@article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2024, title={IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss}, volume={114}, ISSN={["1573-5028"]}, url={https://doi.org/10.1007/s11103-024-01422-3}, DOI={10.1007/s11103-024-01422-3}, abstractNote={AbstractArbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.}, number={2}, journal={PLANT MOLECULAR BIOLOGY}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2024}, month={Apr} }
@article{utley_edwards_budnick_grotewold_sederoff_2024, title={Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism}, url={https://doi.org/10.1101/2024.07.02.601705}, DOI={10.1101/2024.07.02.601705}, abstractNote={ABSTRACT Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3’ and 5’ ends, the backsplice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from its cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in regulation of their cognate RNAs by increasing transcription rates, RNA stability and alternative splicing. We have identified circRNAs from Camelina sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3,447 circRNAs from 2,763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlates with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts. Core ideas First discovery of 3,447 genic and 307 intergenic unique putative circRNAs from Camelina sativa . We identified circRNAs that were regulated in response to seedling de-etiolation. Most circRNAs originate from only one homeolog of the three subgenomes in this allohexaploid Camelina. Alternative splicing of exon skipping and intron retention positively correlate with circRNA occurrence. Validation of KASII circRNAs as an example of lipid metabolism pathways potentially regulated by circRNA.}, author={Utley, Delecia and Edwards, Brianne and Budnick, Asa and Grotewold, Erich and Sederoff, Heike}, year={2024}, month={Jul} }
@article{utley_edwards_budnick_grotewold_sederoff_2024, title={Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism}, volume={12}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20537}, DOI={10.1002/tpg2.20537}, abstractNote={Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3' and 5' ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA, and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts.}, journal={PLANT GENOME}, author={Utley, Delecia and Edwards, Brianne and Budnick, Asa and Grotewold, Erich and Sederoff, Heike}, year={2024}, month={Dec} }
@article{budnick_franklin_utley_edwards_charles_hornstein_sederoff_2024, title={Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus}, volume={1}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20429}, DOI={10.1002/tpg2.20429}, abstractNote={AbstractCircular RNAs (circRNAs) are covalently closed single‐stranded RNAs, generated through a back‐splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high‐confidence circRNA‐expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.}, journal={PLANT GENOME}, author={Budnick, Asa and Franklin, Megan J. and Utley, Delecia and Edwards, Brianne and Charles, Melodi and Hornstein, Eli D. and Sederoff, Heike}, year={2024}, month={Jan} }
@article{hornstein_sederoff_2023, title={Back to the Future: Re-Engineering the Evolutionarily Lost Arbuscular Mycorrhiza Host Trait to Improve Climate Resilience for Agriculture}, volume={9}, ISSN={["1549-7836"]}, url={https://doi.org/10.1080/07352689.2023.2256093}, DOI={10.1080/07352689.2023.2256093}, abstractNote={The coming century in agriculture will be marked by increasing exposure of crops to abiotic stress and disease due to climate change. The plant traits with the strongest potential to mitigate these stresses are complex, and are increasingly recognized to involve interaction with the microbiome. Through symbiosis with soil fungi, plants form arbuscular mycorrhizae (AM) that can alleviate nutrient, water, and temperature stress, and can confer pathogen resistance and increased yield. The portfolio of advantages offered by AM overlaps with the benefits of agriculturally useful plant traits that have been the subject of decades of intensive biotechnological efforts, such as C4 photosynthesis and rhizobial nitrogen fixation. In this article we illustrate the prospective benefits of genetic engineering to produce AM in nonmycorrhizal plants and modify AM in already-mycorrhizal crops. We highlight recent advances which have clarified the key genetic and metabolic components of AM symbiosis, and show that many of these components are involved in other plant biological processes and have already been subject to extensive genetic engineering in nonsymbiotic contexts. We provide a theoretical research roadmap to accomplish engineering of AM into the nonmycorrhizal model Arabidopsis including specific molecular genetic approaches. We conclude that AM is potentially more tractable than other complex plant traits, and that a concerted research initiative for biotechnological manipulation of AM could fill unique needs for agricultural resilience. Finally, we note that engineering of AM provides a potential back door into manipulation of other essential plant traits, including carbon storage, and beneficial microbiome assembly.}, journal={CRITICAL REVIEWS IN PLANT SCIENCES}, author={Hornstein, Eli D. and Sederoff, Heike}, year={2023}, month={Sep} }
@article{charles_edwards_ravishankar_calero_henry_rech_saravitz_you_ade_o'connor_et al._2023, title={Emergent molecular traits of lettuce and tomato grown under wavelength-selective solar cells}, volume={14}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2023.1087707}, abstractNote={The integration of semi-transparent organic solar cells (ST-OSCs) in greenhouses offers new agrivoltaic opportunities to meet the growing demands for sustainable food production. The tailored absorption/transmission spectra of ST-OSCs impacts the power generated as well as crop growth, development and responses to the biotic and abiotic environments. To characterize crop responses to ST-OSCs, we grew lettuce and tomato, traditional greenhouse crops, under three ST-OSC filters that create different light spectra. Lettuce yield and early tomato development are not negatively affected by the modified light environment. Our genomic analysis reveals that lettuce production exhibits beneficial traits involving nutrient content and nitrogen utilization while select ST-OSCs impact regulation of flowering initiation in tomato. These results suggest that ST-OSCs integrated into greenhouses are not only a promising technology for energy-neutral, sustainable and climate-change protected crop production, but can deliver benefits beyond energy considerations.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Charles, Melodi and Edwards, Brianne and Ravishankar, Eshwar and Calero, John and Henry, Reece and Rech, Jeromy and Saravitz, Carole and You, Wei and Ade, Harald and O'Connor, Brendan and et al.}, year={2023}, month={Feb} }
@article{liu_wang_liu_wang_fan_liu_zhang_yang_wang_sederoff_et al._2023, title={Exceptionally high genetic variance of the doubled haploid (DH) population of poplar}, volume={5}, ISSN={["1993-0607"]}, DOI={10.1007/s11676-023-01612-7}, abstractNote={AbstractDoubled haploid (DH) plants have been widely used for breeding and biological research in crops. Populus spp. have been used as model woody plant species for biological research. However, the induction of DH poplar plants is onerous, and limited biological or breeding work has been carried out on DH individuals or populations. In this study, we provide an effective protocol for poplar haploid induction based on an anther culture method. A total of 96 whole DH plant lines were obtained using an F1 hybrid of Populus simonii × P. nigra as a donor tree. The phenotypes of the DH population showed exceptionally high variance when compared to those of half-sib progeny of the donor tree. Each DH line displayed distinct features compared to those of the other DH lines or the donor tree. Additionally, some excellent homozygous lines have the potential to be model plants in genetic and breeding studies.}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Liu, Caixia and Wang, Sui and Liu, Yi and Wang, Meng and Fan, Erqin and Liu, Chen and Zhang, Shikai and Yang, Chuanping and Wang, Junhui and Sederoff, Heike W. W. and et al.}, year={2023}, month={May} }
@article{hornstein_charles_franklin_edwards_vintila_kleiner_sederoff_2023, title={Re-engineering a lost trait:IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss}, url={https://doi.org/10.1101/2023.03.06.531368}, DOI={10.1101/2023.03.06.531368}, abstractNote={AbstractArbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the modelArabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generatedArabidopsisplants expressing a constitutively active form ofInteracting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost fromArabidopsisalong with the AM host trait. We characterize the transcriptomic effect of expressingIPD3inArabidopsiswith and without exposure to the AM fungus (AMF)Rhizophagus irregularis, and compare these results to the AM modelLotus japonicusand itsipd3knockout mutantcyclops-4. Despite its long history as a non-AM species, restoringIPD3in the form of its constitutively active DNA-binding domain toArabidopsisaltered expression of specific gene networks. Surprisingly, the effect of expressingIPD3inArabidopsisand knocking it out inLotuswas strongest in plants not exposed to AMF, which is revealed to be due to changes inIPD3genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM andIPD3inArabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.}, author={Hornstein, Eli D. and Charles, Melodi and Franklin, Megan and Edwards, Brianne and Vintila, Simina and Kleiner, Manuel and Sederoff, Heike}, year={2023}, month={Mar} }
@article{zhao_yuan_wang_wang_chao_sederoff_sederoff_yan_pan_peng_et al._2022, title={Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus}, volume={5}, DOI={10.3389/fmicb.2022.870519}, abstractNote={Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Zhao, Yu and Yuan, Zhibo and Wang, Shuang and Wang, Haoyu and Chao, Yanjie and Sederoff, Ronald R. and Sederoff, Heike and Yan, He and Pan, Jialiang and Peng, Mu and et al.}, year={2022} }
@article{edwards_hornstein_wilson_sederoff_2022, title={High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes}, volume={23}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-022-08918-6}, abstractNote={Abstract
Background
Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.
Results
We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes.
