the high-affinity AL1 binding site is necessary but not sufficient for virus-specific origin activity in vivo. Geminivirus genomes also contain a stem-loop sequence that is required for origin function. A BGMV B mutant with the TGMV stem-loop sequence was replicated by BGMV A, indicating that BGMV AL1 does not discriminate between the two sequences. A BGMV B double mutant, with the TGMV AL1 binding site and stem-loop sequences, was not replicated by either A component, indicating that an additional element in the TGMV origin is required for productive interaction with TGMV AL1. These results suggested that geminivirus replication origins are composed of at least three functional modules: (1) a putative stem-loop structure that is required for replication but does not contribute to virus-specific recognition of the origin, (2) a specific high-affinity binding site for the AL1 protein, and (3) at least one additional element that contributes to specific origin recognition by viral trans-acting factors.}, number={3}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Fontes, E P and Gladfelter, H J and Schaffer, R L and Petty, I T and Hanley-Bowdoin, L}, year={1994}, month={Mar}, pages={405–416} }
 @article{fontes_eagle_sipe_luckow_hanley-bowdoin_1994, title={Interaction between a geminivirus replication protein and origin DNA is essential for viral replication}, volume={269}, journal={Journal of Biological Chemistry}, author={Fontes, E.P.B. and Eagle, P.A. and Sipe, P. and Luckow, V.A. and Hanley-Bowdoin, L.}, year={1994}, pages={8459–8465} }
 @article{pedersen_hanley-bowdoin_1994, title={Molecular Characterization of the AL3 Protein Encoded by a Bipartite Geminivirus}, volume={202}, ISSN={0042-6822}, url={http://dx.doi.org/10.1006/viro.1994.1442}, DOI={10.1006/viro.1994.1442}, abstractNote={The genome of tomato golden mosaic virus (TGMV) is composed of two circular, single-stranded DNA molecules that together contain 6 open reading frames (ORFs). Three of these ORFs (designated AL1, AL2, and AL3) overlap and are specified by multiple polycistronic mRNAs. No RNA specifying the AL3 ORF alone has been detected, suggesting that the AL3 gene product is translated from an internal ORF. A recombinant histidine-tagged-AL3 fusion protein was purified from Escherichia coli and used to raise a polyclonal antiserum. Analysis of protein extracts from healthy plants and plants infected with TGMV by SDS-PAGE and immunoblotting showed that a protein corresponding to the predicted AL3 gene product is produced only in infected plants. This protein comprises approximately 0.05% of the cellular proteins and is present in the soluble and organelle fractions. These results are discussed with respect to the expression and role of the AL3 protein in the viral life cycle.}, number={2}, journal={Virology}, publisher={Elsevier BV}, author={Pedersen, Thomas J. and Hanley-Bowdoin, Linda}, year={1994}, month={Aug}, pages={1070–1075} }
 @article{fontes_luckow_hanley-bowdoin_1992, title={A geminivirus replication protein is a sequence-specific DNA binding protein.}, volume={4}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.4.5.597}, DOI={10.1105/tpc.4.5.597}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component encodes the only viral protein, AL1, that is required for viral replication. We showed that AL1 interacts specifically with TGMV A and B DNA by using an immunoprecipitation assay for AL1:DNA complex formation. In this assay, a monoclonal antibody against AL1 precipitated AL1:TGMV DNA complexes, whereas an unrelated antibody failed to precipitate the complexes. Competition assays with homologous and heterologous DNAs established the specificity of AL1:DNA binding. AL1 produced by transgenic tobacco plants and by baculovirus-infected insect cells exhibited similar DNA binding activity. The AL1 binding site maps to 52 bp on the left side of the common region, a 235-bp region that is highly conserved between the two TGMV genome components. The AL1:DNA binding site does not include the putative hairpin structure that is conserved in the common regions or the equivalent 5' intergenic regions of all geminiviruses. These studies demonstrate that a geminivirus replication protein is a sequence-specific DNA binding protein, and the studies have important implications for the role of this protein in virus replication.}, number={5}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Fontes, E P and Luckow, V A and Hanley-Bowdoin, L}, year={1992}, month={May}, pages={597–608} }
 @inbook{hanley bowdoin_hemenway_1992, title={Transgenic plants expressing viral genes}, booktitle={Genetic Engineering with Plant Viruses}, publisher={CRC Press, Inc}, author={Hanley Bowdoin, L. and Hemenway, C.}, editor={Wilson, T. Michael A. and Davies, Jeffrey W.Editors}, year={1992}, pages={251–295} }
