@article{laosuntisuk_vennapusa_somayanda_leman_jagadish_doherty_2024, title={A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses}, volume={1}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16654}, DOI={10.1111/tpj.16654}, abstractNote={SUMMARY}, journal={PLANT JOURNAL}, author={Laosuntisuk, Kanjana and Vennapusa, Amaranatha and Somayanda, Impa M. and Leman, Adam R. and Jagadish, S. V. Krishna and Doherty, Colleen J.}, year={2024}, month={Jan} } @article{land_sheppard_doherty_perera_2024, title={Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments}, volume={14}, ISSN={["1664-462X"]}, url={http://dx.doi.org/10.3389/fpls.2023.1308713}, DOI={10.3389/fpls.2023.1308713}, abstractNote={IntroductionUnderstanding how plants adapt to the space environment is essential, as plants will be a valuable component of long duration space missions. Several spaceflight experiments have focused on transcriptional profiling as a means of understanding plant adaptation to microgravity. However, there is limited overlap between results from different experiments. Differences in experimental conditions and hardware make it difficult to find a consistent response across experiments and to distinguish the primary effects of microgravity from other spaceflight effects.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Land, Eric S. and Sheppard, James and Doherty, Colleen J. and Perera, Imara Y.}, year={2024}, month={Jan} } @article{schrickx_gyurek_moore_hernandez-pagan_doherty_kudenov_brendan t. o'connor_2024, title={Flexible Self-Powered Organic Photodetector with High Detectivity for Continuous On-Plant Sensing}, volume={2}, ISSN={["2195-1071"]}, DOI={10.1002/adom.202400005}, abstractNote={Abstract}, journal={ADVANCED OPTICAL MATERIALS}, author={Schrickx, Harry M. and Gyurek, Sydney and Moore, Caleb and Hernandez-Pagan, Edmaritz and Doherty, Colleen J. and Kudenov, Michael W. and Brendan T. O'Connor}, year={2024}, month={Feb} } @article{krafft_scarboro_hsieh_doherty_balint-kurti_kudenov_2024, title={Mitigating Illumination-, Leaf-, and View-Angle Dependencies in Hyperspectral Imaging Using Polarimetry}, url={https://doi.org/10.34133/plantphenomics.0157}, DOI={10.34133/plantphenomics.0157}, abstractNote={Automation of plant phenotyping using data from high-dimensional imaging sensors is on the forefront of agricultural research for its potential to improve seasonal yield by monitoring crop health and accelerating breeding programs. A common challenge when capturing images in the field relates to the spectral reflection of sunlight (glare) from crop leaves that, at certain solar incidences and sensor viewing angles, presents unwanted signals. The research presented here involves the convergence of 2 parallel projects to develop a facile algorithm that can use polarization data to decouple light reflected from the surface of the leaves and light scattered from the leaf’s tissue.}, journal={Plant Phenomics}, author={Krafft, Daniel and Scarboro, Clifton G. and Hsieh, William and Doherty, Colleen and Balint-Kurti, Peter and Kudenov, Michael}, year={2024}, month={Jan} } @article{laosuntisuk_vennapusa_somayanda_leman_jagadish_doherty_2023, title={A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses}, url={https://doi.org/10.1101/2023.10.28.564442}, DOI={10.1101/2023.10.28.564442}, abstractNote={Abstract}, author={Laosuntisuk, Kanjana and Vennapusa, Amaranatha and Somayanda, Impa M. and Leman, Adam R. and Jagadish, SV Krishna and Doherty, Colleen J.}, year={2023}, month={Oct} } @misc{tiwari_kumar_subramanian_doherty_jagadish_2023, title={Auxin-cytokinin interplay shapes root functionality under low-temperature stress}, volume={28}, ISSN={["1878-4372"]}, DOI={10.1016/j.tplants.2022.12.004}, abstractNote={Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.}, number={4}, journal={TRENDS IN PLANT SCIENCE}, author={Tiwari, Manish and Kumar, Ritesh and Subramanian, Senthil and Doherty, Colleen J. and Jagadish, S. V. Krishna}, year={2023}, month={Apr}, pages={447–459} } @article{yow_laosuntisuk_young_doherty_gillitt_perkins-veazie_jenny xiang_iorizzo_2023, title={Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple}, volume={13}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-023-45722-y}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Yow, Ashley G. and Laosuntisuk, Kanjana and Young, Roberto A. and Doherty, Colleen J. and Gillitt, Nicholas and Perkins-Veazie, Penelope and Jenny Xiang, Qiu-Yun and Iorizzo, Massimo}, year={2023}, month={Nov} } @article{kudenov_krafft_scarboro_doherty_balint-kurti_2023, title={Hybrid spatial-temporal Mueller matrix imaging spectropolarimeter for high throughput plant phenotyping}, volume={62}, ISSN={["2155-3165"]}, DOI={10.1364/AO.483870}, abstractNote={Many correlations exist between spectral reflectance or transmission with various phenotypic responses from plants. Of interest to us are metabolic characteristics, namely, how