Conclusion
This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
}, number={1}, journal={BMC GENOMICS}, author={Edwards, Brianne and Hornstein, Eli D. and Wilson, Nathan J. and Sederoff, Heike}, year={2022}, month={Oct} }
@article{ravishankar_booth_hollingsworth_ade_sederoff_decarolis_brendan t. o'connor_2022, title={Organic solar powered greenhouse performance optimization and global economic opportunity}, volume={15}, ISSN={["1754-5706"]}, url={https://doi.org/10.1039/D1EE03474J}, DOI={10.1039/D1EE03474J}, abstractNote={This work integrates greenhouse energy demand, solar power production, and plant growth modeling to assess the economic opportunity of organic solar powered greenhouses. Results show these systems have positive economic outlook across broad climates.}, number={4}, journal={ENERGY & ENVIRONMENTAL SCIENCE}, publisher={Royal Society of Chemistry (RSC)}, author={Ravishankar, Eshwar and Booth, Ronald E. and Hollingsworth, Joseph A. and Ade, Harald and Sederoff, Heike and DeCarolis, Joseph F. and Brendan T. O'Connor}, year={2022}, month={Mar} }
@article{wang_lu_zhang_liu_cao_chang_liu_lu_yu_li_et al._2022, title={The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion}, volume={12}, ISSN={["1532-2548"]}, DOI={10.1093/plphys/kiac571}, abstractNote={AbstractAs essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through Bulked Segregant Analysis (BSA) sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.}, journal={PLANT PHYSIOLOGY}, author={Wang, Hanhui and Lu, Yanan and Zhang, Tianxu and Liu, Zhi and Cao, Li and Chang, Qiaoying and Liu, Yueying and Lu, Xin and Yu, Song and Li, Huiyu and et al.}, year={2022}, month={Dec} }
@misc{li_li_zhao_pang_wei_tigabu_chiang_sederoff_sederoff_zhao_2021, title={An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use}, volume={7}, ISSN={["2311-7524"]}, DOI={10.3390/horticulturae7080252}, abstractNote={Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use.}, number={8}, journal={HORTICULTURAE}, author={Li, Yan and Li, Xiang and Zhao, Ming-Hui and Pang, Zhong-Yi and Wei, Jia-Tong and Tigabu, Mulualem and Chiang, Vincent L. and Sederoff, Heike and Sederoff, Ronald and Zhao, Xi-Yang}, year={2021}, month={Aug} }
@article{ravishankar_charles_xiong_henry_swift_rech_calero_cho_booth_kim_et al._2021, title={Balancing crop production and energy harvesting in organic solar-powered greenhouses}, volume={2}, ISSN={["2666-3864"]}, DOI={10.1016/j.xcrp.2021.100381}, abstractNote={Adding semitransparent organic solar cells (ST-OSCs) to a greenhouse structure enables simultaneous plant cultivation and electricity generation, thereby reducing the greenhouse energy demand. However, there is a need to establish the impact of such systems on plant growth and indoor climate and to optimize system tradeoffs. In this work, we consider plant growth under OSCs and system-relevant design. We evaluate the growth of red leaf lettuce under ST-OSC filters and compare the impact of three different OSC active layers that have unique transmittance. We find no significant differences in the fresh weight and chlorophyll content of the lettuce grown under these OSC filters. In addition, OSCs provide an opportunity for further light and thermal management of the greenhouse through device design and optical coatings. The OSCs can thus affect plant growth, power generation, and thermal load of the greenhouse, and this design trade space is reviewed and exemplified.}, number={3}, journal={CELL REPORTS PHYSICAL SCIENCE}, publisher={Elsevier BV}, author={Ravishankar, Eshwar and Charles, Melodi and Xiong, Yuan and Henry, Reece and Swift, Jennifer and Rech, Jeromy and Calero, John and Cho, Sam and Booth, Ronald E. and Kim, Taesoo and et al.}, year={2021}, month={Mar} }
@article{wang_chen_ali_zhang_wang_zhang_wang_zhang_xie_jiang_et al._2021, title={Epigenetic modification associated with climate regulates betulin biosynthesis in birch}, volume={12}, ISSN={["1993-0607"]}, DOI={10.1007/s11676-021-01424-7}, abstractNote={AbstractThe Betula genus contains pentacyclic triterpenoid betulin known for its environmental adaptation and medicinal properties. However, the mechanisms underlying betulin biosynthesis responding to climate change remain unclear. In this study, the role of epigenetic modification (DNA methylation) in betulin biosynthesis was examined and how climatic factors influence it. Whole-genome bisulfite sequencing was performed for greenhouse-grown Chinese white birch (Betula platyphylla Sukaczev) treated with DNA methylation inhibitor zebularine (ZEB) and a natural birch population in Northeast China. ZEB treatment significantly affected the CHH methylation level of transposable elements and betulin content in a hormesis dose-dependent manner. The methylation and expression of bHLH9, a key transcriptional factor controlling betulin biosynthesis, were also consistently affected by ZEB treatment as a hormetic dose–response. In the natural population, there was a positive correlation between promoter methylation of bHLH9 and summer precipitation, while winter temperature was negatively correlated. Thus climate-dependent methylation of bHLH9 regulates the expression of downstream genes involved in betulin biosynthesis. This study highlights the role of environmental signals to induce epigenetic changes that result in betulin production, possibly helping to develop resilient plants to combat ongoing climate change and enhance secondary metabolite production.}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Wang, Jiang and Chen, Bowei and Ali, Shahid and Zhang, Tianxu and Wang, Yu and Zhang, He and Wang, Lishan and Zhang, Yonglan and Xie, Linan and Jiang, Tingbo and et al.}, year={2021}, month={Dec} }
@article{ravishankar_booth_saravitz_sederoff_ade_brendan t. o'connor_2020, title={Achieving Net Zero Energy Greenhouses by Integrating Semitransparent Organic Solar Cells}, volume={4}, ISSN={["2542-4351"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85079138223&partnerID=MN8TOARS}, DOI={10.1016/j.joule.2019.12.018}, abstractNote={Greenhouses vastly increase agricultural land-use efficiency. However, they also consume significantly more energy than conventional farming due in part to conditioning the greenhouse space. One way to mitigate the increase in energy consumption is to integrate solar modules onto the greenhouse structure. Semitransparent organic solar cells (OSCs) are particularly attractive given that their spectral absorption can be tuned to minimize the attenuation of sunlight over the plants photosynthetically active spectrum. Here, the benefits of integrating OSCs on the net energy demand of greenhouses within the U.S. are determined through a detailed energy balance model. We find that these systems can have an annual surplus of energy in warm and moderate climates. Furthermore, we show that sunlight reduction entering the greenhouse can be minimized with appropriate design. These results demonstrate that OSCs are an excellent candidate for implementing in greenhouses and provide an opportunity to diversify sustainable energy generation technology.}, number={2}, journal={JOULE}, author={Ravishankar, Eshwar and Booth, Ronald E. and Saravitz, Carole and Sederoff, Heike and Ade, Harald W. and Brendan T. O'Connor}, year={2020}, month={Feb}, pages={490–506} }
@misc{niu_wang_yuan_sederoff_sederoff_chiang_borriss_2020, title={Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease}, volume={11}, ISSN={["1664-302X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85094139988&partnerID=MN8TOARS}, DOI={10.3389/fmicb.2020.585404}, abstractNote={Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Niu, Ben and Wang, Weixiong and Yuan, Zhibo and Sederoff, Ronald R. and Sederoff, Heike and Chiang, Vincent L. and Borriss, Rainer}, year={2020}, month={Oct} }
@article{liu_li_wang_fan_yang_wang_fu_ge_sederoff_sederoff_et al._2021, title={Qu-2, a robust poplar suspension cell line for molecular biology}, volume={32}, ISSN={["1993-0607"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85097191965&partnerID=MN8TOARS}, DOI={10.1007/s11676-020-01266-9}, abstractNote={AbstractPopulus spp. have long been used as model woody plant species for molecular biology research. However, tissues of poplar are often recalcitrant to experimental procedures for molecular studies. We generated a hormone autotrophic poplar suspension cell line from a hybrid of Populus alba × P. berolinensis ‘Yinzhong’, named Qu-2. Qu-2 cells are suitable as a model biological system for studying woody plants. Qu-2 cells have many advantages over suspension cell lines derived so far from any other woody plants. Qu-2 cells are very easy to cultivate and can grow on several common plant culture media without the addition of any plant hormone. They show exceptionally high growth rates, reaching an approximately 150-fold increase in biomass after one week of culturing. Another important unique characteristic of Qu-2 cells is that they can be cryopreserved and readily reactivated. Qu-2 cells are suitable for molecular manipulations such as protoplast production, transient transformation, and RNA-seq analysis. Therefore, Qu-2 cells have the great potential to be an excellent model cell line in tree molecular biological research, ranging from physiology to gene function. The Qu-2 cells will be made available to the plant community for research.}, number={2}, journal={JOURNAL OF FORESTRY RESEARCH}, author={Liu, Caixia and Li, Kailong and Wang, Meng and Fan, Erqin and Yang, Chuanping and Wang, Junhui and Fu, Pengyue and Ge, Xiaolan and Sederoff, Heike W. and Sederoff, Ronald R. and et al.}, year={2021}, month={Apr}, pages={733–740} }
@article{leebens-mack_barker_carpenter_deyholos_gitzendanner_graham_grosse_li_melkonian_mirarab_et al._2019, title={One thousand plant transcriptomes and the phylogenomics of green plants}, volume={574}, ISSN={["1476-4687"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85074238403&partnerID=MN8TOARS}, DOI={10.1038/s41586-019-1693-2}, abstractNote={AbstractGreen plants (Viridiplantae) include around 450,000–500,000 species1,2of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.}, number={7780}, journal={NATURE}, author={Leebens-Mack, James H. and Barker, Michael S. and Carpenter, Eric J. and Deyholos, Michael K. and Gitzendanner, Matthew A. and Graham, Sean W. and Grosse, Ivo and Li, Zheng and Melkonian, Michael and Mirarab, Siavash and et al.}, year={2019}, month={Oct}, pages={679-+} }