 @article{hanley-bowdoin_elmer_rogers_1990, title={Expression of functional replication protein from tomato golden mosaic virus in transgenic tobacco plants.}, volume={87}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.87.4.1446}, DOI={10.1073/pnas.87.4.1446}, abstractNote={The A component of the bipartite genome of the geminivirus tomato golden mosaic virus (TGMV) encodes the viral protein (AL1) that is required for viral DNA replication. We have constructed transgenic Nicotiana benthamiana plants in which the AL1 open reading frame is transcribed under the control of the cauliflower mosaic virus 35S promoter. The transgenic plants, which were phenotypically normal, produced a single transcript from the 35S-AL1 construct and a 40-kDa protein that cross-reacted with a polyclonal antiserum raised against AL1 protein overproduced in Escherichia coli. Six of nine transgenic lines complemented a TGMV A variant with a mutation in AL1 when coinoculated with the B component of the TGMV genome. Single- and double-stranded forms of the B component were synthesized in leaf discs from a complementing, transgenic line in the absence of TGMV A. These results establish that the transgenic plants express functional AL1 protein and show that this viral protein is not only required, but sufficient, for single- and double-stranded replication of TGMV DNA in the presence of host proteins. These results also show that the AL1 protein is not by itself a determinant of disease or pathogenesis.}, number={4}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Hanley-Bowdoin, L. and Elmer, J. S. and Rogers, S. G.}, year={1990}, month={Feb}, pages={1446–1450} }
 @article{hanley-bowdoin_elmer_rogers_1989, title={Functional expression of the leftward open reading frames of the A component of tomato golden mosaic virus in transgenic tobacco plants.}, volume={1}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.1.11.1057}, DOI={10.1105/tpc.1.11.1057}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. We have constructed Nicotiana benthamiana plants that are transgenic for the three overlapping open reading frames, AL1, AL2, and AL3, from the left side of TGMV A. In the transgenic plants, the AL open reading frames are under the control of the cauliflower mosaic virus (CaMV) 35S promoter. In TGMV infectivity assays, seven of 10 transgenic lines complemented TGMV A variants with mutations in AL1, AL2, or AL3 when co-inoculated with the B component. The 35S-AL construct was transcribed as a single RNA species in the transgenic plants, indicating that AL1, AL2, and AL3 were expressed from a polycistronic mRNA. This differs from the complex transcription pattern in TGMV-infected plants, which contains five AL transcripts. There was no quantitative correlation between the efficiency of complementation in the infectivity assay and the level of expression of transgenic AL RNA in the leaves of a transgenic line. One line that failed to complement defects in AL1, AL2, and AL3 in infectivity assays contained high levels of transgenic AL RNA and functional AL1 protein. These results provide evidence that chromosomal position can affect the cell- and tissue-specific transcription of the 35S promoter in transgenic plants. Comparison of the complementing plants and wild-type infected plants may provide insight into the TGMV infection process and the use of the CaMV 35S promoter for gene expression in transgenic plants.}, number={11}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Hanley-Bowdoin, L and Elmer, J S and Rogers, S G}, year={1989}, month={Nov}, pages={1057–1067} }
 @article{hanley-bowdoin_chua_1989, title={Transcriptional interaction between the promoters of the maize chloroplast genes which encode the β subunit of ATP synthase and the large subunit of ribulose 1,5-bisphosphate carboxylase}, volume={215}, ISSN={0026-8925 1432-1874}, url={http://dx.doi.org/10.1007/bf00339720}, DOI={10.1007/bf00339720}, abstractNote={The genes encoding the beta subunit of ATP synthase and the large subunit of ribulose 1,5-bisphosphate carboxylase are located on opposite strands of the maize chloroplast genome. Their transcription start sites are separated by a 159 bp sequence that includes the promoters for both genes. The effects of deleting or modifying one of the two promoters on transcription from the adjacent, unaltered promoter were assessed in vitro using maize chloroplast extracts to transcribe cloned maize DNA templates. When the atpB promoter was disrupted by an 8 bp insertion, rbcL transcription was not altered. When the rbcL promoter was disrupted by a 2 bp insertion, atpB transcription decreased, whereas when the rbcL promoter region was deleted, atpB transcription increased. Activity of the atpB promoter was also reduced when the + 2 bp-rbcL promoter template was transcribed in vitro by Escherichia coli RNA polymerase. The changes in atpB transcriptional efficiency were only seen when the atpB and rbcL promoters were closely spaced on the same template molecule. These results established that the atpB and rbcL promoters interact in vitro in a cis and spacing dependent manner. The interaction may have physiological relevance in vivo.}, number={2}, journal={Molecular and General Genetics MGG}, publisher={Springer Science and Business Media LLC}, author={Hanley-Bowdoin, Linda and Chua, Nam-Hai}, year={1989}, month={Jan}, pages={217–224} }