the various polarimetric components of plants may correlate to underlying environmental, metabolic, and genotypic differences among different varieties within a given species, as conducted during large field experimental trials. In this paper, we overview a portable Mueller matrix imaging spectropolarimeter, optimized for field use, by combining a temporal and spatial modulation scheme. Key aspects of the design include minimizing the measurement time while maximizing the signal-to-noise ratio by mitigating systematic error. This was achieved while maintaining an imaging capability across multiple measurement wavelengths, spanning the blue to near-infrared spectral region (405–730 nm). To this end, we present our optimization procedure, simulations, and calibration methods. Validation results, which were taken in redundant and non-redundant measurement configurations, indicated that the polarimeter provides average absolute errors of (5.3±2.2)×10−3 and (7.1±3.1)×10−3, respectively. Finally, we provide preliminary field data (depolarization, retardance, and diattenuation) to establish baselines of barren and non-barren Zea maize hybrids (G90 variety), as captured from various leaf and canopy positions during our summer 2022 field experiments. Results indicate that subtle variations in retardance and diattenuation versus leaf canopy position may be present before they are clearly visible in the spectral transmission.}, number={8}, journal={APPLIED OPTICS}, author={Kudenov, Michael W. and Krafft, Danny and Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter}, year={2023}, month={Mar}, pages={2078–2091} } @misc{laosuntisuk_elorriaga_doherty_2023, title={The Game of Timing: Circadian Rhythms Intersect with Changing Environments}, volume={74}, ISSN={["1545-2123"]}, DOI={10.1146/annurev-arplant-070522-065329}, abstractNote={ Recurring patterns are an integral part of life on Earth. Through evolution or breeding, plants have acquired systems that coordinate with the cyclic patterns driven by Earth's movement through space. The biosystem responses to these physical rhythms result in biological cycles of daily and seasonal activity that feed back into the physical cycles. Signaling networks to coordinate growth and molecular activities with these persistent cycles have been integrated into plant biochemistry. The plant circadian clock is the coordinator of this complex, multiscale, temporal schedule. However, we have detailed knowledge of the circadian clock components and functions in only a few species under controlled conditions. We are just beginning to understand how the clock functions in real-world conditions. This review examines what we know about the circadian clock in diverse plant species, the challenges with extrapolating data from controlled environments, and the need to anticipate how plants will respond to climate change. }, journal={ANNUAL REVIEW OF PLANT BIOLOGY}, author={Laosuntisuk, Kanjana and Elorriaga, Estefania and Doherty, Colleen J.}, year={2023}, pages={511–538} } @article{horvath_doherty_desai_clark_anderson_chao_2023, title={Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions}, volume={15}, ISSN={["2041-2851"]}, DOI={10.1093/aobpla/plad013}, abstractNote={Abstract}, number={3}, journal={AOB PLANTS}, author={Horvath, David P. and Doherty, Colleen J. and Desai, Jigar and Clark, Natalie and Anderson, James V and Chao, Wun S.}, year={2023}, month={Jun} } @article{laosuntisuk_desai_doherty_2022, title={Arabidopsis cell suspension culture that lacks circadian rhythms can be recovered by constitutive ELF3 expression}, volume={5}, url={https://doi.org/10.1101/2022.05.12.491735}, DOI={10.1101/2022.05.12.491735}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Laosuntisuk, Kanjana and Desai, Jigar S. and Doherty, Colleen J.}, year={2022}, month={May} } @article{knight_doherty_nielsen_2022, title={Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data}, url={https://doi.org/10.1101/2022.12.01.518235}, DOI={10.1101/2022.12.01.518235}, abstractNote={Abstract}, author={Knight, Montana S. and Doherty, Colleen J. and Nielsen, Dahlia M.}, year={2022}, month={Dec} } @article{tolsma_torres_richards_perera_doherty_2022, title={Evaluating the Effects of the Circadian Clock and Time of Day on Plant Gravitropic Responses}, volume={2368}, ISBN={["978-1-0716-1676-5"]}, ISSN={["1940-6029"]}, url={https://doi.org/10.1007/978-1-0716-1677-2_19}, DOI={10.1007/978-1-0716-1677-2_19}, abstractNote={Circadian rhythms are regular oscillations of an organism's physiology with a period of approximately 24 h. In the model plant Arabidopsis thaliana, circadian rhythms regulate a suite of physiological processes, including transcription, photosynthesis, growth, and flowering. The circadian clock and external rhythmic factors have extensive control of the underlying biochemistry and physiology. Therefore, it is critical to consider the time of day when performing gravitropism experiments, even if the circadian clock is not a focus of study. We describe the critical factors and methods to be considered and methods to investigate the possible circadian regulation of gravitropic responses.