@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={SUMMARYRNA‐Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA‐Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike‐ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike‐ins as a normalization control produces differences in RNA‐Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike‐ins with 3' RNA‐Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.}, 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.MethodsPlant Signaling (PS) and Plant RNA Regulation (PRR) were two separate spaceflight experiments conducted on the International Space Station utilizing the European Modular Cultivation System (EMCS). The EMCS provided a lighted environment for plant growth with centrifugal capabilities providing an onboard 1 g control.Results and discussionAn RNA-Seq analysis of shoot samples from PS and PRR revealed a significant overlap of genes differentially expressed in microgravity between the two experiments. Relative to onboard 1 g controls, genes involved in transcriptional regulation, shoot development, and response to auxin and light were upregulated in microgravity in both experiments. Conversely, genes involved in defense response, abiotic stress, Ca++ signaling, and cell wall modification were commonly downregulated in both datasets. The downregulation of stress responses in microgravity in these two experiments is interesting as these pathways have been previously observed as upregulated in spaceflight compared to ground controls. Similarly, we have observed many stress response genes to be upregulated in the 1 g onboard control compared to ground reference controls; however these genes were specifically downregulated in microgravity. In addition, we analyzed the sRNA landscape of the 1 g and microgravity (μ g) shoot samples from PRR. We identified three miRNAs (miR319c, miR398b, and miR8683) which were upregulated in microgravity, while several of their corresponding target genes were found to be downregulated in microgravity. Interestingly, the downregulated target genes are enriched in those encoding chloroplast-localized enzymes and proteins. These results uncover microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.}, 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={AbstractOrganic photodetectors (OPDs) exhibit performance on par with inorganic detectors (e.g., Si) but can be ultrathin, ultra‐lightweight, flexible, and mechanically resilient, opening up opportunities for novel applications including optical sensors for continuous human and plant health monitoring. Here, a high‐performance flexible self‐powered OPD designed for on‐plant optical sensing is developed. The OPD employs an electrode consisting of Ag nanowires (NWs) embedded in a UV‐curable resin to achieve a flexible and thin form factor. In addition, the OPD active layer consisting of D18‐Cl and Y6 is sequentially cast to reduce dark current. The flexible OPD is sensitive to 400–950 nm wavelengths and exhibits photodetector characteristics comparable to state‐of‐the‐art rigid OPDs. The responsivity reaches values of 0.47 A W−1 and specific detectivity exceeds 1012 Jones. Owing to the embedded Ag NW electrodes in a thin substrate (t = 20 µm) and sequentially cast active layers, the detector demonstrates excellent bending stability. The photocurrent remains steady across 4000 cycles with a bending radius of 2 mm. The flexible OPD is demonstrated to effectively detect plant uptake of the rare‐earth metal terbium and sense time‐dependent chlorophyll fluorescence. Thus, this work highlights the potential for OPDs as on‐plant sensors to advance precision agriculture.}, 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.
          
            The first project is a mast-mounted hyperspectral imaging polarimeter (HIP) that can image a maize field across multiple diurnal cycles throughout a growing season. The second project is a multistatic fiber-based Mueller matrix bidirectional reflectance distribution function (mmBRDF) instrument which measures the polarized light-scattering behavior of individual maize leaves. The mmBRDF data was fitted to an existing model, which outputs parameters that were used to run simulations. The simulated data were then used to train a shallow neural network which works by comparing unpolarized 2-band vegetation index (VI) with linearly polarized data from the low-reflectivity bands of the VI. Using GNDVI and red-edge reflection ratio we saw an improvement of an order of magnitude or more in the mean error (
            ϵ
            ) and a reduction spanning 1.5 to 2.7 in their standard deviation (
            ϵ
            
              σ
            
            ) after applying the correction network on the HIP sensor data.