@article{lai_karam_sederoff_ducoste_de los reyes_2019, title={Relating nitrogen concentration and light intensity to the growth and lipid accumulation of Dunaliella viridis in a photobioreactor}, volume={31}, ISSN={0921-8971 1573-5176}, url={http://dx.doi.org/10.1007/s10811-019-01897-4}, DOI={10.1007/s10811-019-01897-4}, number={6}, journal={Journal of Applied Phycology}, publisher={Springer Science and Business Media LLC}, author={Lai, Yi-Chun and Karam, Amanda L. and Sederoff, Heike W. and Ducoste, Joel J. and de los Reyes, Francis L.}, year={2019}, month={Aug}, pages={3397–3409} }
@article{suchoff_perkins-veazie_sederoff_schultheis_kleinhenz_louws_gunter_2018, title={Grafting the Indeterminate Tomato Cultivar Moneymaker onto Multifort Rootstock Improves Cold Tolerance}, volume={53}, ISSN={["2327-9834"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85057832928&partnerID=MN8TOARS}, DOI={10.21273/HORTSCI13311-18}, abstractNote={Tomato (Solanum lycopersicum L.) is a warm-season, cold-sensitive crop that shows slower growth and development at temperatures below 18 °C. Improving suboptimal temperature tolerance would allow earlier planting of field-grown tomato and a reduction in energy inputs for heating greenhouses. Grafting tomato onto high-altitude Solanum habrochaites (S. Knapp and D.M. Spooner) accessions has proven effective at improving scion suboptimal temperature tolerance in limited experiments. This study was conducted to determine whether commercially available tomato rootstocks with differing parental backgrounds and root system morphologies can improve the tolerance of scion plants to suboptimal temperature. Two controlled environment growth chambers were used and maintained at either optimal (25 °C day/20 °C night) or suboptimal (15 °C day/15 °C night) temperatures. The cold-sensitive tomato cultivar Moneymaker was used as the nongrafted and self-grafted control as well as scion grafted on ‘Multifort’ (S. lycopersicum × S. habrochaites), ‘Shield’ (S. lycopersicum), and S. habrochaites LA1777 rootstocks. Plants were grown for 10 days in 3.8 L plastic containers filled with a mixture of calcined clay and sand. ‘Multifort’ rootstock significantly reduced the amount of cold-induced stress as observed by larger leaf area and higher levels of CO2 assimilation and photosystem II quantum efficiency. ‘Multifort’ had significantly longer roots, having 42% to 56% more fine root (diameter less than 0.5 mm) length compared with the other nongrafted and grafted treatments. Leaf starch concentration was significantly lower in ‘Multifort’-grafted plants at suboptimal temperatures compared with the self-grafted and nongrafted controls and the ‘Shield’-grafted plants at the same temperature. The ability for ‘Multifort’ to maintain root growth at suboptimal temperatures may improve root system sink strength, thereby promoting movement of photosynthate from leaf to root even under cold conditions. This work demonstrates that a commercially available rootstock can be used to improve suboptimal temperature tolerance in cold-sensitive ‘Moneymaker’ scions.}, number={11}, journal={HORTSCIENCE}, author={Suchoff, David H. and Perkins-Veazie, Penelope and Sederoff, Heike W. and Schultheis, Jonathan R. and Kleinhenz, Matthew D. and Louws, Frank J. and Gunter, Christopher C.}, year={2018}, month={Nov}, pages={1610–1617} }
@article{dums_murphree_vasani_young_sederoff_2018, title={Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented With Ammonium Derived From Glutamine}, volume={5}, ISSN={["2296-7745"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85052906510&partnerID=MN8TOARS}, DOI={10.3389/fmars.2018.00311}, abstractNote={Algal biofuel production requires an input of synthetic nitrogen fertilizer. Fertilizer synthesized via the Haber-Bosch process produces CO2 as a waste byproduct and represents a substantial financial and energy investment. Reliance on synthetic fertilizer attenuates the environmental significance and economic viability of algae production systems. To lower fertilizer input, the waste streams of algal production systems can be recycled to provide alternative sources of nitrogen such as amino acids to the algae. The halophytic green alga Dunaliella viridis can use ammonium (NH4+) derived from the abiotic degradation of amino acids, and previously, supplementation of NH4+ from glutamine degradation was shown to support acceptable levels of growth and increased neutral lipid production compared to nitrate. To understand the effect of glutamine-released NH4+ on algae growth and physiology, metabolite levels, growth parameters, and transcript profiles of D. viridis cultures were observed in a time course after transition from media containing nitrate as a sole N source to medium containing glutamine, glutamate, or a N-depleted medium. Growth parameters were similar between glutamine (NH4+) and nitrate supplemented cultures, however, metabolite data showed that the glutamine supplemented cultures (NH4+) more closely resembled cultures under nitrogen starvation (N-depleted and glutamate supplementation). Neutral lipid accumulation was the same in nitrate and glutamine-derived NH4+ cultures. However, glutamine-derived NH4+ caused a transcriptional response in the immediate hours after inoculation of the culture. The strong initial response of cultures to NH4+ changed over the course of days to closely resemble that of nitrogen starvation. These observations suggest that release of NH4+ from glutamine was sufficient to maintain growth, but not high enough to trigger a cell transition to a nitrogen replete state. Comparative transcript profiling of the nitrogen-starved and nitrate-supplied cultures show an overall downregulation of fatty acid synthesis and a shift to starch synthesis and accumulation. The results indicate that a continuous, amino acid derived slow release of NH4+ to algae cultures could reduce the amount of synthetic nitrogen needed for growth, but optimization is needed to balance nitrogen starvation and cell division.}, number={AUG}, journal={FRONTIERS IN MARINE SCIENCE}, author={Dums, Jacob and Murphree, Colin and Vasani, Naresh and Young, Danielle and Sederoff, Heike}, year={2018}, month={Aug} }
@article{hu_wu_dalal_vasani_lopez_sederoff_qu_2017, title={Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa}, volume={12}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85013067776&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0172296}, abstractNote={With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production.}, number={2}, journal={PLOS ONE}, author={Hu, Zhaohui and Wu, Qian and Dalal, Jyoti and Vasani, Naresh and Lopez, Harry O. and Sederoff, Heike W. and Qu, Rongda}, year={2017}, month={Feb} }
@article{murphree_dums_jain_zhao_young_khoshnoodi_tikunov_macdonald_pilot_sederoff_et al._2017, title={Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth}, volume={8}, ISSN={["1664-462X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85021390666&partnerID=MN8TOARS}, DOI={10.3389/fpls.2017.00847}, abstractNote={Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Murphree, C. A. and Dums, J. T. and Jain, S. K. and Zhao, C. S. and Young, D. Y. and Khoshnoodi, N. and Tikunov, A. and Macdonald, J. and Pilot, G. and Sederoff, Heike and et al.}, year={2017}, month={May} }
@article{karam_mcmillan_lai_de los reyes_sederoff_grunden_ranjithan_levis_ducoste_2017, title={Construction and Setup of a Bench-scale Algal Photosynthetic Bioreactor with Temperature, Light, and pH Monitoring for Kinetic Growth Tests}, volume={2017}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/55545}, DOI={10.3791/55545}, abstractNote={The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software.}, number={124}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Karam, Amanda L. and McMillan, Catherine C. and Lai, Yi-Chun and de los Reyes, Francis L., III and Sederoff, Heike W. and Grunden, Amy M. and Ranjithan, Ranji S. and Levis, James W. and Ducoste, Joel J.}, year={2017}, month={Jun} }
@article{karam_mcmillan_lai_reyes_sederoff_grunden_ranjithan_levis_ducoste_2017, title={Construction and setup of a bench-scale algal photosynthetic bioreactor with temperature, light, and ph monitoring for kinetic growth tests}, DOI={10.3791/55545-v}, abstractNote={The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software.}, number={124}, journal={Jove-Journal of Visualized Experiments}, author={Karam, A. L. and McMillan, C. C. and Lai, Y. C. and Reyes, F. L. and Sederoff, H. W. and Grunden, A. M. and Ranjithan, R. S. and Levis, J. W. and Ducoste, J. J.}, year={2017} }
@article{dalal_lewis_tietz_brown_brown_palme_muday_sederoff_2016, title={ROSY1, a novel regulator of gravitropic response is a stigmasterol binding protein}, volume={196-197}, ISSN={["1618-1328"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84962208471&partnerID=MN8TOARS}, DOI={10.1016/j.jplph.2016.03.011}, abstractNote={The gravitropic bending in plant roots is caused by asymmetric cell elongation. This requires an asymmetric increase in cell surface and therefore plasma membrane components such as lipids, sterols, and membrane proteins. We have identified an early gravity-regulated protein in Arabidopsis thaliana root apices that binds stigmasterol and phosphoethanolamines. This root-specific protein interacts with the membrane transport protein synaptotagmin-1 and was therefore named InteractoR Of SYnaptotagmin1 (ROSY1). While interactions between ML-domain proteins with membrane transport proteins and their impact have been reported from animal cell systems, this is the first report of such an interaction in a plant system. Homozygous mutants of ROSY1 exhibit decreased basipetal auxin transport, a faster root gravitropic response, and an increase in salt stress tolerance. Our results suggest that ROSY1 plays a role in root gravitropism, possibly by facilitating membrane trafficking and asymmetric cell elongation via its interaction with synaptotagmin-1.}, journal={JOURNAL OF PLANT PHYSIOLOGY}, author={Dalal, Jyoti and Lewis, Daniel R. and Tietz, Olaf and Brown, Erica M. and Brown, Christopher S. and Palme, Klaus and Muday, Gloria K. and Sederoff, Heike W.}, year={2016}, month={Jun}, pages={28–40} }