 @article{lam_hanley bowdoin_chua_1988, title={Characterization of a chloroplast sequence-specific DNA binding factor}, volume={263}, journal={Journal of Biological Chemistry}, author={Lam, E. and Hanley Bowdoin, L. and Chua, N. H.}, year={1988}, pages={8288–8293} }
 @article{hanley-bowdoin_chua_1988, title={Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide}, volume={10}, ISSN={0167-4412 1573-5028}, url={http://dx.doi.org/10.1007/bf00029880}, DOI={10.1007/bf00029880}, abstractNote={We have mapped and cloned the wheat chloroplast gene (psbA) that encodes the 32 kd polypeptide of Photosystem II. The psbA gene is located in the large single copy region adjacent to one inverted repeat and is transcribed toward the latter. The sequence of the 5' end of the wheat gene is homologous with dicot psbA genes. We have located the 5' terminus of the wheat psbA RNA to a position 83 nt upstream of its coding region. The same psbA RNA species was capped in vitro by guanylyltransferase, establishing that its 5' end is a transcription start site. Regions which resemble procaryotic -10 and -35 promoter elements are located immediately upstream of the wheat psbA transcription initiation site.}, number={4}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Hanley-Bowdoin, Linda and Chua, Nam-Hai}, year={1988}, pages={303–310} }
 @article{hanley-bowdoin_elmer_rogers_1988, title={Transient expression of heterologous RNAs using tomato golden mosaic virus}, volume={16}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/16.22.10511}, DOI={10.1093/nar/16.22.10511}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules designated as components A and B. The A component contains the only virally-encoded function required for autonomous replication in infected plant cells. We used agroinoculation of petunia leaf discs with the A component to develop a transient expression system which permits direct examination of viral transcripts by S1 nuclease protection. The AR1 gene, which encodes the TGMV coat protein, was transcribed transiently in leaf discs after agroinoculation of TGMV a DNA. Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. The AL open reading frames of TGMV A were also expressed transiently in leaf discs. The ratio between AR1 RNA and the major leftward RNA was constant and was used to normalize AR1 transcription for viral DNA copy number. The bacterial genes encoding chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) were transiently expressed in leaf discs from the AR1 promoter in TGMV A. The levels of AR1 and GUS RNAs were similar in leaf discs after adjusting for viral DNA copy number, while CAT RNA was less abundant. The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants.}, number={22}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Hanley-Bowdoin, L. and Elmer, J. S. and Rogers, S. G.}, year={1988}, month={Nov}, pages={10511–10528} }
 @article{hanley-bowdoin_chua_1987, title={Chloroplast promoters}, volume={12}, ISSN={0968-0004}, url={http://dx.doi.org/10.1016/0968-0004(87)90033-8}, DOI={10.1016/0968-0004(87)90033-8}, abstractNote={DNA sequences required for accurate initiation of chloroplast transcription have been characterized in higher plants using chloroplast in vitro transcription systems. Although chloroplast promoters resemble bacterial promoters, they also have some unique properties.}, journal={Trends in Biochemical Sciences}, publisher={Elsevier BV}, author={Hanley-Bowdoin, Linda and Chua, Nam-Hai}, year={1987}, month={Jan}, pages={67–70} }