}, journal={PLANT GRAVITROPISM}, publisher={Springer US}, author={Tolsma, Joseph S. and Torres, Jacob J. and Richards, Jeffrey T. and Perera, Imara Y. and Doherty, Colleen J.}, year={2022}, pages={301–319} } @article{scarboro_doherty_balint-kurti_kudenov_2022, title={Multistatic fiber-based system for measuring the Mueller matrix bidirectional reflectance distribution function}, volume={61}, ISSN={["2155-3165"]}, DOI={10.1364/AO.470608}, abstractNote={Bidirectionality effects can be a significant confounding factor when measuring hyperspectral reflectance data. The bidirectional reflectance distribution function (BRDF) can effectively characterize the reflectivity of surfaces to correct remote sensing measurements. However, measuring BRDFs can be time-consuming, especially when collecting Mueller matrix BRDF (mmBRDF) measurements of a surface via conventional goniometric techniques. In this paper, we present a system for collecting mmBRDF measurements using static optical fiber detectors that sample the hemisphere surrounding an object. The entrance to each fiber contains a polarization state analyzer configuration, allowing for the simultaneous acquisition of the Stokes vector intensity components at many altitudinal and azimuthal viewing positions. We describe the setup, calibration, and data processing used for this system and present its performance as applied to mmBRDF measurements of a ground glass diffuser.}, number={33}, journal={APPLIED OPTICS}, author={Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter J. and Kudenov, Michael W.}, year={2022}, month={Nov}, pages={9832–9842} } @misc{laosuntisuk_doherty_2022, title={The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures}, volume={50}, ISSN={["1470-8752"]}, url={https://doi.org/10.1042/BST20190572}, DOI={10.1042/BST20190572}, abstractNote={Increasing temperatures impact plant biochemistry, but the effects can be highly variable. Both external and internal factors modulate how plants respond to rising temperatures. One such factor is the time of day or season the temperature increase occurs. This timing significantly affects plant responses to higher temperatures altering the signaling networks and affecting tolerance levels. Increasing overlaps between circadian signaling and high temperature responses have been identified that could explain this sensitivity to the timing of heat stress. ELF3, a circadian clock component, functions as a thermosensor. ELF3 regulates thermoresponsive hypocotyl elongation in part through its cellular localization. The temperature sensitivity of ELF3 depends on the length of a polyglutamine region, explaining how plant temperature responses vary between species. However, the intersection between the circadian system and increased temperature stress responses is pervasive and extends beyond this overlap in thermosensing. Here, we review the network responses to increased temperatures, heat stress, and the impacts on the mechanisms of gene expression from transcription to translation, highlighting the intersections between the elevated temperature and heat stress response pathways and circadian signaling, focusing on the role of ELF3 as a thermosensor.}, number={3}, journal={BIOCHEMICAL SOCIETY TRANSACTIONS}, publisher={Portland Press Ltd.}, author={Laosuntisuk, Kanjana and Doherty, Colleen J.}, year={2022}, month={Jun}, pages={1151–1165} } @article{kudenov_krafft_scarboro_doherty_balint-kurti_2021, title={Fieldable Mueller matrix imaging spectropolarimeter using a hybrid spatial and temporal modulation scheme}, volume={11833}, ISSN={["1996-756X"]}, DOI={10.1117/12.2593970}, abstractNote={Many correlations exist between spectral reflectance and various phenotypic responses from plants. Of interest to us are structural characteristics; namely, how the various spectral and polarimetric components may correlate to underlying environmental, metabolic, and genotypic differences among plant varieties within a given species. In this paper, we overview a portable Mueller matrix imaging spectropolarimeter that has been optimized for field use. Key aspects to the design included minimizing the measurement time while maximizing signal-to-noise ratio with low systematic errors. These goals must be achieved while maintaining an imaging capability across multiple measurement wavelengths, spanning the blue to near-infrared spectral region. To this end, we will review our optimization procedure, simulations, and experimental results, including preliminary field data taken from our summer 2021 field trials.