          }, 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={AbstractRNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3’ RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.}, 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={<h2>Abstract</h2> 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={AbstractPineapple originates from tropical regions in South America and is therefore significantly impacted by cold stress. Periodic cold events in the equatorial regions where pineapple is grown may induce early flowering, also known as precocious flowering, resulting in monetary losses due to small fruit size and the need to make multiple passes for harvesting a single field. Currently, pineapple is one of the most important tropical fruits in the world in terms of consumption, and production losses caused by weather can have major impacts on worldwide exportation potential and economics. To further our understanding of and identify mechanisms for low-temperature tolerance in pineapple, and to identify the relationship between low-temperature stress and flowering time, we report here a transcriptomic analysis of two pineapple genotypes in response to low-temperature stress. Using meristem tissue collected from precocious flowering-susceptible MD2 and precocious flowering-tolerant Dole-17, we performed pairwise comparisons and weighted gene co-expression network analysis (WGCNA) to identify cold stress, genotype, and floral organ development-specific modules. Dole-17 had a greater increase in expression of genes that confer cold tolerance. The results suggested that low temperature stress in Dole-17 plants induces transcriptional changes to adapt and maintain homeostasis. Comparative transcriptomic analysis revealed differences in cuticular wax biosynthesis, carbohydrate accumulation, and vernalization-related gene expression between genotypes. Cold stress induced changes in ethylene and abscisic acid-mediated pathways differentially between genotypes, suggesting that MD2 may be more susceptible to hormone-mediated early flowering. The differentially expressed genes and module hub genes identified in this study are potential candidates for engineering cold tolerance in pineapple to develop new varieties capable of maintaining normal reproduction cycles under cold stress. In addition, a total of 461 core genes involved in the development of reproductive tissues in pineapple were also identified in this study. This research provides an important genomic resource for understanding molecular networks underlying cold stress response and how cold stress affects flowering time in pineapple.}, 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
               A new paradigm suggests weeds primarily reduce crop yield by altering crop developmental and physiological processes long before the weeds reduce resources through competition. Multiple studies have implicated stress response pathways are activated when crops such as maize are grown in close proximity with weeds during the first 4–8 weeks of growth—the point at which weeds have their greatest impact on subsequent crop yields. To date, these studies have mostly focused on the response of above-ground plant parts and have not examined the early signal transduction processes associated with maize root response to weeds. To investigate the impact of signals from a below-ground competitor on the maize root transcriptome when most vulnerable to weed pressure, a system was designed to expose maize to only below-ground signals. Gene set enrichment analyses identified over-represented ontologies associated with oxidative stress signalling throughout the time of weed exposure, with additional ontologies associated with nitrogen use and transport and abscisic acid (ABA) signalling, and defence responses being enriched at later time points. Enrichment of promoter motifs indicated over-representation of sequences known to bind FAR-RED IMPAIRED RESPONSE 1 (FAR1), several AP2/ERF transcription factors and others. Likewise, co-expression networks were identified using Weighted-Gene Correlation Network Analysis (WGCNA) and Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) algorithms. WGCNA highlighted the potential roles of several transcription factors including a MYB 3r-4, TB1, WRKY65, CONSTANS-like5, ABF3, HOMEOBOX 12, among others. These studies also highlighted the role of several specific proteins involved in ABA signalling as being important for the initiation of the early response of maize to weeds. SC-ION highlighted potential roles for NAC28, LOB37, NAC58 and GATA2 transcription factors, among many others.}, 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={AbstractCallus and cell suspension culture techniques are valuable tools in plant biotechnology and are widely used in fundamental and applied research. For studies in callus and cell suspension cultures to be relevant, it is essential to know if the underlying biochemistry is similar to intact plants. This study examined the expression of core circadian genes in Arabidopsis callus from the cell suspension named AT2 and found that the circadian rhythms were impaired. The circadian waveforms are similar to intact plants in the light/dark cycles, but the circadian expression in the AT2 callus stopped in the free-running, constant light conditions. Temperature cycles could drive the rhythmic expression in constant conditions, but there were novel peaks at the point of temperature transitions unique to each clock gene. We found that callus freshly induced from seedlings had normal oscillations, like intact plants, suggesting that the loss of the circadian oscillation in the AT2 callus was specific to this callus. We determined that neither the media composition nor the source of the AT2 callus caused this disruption. We observed thatELF3expression was not differentially expressed between dawn and dusk in both entrained, light-dark cycles and constant light conditions. Overexpression ofELF3in the AT2 callus partially recovers the circadian oscillation in the AT2 callus. This work shows that while callus and cell suspension cultures can be valuable tools for investigating plant responses, careful evaluation of their phenotype is important. Moreover, the altered circadian rhythms under constant light and temperature cycles in the AT2 callus could be useful backgrounds to understand the connections driving circadian oscillators and light and temperature sensing at the cellular level.