 @inbook{orozco_mullet_hanley-bowdoin_chua_1986, title={In vitro transcription of chloroplast protein genes}, ISBN={9780121820183}, ISSN={0076-6879}, url={http://dx.doi.org/10.1016/0076-6879(86)18076-1}, DOI={10.1016/0076-6879(86)18076-1}, abstractNote={This chapter discusses the methods that are useful for the in vitro analysis of plastid gene expression. Many plastid genes have multiple transcripts in vivo that may be the result of transcription initiation and subsequent RNA processing events. Heterologous chloroplast transcription extracts may be useful for the analysis of plastid RNA processing. To characterize the potential regulatory nature of the plastid RNA and other plastid DNA sequences, the use of a homologous plastid in vitro transcription system is required. The criteria for such a transcription system are ease of preparation, accuracy of transcription initiation, and stability of enzyme activity. The optimal time and temperature of the in vitro transcription reaction varies with the gene transcribed and the extract employed. Part of this variance may be due to specific RNA processing and nonspecific degradation of in vitro transcripts by endogenous ribonucleases in the chloroplast extracts.}, booktitle={Methods in Enzymology}, publisher={Elsevier}, author={Orozco, Emil M., Jr. and Mullet, John E. and Hanley-Bowdoin, Linda and Chua, Nam-Hai}, year={1986}, pages={232–253} }
 @article{hanley-bowdoin_orozco_chua_1985, title={In vitro synthesis and processing of a maize chloroplast transcript encoded by the ribulose 1,5-bisphosphate carboxylase large subunit gene.}, volume={5}, ISSN={0270-7306 1098-5549}, url={http://dx.doi.org/10.1128/mcb.5.10.2733}, DOI={10.1128/mcb.5.10.2733}, abstractNote={The large subunit gene (rbcL) of ribulose 1,5-bisphosphate carboxylase was transcribed in vitro by using maize and pea chloroplast extracts and a cloned plastid DNA template containing 172 base pairs (bp) of the maize rbcL protein-coding region and 791 bp of upstream sequences. Three major in vitro RNA species were synthesized which correspond to in vivo maize rbcL RNAs with 5' termini positioned 300, 100 to 105, and 63 nucleotides upstream of the protein-coding region. A deletion of 109 bp, including the "-300" 5' end (the 5' end at position -300), depressed all rbcL transcription in vitro. A plasmid DNA containing this 109-bp fragment was sufficient to direct correct transcription initiation in vitro. A cloned template, containing 191 bp of plastid DNA which includes the -105 and -63 rbcL termini, did not support transcription in vitro. Exogenously added -300 RNA could be converted to the -63 transcript by maize chloroplast extract. These results established that the -300 RNA is the primary maize rbcL transcript, the -63 RNA is a processed form of the -300 transcript, and synthesis of the -105 RNA is dependent on the -300 region. The promoter for the maize rbcL gene is located within the 109 bp flanking the -300 site. Mutagenesis of the 109-bp chloroplast sequence 11 bp upstream of the -300 transcription initiation site reduced rbcL promoter activity in vitro.}, number={10}, journal={Molecular and Cellular Biology}, publisher={American Society for Microbiology}, author={Hanley-Bowdoin, L and Orozco, E M, Jr and Chua, N H}, year={1985}, month={Oct}, pages={2733–2745} }
 @inbook{hanley-bowdoin_orozco_chua_1985, title={Transcription of chloroplast genes by homo-logous and heterologous RNA polymerases}, booktitle={Molecular biology of the photosynthetic apparatus}, publisher={Cold Spring Harbor Press}, author={Hanley-Bowdoin, L. and Orozco, E.M. and Chua, N. H}, editor={Steinback, Katherine E. and Bonitz, Susan and Arntzen, Charles J. and Bogorad, LawrenceEditors}, year={1985}, pages={311–318} }
 @article{hanley-bowdoin_lane_1983, title={A novel protein programmed by the mRNA conserved in dry wheat embryos. The principal site of cysteine incorporation during early germination}, volume={135}, ISSN={0014-2956 1432-1033}, url={http://dx.doi.org/10.1111/j.1432-1033.1983.tb07611.x}, DOI={10.1111/j.1432-1033.1983.tb07611.x}, abstractNote={If bulk mRNA from dry wheat embryos (wheat germ) is used to direct cell‐free incorporation of [35S]cysteine into proteins, a striking proportion of the total radioactivity is channeled into a single protein. During early postimbibition development, when protein synthesis is directed by the mRNA conserved in dry embryos, incorporation of cysteine is preponderantly (20–25%) directed into synthesis of this one protein: the ‘early’ cysteine‐labeled protein (Ec). When conserved mRNA from the dry embryos has been fully degraded, as when cellular or cell‐free protein synthesis is directed by the mRNA in germinated embryos, synthesis of Ec is not detected. Reliable detection of Ec requires prior alkylation of wheat embryo proteins, and it was especially interesting to find that when wheat embryo proteins are alkylated by iodo[14C]acetamide, two proteins co‐dominate the distribution of radioalkylated products in dodecylsulphate/polyacrylamide gels: Ec and wheat germ agglutinin. Using co‐electrophoresis with the isotopically labeled protein to detect a dye‐staining counterpart, Ec has been purified by combined cation‐exchange and gel‐filtration chromatography of alkylated wheat germ proteins. The purified protein can be recovered in milligram quantity (5–10 mg/100 g wheat germ) and compositional analysis shows that it is unusually rich in cysteine (approx. 15%) and glycine (approx. 17%), as is wheat germ agglutinin.}, number={1}, journal={European Journal of Biochemistry}, publisher={Wiley}, author={Hanley-Bowdoin, Linda and Lane, Byron G.}, year={1983}, month={Sep}, pages={9–15} }