}, journal={POLARIZATION SCIENCE AND REMOTE SENSING X}, author={Kudenov, Michael W. and Krafft, Danny and Scarboro, Clifton G. and Doherty, Colleen J. and Balint-Kurti, Peter}, year={2021} } @article{bheemanahalli_knight_quinones_doherty_jagadish_2021, title={Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice}, volume={11}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-021-85921-z}, DOI={10.1038/s41598-021-85921-z}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Bheemanahalli, Raju and Knight, Montana and Quinones, Cherryl and Doherty, Colleen J. and Jagadish, S. V. Krishna}, year={2021}, month={Mar} } @article{scarboro_ruzsa_doherty_kudenov_2021, title={Quantification of gray mold infection in lettuce using a bispectral imaging system under laboratory conditions}, volume={5}, ISSN={["2475-4455"]}, url={https://doi.org/10.1002/pld3.317}, DOI={10.1002/pld3.317}, abstractNote={Abstract}, number={3}, journal={PLANT DIRECT}, publisher={Wiley}, author={Scarboro, Clifton G. and Ruzsa, Stephanie M. and Doherty, Colleen J. and Kudenov, Michael W.}, year={2021}, month={Mar} } @article{tolsma_ryan_torres_richards_richardson_land_perera_doherty_2021, title={The Circadian-clock Regulates the Arabidopsis Gravitropic Response}, url={https://doi.org/10.2478/gsr-2021-0014}, DOI={10.2478/gsr-2021-0014}, abstractNote={Abstract}, journal={Gravitational and Space Research}, author={Tolsma, Joseph S. and Ryan, Kaetlyn T. and Torres, Jacob J. and Richards, Jeffrey T. and Richardson, Zach and Land, Eric S. and Perera, Imara Y. and Doherty, Colleen J}, year={2021}, month={Jan} } @article{sheppard_land_toennisson_doherty_perera_2021, title={Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots}, volume={11}, ISSN={["2075-1729"]}, url={https://doi.org/10.3390/life11101010}, DOI={10.3390/life11101010}, abstractNote={Although many reports characterize the transcriptional response of Arabidopsis seedlings to microgravity, few investigate the effect of partial or fractional gravity on gene expression. Understanding plant responses to fractional gravity is relevant for plant growth on lunar and Martian surfaces. The plant signaling flight experiment utilized the European Modular Cultivation System (EMCS) onboard the International Space Station (ISS). The EMCS consisted of two rotors within a controlled chamber allowing for two experimental conditions, microgravity (stationary rotor) and simulated gravity in space. Seedlings were grown for 5 days under continuous light in seed cassettes. The arrangement of the seed cassettes within each experimental container results in a gradient of fractional g (in the spinning rotor). To investigate whether gene expression patterns are sensitive to fractional g, we carried out transcriptional profiling of root samples exposed to microgravity or partial g (ranging from 0.53 to 0.88 g). Data were analyzed using DESeq2 with fractional g as a continuous variable in the design model in order to query gene expression across the gravity continuum. We identified a subset of genes whose expression correlates with changes in fractional g. Interestingly, the most responsive genes include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins.}, number={10}, journal={LIFE-BASEL}, author={Sheppard, James and Land, Eric S. and Toennisson, Tiffany Aurora and Doherty, Colleen J. and Perera, Imara Y.}, year={2021}, month={Oct} } @article{desai_lawas_valente_leman_grinevich_jagadish_doherty_2021, title={Warm nights disrupt transcriptome rhythms in field-grown rice panicles}, volume={118}, ISSN={["0027-8424"]}, url={https://doi.org/10.1073/pnas.2025899118}, DOI={10.1073/pnas.2025899118}, abstractNote={Significance}, number={25}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Desai, Jigar S. and Lawas, Lovely Mae F. and Valente, Ashlee M. and Leman, Adam R. and Grinevich, Dmitry O. and Jagadish, S. V. Krishna and Doherty, Colleen J.}, year={2021}, month={Jun} } @article{vennapusa_somayanda_doherty_jagadish_2020, title={A universal method for high-quality RNA extraction from plant tissues rich in starch, proteins and fiber}, volume={10}, ISSN={["2045-2322"]}, url={https://europepmc.org/articles/PMC7547072}, DOI={10.1038/s41598-020-73958-5}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Vennapusa, Amaranatha R. and Somayanda, Impa M. and Doherty, Colleen J. and Jagadish, S. V. Krishna}, year={2020}, month={Oct} } @article{current status of the multinational arabidopsis community_2020, volume={4}, url={http://dx.doi.org/10.1002/pld3.248}, DOI={10.1002/pld3.248}, abstractNote={Abstract}, number={7}, journal={Plant Direct}, publisher={Wiley}, year={2020}, month={Jul} } @article{scarboro_ruzsa_doherty_kudenov_2020, title={Detection of Gray Mold Infection in Plants Using a Multispectral Imaging System}, volume={4}, url={https://doi.org/10.1101/2020.04.23.051300}, DOI={10.1101/2020.04.23.051300}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Scarboro, Clifton G. and Ruzsa, Stephanie M. and Doherty, Colleen J. and Kudenov, Michael W.