}, 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={AbstractUnderstanding the effects of space radiation and microgravity on DNA integrity is critical to assess the impact of long-term spaceflight. However, studying spaceflight’s effect on terrestrial life is difficult. NASA created GeneLab, a public Omics database for spaceflight-related data, to help combat these limitations. While GeneLab has very few DNA-based data sets, transcriptome information is abundant. This study used RNA-Seq data from GeneLab to examine DNA sequence variants linked to spaceflight stress exposure. More mutations were observed in spaceflight samples than in the ground control samples. This increase in variants was not reduced in samples grown under artificial gravity in space, suggesting that microgravity did not significantly affect the amount of DNA damage in this experiment. There was also an increase in transversion mutations, consistent with known forms of radiation-induced damage. This work demonstrates that RNA-Seq data is a useful resource for evaluating DNA damage from spaceflight and provides a baseline for the types of mutations that could be detected.}, author={Knight, Montana S. and Doherty, Colleen J. and Nielsen, Dahlia M.}, year={2022}, month={Dec} }
 @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{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{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={AbstractHigh night temperatures (HNT) are shown to significantly reduce rice (Oryza sativa L.) yield and quality. A better understanding of the genetic architecture of HNT tolerance will help rice breeders to develop varieties adapted to future warmer climates. In this study, a diverse indica rice panel displayed a wide range of phenotypic variability in yield and quality traits under control night (24 °C) and higher night (29 °C) temperatures. Genome-wide association analysis revealed 38 genetic loci associated across treatments (18 for control and 20 for HNT). Nineteen loci were detected with the relative changes in the traits between control and HNT. Positive phenotypic correlations and co-located genetic loci with previously cloned grain size genes revealed common genetic regulation between control and HNT, particularly grain size. Network-based predictive models prioritized 20 causal genes at the genetic loci based on known gene/s expression under HNT in rice. Our study provides important insights for future candidate gene validation and molecular marker development to enhance HNT tolerance in rice. Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.}, 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={AbstractGray mold disease caused by the fungus Botrytis cinerea damages many crop hosts worldwide and is responsible for heavy economic losses. Early diagnosis and detection of the disease would allow for more effective crop management practices to prevent outbreaks in field or greenhouse settings. Furthermore, having a simple, non‐invasive way to quantify the extent of gray mold disease is important for plant pathologists interested in measuring infection rates. In this paper, we design and build a bispectral imaging system for discriminating between leaf regions infected with gray mold and those that remain unharmed on a lettuce (Lactuca spp.) host. First, we describe a method to select two optimal (high contrast) spectral bands from continuous hyperspectral imagery (450–800 nm). We then explain the process of building a system based on these two spectral bands, located at 540 and 670 nm. The resultant system uses two cameras, with a narrow band‐pass spectral filter mounted on each, to measure the bispectral reflectance of a lettuce leaf. The two resulting images are combined using a normalized difference calculation that produces a single image with high contrast between the leaves’ infected and healthy regions. A classifier was then created based on the thresholding of single pixel values. We demonstrate that this simple classification produces a true‐positive rate of 95.25% with a false‐positive rate of 9.316% in laboratory conditions.}, 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
               For long-term space missions, it is necessary to understand how organisms respond to changes in gravity. Plant roots are positively gravitropic; the primary root grows parallel to gravity's pull even after being turned away from the direction of gravity. We examined if this gravitropic response varies depending on the time of day reorientation occurs. When plants were reoriented in relation to the gravity vector or placed in simulated microgravity, the magnitude of the root gravitropic response varied depending on the time of day the initial change in gravity occurred. The response was greatest when plants were reoriented at dusk, just before a period of rapid growth, and were minimal just before dawn as the plants entered a period of reduced root growth. We found that this variation in the magnitude of the gravitropic response persisted in constant light (CL) suggesting the variation is circadian-regulated. Gravitropic responses were disrupted in plants with disrupted circadian clocks, including plants overexpressing Circadian-clock Associated 1 (CCA1) and elf3-2, in the reorientation assay and on a 2D clinostat. These findings indicate that circadian-regulated pathways modulate the gravitropic responses, thus, highlighting the importance of considering and recording the time of day gravitropic experiments are performed.}, 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