 @article{grzelczak_sattolo_hanley-bowdoin_kennedy_lane_1982, title={Synthesis and turnover of proteins and mRNA in germinating wheat embryos}, volume={60}, ISSN={0008-4018}, url={http://dx.doi.org/10.1139/o82-046}, DOI={10.1139/o82-046}, abstractNote={ The most prominent methionine-labeled protein made when cell-free systems are programmed with bulk mRNA from dry wheat embryos has been identified with what may be the most abundant protein in dry wheat embryos. The protein has been brought to purity and has a distinctive amino acid composition, Gly and Glx accounting for almost 40% of the total amino acids. Designated E because of its conspicuous association with early imbibition of dry wheat embryos, the protein and its mRNA are abundant during the "early" phase (0–1 h) of postimbibition development, and easily detected during "lag" phase (1–5 h), but they are almost totally degraded soon after entry into the "growth" phase of development, by about 10 h postimbibition.The most prominent methionine-labeled protein peculiar to the cell-free translational capacity of bulk mRNA from "growth" phase embryos is not detected as a product of in vivo synthesis. Its electrophoretic properties and its time course of emergence, after 5 h postimbibition development, suggest that this major product of cell-free synthesis may be an in vitro counterpart to a prominent methionine-labeled protein made only in vivo, by "growth" phase embryos. Designated G because of its conspicuous association with "growth" phase development, the cell-free product does not comigrate with any prominent dye-stained band in electrophoretic distributions of wheat proteins. The suspected cellular counterpart to G, also, does not comigrate with a prominent dye-stained wheat protein during electrophoresis, and although found in particulate as well as soluble fractions of wheat embryo homogenates it is not concentrated in either nuclei or mitochondria, as isolated. }, number={3}, journal={Canadian Journal of Biochemistry}, publisher={Canadian Science Publishing}, author={Grzelczak, Zbyszko F. and Sattolo, Mark H. and Hanley-Bowdoin, Linda K. and Kennedy, Theresa D. and Lane, Byron G.}, year={1982}, month={Mar}, pages={389–397} }
 @article{kennedy_hanley-bowdoin_lane_1981, title={Structural integrity of RNA and translational integrity of ribosomes in nuclease-treated cell-free protein synthesizing systems prepared from wheat germ and rabbit reticulocytes}, volume={256}, journal={Journal of Biological Chemistry}, author={Kennedy, T.D. and Hanley-Bowdoin, L. and Lane, B.G}, year={1981}, pages={5802–5809} }
 @article{bellvé_anderson_hanley-bowdoin_1975, title={Synthesis and amino acid composition of basic proteins in mammalian sperm nuclei}, volume={47}, ISSN={0012-1606}, url={http://dx.doi.org/10.1016/0012-1606(75)90289-4}, DOI={10.1016/0012-1606(75)90289-4}, abstractNote={The basic chromosomal proteins (SCP) of human, mouse, rabbit and guinea pig sperm nuclei were characterized by polyacrylamide gel electrophoresis and amino acid analysis. Spermatozoa were decapitated with 1% SDS and the nuclei recovered by density gradient centrifugation. Examination by Nomarski and electron microscopy revealed the nuclei to be intact and 99% pure. The basic proteins were extracted from nuclei, aminoethylated and purified by ion exchange chromatography and gel filtration chromatography. The SCP of human, rabbit and guinea pig gave single protein bands with similar mobilities when subjected to polyacrylamide gel electrophoresis. In contrast, aminoethylated mouse SCP consisted of two proteins, SCP·AE1 and SCP·AE2, which had different electrophoretic mobilities. The SCP of these mammalian species were characteristically rich in arginine (47–54.4%) and cysteine (7.7–12.2%). Major differences existed in the amino acid compositions of these proteins. Mouse and human SCP were rich in histidine (12.2 and 7.7%, respectively) and guinea pig was high in tyrosine (11.7%) and phenylalanine (3.5%). Valine was detected only in rabbit SCP and proline in human and guinea pig. Aspartic acid, methionine and tryptophan were not detected in all four species. Studies on the incorporation of [3H]arginine into mouse SCP demonstrated that these basic proteins are synthesized during the terminal stages of spermatogenesis and are subsequently conserved.}, number={2}, journal={Developmental Biology}, publisher={Elsevier BV}, author={Bellvé, Anthony R. and Anderson, Everett and Hanley-Bowdoin, Linda}, year={1975}, month={Dec}, pages={349–365} }