}, year={2020}, month={Apr} } @article{slabaugh_desai_sartor_lawas_krishna jagadish_doherty_2019, title={Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome}, volume={25}, ISSN={["1469-9001"]}, url={https://doi.org/10.1261/rna.070227.118}, DOI={10.1261/rna.070227.118}, abstractNote={RNA-seq analysis has enabled the evaluation of transcriptional changes in many species including nonmodel organisms. However, in most species only a single reference genome is available and RNA-seq reads from highly divergent varieties are typically aligned to this reference. Here, we quantify the impacts of the choice of mapping genome in rice where three high-quality reference genomes are available. We aligned RNA-seq data from a popular productive rice variety to three different reference genomes and found that the identification of differentially expressed genes differed depending on which reference genome was used for mapping. Furthermore, the ability to detect differentially used transcript isoforms was profoundly affected by the choice of reference genome: Only 30% of the differentially used splicing features were detected when reads were mapped to the more commonly used, but more distantly related reference genome. This demonstrated that gene expression and splicing analysis varies considerably depending on the mapping reference genome, and that analysis of individuals that are distantly related to an available reference genome may be improved by acquisition of new genomic reference material. We observed that these differences in transcriptome analysis are, in part, due to the presence of single nucleotide polymorphisms between the sequenced individual and each respective reference genome, as well as annotation differences between the reference genomes that exist even between syntenic orthologs. We conclude that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome analysis.}, number={6}, journal={RNA}, publisher={Cold Spring Harbor Laboratory}, author={Slabaugh, Erin and Desai, Jigar S. and Sartor, Ryan C. and Lawas, Lovely Mae F. and Krishna Jagadish, S. V. and Doherty, Colleen J.}, year={2019}, month={Jun}, pages={669–684} } @article{doherty_friesner_gregory_loraine_megraw_meyers_provart_slotkin_town_assmann_et al._2019, title={Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future}, volume={3}, ISSN={["2475-4455"]}, DOI={10.1002/pld3.109}, abstractNote={Abstract}, number={1}, journal={PLANT DIRECT}, author={Doherty, Colleen and Friesner, Joanna and Gregory, Brian and Loraine, Ann and Megraw, Molly and Meyers, Blake C. and Provart, Nicholas and Slotkin, R. Keith and Town, Chris and Assmann, Sarah M. and et al.}, year={2019}, month={Jan} } @article{argueso_assmann_birnbaum_chen_dinneny_doherty_eveland_friesner_greenlee_law_et al._2019, title={Directions for research and training in plant omics: Big Questions and Big Data}, volume={3}, ISSN={2475-4455}, url={http://dx.doi.org/10.1002/PLD3.133}, DOI={10.1002/pld3.133}, abstractNote={Abstract}, number={4}, journal={Plant Direct}, publisher={Wiley}, author={Argueso, Cristiana T. and Assmann, Sarah M. and Birnbaum, Kenneth D. and Chen, Sixue and Dinneny, José R. and Doherty, Colleen J. and Eveland, Andrea L. and Friesner, Joanna and Greenlee, Vanessa R. and Law, Julie A. and et al.}, year={2019}, month={Apr}, pages={e00133} } @article{moghimi_desai_bheemanahalli_impa_vennapusa_sebela_perumal_doherty_jagadish_2019, title={New candidate loci and marker genes on chromosome 7 for improved chilling tolerance in sorghum}, volume={4}, url={http://dx.doi.org/10.1093/jxb/erz143}, DOI={10.1093/jxb/erz143}, abstractNote={Abstract}, journal={J. Exp. Bot}, publisher={Oxford University Press (OUP)}, author={Moghimi, Naghmeh and Desai, Jigar S and Bheemanahalli, Raju and Impa, Somayanda M and Vennapusa, Amaranatha Reddy and Sebela, David and Perumal, Ramasamy and Doherty, Colleen J and Jagadish, S V Krishna}, year={2019}, month={Apr} } @article{grinevich_desai_stroup_duan_slabaugh_doherty_2019, title={Novel transcriptional responses to heat revealed by turning up the heat at night}, volume={101}, url={https://doi.org/10.1007/s11103-019-00873-3}, DOI={10.1007/s11103-019-00873-3}, abstractNote={The circadian clock controls many molecular activities, impacting experimental interpretation. We quantify the genome-wide effects of time-of-day on the heat-shock response and the effects of “diurnal bias” in stress experiments. Heat stress has significant adverse effects on plant productivity worldwide. Most experiments examining heat stress are performed during daytime hours, generating a ‘diurnal bias’ in the pathways and regulatory mechanisms identified. Such bias may confound downstream interpretations and limit our understanding of the full response to heat stress. Here we show that the transcriptional and physiological responses to a sudden heat shock in Arabidopsis are profoundly sensitive to the time of day. We observe that plant tolerance and acclimation to heat shock vary throughout the