@article{dalal_yalamanchili_hovary_ji_rodriguez-welsh_aslett_ganapathy_grunden_sederoff_qu_et al._2015, title={A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants}, volume={81}, ISSN={["1095-9890"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938634755&partnerID=MN8TOARS}, DOI={10.1016/j.plasmid.2015.06.003}, abstractNote={The rapidly advancing field of plant synthetic biology requires transforming plants with multiple genes. This has sparked a growing interest in flexible plant transformation vectors, which can be used for multi-gene transformations. We have developed a novel binary vector series, named the PC-GW series (GenBank: KP826769-KP826773), for Agrobacterium-mediated plant transformation. The PC-GW vectors use the pCAMBIA vector backbone, and contain NPTII, hpt, bar, mCherry or egfp genes as selectable markers for plant transformation. In a modified multiple cloning site (MCS) of the T-DNA region, we have placed the attR1, attR2 and ccdB sequences for rapid cloning of one to four genes by Gateway™-assisted recombination. In addition, we have introduced four meganuclease sites, and other restriction sites for multi-gene vector construction. Finally, we have placed a CaMV 35S promoter and a 35S terminator on the 5' and 3' ends of the MCS. The CaMV 35S promoter is flanked by PstI restriction sites that can be used to replace it with another promoter sequence if needed. The PC-GW vectors provide choices for selectable markers, cloning methods, and can accommodate up to eight gene constructs in a single T-DNA, thereby significantly reducing the number of transformations or crosses needed to generate multi-transgene expressing plants.}, journal={PLASMID}, author={Dalal, J. and Yalamanchili, R. and Hovary, C. La and Ji, M. and Rodriguez-Welsh, M. and Aslett, D. and Ganapathy, S. and Grunden, A. and Sederoff, Heike and Qu, R. D. and et al.}, year={2015}, month={Sep}, pages={55–62} }
@article{dalal_lopez_vasani_hu_swift_yalamanchili_dvora_lin_xie_qu_et al._2015, title={A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa}, volume={8}, ISSN={["1754-6834"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84945972179&partnerID=MN8TOARS}, DOI={10.1186/s13068-015-0357-1}, abstractNote={Camelina sativa is an oilseed crop with great potential for biofuel production on marginal land. The seed oil from camelina has been converted to jet fuel and improved fuel efficiency in commercial and military test flights. Hydrogenation-derived renewable diesel from camelina is environmentally superior to that from canola due to lower agricultural inputs, and the seed meal is FDA approved for animal consumption. However, relatively low yield makes its farming less profitable. Our study is aimed at increasing camelina seed yield by reducing carbon loss from photorespiration via a photorespiratory bypass. Genes encoding three enzymes of the Escherichia coli glycolate catabolic pathway were introduced: glycolate dehydrogenase (GDH), glyoxylate carboxyligase (GCL) and tartronic semialdehyde reductase (TSR). These enzymes compete for the photorespiratory substrate, glycolate, convert it to glycerate within the chloroplasts, and reduce photorespiration. As a by-product of the reaction, CO2 is released in the chloroplast, which increases photosynthesis. Camelina plants were transformed with either partial bypass (GDH), or full bypass (GDH, GCL and TSR) genes. Transgenic plants were evaluated for physiological and metabolic traits.Expressing the photorespiratory bypass genes in camelina reduced photorespiration and increased photosynthesis in both partial and full bypass expressing lines. Expression of partial bypass increased seed yield by 50-57 %, while expression of full bypass increased seed yield by 57-73 %, with no loss in seed quality. The transgenic plants also showed increased vegetative biomass and faster development; they flowered, set seed and reached seed maturity about 1 week earlier than WT. At the transcriptional level, transgenic plants showed differential expression in categories such as respiration, amino acid biosynthesis and fatty acid metabolism. The increased growth of the bypass transgenics compared to WT was only observed in ambient or low CO2 conditions, but not in elevated CO2 conditions.The photorespiratory bypass is an effective approach to increase photosynthetic productivity in camelina. By reducing photorespiratory losses and increasing photosynthetic CO2 fixation rates, transgenic plants show dramatic increases in seed yield. Because photorespiration causes losses in productivity of most C3 plants, the bypass approach may have significant impact on increasing agricultural productivity for C3 crops.}, number={1}, journal={BIOTECHNOLOGY FOR BIOFUELS}, author={Dalal, Jyoti and Lopez, Harry and Vasani, Naresh B. and Hu, Zhaohui and Swift, Jennifer E. and Yalamanchili, Roopa and Dvora, Mia and Lin, Xiuli and Xie, Deyu and Qu, Rongda and et al.}, year={2015}, month={Oct} }
@article{delaux_radhakrishnan_jayaraman_cheem_malbreil_volkening_sekimoto_nishiyama_melkonian_pokorny_et al._2015, title={Algal ancestor of land plants was preadapted for symbiosis}, volume={112}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84945402783&partnerID=MN8TOARS}, DOI={10.1073/pnas.1515426112}, abstractNote={Significance
Colonization of land by plants was a critical event for the emergence of extant ecosystems. The innovations that allowed the algal ancestor of land plants to succeed in such a transition remain unknown. Beneficial interaction with symbiotic fungi has been proposed as one of these innovations. Here we show that the genes required for this interaction appeared in a stepwise manner: Some evolved before the colonization of land by plants and others first appeared in land plants. We thus propose that the algal ancestor of land plants was preadapted for interaction with beneficial fungi and employed these gene networks to colonize land successfully.}, number={43}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Delaux, Pierre-Marc and Radhakrishnan, Guru V. and Jayaraman, Dhileepkumar and Cheem, Jitender and Malbreil, Mathilde and Volkening, Jeremy D. and Sekimoto, Hiroyuki and Nishiyama, Tomoaki and Melkonian, Michael and Pokorny, Lisa and et al.}, year={2015}, month={Oct}, pages={13390–13395} }
@article{srirangan_sauer_howard_dvora_dums_backman_sederoff_2015, title={Interaction of Temperature and Photoperiod Increases Growth and Oil Content in the Marine Microalgae Dunaliella viridis}, volume={10}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84930682335&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0127562}, abstractNote={Eukaryotic marine microalgae like Dunaliella spp. have great potential as a feedstock for liquid transportation fuels because they grow fast and can accumulate high levels of triacylgycerides with little need for fresh water or land. Their growth rates vary between species and are dependent on environmental conditions. The cell cycle, starch and triacylglycerol accumulation are controlled by the diurnal light:dark cycle. Storage compounds like starch and triacylglycerol accumulate in the light when CO2 fixation rates exceed the need of assimilated carbon and energy for cell maintenance and division during the dark phase. To delineate environmental effects, we analyzed cell division rates, metabolism and transcriptional regulation in Dunaliella viridis in response to changes in light duration and growth temperatures. Its rate of cell division was increased under continuous light conditions, while a shift in temperature from 25°C to 35°C did not significantly affect the cell division rate, but increased the triacylglycerol content per cell several-fold under continuous light. The amount of saturated fatty acids in triacylglycerol fraction was more responsive to an increase in temperature than to a change in the light regime. Detailed fatty acid profiles showed that Dunaliella viridis incorporated lauric acid (C12:0) into triacylglycerol after 24 hours under continuous light. Transcriptome analysis identified potential regulators involved in the light and temperature-induced lipid accumulation in Dunaliella viridis.}, number={5}, journal={PLOS ONE}, author={Srirangan, Soundarya and Sauer, Marie-Laure and Howard, Brian and Dvora, Mia and Dums, Jacob and Backman, Patrick and Sederoff, Heike}, year={2015}, month={May} }
@inbook{dalal_land_vasani_he_smith_rodriguez-welsh_perera_sederoff_2015, title={Methods for RNA Profiling of Gravi-Responding Plant Tissues}, volume={1309}, ISBN={9781493926961 9781493926978}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-4939-2697-8_9}, DOI={10.1007/978-1-4939-2697-8_9}, abstractNote={Plant transcriptional responses to gravity stimulation by reorientation are among the fastest measured in any tissue or species. Upon reorientation, changes in abundance of specific mRNAs can be measured within seconds or minutes, for plastid or nuclear encoded genes, respectively. Identifying fast gravity-induced transcripts has been made possible by the development of high-throughput technology for qualitative and quantitative RNA analysis. RNA profiling has undergone further rapid development due to its enormous potential in basic sciences and medical applications. We describe here the current and most widely used methods to profile the changes in an entire transcriptome by high-throughput sequencing of RNA fractions (RNAseq) and single gene transcript analysis using real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).}, booktitle={Methods in Molecular Biology}, publisher={Springer New York}, author={Dalal, Jyoti and Land, Eric and Vasani, Naresh and He, Luyan and Smith, Caroline and Rodriguez-Welsh, Maria and Perera, Imara Y. and Sederoff, Heike}, year={2015}, pages={91–117} }