          The effects of warmer nighttime temperatures (WNT) on crops are one poorly understood dimension of climate change. WNT result from the asymmetrical increase in nighttime versus daytime temperatures. In rice, WNT reduce grain yield and quality. WNT reduce the amplitude of daily temperature cycles plants use to set their circadian clock. Therefore, we examined how WNT affect the timing of molecular activities. In field-grown plants, WNT alter the daily pattern of the transcriptome. Genes with strong rhythmic expression and those under circadian control are affected most by WNT. Many candidate regulators of the disrupted genes are circadian clock associated, emphasizing the altered timing under WNT. The pathways and mechanisms identified can assist efforts to identify lines tolerant to WNT.}, 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={AbstractUsing existing protocols, RNA extracted from seeds rich in starch often results in poor quality RNA, making it inappropriate for downstream applications. Though some methods are proposed for extracting RNA from plant tissue rich in starch and other polysaccharides, they invariably yield less and poor quality RNA. In order to obtain high yield and quality RNA from seeds and other plant tissues including roots a modified SDS-LiCl method was compared with existing methods, including TRIZOL kit (Invitrogen), Plant RNeasy mini kit (Qiagen), Furtado (2014) method, and CTAB-LiCl method. Modifications in the extraction buffer and solutions used for RNA precipitation resulted in a robust method for extracting RNA in seeds and roots, where extracting quality RNA is challenging. The modified SDS-LiCl method revealed intense RNA bands through gel electrophoresis and a nanodrop spectrophotometer detected ratios of ≥ 2 and 1.8 for A260/A230 and A260/A280, respectively. The absence of starch co-precipitation during RNA extraction resulted in enhanced yield and quality of RNA with RIN values of 7–9, quantified using a bioanalyzer. The high-quality RNA obtained was demonstrated to be suitable for downstream applications, such as cDNA synthesis, gene amplification, and RT-qPCR. The method was also effective in extracting RNA from seeds of other cereals including field-grown sorghum and corn. The modified SDS-LiCl method is a robust and highly reproducible RNA extraction method for plant tissues rich in starch and other secondary metabolites. The modified SDS-LiCl method successfully extracted high yield and quality RNA from mature, developing, and germinated seeds, leaves, and roots exposed to different abiotic stresses.}, 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={AbstractThe multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community.}, 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}, url={https://doi.org/10.1101/2020.04.23.051300}, DOI={10.1101/2020.04.23.051300}, abstractNote={AbstractGray mold disease caused by the fungus Botrytis cinerea damages many crop hosts worldwide and is responsible for heavy economic losses. Early diagnosis and detection of the disease would allow for more effective crop management practices to prevent outbreaks in field or greenhouse settings. Furthermore, having a simple, non-invasive way to quantify the extent of gray mold disease is important for plant pathologists interested in quantifying infection rates. In this paper, we design and build a multispectral imaging system for discriminating between leaf regions, infected with gray mold, and those that remain unharmed on a lettuce (Lactuca spp.) host. First, we describe a method to select two optimal (high contrast) spectral bands from continuous hyperspectral imagery (450-800 nm). We then built a system based on these two spectral bands, located at 540 and 670 nm. The resultant system uses two cameras, with a narrow band-pass spectral filter mounted on each, to measure the multispectral reflectance of a lettuce leaf. The two resulting images are combined using a normalized difference calculation that produces a single image with high contrast between the leaves’ infected and healthy regions. A classifier was then created based on the thresholding of single pixel values. We demonstrate that this simple classification produces a true positive rate of 95.25% with a false positive rate of 9.316%.}, 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={AbstractEffective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly‐shared resources. These resources include reference genome sequence data and an ever‐increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community‐defined common standards for data and metadata, and accessible and user‐friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less‐established standards (e.g., phenomics, metabolomics). Community‐established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a “one‐stop shop” website, an Arabidopsis “Super‐Portal” to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy‐in and participation in its establishment and development to encourage adoption.}, 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={AbstractA key remit of the NSF‐funded “Arabidopsis Research and Training for the 21st Century” (ART‐21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART‐21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post‐doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.}, 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