day and are maximal at dusk. Consistently, over 75% of heat-responsive transcripts show a time of day-dependent response, including many previously characterized heat-response genes. This temporal sensitivity implies a complex interaction between time and temperature where daily variations in basal transcription influence thermotolerance. When we examined these transcriptional responses, we uncovered novel night-response genes and cis-regulatory elements, underpinning new aspects of heat stress responses not previously appreciated. Exploiting this temporal variation can be applied to most environmental responses to understand the underlying network wiring. Therefore, we propose that using time as a perturbagen is an approach that will enhance our understanding of plant regulatory networks and responses to environmental stresses.}, number={1-2}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Grinevich, Dmitry O. and Desai, Jigar S. and Stroup, Kevin P. and Duan, Jiaqi and Slabaugh, Erin and Doherty, Colleen J.}, year={2019}, month={Sep}, pages={1–19} } @article{liebelt_jordan_doherty_2019, title={Only a matter of time: the impact of daily and seasonal rhythms on phytochemicals}, volume={18}, url={https://doi.org/10.1007/s11101-019-09617-z}, DOI={10.1007/s11101-019-09617-z}, number={6}, journal={Phytochemistry Reviews}, publisher={Springer Science and Business Media LLC}, author={Liebelt, Donna J. and Jordan, Juliette T. and Doherty, Colleen J.}, year={2019}, month={Dec}, pages={1409–1433} } @article{desai_lawas_valente_leman_grinevich_jagadish_doherty_2019, title={Warm nights disrupt global transcriptional rhythms in field-grown rice panicles}, volume={7}, url={https://doi.org/10.1101/702183}, DOI={10.1101/702183}, abstractNote={ABSTRACT}, publisher={Cold Spring Harbor Laboratory}, author={Desai, Jigar S. and Lawas, Lovely Mae F. and Valente, Ashlee M. and Leman, Adam R. and Grinevich, Dmitry O. and Jagadish, S.V. Krishna and Doherty, Colleen J.}, year={2019}, month={Jul} } @article{desai_slabaugh_liebelt_fredenberg_gray_jagadish_wilkins_doherty_2018, title={Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance}, volume={9}, ISSN={["1664-462X"]}, url={http://dx.doi.org/10.3389/fpls.2018.01585}, DOI={10.3389/fpls.2018.01585}, abstractNote={In many plant species, the time of day at which flowers open to permit pollination is tightly regulated. Proper time of flower opening, or Time of Day of Anther Appearance (TAA), may coordinate flowering opening with pollinator activity or may shift temperature sensitive developmental processes to cooler times of the day. The genetic mechanisms that regulate the timing of this process in cereal crops are unknown. To address this knowledge gap, it is necessary to establish a monocot model system that exhibits variation in TAA. Here, we examine the suitability of Setaria viridis, the model for C4 photosynthesis, for such a role. We developed an imaging system to monitor the temporal regulation of growth, flower opening time, and other physiological characteristics in Setaria. This system enabled us to compare Setaria varieties Ames 32254, Ames 32276, and PI 669942 variation in growth and daily flower opening time. We observed that TAA occurs primarily at night in these three Setaria accessions. However, significant variation between the accessions was observed for both the ratio of flowers that open in the day vs. night and the specific time of day where the rate is maximal. Characterizing this physiological variation is a requisite step toward uncovering the molecular mechanisms regulating TAA. Leveraging the regulation of TAA could provide researchers with a genetic tool to improve crop productivity in new environments.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Desai, Jigar S. and Slabaugh, Erin and Liebelt, Donna J. and Fredenberg, Jacob D. and Gray, Benjamin N. and Jagadish, S. V. Krishna and Wilkins, Olivia and Doherty, Colleen J.}, year={2018}, month={Oct} } @article{desai_sartor_lawas_jagadish_doherty_2017, title={Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes}, url={https://doi.org/10.1038/s41598-017-17143-1}, DOI={10.1038/s41598-017-17143-1}, abstractNote={Abstract}, journal={Scientific Reports}, author={Desai, Jigar S. and Sartor, Ryan C. and Lawas, Lovely Mae and Jagadish, S. V. Krishna and Doherty, Colleen J.}, year={2017}, month={Dec} } @article{shani_salehin_zhang_sanchez_doherty_wang_mangado_song_tal_pisanty_et al._2017, title={Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors}, volume={27}, ISSN={["1879-0445"]}, DOI={10.1016/j.cub.2016.12.016}, abstractNote={The Aux/IAA proteins are auxin-sensitive repressors that mediate diverse physiological and developmental processes in plants [1, 2]. There are 29 Aux/IAA genes in Arabidopsis that exhibit unique but partially overlapping patterns of expression [3]. Although some studies have suggested that individual Aux/IAA genes have specialized function, genetic analyses of the family have been limited by the scarcity of loss-of-function phenotypes [4]. Furthermore, with a few exceptions, our knowledge of the factors that regulate Aux/IAA expression is limited [1, 5]. We hypothesize that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response. Here, we describe a screen for transcription factors (TFs) that regulate the Aux/IAA genes. We identify TFs from 38 families, including 26 members of the DREB/CBF family. Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19 genes in response to abiotic stress. Recessive mutations in these IAA genes result in decreased tolerance to stress conditions, demonstrating a role for auxin in abiotic stress. Our results demonstrate that stress pathways interact with the auxin gene regulatory network (GRN) through transcription of the Aux/IAA genes. We propose that the Aux/IAA genes function as hubs that integrate genetic and environmental information to achieve the appropriate developmental or physiological outcome.}, number={3}, journal={CURRENT BIOLOGY}, author={Shani, Eilon and Salehin, Mohammad and Zhang, Yuqin and Sanchez, Sabrina E. and Doherty, Colleen and Wang, Renhou and Mangado, Cristina Castillejo and Song, Liang and Tal, Iris and Pisanty, Odelia and et al.}, year={2017}, month={Feb}, pages={437–444} } @article{friesner_assmann_bastow_bailey-serres_beynon_brendel_buell_bucksch_busch_demura_et al._2017, title={The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology}, volume={175}, ISSN={["1532-2548"]}, url={http://dx.doi.org/10.1104/pp.17.01490}, DOI={10.1104/pp.17.01490}, abstractNote={Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.}, number={4}, journal={PLANT PHYSIOLOGY}, author={Friesner, Joanna and Assmann, Sarah M. and Bastow, Ruth and Bailey-Serres, Julia and Beynon, Jim and Brendel, Volker and Buell, C. Robin and Bucksch, Alexander and Busch, Wolfgang and Demura, Taku and et al.}, year={2017}, month={Dec}, pages={1499–1509} } @article{desai_sartor_lawas_jagadish_doherty_2016, title={Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes}, volume={12}, url={https://doi.org/10.1101/093807}, DOI={10.1101/093807}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Desai, Jigar S. and Sartor, Ryan C. and Lawas, Lovely Mae and Jagadish, SV Krishna and Doherty, Colleen J.}, year={2016}, month={Dec} } @article{genome-wide identification of cca1 targets uncovers an expanded clock network in arabidopsis._2015, url={https://europepmc.org/articles/PMC4553765}, DOI={10.1073/pnas.1513609112}, abstractNote={Significance}, journal={Proceedings of the National Academy of Sciences of the United States of America}, year={2015}, month={Aug} } @article{regulation of the arabidopsis cbf regulon by a complex low-temperature regulatory network._2015, url={https://doi.org/10.1111/tpj.12796}, DOI={10.1111/tpj.12796}, abstractNote={Summary}, journal={The Plant journal : for cell and molecular biology}, year={2015}, month={Mar} } @article{a genome-scale resource for the functional characterization of arabidopsis transcription factors._2014, url={http://europepmc.org/articles/PMC4125603}, DOI={10.1016/j.celrep.2014.06.033}, abstractNote={Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.}, journal={Cell reports}, year={2014}, month={Jul} } @article{arabidopsis circadian clock protein, toc1, is a dna-binding transcription factor._2012, url={http://europepmc.org/articles/PMC3286946}, DOI={10.1073/pnas.1200355109}, abstractNote={ The first described feedback loop of the Arabidopsis circadian clock is based on reciprocal regulation between TIMING OF CAB EXPRESSION 1 (TOC1) and CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1)/LATE ELONGATED HYPOCOTYL (LHY). CCA1 and LHY are Myb transcription factors that bind directly to the TOC1 promoter to negatively regulate its expression. Conversely, the activity of TOC1 has remained less well characterized. Genetic data support that TOC1 is necessary for the reactivation of CCA1 / LHY , but there is little description of its biochemical function. Here we show that TOC1 occupies specific genomic regions in the CCA1 and LHY promoters. Purified TOC1 binds directly to DNA through its CCT domain, which is similar to known DNA-binding domains. Chemical induction and transient overexpression of TOC1 in Arabidopsis seedlings cause repression of CCA1 / LHY expression, demonstrating that TOC1 can repress direct targets, and mutation or deletion of the CCT domain prevents this repression showing that DNA-binding is necessary for TOC1 action. Furthermore, we use the Gal4/UAS system in Arabidopsis to show that TOC1 acts as a general transcriptional repressor, and that repression activity is in the pseudoreceiver domain of the protein. To identify the genes regulated by TOC1 on a genomic scale, we couple TOC1 chemical induction with microarray analysis and identify previously unexplored potential TOC1 targets and output