@article{wang_allen_campos_cade_dean_dvora_immer_mixson_srirangan_sauer_et al._2013, title={ASI: Dunaliella marine microalgae to drop-in replacement liquid transportation fuel}, volume={32}, ISSN={1944-7442}, url={http://dx.doi.org/10.1002/EP.11855}, DOI={10.1002/EP.11855}, abstractNote={Microalgae are a promising biofuels feedstock, theoretically yielding concentrations of triacylglycerides (TAGs) per unit area that are far higher than traditional feedstocks due to their rapid growth. Dunaliella is particularly advantageous as a feedstock because it is currently commercially mass cultured, thrives in salt water, and has no cell wall. Fourteen strains of Dunaliella have been investigated for growth rates and lipid production in mass culture and tested for enhanced lipid production under a range of environmental stressors including salinity, pH, nitrogen and phosphorus limitation, and light regime. The nuclear genome has been sequenced for four of these strains, with the objective of increasing carbon flux through genetic engineering. Electroflocculation followed by osmotic membrane rupturing may be a very energy and cost efficient means of harvesting the lipid bodies from Dunaliella. A technically feasible and scalable thermo‐catalytic process to convert the lipids into replacements for liquid transportation fuels has been developed. The lipids were converted into long‐chain alkanes through continuous thermal hydrolysis followed by fed‐batch thermo‐catalytic decarboxylation. These alkanes can be reformed into renewable diesel via conventional catalytic hydrocarbon isomerization reactions to improve cold flow properties, if desired. © 2013 American Institute of Chemical Engineers Environ Prog, 32: 916–925, 2013}, number={4}, journal={Environmental Progress & Sustainable Energy}, publisher={Wiley}, author={Wang, Wei-Cheng and Allen, Elle and Campos, Andrew A. and Cade, Rushyannah Killens and Dean, Lisa and Dvora, Mia and Immer, Jeremy G. and Mixson, Stephanie and Srirangan, Soundarya and Sauer, Marie-Laure and et al.}, year={2013}, month={Sep}, pages={916–925} }
@article{howard_hu_babaoglu_chandra_borghi_tan_he_winter-sederoff_gassmann_veronese_et al._2013, title={High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants}, volume={8}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84885077606&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0074183}, abstractNote={We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events – more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens.}, number={10}, journal={PLOS ONE}, author={Howard, Brian E. and Hu, Qiwen and Babaoglu, Ahmet Can and Chandra, Manan and Borghi, Monica and Tan, Xiaoping and He, Luyan and Winter-Sederoff, Heike and Gassmann, Walter and Veronese, Paola and et al.}, year={2013}, month={Oct} }
@article{fang_blackmon_staton_nelson_kubisiak_olukolu_henry_zhebentyayeva_saski_cheng_et al._2013, title={A physical map of the Chinese chestnut (Castanea mollissima) genome and its integration with the genetic map}, volume={9}, ISSN={["1614-2950"]}, DOI={10.1007/s11295-012-0576-6}, abstractNote={Three Chinese chestnut bacterial artificial chromosome (BAC) libraries were developed and used for physical map construction. Specifically, high information content fingerprinting was used to assemble 126,445 BAC clones into 1,377 contigs and 12,919 singletons. Integration of the dense Chinese chestnut genetic map with the physical map was achieved via high-throughput hybridization using overgo probes derived from sequence-based genetic markers. A total of 1,026 probes were anchored to the physical map including 831 probes corresponding to 878 expressed sequence tag-based markers. Within the physical map, three BAC contigs were anchored to the three major fungal blight-resistant quantitative trait loci on chestnut linkage groups B, F, and G. A subset of probes corresponding to orthologous genes in poplar showed only a limited amount of conserved gene order between the poplar and chestnut genomes. The integrated genetic and physical map of Chinese chestnut is available at www.fagaceae.org/physical_maps .}, number={2}, journal={TREE GENETICS & GENOMES}, author={Fang, Guang-Chen and Blackmon, Barbara P. and Staton, Margaret E. and Nelson, C. Dana and Kubisiak, Thomas L. and Olukolu, Bode A. and Henry, David and Zhebentyayeva, Tatyana and Saski, Christopher A. and Cheng, Chun-Huai and et al.}, year={2013}, month={Apr}, pages={525–537} }
@article{rueschhoff_gillikin_sederoff_daub_2013, title={The SOS4 pyridoxal kinase is required for maintenance of vitamin B-6-mediated processes in chloroplasts}, volume={63}, ISSN={["0981-9428"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84872415352&partnerID=MN8TOARS}, DOI={10.1016/j.plaphy.2012.12.003}, abstractNote={Vitamin B(6) (pyridoxal 5'-phosphate and its vitamers) is an important cofactor in numerous enzymatic reactions. In spite of its importance, the consequences of altering vitamin B(6) content on plant growth and development are not well understood. This study compares two mutants for vitamin B(6)-metabolizing enzymes in Arabidopsis thaliana: a pdx1.3 mutant in the de novo synthesis pathway and a salvage pathway sos4 mutant that accumulates more vitamin B(6). We show that despite a difference in total B(6) content in leaf tissue, both mutants share similar phenotypes, including chlorosis, decreased size, altered chloroplast ultrastructure, and root sensitivity to sucrose. Assay of B(6) vitamer content from isolated chloroplasts showed that, despite differing B(6) vitamer content in whole leaf tissue, both mutants share a common deficiency in total and phosphorylated vitamers in chloroplasts. One of the splice variants of the SOS4 proteins was shown to be located in the chloroplast. Our data indicate that some of the phenotypic consequences shared between the pdx1.3 and sos4 mutants are due to B(6) deficiency in chloroplasts, and show that SOS4 is required for maintenance of phosphorylated B(6) vitamer concentrations in chloroplasts. Further, our data are consistent with a diffusion model for transport of vitamin B(6) into chloroplasts.}, journal={PLANT PHYSIOLOGY AND BIOCHEMISTRY}, author={Rueschhoff, Elizabeth E. and Gillikin, Jeffrey W. and Sederoff, Heike W. and Daub, Margaret E.}, year={2013}, month={Feb}, pages={281–291} }
@article{tsou_lee_allen_winter-sederoff_robertson_2012, title={An ER-targeted calcium-binding peptide confers salt and drought tolerance mediated by CIPK6 in Arabidopsis}, volume={235}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84857634774&partnerID=MN8TOARS}, DOI={10.1007/s00425-011-1522-9}, abstractNote={Different plant organelles have high internal stores of Ca(2+) compared to the cytoplasm and could play independent roles in stress responses or signal transduction. We used a GFP fusion with the C-domain of calreticulin, which shows low-affinity, high capacity Ca(2+) binding in the ER, as a calcium-binding peptide (CBP) to specifically increase stores in the ER and nucleus. Despite the presence of a signal sequence and KDEL retention sequence, our work and previous studies (Brandizzi et al. Plant Journal 34:269-281, 2003) demonstrated both ER and nuclear localization of GFP-CBP. Under normal conditions, GFP-CBP-expressing lines had ~25% more total Ca(2+) and higher levels of chlorophyll and seed yield than wild type and GFP controls. CBP-expressing plants also had better survival under intermittent drought or high salt treatments and increased root growth. One member of the CIPK (calcineurin B-like interacting protein kinase) gene family, CIPK6, was up-regulated in CBP-expressing plants, even under non-stress conditions. A null mutation in cipk6 abolished the increased stress tolerance of CBP-transgenic plants, as well as the CBP-mediated induction of two stress-associated genes, DREB1A and RD29A, under non-stress conditions. Although this suggested that it was the induction of CIPK6, rather than localized changes in Ca(2+), that resulted in increased survival under adverse conditions, CIPK6 induction still required Ca(2+). This work demonstrates that ER (or nuclear) Ca(2+) can directly participate in signal transduction to alter gene expression. The discovery of a method for increasing Ca(2+) levels without deleterious effects on plant growth may have practical applications.}, number={3}, journal={PLANTA}, author={Tsou, Pei-Lan and Lee, Sang Yoon and Allen, Nina Stromgren and Winter-Sederoff, Heike and Robertson, Dominique}, year={2012}, month={Mar}, pages={539–552} }
@article{silva_laska_brown_sederoff_khodakovskaya_2011, title={Arabidopsis thaliana calcium-dependent lipid-binding protein (AtCLB): a novel repressor of abiotic stress response}, volume={62}, ISSN={["1460-2431"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79957467259&partnerID=MN8TOARS}, DOI={10.1093/jxb/erq468}, abstractNote={Ca(2+) is an important second messenger in plant signal transduction pathways regulating stress-induced gene expression. Functional analysis of plant proteins containing Ca(2+)-binding domains (C2 domains) will help us understand the mechanisms behind the role of transcriptional regulators in the Ca(2+) signalling pathway and open new perspectives for crop genetic improvement. We identified a novel transcriptional regulator, a Ca(2+)-dependent lipid-binding protein (AtCLB) containing a C2 domain. AtCLB binds specifically to the promoter of the Arabidopsis thalianol synthase gene (AtTHAS1), whose expression is induced by gravity and light. Here we describe the role of the Atclb gene encoding the AtCLB protein. Expression of the Atclb gene was documented in all analysed tissues of Arabidopsis (leaf, root, stem, flower, and silique) by real-time PCR analysis. Immunofluorescence analysis revealed that AtCLB protein is localized in the nucleus of cells in Arabidopsis root tips. We demonstrated that the AtCLB protein was capable of binding to the membrane lipid ceramide. The role of the Atclb gene in negatively regulating responses to abiotic stress in Arabidopsis thaliana was identified. The loss of the Atclb gene function confers an enhanced drought and salt tolerance and a modified gravitropic response in T-DNA insertion knockout mutant lines. Expression of AtTHAS1 in Atclb knockout mutant lines was increased compared with wild type and a 35S-Atclb overexpression line suggesting AtCLB as a transcriptional repressor of AtTHAS1.}, number={8}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Silva, Kanishka and Laska, Bozena and Brown, Christopher and Sederoff, Heike Winter and Khodakovskaya, Mariya}, year={2011}, month={May}, pages={2679–2689} }