               Sorghum is often exposed to suboptimal low temperature stress under field conditions, particularly at the seedling establishment stage. Enhancing chilling tolerance will facilitate earlier planting and so minimize the negative impacts of other stresses experienced at later growth stages. Genome-wide association mapping was performed on a sorghum association panel grown under control (30/20 °C; day/night) and chilling (20/10 °C) conditions. Genomic regions on chromosome 7, controlling the emergence index and seedling (root and shoot) vigor, were associated with increased chilling tolerance but they did not co-localize with undesirable tannin content quantitative trait loci (QTLs). Shoot and root samples from highly contrasting haplotype pairs expressing differential responses to chilling stress were used to identify candidate genes. Three candidate genes (an alpha/beta hydrolase domain protein, a DnaJ/Hsp40 motif-containing protein, and a YTH domain-containing RNA-binding protein) were expressed at significantly higher levels under chilling stress in the tolerant haplotype compared with the sensitive haplotype and BTx623. Moreover, two CBF/DREB1A transcription factors on chromosome 2 showed a divergent response to chilling in the contrasting haplotypes. These studies identify haplotype differences on chromosome 7 that modulate chilling tolerance by either regulating CBF or feeding back into this signaling pathway. We have identified new candidate genes that will be useful markers in ongoing efforts to develop tannin-free chilling-tolerant sorghum hybrids.}, 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={ABSTRACTIn rice, a small increase in nighttime temperatures reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the normal day to night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase on field-grown rice panicles acclimated to 2-3°C WNT. Rhythmically expressed transcripts were more sensitive to WNT than non-rhythmic transcripts. The system-wide transcriptional perturbations suggest that WNT disrupts the tight temporal coordination between internal molecular events and the environment resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and candidates that can be targeted to enhance tolerance to WNT.}, 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={AbstractOrganisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here: http://github.com/DohertyLab/ExRANGES. To install the package type: devtools::install_github(“DohertyLab/ExRANGES”).}, 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}, url={https://doi.org/10.1101/093807}, DOI={10.1101/093807}, abstractNote={AbstractOrganisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here:http://github.com/DohertyLab/ExRANGES.To install the package type:devtools::install_github(“DohertyLab/ExRANGES”)}, 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
          
            The circadian clock, an endogenous time-keeping mechanism common to most species, allows organisms to coordinate biological processes with specific times of day. In plants, the role of the clock extends to almost every aspect of growth and development, including responses to biotic and abiotic stresses. The core molecular components and circuits of the clock have been well studied in the model organism
            Arabidopsis thaliana
            ; however, how this mechanism connects to clock-controlled outputs remains poorly understood. Here, we performed a genome-wide characterization of the direct targets of a key clock component in
            Arabidopsis
            . Our results emphasize the broad role of the plant clock in regulating multiple biological functions and provide direct links between the oscillator and clock-regulated outputs.
          }, 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={SummaryExposure of Arabidopsis thaliana plants to low non‐freezing temperatures results in an increase in freezing tolerance that involves action of the C‐repeat binding factor (CBF) regulatory pathway. CBF1, CBF2 and CBF3, which are rapidly induced in response to low temperature, encode closely related AP2/ERF DNA‐binding proteins that recognize the C‐repeat (CRT)/dehydration‐responsive element (DRE) DNA regulatory element present in the promoters of CBF‐regulated genes. The CBF transcription factors alter the expression of more than 100 genes, known as the CBF regulon, which contribute to an increase in freezing tolerance. In this study, we investigated the extent to which cold induction of the CBF regulon is regulated by transcription factors other than CBF1, CBF2 and CBF3, and whether freezing tolerance is dependent on a functional CBF–CRT/DRE regulatory module. To address these issues we generated transgenic lines that constitutively overexpressed a truncated version of CBF2 that had dominant negative effects on the function of the CBF–CRT/DRE regulatory module, and 11 transcription factors encoded by genes that were rapidly cold‐induced in parallel with the ‘first‐wave’ CBF genes, and determined the effects that overexpressing these proteins had on global gene expression and freezing tolerance. Our results indicate that cold regulation of the CBF regulon involves extensive co‐regulation by other first‐wave transcription factors; that the low‐temperature regulatory network beyond the CBF pathway is complex and highly interconnected; and that the increase in freezing tolerance that occurs with cold acclimation is only partially dependent on the CBF–CRT/DRE regulatory module.}, 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={AbstractThe Arabidopsis thaliana CBF cold response pathway plays a central role in cold acclimation. It is characterized by rapid cold induction of genes encoding the CBF1-3 transcription factors, followed by expression of the CBF gene regulon, which imparts freezing tolerance. Our goal was to further the understanding of the cis-acting elements and trans-acting factors involved in expression of CBF2. We identified seven conserved DNA motifs (CM), CM1 to 7, that are present in the promoters of CBF2 and another rapidly cold-induced gene encoding a transcription factor, ZAT12. The results presented indicate that in the CBF2 promoter, CM4 and CM6 have negative regulatory activity and that CM2 has both negative and positive activity. A Myc binding site in the CBF2 promoter was also found to have positive regulatory effects. Moreover, our results indicate that members of the calmodulin binding transcription activator (CAMTA) family of transcription factors bind to the CM2 motif, that CAMTA3 is a positive regulator of CBF2 expression, and that double camta1  camta3 mutant plants are impaired in freezing tolerance. These results establish a role for CAMTA proteins in cold acclimation and provide a possible point of integrating low-temperature calcium and calmodulin signaling with cold-regulated gene expression.}, journal={The Plant cell}, year={2009}, month={Mar} }