pathways. Taken together, these results define a biochemical action for the core clock protein TOC1 and refine our perspective on how plant clocks function. }, journal={Proceedings of the National Academy of Sciences of the United States of America}, year={2012}, month={Feb} } @article{circadian clock-associated 1 regulates ros homeostasis and oxidative stress responses._2012, url={https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23027948/?tool=EBI}, DOI={10.1073/pnas.1209148109}, abstractNote={ Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in Arabidopsis thaliana . ROS-responsive genes exhibit a time-of-day–specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator, CIRCADIAN CLOCK ASSOCIATED 1 ( CCA1 ), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of EARLY FLOWERING 3 , LUX ARRHYTHMO , and TIMING OF CAB EXPRESSION 1 affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by CCA1 and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses. }, journal={Proceedings of the National Academy of Sciences of the United States of America}, year={2012}, month={Oct} } @article{circadian surprise--it's not all about transcription._2012, url={https://doi.org/10.1126/science.1230008}, DOI={10.1126/science.1230008}, abstractNote={Posttranscriptional regulation plays a substantial role in controlling the mammalian circadian clockwork.}, journal={Science (New York, N.Y.)}, year={2012}, month={Oct} } @article{a comparison of the low temperature transcriptomes and cbf regulons of three plant species that differ in freezing tolerance: solanum commersonii, solanum tuberosum, and arabidopsis thaliana._2011, url={https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21511909/?tool=EBI}, DOI={10.1093/jxb/err066}, abstractNote={Solanum commersonii and Solanum tuberosum are closely related plant species that differ in their abilities to cold acclimate; whereas S. commersonii increases in freezing tolerance in response to low temperature, S. tuberosum does not. In Arabidopsis thaliana, cold-regulated genes have been shown to contribute to freezing tolerance, including those that comprise the CBF regulon, genes that are controlled by the CBF transcription factors. The low temperature transcriptomes and CBF regulons of S. commersonii and S. tuberosum were therefore compared to determine whether there might be differences that contribute to their differences in ability to cold acclimate. The results indicated that both plants alter gene expression in response to low temperature to similar degrees with similar kinetics and that both plants have CBF regulons composed of hundreds of genes. However, there were considerable differences in the sets of genes that comprised the low temperature transcriptomes and CBF regulons of the two species. Thus differences in cold regulatory programmes may contribute to the differences in freezing tolerance of these two species. However, 53 groups of putative orthologous genes that are cold-regulated in S. commersonii, S. tuberosum, and A. thaliana were identified. Given that the evolutionary distance between the two Solanum species and A. thaliana is 112–156 million years, it seems likely that these conserved cold-regulated genes—many of which encode transcription factors and proteins of unknown function—have fundamental roles in plant growth and development at low temperature.}, journal={Journal of experimental botany}, year={2011}, month={Apr} } @article{circadian control of global gene expression patterns._2010, url={https://europepmc.org/articles/PMC4251774}, DOI={10.1146/annurev-genet-102209-163432}, abstractNote={ An internal time-keeping mechanism has been observed in almost every organism studied from archaea to humans. This circadian clock provides a competitive advantage in fitness and survival ( 18 , 30 , 95 , 129 , 137 ). Researchers have uncovered the molecular composition of this internal clock by combining enzymology, molecular biology, genetics, and modeling approaches. However, understanding the mechanistic link between the clock and output responses has been elusive. In three model organisms, Arabidopsis thaliana, Drosophila melanogaster, and Mus musculus, whole-genome expression arrays have enabled researchers to investigate how maintaining a time-keeping mechanism connects to an adaptive advantage. Here, we review the impacts transcriptomics have had on our understanding of the clock and how this molecular clock connects with system-level circadian responses. We explore the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions. }, journal={Annual review of genetics}, year={2010}, month={Jan} } @article{roles for arabidopsis camta transcription factors in cold-regulated gene expression and freezing tolerance._2009, url={https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19270186/?tool=EBI}, DOI={10.1105/tpc.108.063958}, abstractNote={Abstract}, journal={The Plant cell}, year={2009}, month={Mar} }