@article{boss_sederoff_im_moran_grunden_perera_2010, title={Basal Signaling Regulates Plant Growth and Development}, volume={154}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957739073&partnerID=MN8TOARS}, DOI={10.1104/pp.110.161232}, abstractNote={The term signal transduction refers to the classical paradigm where an external stimulus is sensed and initiates an increase in second messengers. Each second messenger transmits and amplifies the signal by activating a subset of downstream pathways. This complex network of interwoven downstream}, number={2}, journal={PLANT PHYSIOLOGY}, author={Boss, Wendy F. and Sederoff, Heike Winter and Im, Yang Ju and Moran, Nava and Grunden, Amy M. and Perera, Imara Y.}, year={2010}, month={Oct}, pages={439–443} }
@inproceedings{henry lamb_burkholder_roberts_sederoff_strikeleather_2010, title={EFRI-HyBi: Algal oils to "drop-in" replacements for petroleum transportation fuels}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-79951504751&partnerID=MN8TOARS}, booktitle={ACS National Meeting Book of Abstracts}, author={Henry Lamb, H. and Burkholder, J. and Roberts, W.L. and Sederoff, H.W. and Strikeleather, L.F.}, year={2010} }
@article{novaes_kirst_chiang_winter-sederoff_sederoff_2010, title={Lignin and Biomass: A Negative Correlation for Wood Formation and Lignin Content in Trees}, volume={154}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957730551&partnerID=MN8TOARS}, DOI={10.1104/pp.110.161281}, abstractNote={Studies in populations of forest tree hybrids have shown a negative correlation of biomass growth (usually measured as wood volume) and lignin content ([Kirst et al., 2004][1]; [Novaes et al., 2009][2]). The control of growth and lignin appears to be highly regulated, implying that selection for}, number={2}, journal={PLANT PHYSIOLOGY}, author={Novaes, Evandro and Kirst, Matias and Chiang, Vincent and Winter-Sederoff, Heike and Sederoff, Ronald}, year={2010}, month={Oct}, pages={555–561} }
@article{salinas mondragon_kajla_perera_brown_sederoff_2010, title={Role of inositol 1,4,5-triphosphate signalling in gravitropic and phototropic gene expression}, volume={33}, ISSN={0140-7791}, url={http://dx.doi.org/10.1111/j.1365-3040.2010.02204.x}, DOI={10.1111/j.1365-3040.2010.02204.x}, abstractNote={ABSTRACTPlants sense light and gravity to orient their direction of growth. One common component in the early events of both phototropic and gravitropic signal transduction is activation of phospholipase C (PLC), which leads to an increase in inositol 1,4,5‐triphosphate (InsP3) levels. The InsP3 signal is terminated by hydrolysis of InsP3 through inositolpolyphosphate‐5‐phosphatases (InsP 5‐ptases). Arabidopsis plants expressing a heterologous InsP 5‐ptase have low basal InsP3 levels and exhibit reduced gravitropic and phototropic bending. Downstream effects of InsP3‐mediated signalling are not understood. We used comparative transcript profiling to characterize gene expression changes in gravity‐ or light‐stimulated Arabidopsis root apices that were manipulated in their InsP3 metabolism either through inhibition of PLC activity or expression of InsP 5‐ptase. We identified InsP3‐dependent and InsP3‐independent co‐regulated gene sets in response to gravity or light stimulation. Inhibition of PLC activity in wild‐type plants caused similar changes in transcript abundance in response to gravitropic and phototropic stimulation as in the transgenic lines. Therefore, we conclude that changes in gene expression in response to gravitropic and phototropic stimulation are mediated by two signal transduction pathways that vary in their dependence on changes in InsP3.}, number={12}, journal={Plant, Cell & Environment}, publisher={Wiley}, author={Salinas Mondragon, Raul E. and Kajla, Jyoti D. and Perera, Imara Y. and Brown, Christopher S. and Sederoff, Heike Winter}, year={2010}, month={Nov}, pages={2041–2055} }
@article{khodakovskaya_sword_wu_perera_boss_brown_sederoff_2010, title={Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato}, volume={8}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-73949085190&partnerID=MN8TOARS}, DOI={10.1111/j.1467-7652.2009.00472.x}, abstractNote={SummaryInositol‐(1,4,5)‐trisphosphate (InsP3) is a second messenger in plants that increases in response to many stimuli. The metabolic consequences of this signalling pathway are not known. We reduced the basal level of InsP3 in tomato (Solanum lycopersicum cv. Micro‐Tom) by expressing the human type I inositol polyphosphate 5‐phosphatase (InsP 5‐ptase) gene. Transgenic lines producing InsP 5‐ptase protein had between 15% and 30% of the basal InsP3 level of control plants. This increased hydrolysis of InsP3 caused dramatic increases in drought tolerance, vegetative biomass and lycopene and hexose concentrations in the fruits. Transcript profiling of root, leaf and fruit tissues identified a small group of genes, including a cell‐wall invertase inhibitor gene, that were differentially regulated in all tissues of the InsP 5‐ptase expressing plants. Significant differences were found in the amounts of carbohydrates and organic phosphate in these plants. Plants with increased hydrolysis of InsP3 in the cytosol also showed increased net CO2‐fixation and sucrose export into sink tissue and storage of hexoses in the source leaves. The increase in biomass was dependent on the supply of inorganic phosphate in the nutrient medium. Uptake and storage of phosphate was increased in the transgene expressing lines. This suggests that in tomato, increased flux through the inositol phosphate pathway uncoupled phosphate sensing from phosphate metabolism. Altering the second messenger, InsP3, revealed multiple coordinated changes in development and metabolism in tomato that have potential for crop improvement.}, number={2}, journal={Plant Biotechnology Journal}, author={Khodakovskaya, M. and Sword, C. and Wu, Q. and Perera, I. Y. and Boss, W. F. and Brown, C. S. and Sederoff, Heike}, year={2010}, pages={170–183} }
@inbook{brown_sederoff_davies_ferl_stankovic_2008, title={Plan(t)s for Space Exploration}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84889307727&partnerID=MN8TOARS}, DOI={10.1002/9780470388297.ch9}, abstractNote={Chapter 9 Plan(t)s for Space Exploration Christopher S. Brown, Christopher S. BrownSearch for more papers by this authorHeike Winter Sederoff, Heike Winter SederoffSearch for more papers by this authorEric Davies, Eric DaviesSearch for more papers by this authorRobert J. Ferl, Robert J. FerlSearch for more papers by this authorBratislav Stankovic, Bratislav StankovicSearch for more papers by this author Christopher S. Brown, Christopher S. BrownSearch for more papers by this authorHeike Winter Sederoff, Heike Winter SederoffSearch for more papers by this authorEric Davies, Eric DaviesSearch for more papers by this authorRobert J. Ferl, Robert J. FerlSearch for more papers by this authorBratislav Stankovic, Bratislav StankovicSearch for more papers by this author Book Editor(s):Simon Gilroy Ph.D., Simon Gilroy Ph.D. Professor of Biology at Pennsylvania State UniversitySearch for more papers by this authorPatrick H. Masson Ph.D., Patrick H. Masson Ph.D. Professor of Genetics, University of WisconsinSearch for more papers by this author First published: 30 October 2007 https://doi.org/10.1002/9780470388297.ch9Citations: 1 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter contains section titled: Introduction Human Missions to Space Life Support Genomics and Space Exploration Nanotechnology Sensors, Biosensors, and Intelligent Machines Plan(t)s for Space Exploration Imagine… Literature Cited Citing Literature Plant Tropisms RelatedInformation}, booktitle={Plant Tropisms}, author={Brown, C.S. and Sederoff, H.W. and Davies, E. and Ferl, R.J. and Stankovic, B.}, year={2008}, pages={183–195} }
@inproceedings{howard_sick_perera_im_winter-sederoff_heber_2007, title={Quality Assessment of Affymetrix GeneChip Data using the EM Algorithm and a Naive Bayes Classifier}, ISBN={1424415098 9781424415090}, url={http://dx.doi.org/10.1109/bibe.2007.4375557}, DOI={10.1109/BIBE.2007.4375557}, abstractNote={Recent research has demonstrated the utility of using supervised classification systems for automatic identification of low quality microarray data. However, this approach requires annotation of a large training set by a qualified expert. In this paper we demonstrate the utility of an unsupervised classification technique based on the Expectation-Maximization (EM) algorithm and naive Bayes classification. On our test set, this system exhibits performance comparable to that of an analogous supervised learner constructed from the same training data.}, booktitle={2007 IEEE 7th International Symposium on BioInformatics and BioEngineering}, publisher={IEEE}, author={Howard, Brian E. and Sick, Beate and Perera, Imara and Im, Yang Ju and Winter-Sederoff, Heike and Heber, Steffen}, year={2007}, month={Oct}, pages={145–150} }
@article{kimbrough_brown_sederoff_2005, title={Co-expression and hormonal regulation of genes in response to gravity and mechanical stimulation in the Arabidopsis root apex.}, volume={18}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-26944462406&partnerID=MN8TOARS}, number={2}, journal={Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology}, author={Kimbrough, J.M. and Brown, C.S. and Sederoff, H.W.}, year={2005}, pages={117–118} }
@article{salinas-mondragon_brogan_ward_perera_boss_brown_sederoff_2005, title={Gravity and light: integrating transcriptional regulation in roots.}, volume={18}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-24944540197&partnerID=MN8TOARS}, number={2}, journal={Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology}, author={Salinas-Mondragon, R. and Brogan, A. and Ward, N. and Perera, I. and Boss, W. and Brown, C.S. and Sederoff, H.W.}, year={2005}, pages={121–122} }
@article{hardin_winter_huber_2004, title={Phosphorylation of the amino terminus of maize sucrose synthase in relation to membrane association and enzyme activity}, volume={134}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-1942437647&partnerID=MN8TOARS}, DOI={10.1104/pp.103.036780}, abstractNote={Abstract
Sucrose synthase (SUS) is phosphorylated on a major, amino-terminal site located at Ser-15 (S15) in the maize (Zea mays) SUS1 protein. Site- and phospho-specific antibodies against a phosphorylated S15 (pS15) peptide allowed direct analysis of S15 phosphorylation in relation to membrane association. Immunoblots of the maize leaf elongation zone, divided into 4-cm segments, demonstrated that the abundance of soluble (s-SUS) and membrane (m-SUS) SUS protein showed distinct positional profiles. The content of m-SUS was maximal in the 4- to 8-cm segment where it represented 9% of total SUS and occurred as a peripheral membrane protein. In contrast, s-SUS was highest in the 12- to 16-cm segment. Relative to s-SUS, m-SUS was hypophosphorylated at S15 in the basal 4 cm but hyperphosphorylated in apical segments. Differing capabilities of the anti-pS15 and anti-S15 peptide antibodies to immunoprecipitate SUS suggested that phosphorylation of S15, or exposure of unphosphorylated SUS to slightly acidic pH, altered the structure of the amino terminus. These structural changes were generally coincident with the increased sucrose cleavage activity that occurs at pH values below 7.5. In vitro S15 phosphorylation of the S170A SUS protein by a maize calcium-dependent protein kinase (CDPK) significantly increased sucrose cleavage activity at low pH. Collectively, the results suggest that (1) SUS membrane binding is controlled in vivo; (2) relative pS15 content of m-SUS depends on the developmental state of the organ; and (3) phosphorylation of S15 affects amino-terminal conformation in a way that may stimulate the catalytic activity of SUS and influence membrane association.}, number={4}, journal={PLANT PHYSIOLOGY}, author={Hardin, SC and Winter, H and Huber, SC}, year={2004}, month={Apr}, pages={1427–1438} }
@article{kimbrough_salinas-mondragon_boss_brown_sederoff_2004, title={The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root Apex}, volume={136}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-16544389872&partnerID=MN8TOARS}, DOI={10.1104/pp.104.044594}, abstractNote={Abstract
Plant root growth is affected by both gravity and mechanical stimulation (Massa GD, Gilroy S [2003] Plant J 33: 435–445). A coordinated response to both stimuli requires specific and common elements. To delineate the transcriptional response mechanisms, we carried out whole-genome microarray analysis of Arabidopsis root apices after gravity stimulation (reorientation) and mechanical stimulation and monitored transcript levels of 22,744 genes in a time course during the first hour after either stimulus. Rapid, transient changes in the relative abundance of specific transcripts occurred in response to gravity or mechanical stimulation, and these transcript level changes reveal clusters of coordinated events. Transcriptional regulation occurs in the root apices within less than 2 min after either stimulus. We identified genes responding specifically to each stimulus as well as transcripts regulated in both signal transduction pathways. Several unknown genes were specifically induced only during gravitropic stimulation (gravity induced genes). We also analyzed the network of transcriptional regulation during the early stages of gravitropism and mechanical stimulation.}, number={1}, journal={PLANT PHYSIOLOGY}, author={Kimbrough, JM and Salinas-Mondragon, R and Boss, WE and Brown, CS and Sederoff, HW}, year={2004}, month={Sep}, pages={2790–2805} }
@article{hardin_tang_scholz_holtgraewe_winter_huber_2003, title={Phosphorylation of sucrose synthase at serine 170: occurrence and possible role as a signal for proteolysis}, volume={35}, ISSN={["1365-313X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0141792977&partnerID=MN8TOARS}, DOI={10.1046/j.1365-313X.2003.01831.x}, abstractNote={SummarySequence analysis identified serine 170 (S170) of the maize (Zea mays L.) SUS1 sucrose synthase (SUS) protein as a possible, second phosphorylation site. Maize leaves contained two calcium‐dependent protein kinase activities and a calcium‐independent kinase activity with characteristics of an sucrose non‐fermenting 1 (SNF1)‐related protein kinase. Phosphorylation of the novel S170 and the known serine 15 (S15) site by these protein kinases was determined in peptide substrates and detected in SUS1 protein substrates utilizing sequence‐ and phosphorylation‐specific antibodies. We demonstrate phosphorylation of S170 in vitro and in vivo. The calcium‐dependent protein kinases phosphorylated both S170 and S15, whereas SNF1‐related protein kinase activity was restricted to S15. Calcium‐dependent protein‐kinase‐mediated S170 and S15 phosphorylation kinetics were determined in wild‐type and mutant SUS1 substrates. These analyses revealed that kinase specificity for S170 was threefold lower than that for S15, and that phosphorylation of S170 was stimulated by prior phosphorylation at the S15 site. The SUS‐binding peptides encoded by early nodulin 40 (ENOD40) specifically antagonized S170 phosphorylation in vitro. A model wherein S170 phosphorylation functions as part of a mechanism targeting SUS for proteasome‐mediated degradation is supported by the observations that SUS proteolytic fragments: (i) were detected and possessed relatively high phosphorylated‐S170 (pS170) stoichiometry; (ii) were spatially coincident with proteasome activity within developing leaves; and (iii) co‐sedimented with proteasome activity. In addition, full‐length pS170‐SUS protein was less stable than S170‐SUS in cultured leaf segments and was stabilized by proteasome inhibition. Post‐translational control of SUS protein level through pS170‐promoted proteolysis may explain the specific and significant decrease in SUS abundance that accompanies the sink‐to‐source transition in developing maize leaves.}, number={5}, journal={PLANT JOURNAL}, author={Hardin, SC and Tang, GQ and Scholz, A and Holtgraewe, D and Winter, H and Huber, SC}, year={2003}, month={Sep}, pages={588–603} }
@article{smith_winter_storer_bussell_schuller_atkins_2002, title={Effect of short-term N2 deficiency on expression of the ureide pathway in cowpea root nodules}, volume={129}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0035983935&partnerID=MN8TOARS}, DOI={10.1104/pp.010714}, abstractNote={Abstract
Root systems of 28-d-old cowpea (Vigna unguiculata L. Walp cv Vita 3: Bradyrhizobiumsp. strain CB756) plants bearing nitrogen-fixing nodules in sand culture were exposed to an atmosphere of Ar:O2 (80:20, v/v) for 48 h and then returned to air. Root systems of control plants were maintained in air throughout. Nodules were harvested at the same times in control and Ar:O2-treated root systems. Activities of two enzymes of de novo purine synthesis, glycinamide ribonucleotide transformylase (GART; EC 2.1.2.2), aminoimidazole ribonucleotide synthetase (AIRS; EC 6.3.3.1), uricase (EC 1.7.3.3), and phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) were measured together with the protein level of each using immune-specific polyclonal antibodies. AIRS activity and protein both declined to very low levels within 6 h in Ar:O2 together with a decline in transcript level of pur5, the encoding gene. GART activity, protein, and transcript (pur3) levels were relatively stable. Uricase activity declined in Ar:O2 as rapidly as AIRS activity but the protein was stable. PEPC activity showed evidence of increased sensitivity to inhibition by malate but the protein level was stable. The data indicate that the flux of fixed N from bacteroids (N2-fixing nodule bacteria) is in some way associated with transcriptional control over pur5and possibly also catabolism of AIRS protein. In contrast, there is limited posttranslational control over GART and PEPC and close posttranslational control over uricase activity. The significance of these different levels of regulation is discussed in relation to the overall control of enhanced expression of plant enzymes in the cowpea symbiosis.}, number={3}, journal={Plant Physiology}, author={Smith, P.M.C. and Winter, H. and Storer, P.J. and Bussell, J.D. and Schuller, K.A. and Atkins, C.A.}, year={2002}, pages={1216–1221} }
@article{winter_huber_2000, title={Regulation of sucrose metabolism in higher plants: Localization and regulation of activity of key enzymes}, volume={19}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033984161&partnerID=MN8TOARS}, DOI={10.1080/07352680091139178}, abstractNote={Sucrose (Suc) plays a central role in plant growth and development. It is a major end product of photosynthesis and functions as a primary transport sugar and in some cases as a direct or indirect regulator of gene expression. Research during the last 2 decades has identified the pathways involved and which enzymes contribute to the control of flux. Availability of metabolites for Suc synthesis and ‘demand’ for products of sucrose degradation are important factors, but this review specifically focuses on the biosynthetic enzyme sucrose-phosphate synthase (SPS), and the degradative enzymes, sucrose synthase (SuSy), and the invertases. Recent progress has included the cloning of genes encoding these enzymes and the elucidation of posttranslational regulatory mechanisms. Protein phosphorylation is emerging as an important mechanism controlling SPS activity in response to various environmental and endogenous signals. In terms of Suc degradation, invertase-catalyzed hydrolysis generally has been associated with cell expansion, whereas SuSy-catalyzed metabolism has been linked with biosynthetic processes (e.g., cell wall or storage products). Recent results indicate that SuSy may be localized in multiple cellular compartments: (1) as a soluble enzyme in the cytosol (as traditionally assumed); (2) associated with the plasma membrane; and (3) associated with the actin cytoskel-eton. Phosphorylation of SuSy has been shown to occur and may be one of the factors controlling localization of the enzyme. The purpose of this review is to summarize some of the recent developments relating to regulation of activity and localization of key enzymes involved in sucrose metabolism in plants.}, number={1}, journal={Critical Reviews in Plant Sciences}, author={Winter, H. and Huber, S.C.}, year={2000}, pages={31–67} }
@misc{winter_huber_2000, title={Regulation of sucrose metabolism in higher plants: Localization and regulation of activity of key enzymes}, volume={35}, ISSN={["1549-7798"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0033829914&partnerID=MN8TOARS}, DOI={10.1080/10409230008984165}, abstractNote={ABSTRACT Sucrose (Sue) plays a central role in plant growth and development. It is a major end product of photosynthesis and functions as a primary transport sugar and in some cases as a direct or indirect regulator of gene expression. Research during the last 2 decades has identified the pathways involved and which enzymes contribute to the control of flux. Availability of metabolites for Sue synthesis and 'demand' for products of sucrose degradation are important factors, but this review specifically focuses on the biosynthetic enzyme sucrose-phosphate synthase (SPS), and the degradative enzymes, sucrose synthase (SuSy), and the invertases. Recent progress has included the cloning of genes encoding these enzymes and the elucidation of posttranslational regulatory mechanisms. Protein phosphorylation is emerging as an important mechanism controlling SPS activity in response to various environmental and endogenous signals. In terms of Sue degradation, invertase-catalyzed hydrolysis generally has been associated with cell expansion, whereas SuSy-catalyzed metabolism has been linked with biosynthetic processes (e.g., cell wall or storage products). Recent results indicate that SuSy may be localized in multiple cellular compartments: (1) as a soluble enzyme in the cytosol (as traditionally assumed); (2) associated with the plasma membrane; and (3) associated with the actin cytoskeleton. Phosphorylation of SuSy has been shown to occur and may be one of the factors controlling localization of the enzyme. The purpose of this review is to summarize some of the recent developments relating to regulation of activity and localization of key enzymes involved in sucrose metabolism in plants.}, number={4}, journal={CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY}, author={Winter, H and Huber, SC}, year={2000}, pages={253–289} }
@article{kuzma_winter_storer_oresnik_atkins_layzell_1999, title={The site of oxygen limitation in soybean nodules}, volume={119}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032838730&partnerID=MN8TOARS}, DOI={10.1104/pp.119.2.399}, abstractNote={Abstract
In legume nodules the [O2] in the infected cells limits respiration and nitrogenase activity, becoming more severe if nodules are exposed to subambient O2 levels. To identify the site of O2 limitation, adenylate pools were measured in soybean (Glycine max) nodules that were frozen in liquid N2 before being ground, lyophilized, sonicated, and separated on density gradients of nonaqueous solvents (heptane/tetrachloroethylene) to yield fractions enriched in bacteroid or plant components. In nodules maintained in air, the adenylate energy charge (AEC = [ATP + 0.5 ADP]/[ATP + ADP + AMP]) was lower in the plant compartment (0.65 ± 0.04) than in the bacteroids (0.76 ± 0.095), but did not change when the nodulated root system was exposed to 10% O2. In contrast, 10% O2decreased the bacteroid AEC to 0.56 ± 0.06, leading to the conclusion that they are the primary site of O2 limitation in nodules. To account for the low but unchanged AEC in the plant compartment and for the evidence that mitochondria are localized in O2-enriched microenvironments adjacent to intercellular spaces, we propose that steep adenylate gradients may exist between the site of ATP synthesis (and ADP use) in the mitochondria and the extra-mitochondrial sites of ATP use (and ADP production) throughout the large, infected cells.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Kuzma, MM and Winter, H and Storer, P and Oresnik, I and Atkins, CA and Layzell, DB}, year={1999}, month={Feb}, pages={399–407} }
@article{collings_winter_wyatt_allen_1998, title={Growth dynamics and cytoskeleton organization during stem maturation and gravity-induced stem bending in Zea mays L.}, volume={207}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032435367&partnerID=MN8TOARS}, DOI={10.1007/s004250050480}, abstractNote={Characterization of gravitropic bending in the maize stem pulvinus, a tissue that functions specifically in gravity responses, demonstrates that the pulvinus is an ideal system for studying gravitropism. Gravistimulation during the second of three developmental phases of the pulvinus induces a gradient of cell elongation across the non-growing cells of the pulvinus, with the most elongation occurring on the lower side. This cell elongation is spatially and temporally separated from normal internodal cell elongation. The three characterized growth phases in the pulvinus correspond closely to a specialized developmental sequence in which structural features typical of cells not fully matured are retained while cell maturation occurs in surrounding internodal and nodal tissue. For example, the lignification of supporting tissue and rearrangement of transverse microtubules to oblique that occur in the internode when cell elongation ceases are delayed for up to 10 d in the adjacent cells of the pulvinus, and only occurs as a pulvinus loses its capacity to respond to gravistimulation. Gravistimulation does not modify this developmental sequence. Neither wall lignification nor rearrangement of transverse microtubules occurs in the rapidly elongating lower side or non-responsive upper side of the pulvinus until the pulvinus loses the capacity to bend further. Gravistimulation does, however, lead to the formation of putative pit fields within the expanding cells of the pulvinus.}, number={2}, journal={PLANTA}, author={Collings, DA and Winter, H and Wyatt, SE and Allen, NS}, year={1998}, month={Dec}, pages={246–258} }
@article{winter_huber_huber_1998, title={Identification of sucrose synthase as an actin-binding protein}, volume={430}, ISSN={["1873-3468"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0032479338&partnerID=MN8TOARS}, DOI={10.1016/S0014-5793(98)00659-0}, abstractNote={Several lines of evidence indicate that sucrose synthase (SuSy) binds both G‐ and F‐actin: (i) presence of SuSy in the Triton X‐100‐insoluble fraction of microsomal membranes (i.e. crude cytoskeleton fraction); (ii) co‐immunoprecipitation of actin with anti‐SuSy monoclonal antibodies; (iii) association of SuSy with in situ phalloidin‐stabilized F‐actin filaments; and (iv) direct binding to F‐actin, polymerized in vitro. Aldolase, well known to interact with F‐actin, interfered with binding of SuSy, suggesting that a common or overlapping binding site may be involved. We postulate that some of the soluble SuSy in the cytosol may be associated with the actin cytoskeleton in vivo.}, number={3}, journal={FEBS LETTERS}, author={Winter, H and Huber, JL and Huber, SC}, year={1998}, month={Jul}, pages={205–208} }
@article{winter_huber_huber_1997, title={Membrane association of sucrose synthase: changes during the graviresponse and possible control by protein phosphorylation}, volume={420}, ISSN={["1873-3468"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0031590792&partnerID=MN8TOARS}, DOI={10.1016/S0014-5793(97)01506-8}, abstractNote={Sucrose synthase (SuSy) plays an important role in sucrose degradation and occurs both as a soluble and as a membrane‐associated enzyme in higher plants. We show that membrane association can vary in vivo in response to gravistimulation, apparently involving SuSy dephosphorylation, and is a reversible process in vitro. Phosphorylation of SuSy has little effect on its activity but decreases its surface hydrophobicity as reported with the fluorescent probe bis‐ANS. We postulate that phosphorylation of SuSy (and perhaps other membrane proteins) is involved in the release of the membrane‐bound enzyme in part as a result of decreased surface hydrophobicity.}, number={2-3}, journal={FEBS LETTERS}, author={Winter, H and Huber, JL and Huber, SC}, year={1997}, month={Dec}, pages={151–155} }
@article{wadham_winter_schuller_1996, title={Regulation of soybean nodule phosphoenolpyruvate carboxylase in vivo}, volume={97}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0030484601&partnerID=MN8TOARS}, DOI={10.1034/j.1399-3054.1996.970316.x}, number={3}, journal={Physiologia Plantarum}, author={Wadham, C. and Winter, H. and Schuller, K.A.}, year={1996}, pages={531–535} }
@article{riens_lohaus_winter_heldt_1994, title={Production and diurnal utilization of assimilates in leaves of spinach (Spinacia oleracea L.) and barley (Hordeum vulgare L.)}, volume={192}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0028112285&partnerID=MN8TOARS}, DOI={10.1007/BF00203587}, number={4}, journal={Planta}, author={Riens, B. and Lohaus, G. and Winter, H. and Heldt, H.W.}, year={1994}, pages={497–501} }
@article{winter_robinson_heldt_1994, title={Subcellular volumes and metabolite concentrations in spinach leaves}, volume={193}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0027976083&partnerID=MN8TOARS}, DOI={10.1007/BF02411558}, number={4}, journal={Planta}, author={Winter, H. and Robinson, D.G. and Heldt, H.W.}, year={1994}, pages={530–535} }
@article{winter_robinson_heldt_1993, title={Subcellular volumes and metabolite concentrations in barley leaves}, volume={191}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0000957432&partnerID=MN8TOARS}, DOI={10.1007/BF00199748}, number={2}, journal={Planta}, author={Winter, H. and Robinson, D.G. and Heldt, H.W.}, year={1993}, pages={180–190} }
@article{winter_lohaus_heldt_1992, title={Phloem transport of amino acids in relation to their cytosolic levels in barley leaves}, volume={99}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-0001566367&partnerID=MN8TOARS}, DOI={10.1104/pp.99.3.996}, abstractNote={A comparison of barley (Hordeum vulgare L.) leaves was made between the cytosolic content of amino acids and sucrose as determined by subcellular fractionation and the corresponding concentration in phloem sap, which was collected continuously for up to 6 days from severed aphid stylets. Because amino acids were found to be almost absent from the vacuoles, and because the amino acid patterns in the stroma and cytosol are similar, whole leaf contents could be taken as a measure of cytosolic amino acid levels for a comparison of data during a diurnal cycle. The results show that the pattern of amino acids in the phloem sap was very similar to the pattern in the cytosol. Therefore, we concluded that the overall process of transfer of amino acids from the cytosol of the source cells into the sieve tubes, although carrier mediated, may be a passive process and that the translocation of amino acids via the sieve tubes requires the mass flow of sucrose driven by the active sucrose transport involved by the phloem loading.}, number={3}, journal={Plant Physiology}, author={Winter, H. and Lohaus, G. and Heldt, H.W.}, year={1992}, pages={996–1004} }